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Sample records for jackknifing

  1. 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...

  2. 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…

  3. A short note on jackknifing the concordance correlation coefficient.

    PubMed

    Feng, Dai; Baumgartner, Richard; Svetnik, Vladimir

    2014-02-10

    Lin's concordance correlation coefficient (CCC) is a very popular scaled index of agreement used in applied statistics. To obtain a confidence interval (CI) for the estimate of CCC, jackknifing was proposed and shown to perform well in simulation as well as in applications. However, a theoretical proof of the validity of the jackknife CI for the CCC has not been presented yet. In this note, we establish a sufficient condition for using the jackknife method to construct the CI for the CCC.

  4. Jackknifing Techniques for Evaluation of Equating Accuracy. Research Report. ETS RR-09-39

    ERIC Educational Resources Information Center

    Haberman, Shelby J.; Lee, Yi-Hsuan; Qian, Jiahe

    2009-01-01

    Grouped jackknifing may be used to evaluate the stability of equating procedures with respect to sampling error and with respect to changes in anchor selection. Properties of grouped jackknifing are reviewed for simple-random and stratified sampling, and its use is described for comparisons of anchor sets. Application is made to examples of item…

  5. Investigation of Alternative Methods Including Jackknifing for Estimating Point Availability of a System.

    DTIC Science & Technology

    1981-09-01

    Properties of two alternative procedures to the Jackknife Point and Confidence Interval Estimation Procedure of Gaver and Chu have been studied. They...Jackknife Point and Confidence Interval Availability Estimation Procedure. Numerical results from simulations are presented in this report. (Author)

  6. Anti-jackknife reverse tracking control of articulated vehicles in the presence of actuator saturation

    NASA Astrophysics Data System (ADS)

    Yuan, H.; Zhu, H.

    2016-10-01

    It is well known that backward motion control of an articulated vehicle is difficult because it is an open loop unstable system and such motion is also dangerous due to 'jackknifing'. In this paper, an anti-jackknife reverse tracking control strategy for autonomous articulated vehicles is proposed based on the combined longitudinal and lateral control scheme. In the proposed lateral-longitudinal control scheme, the major task is to control the reverse heading of the trailer by automatic steering strategies that observe both the anti-jackknife condition and input limitations. The main contribution of this paper is the development of globally asymptotic anti-jackknife stabilising and tracking controls of heading angles with both state and input constraints considered a priori. The proposed control inherently has an anti-windup mechanism that prevents the hitch angle from going beyond any specified critical value to avoid jackknifing, during which time, the steering angle remains at its limit. Stability of the controller is theoretically proven via the Lyapunov argument. Effectiveness of the proposed approach is demonstrated by CarSim and Simulink joint simulations.

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

    ERIC Educational Resources Information Center

    Daniel, Larry G.

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

  8. Confidence limits for air quality model evaluations, as estimated by bootstrap and jackknife resampling methods

    NASA Astrophysics Data System (ADS)

    Hanna, Steven R.

    Air quality models are used to make decisions regarding the construction of industrial plants, the types of fuel that will be burnt and the types of pollution control devices that will be used. It is important to know the uncertainties that are associated with these model predictions. Standard analytical methods found in elementary statistics textbooks for estimating uncertainties are generally not applicable since the distributions of performance measures related to air quality concentrations are not easily transformed to a Gaussian shape. This paper suggests several possible resampling procedures that can be used to calculate uncertainties or confidence limits on air quality model performance. In these resampling methods, many new data sets are drawn from the original data set using an empirical set of rules. A few alternate forms of the socalled bootstrap and jackknife resampling procedures are tested using a concocted data set with a Gaussian parent distributions, with the result that the jackknife is the most efficient procedure to apply, although its confidence bounds are slightly overestimated. The resampling procedures are then applied to predictions by seven air quality models for the Carpinteria coastal dispersion experiment. Confidence intervals on the fractional mean bias and the normalized mean square error are calculated for each model and for differences between models. It is concluded that these uncertainties are sometimes so large for data sets consisting of about 20 elements that it cannot be stated with 95% confidence that the performance measure for the 'best' model is significantly different from that for another model.

  9. Optimal measurements of hemodynamic response latency in fNIRS using the jackknife approach.

    PubMed

    Maheux, Manon; Bisaillon-Sicotte, Étienne; Tabrizi, Shirin; Armony, Jorge L; Lina, Jean-Marc; Jolicoeur, Pierre

    2017-01-01

    Functional near-infrared spectroscopy (fNIRS) permits measurements of changes in the concentration of oxygenated and deoxygenated hemoglobin, typically with a higher sampling rate than with other imaging methods based on the hemodynamic response. We examined the potential of the fNIRS technique to estimate variations in the latency of hemodynamic responses to experimental events and sought optimal methods to maximize the reliability and reproducibility of latency effects. We used Monte Carlo simulations using subsamples of real fNIRS measures to estimate the statistical power of different approaches (such as fixed threshold, percent of peak, fractional-area latency, for both individual-subject estimates and estimates from jackknife averages) to detect a known simulated latency shift. The simulations used measures of hemodynamic responses in the temporal lobe from two groups of young adult participants who listened to auditory stimuli, one with a blocked presentation design and one with an event-related design. We estimated the relative sensitivity of different latency measures and approaches to the measurement of latency effects of different magnitudes using realistic noise and signal-to-noise characteristics. In general, the jackknife approach provided the greatest statistical power to detect a known latency shift, without inflation of Type I error.

  10. Morphological characterization via light and electron microscopy of Atlantic jackknife clam (Ensis directus) hemocytes.

    PubMed

    Preziosi, Brian M; Bowden, Timothy J

    2016-05-01

    The Atlantic jackknife clam, Ensis directus, is currently being researched as a potential species for aquaculture operations in Maine. The goal of this study was to describe the hemocytes of this species for the first time and provide a morphological classification scheme. We viewed hemocytes under light microscopy (using Hemacolor, neutral red, and Pappenheim's stains) as well as transmission electron microscopy (TEM). The 2 main types of hemocytes found were granulocytes and hyalinocytes (agranular cells). The granulocytes were subdivided into large and small granulocytes while the hyalinocytes were subdivided into large and small hyalinocytes. The large hemocytes had both a larger diameter and smaller nucleus to cell diameter ratio than their smaller counterparts. A rare cell type, the vesicular cell, was also observed and it possessed many vesicles but few or no granules. Using TEM, granulocytes were found to contain both electron-lucent and electron-dense granules of various sizes. These numerous granules were the only structures that took up the neutral red stain. Hyalinocytes had few of these granules relative to granulocytes. Large hyalinocytes had both various organelles and large vesicles in their abundant cytoplasm while small hyalinocytes had little room for organelles in their scant cytoplasm. Total hemocyte counts averaged 1.96×10(6) cells mL(-1) while differential hemocyte counts averaged 11% for small hyalinocytes, 12% for large hyalinocytes, 59% for small granulocytes, and 18% for large granulocytes. The results of this study provide a starting point for future studies on E. directus immune function.

  11. Electromyographic activity of the rectus abdominis during a traditional crunch and the basic jackknife exercise with the Ab Lounge™.

    PubMed

    Nelson, Gail A; Bent-Forsythe, Denise A; Roopchand-Martin, Sharmella C

    2012-06-01

    The use of nontraditional exercise devices such as the Ab Lounge™ has been promoted as being as effective as the traditional abdominal crunch in strengthening the abdominal musculature. Evidence for this is lacking, however. The purpose of this study was to compare the degree of activation of the upper and lower rectus abdominis using electromyography (EMG) during a traditional crunch with the basic jackknife using the Ab Lounge™. Twenty-two subjects (6 men and 16 women) were randomly selected from the student population at the University of the West Indies (Mona Campus). The mean age of the participants was 20.5 ± 1.5 years, height 166.4 ± 6.2 cm, weight 64 ± 10.3 kg, and waist-hip ratio 0.7 ± 0.1. Surface EMG was used to assess the muscle activity from the upper and lower rectus abdominis while each exercise was performed. The EMG data were full-wave rectified and normalized using a mathematical model that was set up in Microsoft Excel for Windows XP. Statistical analysis was performed on the data using a univariate analysis of variance with gender as a covariate. Significance was determined by p < 0.05. The mean EMG data recorded for the upper rectus abdominis was significantly higher with the traditional crunch when compared with the basic jackknife performed on the Ab Lounge™ (F = 4.39, p = 0.04). The traditional crunch produced a higher level of activity in the lower rectus abdominis when compared with the basic jackknife, but this was not statistically significant (F = 0.249, p = 0.62). There was no significant interaction between gender and the effect of the type of exercise on upper and lower rectus abdominis activation. These results suggest that the traditional abdominal crunch is more effective than the basic jackknife is in activating the rectus abdominis musculature.

  12. Supplement Analysis for the Watershed Management Program EIS (DOE/EIS-0265/SA-159) - Pine Hollow Watershed Enhancement – Jackknife Watershed Projects

    SciTech Connect

    Stewart, Shannon C.

    2004-07-15

    The Bonneville Power Administration is proposing to fund watershed enhancement activities in the Pine Hollow and Jackknife Canyon Watersheds in conjunction with the Sherman County Soil and Water Conservation District. Activities will include installation of offstream watering facilities and structural improvements for reducing sediment delivery to streams. Nine Water and Sediment Control Basins and 2,000 feet of diversion ditches will be utilized to reduce the erosive forces of water during storm events, effectively allowing sediment to settle out of suspension in the water column. Two wells, two spring developments, and two watering systems will be employed to provide better watering options to rangeland managers, reducing the need for cattle to utilize streams for water.

  13. The effect of temperature and wing morphology on quantitative genetic variation in the cricket Gryllus firmus, with an appendix examining the statistical properties of the Jackknife-MANOVA method of matrix comparison.

    PubMed

    Bégin, M; Roff, D A; Debat, V

    2004-11-01

    We investigated the effect of temperature and wing morphology on the quantitative genetic variances and covariances of five size-related traits in the sand cricket, Gryllus firmus. Micropterous and macropterous crickets were reared in the laboratory at 24, 28 and 32 degrees C. Quantitative genetic parameters were estimated using a nested full-sib family design, and (co)variance matrices were compared using the T method, Flury hierarchy and Jackknife-manova method. The results revealed that the mean phenotypic value of each trait varied significantly among temperatures and wing morphs, but temperature reaction norms were not similar across all traits. Micropterous individuals were always smaller than macropterous individuals while expressing more phenotypic variation, a finding discussed in terms of canalization and life-history trade-offs. We observed little variation between the matrices of among-family (co)variation corresponding to each combination of temperature and wing morphology, with only one matrix of six differing in structure from the others. The implications of this result are discussed with respect to the prediction of evolutionary trajectories.

  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. Data resolution: a jackknife procedure for determining the consistency of molecular marker datasets.

    PubMed

    van Hintum, Th J L

    2007-08-01

    The results of genetic diversity studies using molecular markers not only depend on the biology of the studied objects but also on the quality of the marker data. Poor data quality may hamper the correct answering of biological questions. A new statistic is proposed to estimate the quality of a marker data set with regard to its ability to describe the structure of the biological material under study. This statistic is called data resolution (DR). It is calculated by splitting a marker data set at random into two sets each with half the number of markers. In each set, similarities between all pairs of objects are calculated. Subsequently, the similarities obtained for the two sets are correlated. This process is repeated a large number of times. The average of the correlation coefficients obtained in this way is the DR of the dataset. In the present paper, the DR statistic is applied to four studies involving amplified fragment length polymorphism as well as micro-satellite markers. In addition, some properties and possible applications of DR are discussed, including the prediction of the added value of scoring additional markers, and the determination of which similarity measure is, apart from genetical considerations, most appropriate for analyzing the data.

  16. Prone jackknife position is not necessary to achieve a cylindrical abdominoperineal resection: demonstration of the lithotomy position.

    PubMed

    Keller, Deborah S; Lawrence, Justin K; Delaney, Conor P

    2014-02-01

    This video demonstrates a laparoscopic abdominal perineal resection for a fixed 4.8-cm mass involving the posterior and left rectal walls and left puborectalis, 2 cm from the anal verge (see Video, Supplemental Digital Content 1, http://links.lww.com/DCR/A127). We detail the steps of the procedure, all completed in lithotomy, including lateral-to-medial dissection; identification and protection of the left ureter and presacral nerves; division of the inferior mesenteric artery; medial-to-lateral dissection, with meeting the previous dissection plane; total mesorectal excision and pelvic dissection; perineal dissection and layered closure; and abdominal inspection and colostomy creation. Total operative time was 181 minutes. The specimen total mesorectal excision was complete with a negative circumferential radial margin (greater than 1 cm). Final pathology was T3N2M0.

  17. Jackknife Estimation of Sampling Variance of Ratio Estimators in Complex Samples: Bias and the Coefficient of Variation. Research Report. ETS RR-06-19

    ERIC Educational Resources Information Center

    Oranje, Andreas

    2006-01-01

    A multitude of methods has been proposed to estimate the sampling variance of ratio estimates in complex samples (Wolter, 1985). Hansen and Tepping (1985) studied some of those variance estimators and found that a high coefficient of variation (CV) of the denominator of a ratio estimate is indicative of a biased estimate of the standard error of a…

  18. Weighting Procedures and the Cluster Forming Algorithm for Delete-k Jackknife Variance Estimation for Institutional Surveys. Research Report. ETS RR-06-15

    ERIC Educational Resources Information Center

    Qian, Jiahe

    2006-01-01

    Weighting and variance estimation are two statistical issues involved in survey data analysis for large-scale assessment programs such as the Higher Education Information and Communication Technology (ICT) Literacy Assessment. Because survey data are always acquired by probability sampling, to draw unbiased or almost unbiased inferences for the…

  19. 46 CFR 160.043-1 - Applicable specification and plan.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...: Dwg. No. 160.043-1(b), Jackknife (With Can Opener). (c) Copies on file. A copy of the above... MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant...

  20. 46 CFR 160.043-1 - Applicable specification and plan.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...: Dwg. No. 160.043-1(b), Jackknife (With Can Opener). (c) Copies on file. A copy of the above... MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant...

  1. 46 CFR 160.043-1 - Applicable specification and plan.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...: Dwg. No. 160.043-1(b), Jackknife (With Can Opener). (c) Copies on file. A copy of the above... MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant...

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant Vessels § 160.043-6... manufacturer's type or size designation. (b) Instructions for can opener. With each jackknife the manufacturer shall supply instructions, complete with an illustration, indicating the proper method for using the...

  3. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant Vessels § 160.043-6... manufacturer's type or size designation. (b) Instructions for can opener. With each jackknife the manufacturer shall supply instructions, complete with an illustration, indicating the proper method for using the...

  4. Parametric and Nonparametric Estimation of the Mean Number of Customers in Service for an M/G/Infinity Queue.

    DTIC Science & Technology

    1986-03-01

    GROUP M/G/00 queueing model, simulation, Parametric estimation , Nonparametric estimati on, Paired-jackknife, Separated- jackknife, Bootstrap, 9...12 III. PARAMETRIC ESTIMATION METHOD .... ........... .14 A. DESCRIPTION ...... ................. 14 B. EXPONENTIAL SERVICE TIME...shall call parametric estimation " and "nonparametric estimation". In the parametric estimation case, a particular probabilistic model is specified for the

  5. 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.

  6. 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…

  7. 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…

  8. 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.

  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. 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…

  11. 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...

  12. Statistical-Dynamical Forecasting of Tropical Cyclogenesis in the North Atlantic at Intraseasonal Lead Times

    DTIC Science & Technology

    2009-06-01

    black dot represents TC Beryl that formed on 13 August 2000. Contours start at 1 percent and are in 1 percent increments...of 2000, constructed from a 40 percent NTCI model that jackknifed year 2000. The black dot represents TC Beryl that formed on 13 August 2000

  13. A Comparison of Rasch Person Analysis and Robust Estimators.

    ERIC Educational Resources Information Center

    Smith, Richard M.

    1985-01-01

    Standard maximum likeliheed estimation was compared using two forms of robust estimation, BIWEIGHT (based on Tukey's Biweight) and AMTJACK (AMT-Robustified Jackknife), and Rasch model person analysis. The two procedures recovered the generating parameters, but Rasch person analysis also helped to identify the nature of a response disturbance. (GDC)

  14. 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

    2014-03-01

    The life table and consumption rate of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) reared on asparagus, Asparagus officinalis L. (Asparagales: Asparagaceae) were studied under laboratory conditions to assess their interaction. Development, survival, fecundity, and consumption data were analyzed by the age-stage, twosex life table. This study indicated that asparagus is a natural host of H. armigera. However, the poor nutritional content in asparagus foliage and the poor fitness of H. armigera that fed on asparagus indicated that asparagus is a suboptimal host in comparison to hybrid sweet corn. The uncertainty associated with life table parameters was estimated by using jackknife and bootstrap techniques, and the results were compared for statistical inference. The intrinsic rate of increase (r), finite rate of increase (λ), 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.

  15. Do QEEG topographic map data have a multivariate normal distribution? Implications for tests of individual maps.

    PubMed

    Lawson, J S; Adams, S J; Brunet, D G; Criollo, M; Galin, H; MacCrimmon, D J

    1998-01-01

    The study was designed to test whether topographic map data expressed in log power units have a multivariate normal (MVN) distribution in a healthy population, and to determine if any deviation from normality poses serious difficulties for the use of standard multivariate statistical tests in assessing the significance of deformations of the map in individual cases. Data on 361 healthy adults using 20 electrodes in the classic 10/20 configuration were recorded in six frequency bands. The log-transformed power data were shown to deviate markedly from MVN. The actual distributions of multivariate tests were computed for the sample using the 'jackknife' method, and shown to deviate markedly from the F-distributions that would be expected for MVN data. These 'jackknife' sampling distributions were then used to demonstrate significant deformations in the topographic maps of a patient who had sustained traumatic head injury.

  16. Statistical genetics of an annual plant, Impatiens capensis. I. Genetic basis of quantitative variation.

    PubMed

    Mitchell-Olds, T; Bergelson, J

    1990-02-01

    Analysis of quantitative genetics in natural populations has been hindered by computational and methodological problems in statistical analysis. We developed and validated a jackknife procedure to test for existence of broad sense heritabilities and dominance or maternal effects influencing quantitative characters in Impatiens capensis. Early life cycle characters showed evidence of dominance and/or maternal effects, while later characters exhibited predominantly environmental variation. Monte Carlo simulations demonstrate that these jackknife tests of variance components are extremely robust to heterogeneous error variances. Statistical methods from human genetics provide evidence for either a major locus influencing germination date, or genes that affect phenotypic variability per se. We urge explicit consideration of statistical behavior of estimation and testing procedures for proper biological interpretation of statistical results.

  17. Estimators for the truncated beta-binomial distribution

    SciTech Connect

    Atwood, C.L.

    1980-01-01

    Let X have a beta-binomial(m,p,theta) distribution, truncated such that X > t for t = 0 or 1. Suppose that independent observations of X are available. A consistent estimator of (p,theta) is given, based on the first three sample moments. This may be used as a start for maximum likelihood estimation or jackknifing. The standard assumptions for a C(..cap alpha..) is truncated binomial do not hold; however, a test is proposed based on jackknifing the sample variance of X. Some Monte Carlo comparisons are given. For moderately small data sets, these comparisons show that the moment estimator is often superior to the MLE, and the C(..cap alpha..) test is superior to other proposed tests, in spite of its lack of theoretical justification. 3 figures, 5 tables.

  18. 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.

  19. An Application of Discriminant Analysis to the Selection of Software Cost Estimating Models.

    DTIC Science & Technology

    1984-09-01

    32 List of Tables Table Page I. Summary of Stepwise Classification Scores ..... 29 II. Mean Values for Variables by Model-Group ...... 30 III...by the classification function. The stability will be measured by the difference between the jackknifed and unjackknifed classification score . The...classification score . The biased or unjackknifed method, calculates the discriminant function using all twenty-five projects. The bias occurs because the

  20. Simulation Study of Estimators for the Survival Probability of a First Passage Time for a Semi-Markov Process Using Censored Data

    DTIC Science & Technology

    1988-09-01

    Finite state space semi-Markov process find application in many areas. Often interest centers on whether or not the process has hit a particular state before a time t. This thesis reports results of a simulation study of the small behavior for three estimators of the survival probability of a first passage time for a semi-Markov process using censored data. Keywords: Semi- Markov; Kaplan Meier estimator; Confidence interval ; Jackknife; Problem; Theses.

  1. 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.

  2. A comparison of confidence interval methods for the concordance correlation coefficient and intraclass correlation coefficient with small number of raters.

    PubMed

    Feng, Dai; Svetnik, Vladimir; Coimbra, Alexandre; Baumgartner, Richard

    2014-01-01

    The intraclass correlation coefficient (ICC) with fixed raters or, equivalently, the concordance correlation coefficient (CCC) for continuous outcomes is a widely accepted aggregate index of agreement in settings with small number of raters. Quantifying the precision of the CCC by constructing its confidence interval (CI) is important in early drug development applications, in particular in qualification of biomarker platforms. In recent years, there have been several new methods proposed for construction of CIs for the CCC, but their comprehensive comparison has not been attempted. The methods consisted of the delta method and jackknifing with and without Fisher's Z-transformation, respectively, and Bayesian methods with vague priors. In this study, we carried out a simulation study, with data simulated from multivariate normal as well as heavier tailed distribution (t-distribution with 5 degrees of freedom), to compare the state-of-the-art methods for assigning CI to the CCC. When the data are normally distributed, the jackknifing with Fisher's Z-transformation (JZ) tended to provide superior coverage and the difference between it and the closest competitor, the Bayesian method with the Jeffreys prior was in general minimal. For the nonnormal data, the jackknife methods, especially the JZ method, provided the coverage probabilities closest to the nominal in contrast to the others which yielded overly liberal coverage. Approaches based upon the delta method and Bayesian method with conjugate prior generally provided slightly narrower intervals and larger lower bounds than others, though this was offset by their poor coverage. Finally, we illustrated the utility of the CIs for the CCC in an example of a wake after sleep onset (WASO) biomarker, which is frequently used in clinical sleep studies of drugs for treatment of insomnia.

  3. 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

  4. 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

  5. The Purley train crash mechanism: injuries and prevention.

    PubMed Central

    Fothergill, N J; Ebbs, S R; Reese, A; Partridge, R J; Mowbray, M; Southcott, R D; Hashemi, K

    1992-01-01

    On the afternoon of Saturday 4th March 1989 two trains, both bound for London Victoria Station, collided. Part of the rear train rolled down a steep railway embankment and jack-knifed against a tree. The mechanism of the crash and the injuries sustained by the 55 victims who were seen in the A&E Department of the Mayday University Hospital are described. Improvements in signalling technology and design of rolling stock which may reduce both the risk of collision and severity of injury in future accidents are discussed. Images Fig. 1 PMID:1388485

  6. Aircraft Crash Survival Design Guide. Volume 2. Aircraft Crash Environment and Human Tolerance

    DTIC Science & Technology

    1980-01-01

    spine can produce spinal fracture through flex- ure that results from jackknife bending over a lap- belt-only restraint. The lap belt might inflict...injuries to the internal organs if it is not re- tained on the pelvic girdle but is allowed to exert its force above the iliac crests in the soft...exerted by deceleration of the thighs and lower legs accom- panied by lap belt slippage up and over the iliac crests. Lap belt slippage up and over the

  7. Detection method of nonlinearity errors by statistical signal analysis in heterodyne Michelson interferometer.

    PubMed

    Hu, Juju; Hu, Haijiang; Ji, Yinghua

    2010-03-15

    Periodic nonlinearity that ranges from tens of nanometers to a few nanometers in heterodyne interferometer limits its use in high accuracy measurement. A novel method is studied to detect the nonlinearity errors based on the electrical subdivision and the analysis method of statistical signal in heterodyne Michelson interferometer. Under the movement of micropositioning platform with the uniform velocity, the method can detect the nonlinearity errors by using the regression analysis and Jackknife estimation. Based on the analysis of the simulations, the method can estimate the influence of nonlinearity errors and other noises for the dimensions measurement in heterodyne Michelson interferometer.

  8. 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.

  9. PsN-Toolkit--a collection of computer intensive statistical methods for non-linear mixed effect modeling using NONMEM.

    PubMed

    Lindbom, Lars; Pihlgren, Pontus; Jonsson, E Niclas; Jonsson, Niclas

    2005-09-01

    PsN-Toolkit is a collection of statistical tools for pharmacometric data analysis using the non-linear mixed effect modeling software NONMEM. The toolkit is object oriented and written in the programming language Perl using the programming library Perl-speaks-NONMEM (PsN). Five methods: the Bootstrap, the Jackknife, Log-likelihood Profiling, Case-deletion Diagnostics and Stepwise Covariate Model building are included as separate classes and may be used in user-written Perl scripts or through stand-alone command line applications. The tools are designed with the ability to cooperate and with an emphasis on common structures for workflow and result handling. Parallel execution of independent tool sections is supported on shared memory multiprocessor (SMP) computers, Mosix/openMosix clusters and distributed computing environments following the NorduGrid standard. In conclusion, PsN-Toolkit makes it easier to use the Bootstrap, the Jackknife, Log-likelihood Profiling, Case-deletion Diagnostics and Stepwise Covariate Model building in pharmacometric data analysis.

  10. Statistical analysis of SHAPE-directed RNA secondary structure modeling.

    PubMed

    Ramachandran, Srinivas; Ding, Feng; Weeks, Kevin M; Dokholyan, Nikolay V

    2013-01-29

    The ability to predict RNA secondary structure is fundamental for understanding and manipulating RNA function. The information obtained from selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments greatly improves the accuracy of RNA secondary structure prediction. Recently, Das and colleagues [Kladwang, W., et al. (2011) Biochemistry 50, 8049-8056] proposed a "bootstrapping" approach for estimating the variance and helix-by-helix confidence levels of predicted secondary structures based on resampling (randomizing and summing) the measured SHAPE data. We show that the specific resampling approach described by Kladwang et al. introduces systematic errors and underestimates confidence in secondary structure prediction using SHAPE data. Instead, a leave-data-out jackknife approach better estimates the influence of a given experimental data set on SHAPE-directed secondary structure modeling. Even when 35% of the data were left out in the jackknife approach, the confidence levels of SHAPE-directed secondary structure prediction were significantly higher than those calculated by Das and colleagues using bootstrapping. Helix confidence levels were thus underestimated in the recent study, and the resampling approach implemented by Kladwang et al. is not an appropriate metric for evaluating SHAPE-directed secondary structure modeling.

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

    SciTech Connect

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

    2015-12-31

    Data re-sampling methods such as the delete-one jackknife are a common tool for estimating the covariance of large scale structure probes. In this paper we investigate the concepts of internal covariance estimation in the context of cosmic shear two-point statistics. We demonstrate how to use log-normal simulations of the convergence field and the corresponding shear field to carry out realistic tests of internal covariance estimators and find that most estimators such as jackknife or sub-sample covariance can reach a satisfactory compromise between bias and variance of the estimated covariance. In a forecast for the complete, 5-year DES 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 $\\Omega_m$-$\\sigma_8$ plane as measured with internally estimated covariance matrices is on average $\\gtrsim 85\\%$ of the volume derived from the true covariance matrix. The uncertainty on the parameter combination $\\Sigma_8 \\sim \\sigma_8 \\Omega_m^{0.5}$ derived from internally estimated covariances is $\\sim 90\\%$ of the true uncertainty.

  12. Estimation of the Time Interval between the Administration of Heroin and the Sampling of Blood in Chronic Inhalers.

    PubMed

    Dubois, Nathalie; Hallet, Claude; Seidel, Laurence; Demaret, Isabelle; Luppens, David; Ansseau, Marc; Rozet, Eric; Albert, Adelin; Hubert, Philippe; Charlier, Corinne

    2015-05-01

    To develop a model for estimating the time delay between last heroin consumption and blood sampling in chronic drug users. Eleven patients, all heroin inhalers undergoing detoxification, were included in the study. Several plasma samples were collected during the detoxification procedure and analyzed for the heroin metabolites 6-acetylmorphine (6AM), morphine (MOR), morphine-6-glucuronide (M6G) and morphine-3-glucuronide (M3G), according to a UHPLC/MSMS method. The general linear mixed model was applied to time-related concentrations and a pragmatic four-step delay estimation approach was proposed based on the simultaneous presence of metabolites in plasma. Validation of the model was carried out using the jackknife technique on the 11 patients, and on a group of 7 test patients. Quadratic equations were derived for all metabolites except 6AM. The interval delay estimation was 2-4 days when only M3G present in plasma, 1-2 days when M6G and M3G were both present, 0-1 day when MOR, M6G and M3G were present and <2 h for all metabolites present. The 'jackknife' correlation between declared and actual estimated delays was 0.90. The overall precision of the delay estimates was 8-9 h. The delay between last heroin consumption and blood sampling in chronic drug users can be satisfactorily predicted from plasma heroin metabolites.

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

    DOE PAGES

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

    2015-12-31

    Data re-sampling methods such as the delete-one jackknife are a common tool for estimating the covariance of large scale structure probes. In this paper we investigate the concepts of internal covariance estimation in the context of cosmic shear two-point statistics. We demonstrate how to use log-normal simulations of the convergence field and the corresponding shear field to carry out realistic tests of internal covariance estimators and find that most estimators such as jackknife or sub-sample covariance can reach a satisfactory compromise between bias and variance of the estimated covariance. In a forecast for the complete, 5-year DES 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 themore » $$\\Omega_m$$-$$\\sigma_8$$ plane as measured with internally estimated covariance matrices is on average $$\\gtrsim 85\\%$$ of the volume derived from the true covariance matrix. The uncertainty on the parameter combination $$\\Sigma_8 \\sim \\sigma_8 \\Omega_m^{0.5}$$ derived from internally estimated covariances is $$\\sim 90\\%$$ of the true uncertainty.« less

  14. 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.

  15. [Sampling effort and floristic atlases: survey completeness of localities and description of knowledge gaps].

    PubMed

    Vallet, Jeanne; Rambaud, Maëlle; Coquel, Loïc; Poncet, Laurent; Hendoux, Frédéric

    2012-12-01

    Floristic atlases have an important input to flora conservation planning even though their data quality varied greatly across countries. This study aimed to assess survey completeness of cells of floristic atlases. Then, a surveying guide is designed to overcome as efficiently as possible sampling biases. A review and analyses on a wide dataset were carried out to select an estimator of the true species richness of surveyed cells. The Jackknife 1, a non-parametric estimator, appeared as the best compromise for regional floristic atlases. The number of records in each cell was used as an estimator of sampling effort. The ratio between the observed species richness and the estimated species richness measures the completeness of inventories in each surveyed cell. Eighteen variables were selected to describe current inventories and design new surveys. These variables highlight locations, periods and species to be given priority in future studies.

  16. Cascaded multiple classifiers for secondary structure prediction.

    PubMed Central

    Ouali, M.; King, R. D.

    2000-01-01

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

  17. 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.

  18. Predict protein structural class for low-similarity sequences by evolutionary difference information into the general form of Chou's pseudo amino acid composition.

    PubMed

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang

    2014-08-21

    Knowledge of protein structural class plays an important role in characterizing the overall folding type of a given protein. At present, it is still a challenge to extract sequence information solely using protein sequence for protein structural class prediction with low similarity sequence in the current computational biology. In this study, a novel sequence representation method is proposed based on position specific scoring matrix for protein structural class prediction. By defined evolutionary difference formula, varying length proteins are expressed as uniform dimensional vectors, which can represent evolutionary difference information between the adjacent residues of a given protein. To perform and evaluate the proposed method, support vector machine and jackknife tests are employed on three widely used datasets, 25PDB, 1189 and 640 datasets with sequence similarity lower than 25%, 40% and 25%, respectively. Comparison of our results with the previous methods shows that our method may provide a promising method to predict protein structural class especially for low-similarity sequences.

  19. Persistent topographic quantitative EEG sequelae of chronic marihuana use: a replication study and initial discriminant function analysis.

    PubMed

    Struve, F A; Straumanis, J J; Patrick, G

    1994-04-01

    In a previous pilot study using psychiatric patients we reported that daily marihuana users had significant elevations of (1) Absolute Alpha Power, (2) Relative Alpha Power, and (3) Interhemispheric Alpha Coherence over both frontal and frontal-central areas when contrasted with subjects who did not use marihuana. We referred to this phenomenon as Hyperfrontality of Alpha. The study presented here is a successful replication of our previous findings using new samples of subjects and identical methods. Post hoc analyses based on the combined sample from both studies suggest that variables of psychiatric diagnoses and medication did not bias our results. In addition, a discriminant function analysis using quantitative EEG variables as candidate predictors generated a 95% correct THC user versus nonuser classification accuracy which received a successful jackknife replication.

  20. A Hybrid Classification System for Heart Disease Diagnosis Based on the RFRS Method

    PubMed Central

    Su, Qiang; Zhang, Mo; Zhu, Yanhong; Wang, Qiugen; Wang, Qian

    2017-01-01

    Heart disease is one of the most common diseases in the world. The objective of this study is to aid the diagnosis of heart disease using a hybrid classification system based on the ReliefF and Rough Set (RFRS) method. The proposed system contains two subsystems: the RFRS feature selection system and a classification system with an ensemble classifier. The first system includes three stages: (i) data discretization, (ii) feature extraction using the ReliefF algorithm, and (iii) feature reduction using the heuristic Rough Set reduction algorithm that we developed. In the second system, an ensemble classifier is proposed based on the C4.5 classifier. The Statlog (Heart) dataset, obtained from the UCI database, was used for experiments. A maximum classification accuracy of 92.59% was achieved according to a jackknife cross-validation scheme. The results demonstrate that the performance of the proposed system is superior to the performances of previously reported classification techniques. PMID:28127385

  1. 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.

  2. A new methodology to define homogeneous regions through an entropy based clustering method

    NASA Astrophysics Data System (ADS)

    Ridolfi, E.; Rianna, M.; Trani, G.; Alfonso, L.; Di Baldassarre, G.; Napolitano, F.; Russo, F.

    2016-10-01

    One of the most crucial steps in flow frequency studies is the definition of Homogenous Regions (HRs), i.e. areas with similar hydrological behavior. This is essential in ungauged catchments, as HR allows information to be transferred from a neighboring river basin. This study proposes a new, entropy-based approach to define HRs, in which regions are defined as homogeneous if their hydrometric stations capture redundant information. The problem is handled through the definition of the Information Transferred Index (ITI) as the ratio between redundant information and the total information provided by pairs of stations. The methodology is compared with a traditional, distance-based clustering method through a Monte Carlo experiment and a jack-knife procedure. Results indicate that the ITI-based method performs well, adding value to current methodologies to define HRs.

  3. Geary autocorrelation and DCCA coefficient: Application to predict apoptosis protein subcellular localization via PSSM

    NASA Astrophysics Data System (ADS)

    Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

    2017-02-01

    Apoptosis is a fundamental process controlling normal tissue homeostasis by regulating a balance between cell proliferation and death. Predicting subcellular location of apoptosis proteins is very helpful for understanding its mechanism of programmed cell death. Prediction of apoptosis protein subcellular location is still a challenging and complicated task, and existing methods mainly based on protein primary sequences. In this paper, we propose a new position-specific scoring matrix (PSSM)-based model by using Geary autocorrelation function and detrended cross-correlation coefficient (DCCA coefficient). Then a 270-dimensional (270D) feature vector is constructed on three widely used datasets: ZD98, ZW225 and CL317, and support vector machine is adopted as classifier. The overall prediction accuracies are significantly improved by rigorous jackknife test. The results show that our model offers a reliable and effective PSSM-based tool for prediction of apoptosis protein subcellular localization.

  4. Detrended cross-correlation coefficient: Application to predict apoptosis protein subcellular localization.

    PubMed

    Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

    2016-12-01

    Apoptosis, or programed cell death, plays a central role in the development and homeostasis of an organism. Obtaining information on subcellular location of apoptosis proteins is very helpful for understanding the apoptosis mechanism. The prediction of subcellular localization of an apoptosis protein is still a challenging task, and existing methods mainly based on protein primary sequences. In this paper, we introduce a new position-specific scoring matrix (PSSM)-based method by using detrended cross-correlation (DCCA) coefficient of non-overlapping windows. Then a 190-dimensional (190D) feature vector is constructed on two widely used datasets: CL317 and ZD98, and support vector machine is adopted as classifier. To evaluate the proposed method, objective and rigorous jackknife cross-validation tests are performed on the two datasets. The results show that our approach offers a novel and reliable PSSM-based tool for prediction of apoptosis protein subcellular localization.

  5. Classification of lung nodules in diagnostic CT: an approach based on 3D vascular features, nodule density distribution, and shape features

    NASA Astrophysics Data System (ADS)

    Lo, Shih-Chung B.; Hsu, Li-Yueh; Freedman, Matthew T.; Lure, Yuan Ming F.; Zhao, Hui

    2003-05-01

    We have developed various segmentation and analysis methods for the quantification of lung nodules in thoracic CT. Our methods include the enhancement of lung structures followed by a series of segmentation methods to extract the nodule and to form 3D configuration at an area of interest. The vascular index, aspect ratio, circularity, irregularity, extent, compactness, and convexity were also computed as shape features for quantifying the nodule boundary. The density distribution of the nodule was modeled based on its internal homogeneity and/or heterogeneity. We also used several density related features including entropy, difference entropy as well as other first and second order moments. We have collected 48 cases of lung nodules scanned by thin-slice diagnostic CT. Of these cases, 24 are benign and 24 are malignant. A jackknife experiment was performed using a standard back-propagation neural network as the classifier. The LABROC result showed that the Az of this preliminary study is 0.89.

  6. Predicting subcellular location of apoptosis proteins with pseudo amino acid composition: approach from amino acid substitution matrix and auto covariance transformation.

    PubMed

    Yu, Xiaoqing; Zheng, Xiaoqi; Liu, Taigang; Dou, Yongchao; Wang, Jun

    2012-05-01

    Apoptosis proteins are very important for understanding the mechanism of programmed cell death. Obtaining information on subcellular location of apoptosis proteins is very helpful to understand the apoptosis mechanism. In this paper, based on amino acid substitution matrix and auto covariance transformation, we introduce a new sequence-based model, which not only quantitatively describes the differences between amino acids, but also partially incorporates the sequence-order information. This method is applied to predict the apoptosis proteins' subcellular location of two widely used datasets by the support vector machine classifier. The results obtained by jackknife test are quite promising, indicating that the proposed method might serve as a potential and efficient prediction model for apoptosis protein subcellular location prediction.

  7. A quantitative structure-activity relationship study on a few series of anti-hepatitis C virus agents.

    PubMed

    Varshney, Jonish; Sharma, Anjana; Gupta, Satya P

    2012-05-01

    A 2-Dimensional Quantitative Structure-Activity Relationship study has been performed on 2 series of hepatitis C virus (HCV) inhibitors, i.e., Isothiazoles and Thiazolones. In each case significant correlations are found between the anti-HCV potencies and some physicochemical, electronic and steric properties of the compounds, indicating that for the first series the activity is controlled by density and two indicator parameters (one for halogen and other for methyl), while for the second series density, Hammett constant and Kier's first order valence molecular connectivity index are important for anti-HCV activity. The validity of the correlation has been judged by leave-one-out jackknife procedure and predicting the activity of some test compounds. Using the correlations obtained, some new compounds of high potency have been predicted in each series.

  8. Comparative analysis on determinants of self-rated health among non-Hispanic White, Hispanic, and Asian American older adults.

    PubMed

    Min, Jong Won; Rhee, Siyon; Lee, Sang E; Rhee, Jessica; Tran, Thanh

    2014-06-01

    The purpose of the study is (1) to compare the effects of factors on self-rated health (SRH) among older non-Hispanic Whites (NHW), Hispanic, and Asian Californians and (2) to provide estimated influence size of each factor on SRH. This study analyzed secondary data drawn from the 2005 California Health Interview Survey. Binary logit regressions were used to analyze data with the Jackknife replication sampling weights. Significant differences were found in SRH among the three groups. Hispanics and Asians reported poorer health than NHW. Socioeconomic status, acculturation, and health access significantly accounted for an association between ethnicity and SRH. However, the magnitudes of their effects on SRH varied across the groups and by the factors examined. This study discusses and concludes with some recommendations on the opportunities presented by the Affordable Care Act and Healthy People 2020.

  9. Identification of mitochondrial proteins of malaria parasite using analysis of variance.

    PubMed

    Ding, Hui; Li, Dongmei

    2015-02-01

    As a parasitic protozoan, Plasmodium falciparum (P. falciparum) can cause malaria. The mitochondrial proteins of malaria parasite play important roles in the discovery of anti-malarial drug targets. Thus, accurate identification of mitochondrial proteins of malaria parasite is a key step for understanding their functions and finding potential drug targets. In this work, we developed a sequence-based method to identify the mitochondrial proteins of malaria parasite. At first, we extended adjoining dipeptide composition to g-gap dipeptide composition for discretely formulating the protein sequences. Subsequently, the analysis of variance (ANOVA) combined with incremental feature selection (IFS) was used to pick out the optimal features. Finally, the jackknife cross-validation was used to evaluate the performance of the proposed model. Evaluation results showed that the maximum accuracy of 97.1% could be achieved by using 101 optimal 5-gap dipeptides. The comparison with previous methods demonstrated that our method was accurate and efficient.

  10. Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition.

    PubMed

    Song, Jiang-Ning; Wang, Ming-Lei; Li, Wei-Jiang; Xu, Wen-Bo

    2004-05-21

    In this paper, a novel approach has been introduced to predict the disulfide-bonding state of cysteines in proteins by means of a linear discriminator based on their dipeptide composition. The prediction is performed with a newly enlarged dataset with 8114 cysteine-containing segments extracted from 1856 non-homologous proteins of well-resolved three-dimensional structures. The oxidation of cysteines exhibits obvious cooperativity: almost all cysteines in disulfide-bond-containing proteins are in the oxidized form. This cooperativity can be well described by protein's dipeptide composition, based on which the prediction accuracy of the oxidation form of cysteines scores as high as 89.1% and 85.2%, when measured on cysteine and protein basis using the rigorous jack-knife procedure, respectively. The result demonstrates the applicability of this new relatively simple method and provides superior prediction performance compared with existing methods for the prediction of the oxidation states of cysteines in proteins.

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

    PubMed

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

    2015-11-10

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

  12. Bayesian methods of confidence interval construction for the population attributable risk from cross-sectional studies.

    PubMed

    Pirikahu, Sarah; Jones, Geoffrey; Hazelton, Martin L; Heuer, Cord

    2016-08-15

    Population attributable risk measures the public health impact of the removal of a risk factor. To apply this concept to epidemiological data, the calculation of a confidence interval to quantify the uncertainty in the estimate is desirable. However, because perhaps of the confusion surrounding the attributable risk measures, there is no standard confidence interval or variance formula given in the literature. In this paper, we implement a fully Bayesian approach to confidence interval construction of the population attributable risk for cross-sectional studies. We show that, in comparison with a number of standard Frequentist methods for constructing confidence intervals (i.e. delta, jackknife and bootstrap methods), the Bayesian approach is superior in terms of percent coverage in all except a few cases. This paper also explores the effect of the chosen prior on the coverage and provides alternatives for particular situations. Copyright © 2016 John Wiley & Sons, Ltd.

  13. Using compound similarity and functional domain composition for prediction of drug-target interaction networks.

    PubMed

    Chen, Lei; He, Zhi-Song; Huang, Tao; Cai, Yu-Dong

    2010-11-01

    Study of interactions between drugs and target proteins is an essential step in genomic drug discovery. It is very hard to determine the compound-protein interactions or drug-target interactions by experiment alone. As supplementary, effective prediction model using machine learning or data mining methods can provide much help. In this study, a prediction method based on Nearest Neighbor Algorithm and a novel metric, which was obtained by combining compound similarity and functional domain composition, was proposed. The target proteins were divided into the following groups: enzymes, ion channels, G protein-coupled receptors, and nuclear receptors. As a result, four predictors with the optimal parameters were established. The overall prediction accuracies, evaluated by jackknife cross-validation test, for four groups of target proteins are 90.23%, 94.74%, 97.80%, and 97.51%, respectively, indicating that compound similarity and functional domain composition are very effective to predict drug-target interaction networks.

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

    PubMed

    Emura, Takeshi; Konno, Yoshihiko; Michimae, Hirofumi

    2015-07-01

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

  15. Predicting protein structural class by incorporating patterns of over-represented k-mers into the general form of Chou's PseAAC.

    PubMed

    Qin, Yu-Fang; Wang, Chun-Hua; Yu, Xiao-Qing; Zhu, Jie; Liu, Tai-Gang; Zheng, Xiao-Qi

    2012-04-01

    Computational prediction of protein structural class based on sequence data remains a challenging problem in current protein science. In this paper, a new feature extraction approach based on relative polypeptide composition is introduced. This approach could take into account the background distribution of a given k-mer under a Markov model of order k-2, and avoid the curse of dimensionality with the increase of k by using a T-statistic feature selection strategy. The selected features are then fed to a support vector machine to perform the prediction. To verify the performance of our method, jackknife cross-validation tests are performed on four widely used benchmark datasets. Comparison of our results with existing methods shows that our method provides satisfactory performance for structural class prediction.

  16. Using principal component analysis and support vector machine to predict protein structural class for low-similarity sequences via PSSM.

    PubMed

    Zhang, Shengli; Ye, Feng; Yuan, Xiguo

    2012-01-01

    The accurate identification of protein structure class solely using extracted information from protein sequence is a complicated task in the current computational biology. Prediction of protein structural class for low-similarity sequences remains a challenging problem. In this study, the new computational method has been developed to predict protein structural class by fusing the sequence information and evolution information to represent a protein sample. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark data-sets, 1189 and 25PDB with sequence similarity lower than 40 and 25%, respectively. Comparison of our results with other methods shows that the proposed method by us is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity data-sets.

  17. A protein structural classes prediction method based on PSI-BLAST profile.

    PubMed

    Ding, Shuyan; Yan, Shoujiang; Qi, Shuhua; Li, Yan; Yao, Yuhua

    2014-07-21

    Knowledge of protein structural classes plays an important role in understanding protein folding patterns. Prediction of protein structural class based solely on sequence data remains to be a challenging problem. In this study, we extract the long-range correlation information and linear correlation information from position-specific score matrix (PSSM). A total of 3600 features are extracted, then, 278 features are selected by a filter feature selection method based on 1189 dataset. To verify the performance of our method (named by LCC-PSSM), jackknife tests are performed on three widely used low similarity benchmark datasets. Comparison of our results with the existing methods shows that our method provides the favorable performance for protein structural class prediction. Stand-alone version of the proposed method (LCC-PSSM) is written in MATLAB language and it can be downloaded from http://bioinfo.zstu.edu.cn/LCC-PSSM/.

  18. 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.

  19. Predicting Presynaptic and Postsynaptic Neurotoxins by Developing Feature Selection Technique

    PubMed Central

    Yang, Yunchun; Zhang, Chunmei; Chen, Rong; Huang, Po

    2017-01-01

    Presynaptic and postsynaptic neurotoxins are proteins which act at the presynaptic and postsynaptic membrane. Correctly predicting presynaptic and postsynaptic neurotoxins will provide important clues for drug-target discovery and drug design. In this study, we developed a theoretical method to discriminate presynaptic neurotoxins from postsynaptic neurotoxins. A strict and objective benchmark dataset was constructed to train and test our proposed model. The dipeptide composition was used to formulate neurotoxin samples. The analysis of variance (ANOVA) was proposed to find out the optimal feature set which can produce the maximum accuracy. In the jackknife cross-validation test, the overall accuracy of 94.9% was achieved. We believe that the proposed model will provide important information to study neurotoxins. PMID:28303250

  20. The Development of a Statistical Decision Aid for Psychiatric Case Identification of Alcohol Use Disorder in the Eastern Baltimore Community

    PubMed Central

    Rizik, Peter D.

    1984-01-01

    The development of a case identification decision support tool in a Public Health setting is presented in this research. The analytic problem is described as the classification problem (Duda and Hart, 1974). Using logistic regression with a variable selection option enables iterative improvements in classification criteria through dimensionality reduction and subspace modification. The performance of the classifier on new samples is simulated by a subset jackknife technique which trains the model on one portion of the sample and tests on the other portion. Repeating this several times gives estimates of case detection and suggests underlying patterns of predictive variable sets through key variable selections and parameter estimate stability. From these estimates, positive and negative predictive values and referral rates can be estimated for proper evaluation of the tool.

  1. 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 δ(13)C, δ(15)N, and δ(18)O compositions were in agreement with those previously reported for green coffee beans. The δ(15)N composition was seen to be related to organic cultivation, reflected in both δ(2)H and δ(18)O compositions. The δ(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.

  2. Trajectory Clustering: a Non-Parametric Method for Grouping Gene Expression Time Courses, with Applications to Mammary Development

    PubMed Central

    Phang, T.L.; Neville, M.C.; Rudolph, M.; Hunter, L.

    2008-01-01

    Trajectory clustering is a novel and statistically well-founded method for clustering time series data from gene expression arrays. Trajectory clustering uses non-parametric statistics and is hence not sensitive to the particular distributions underlying gene expression data. Each cluster is clearly defined in terms of direction of change of expression for successive time points (its ‘trajectory’), and therefore has easily appreciated biological meaning. Applying the method to a dataset from mouse mammary gland development, we demonstrate that it produces different clusters than Hierarchical, K-means, and Jackknife clustering methods, even when those methods are applied to differences between successive time points. Compared to all of the other methods, trajectory clustering was better able to match a manual clustering by a domain expert, and was better able to cluster groups of genes with known related functions. PMID:12603041

  3. A Method for WD40 Repeat Detection and Secondary Structure Prediction

    PubMed Central

    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

  4. Review and research on feature selection methods from NMR data in biological fluids. Presentation of an original ensemble method applied to atherosclerosis field.

    PubMed

    Semmar, Nabil; Canlet, Cecile; Delplanque, Bernadette; Ruyet, Pascale Le; Paris, Alain; Martin, Jean-Charles

    2014-01-01

    Metabolic pools of biological matrices can be extensively analyzed by NMR. Measured data consist of hundreds of NMR signals with different chemical shifts and intensities representing different metabolites' types and levels, respectively. Relevant predictive NMR signals need to be extracted from the pool using variable selection methods. This paper presents both a review and research on this metabolomics field. After reviews on discriminant potentials and statistical analyses of NMR data in biological fields, the paper presents an original approach to extract a small number of NMR signals in a biological matrix A (BM-A) in order to predict metabolic levels in another biological matrix B (BM-B). Initially, NMR dataset of BM-A was decomposed into several row-column homogeneous blocks using hierarchical cluster analysis (HCA). Then, each block was subjected to a complete set of Jackknifed correspondence analysis (CA) by removing separately each individual (row). Each CA condensed the numerous NMR signals into some principal components (PCs). The different PCs representing the (n - 1) active individuals were used as latent variables in a stepwise multi-linear regression to predict metabolic levels in BM-B. From the built regression model, metabolite level in the outside individual was predicted (for next model validation). >From all the PCs-based regression models resulting from all the jackknifed CA applied on all the individuals, the most contributive NMR signals were identified by their highest absolute contributions to PCs. Finally, these selected NMR signals (measured in BMA) were used to build final population and sub-population regression models predicting metabolite levels in BM-B.

  5. Pharmacokinetics of amantadine in cats.

    PubMed

    Siao, K T; Pypendop, B H; Stanley, S D; Ilkiw, J E

    2011-12-01

    This study reports the pharmacokinetics of amantadine in cats, after both i.v. and oral administration. Six healthy adult domestic shorthair female cats were used. Amantadine HCl (5 mg/kg, equivalent to 4 mg/kg amantadine base) was administered either intravenously or orally in a crossover randomized design. Blood samples were collected immediately prior to amantadine administration, and at various times up to 1440 min following intravenous, or up to 2880 min following oral administration. Plasma amantadine concentrations were determined by liquid chromatography-mass spectrometry, and plasma amantadine concentration-time data were fitted to compartmental models. A two-compartment model with elimination from the central compartment best described the disposition of amantadine administered intravenously in cats, and a one-compartment model best described the disposition of oral amantadine in cats. After i.v. administration, the apparent volume of distribution of the central compartment and apparent volume of distribution at steady-state [mean ± SEM (range)], and the clearance and terminal half-life [harmonic mean ± jackknife pseudo-SD (range)] were 1.5 ± 0.3 (0.7-2.5) L/kg, 4.3 ± 0.2 (3.7-5.0) L/kg, 8.2 ± 2.1 (5.9-11.4) mL·min/kg, and 348 ± 49 (307-465) min, respectively. Systemic availability [mean ± SEM (range)] and terminal half-life after oral administration [harmonic mean ± jackknife pseudo-SD (range)] were 130 ± 11 (86-160)% and 324 ± 41 (277-381) min, respectively.

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

  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

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

    PubMed Central

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

    2004-01-01

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

  9. [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.

  10. Comparing performances of logistic regression and neural networks for predicting melatonin excretion patterns in the rat exposed to ELF magnetic fields.

    PubMed

    Jahandideh, Samad; Abdolmaleki, Parviz; Movahedi, Mohammad Mehdi

    2010-02-01

    Various studies have been reported on the bioeffects of magnetic field exposure; however, no consensus or guideline is available for experimental designs relating to exposure conditions as yet. In this study, logistic regression (LR) and artificial neural networks (ANNs) were used in order to analyze and predict the melatonin excretion patterns in the rat exposed to extremely low frequency magnetic fields (ELF-MF). Subsequently, on a database containing 33 experiments, performances of LR and ANNs were compared through resubstitution and jackknife tests. Predictor variables were more effective parameters and included frequency, polarization, exposure duration, and strength of magnetic fields. Also, five performance measures including accuracy, sensitivity, specificity, Matthew's Correlation Coefficient (MCC) and normalized percentage, better than random (S) were used to evaluate the performance of models. The LR as a conventional model obtained poor prediction performance. Nonetheless, LR distinguished the duration of magnetic fields as a statistically significant parameter. Also, horizontal polarization of magnetic fields with the highest logit coefficient (or parameter estimate) with negative sign was found to be the strongest indicator for experimental designs relating to exposure conditions. This means that each experiment with horizontal polarization of magnetic fields has a higher probability to result in "not changed melatonin level" pattern. On the other hand, ANNs, a more powerful model which has not been introduced in predicting melatonin excretion patterns in the rat exposed to ELF-MF, showed high performance measure values and higher reliability, especially obtaining 0.55 value of MCC through jackknife tests. Obtained results showed that such predictor models are promising and may play a useful role in defining guidelines for experimental designs relating to exposure conditions. In conclusion, analysis of the bioelectromagnetic data could result in

  11. Integrating local pastoral knowledge, participatory mapping, and species distribution modeling for risk assessment of invasive rubber vine (Cryptostegia grandiflora) in Ethiopia’s Afar region

    USGS Publications Warehouse

    Luizza, Matthew; Wakie, Tewodros; Evangelista, Paul; Jarnevich, Catherine S.

    2016-01-01

    The threats posed by invasive plants span ecosystems and economies worldwide. Local knowledge of biological invasions has proven beneficial for invasive species research, but to date no work has integrated this knowledge with species distribution modeling for invasion risk assessments. In this study, we integrated pastoral knowledge with Maxent modeling to assess the suitable habitat and potential impacts of invasive Cryptostegia grandiflora Robx. Ex R.Br. (rubber vine) in Ethiopia’s Afar region. We conducted focus groups with seven villages across the Amibara and Awash-Fentale districts. Pastoral knowledge revealed the growing threat of rubber vine, which to date has received limited attention in Ethiopia, and whose presence in Afar was previously unknown to our team. Rubber vine occurrence points were collected in the field with pastoralists and processed in Maxent with MODIS-derived vegetation indices, topographic data, and anthropogenic variables. We tested model fit using a jackknife procedure and validated the final model with an independent occurrence data set collected through participatory mapping activities with pastoralists. A Multivariate Environmental Similarity Surface analysis revealed areas with novel environmental conditions for future targeted surveys. Model performance was evaluated using area under the receiver-operating characteristic curve (AUC) and showed good fit across the jackknife models (average AUC = 0.80) and the final model (test AUC = 0.96). Our results reveal the growing threat rubber vine poses to Afar, with suitable habitat extending downstream of its current known location in the middle Awash River basin. Local pastoral knowledge provided important context for its rapid expansion due to acute changes in seasonality and habitat alteration, in addition to threats posed to numerous endemic tree species that provide critical provisioning ecosystem services. This work demonstrates the utility of integrating local ecological

  12. Abundance and species richness of Coreoidea (Hemiptera: Heteroptera) from Parque Estadual do Turvo, Southern Brazil.

    PubMed

    Barcellos, Aline; Schmidt, Letícia S; Brailovsky, Harry

    2008-01-01

    The coreoid fauna from Neotropics is poorly known, especially in terms of community studies. Aiming at contributing to this knowledge, a two-year study was carried out at Parque Estadual do Turvo, Municipality of Derrubadas, state of Rio Grande do Sul, Brazil, to evaluate the composition, abundance and species richness of Coreoidea. Samplings were conducted in the springs of 2003 and 2004 (October), and autumns of 2004 and 2005 (May), using beating tray method, along two trails of the park. Sampling effort (hours X collectors) totaled 153h. A total of 282 individuals of Coreoidea were collected, distributed in 28 species of Alydidae, Coreidae and Rhopalidae. The most abundant species was the coreid Cebrenis supina Brailovsky, representing 16% of the collected individuals, followed by the rhopalids Jadera aeola (Dallas), and Harmostes sp., with 12.1% and 11.7%, respectively. The estimated richnesses by Chao 1, Chao 2, Jackknife 1 and Jackknife 2 indicated that the observed richness corresponds to 70% to 80% of the expected for the area. The estimated richness through rarefaction was significantly higher in spring 2003 and autumn 2004 than in the other periods. There was no significant difference, however, between spring of 2003 and autumn of 2004, and between spring of 2004 and autumn of 2005, for the same parameter. Yucumã and Garcia trails did not differ significantly for the estimated richness. Singletons and doubletons represented 32.1% of the recorded species. Additionally, eight other species were obtained qualitatively by using, besides beating tray without protocol, manual collection.

  13. 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

  14. 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

  15. Forecasting natural aquifer discharge using a numerical model and convolution.

    PubMed

    Boggs, Kevin G; Johnson, Gary S; Van Kirk, Rob; Fairley, Jerry P

    2014-01-01

    If the nature of groundwater sources and sinks can be determined or predicted, the data can be used to forecast natural aquifer discharge. We present a procedure to forecast the relative contribution of individual aquifer sources and sinks to natural aquifer discharge. Using these individual aquifer recharge components, along with observed aquifer heads for each January, we generate a 1-year, monthly spring discharge forecast for the upcoming year with an existing numerical model and convolution. The results indicate that a forecast of natural aquifer discharge can be developed using only the dominant aquifer recharge sources combined with the effects of aquifer heads (initial conditions) at the time the forecast is generated. We also estimate how our forecast will perform in the future using a jackknife procedure, which indicates that the future performance of the forecast is good (Nash-Sutcliffe efficiency of 0.81). We develop a forecast and demonstrate important features of the procedure by presenting an application to the Eastern Snake Plain Aquifer in southern Idaho.

  16. Resampling methods for model fitting and model selection.

    PubMed

    Babu, G Jogesh

    2011-11-01

    Resampling procedures for fitting models and model selection are considered in this article. Nonparametric goodness-of-fit statistics are generally based on the empirical distribution function. The distribution-free property of these statistics does not hold in the multivariate case or when some of the parameters are estimated. Bootstrap methods to estimate the underlying distributions are discussed in such cases. The results hold not only in the case of one-dimensional parameter space, but also for the vector parameters. Bootstrap methods for inference, when the data is from an unknown distribution that may or may not belong to a specified family of distributions, are also considered. Most of the information criteria-based model selection procedures such as the Akaike information criterion, Bayesian information criterion, and minimum description length use estimation of bias. The bias, which is inevitable in model selection problems, arises mainly from estimating the distance between the "true" model and an estimated model. A jackknife type procedure for model selection is discussed, which instead of bias estimation is based on bias reduction.

  17. Relative importance of meteorological and geographical factors in the distribution of Fasciola hepatica infestation in farmed sheep in Qinghai province, China

    PubMed Central

    Qin, Hongyu; Gao, Xiang; Wang, Hongbin; Xiao, Jianhua

    2016-01-01

    Fasciola hepatica is an important trematode parasite of economic importance that infests sheep and cattle worldwide. We conducted a detailed investigation into the spatial distribution of F. hepatica infestation in farmed sheep in Qinghai (Wutumeiren) province, Mainland China. Mathematical modelling was used to assess the inter-relationships between meteorological and geographical factors and the risk of F. hepatica infestation across the province. A capture enzyme-linked immunosorbent assay (ELISA) test (MM3-SERO) was used to detect F. hepatica infestation. A niche model based on the maximum entropy method (MaxEnt) was used to estimate the influence of meteorological and geographical factors on the observed spatial distribution of F. hepatica infestation. Results of jackknife analysis indicated that temperature, precipitation, solar radiation, digital elevation and slope were associated with the occurrence of F. hepatica infestation, and that infestation rates were significantly higher among animals from districts with a high percentage of grassland habitat. The findings indicate that meteorological and geographical factors may be important variables affecting the distribution of F. hepatica infestation and should be taken into account in the development of future surveillance and control programmes for fascioliasis. PMID:28000591

  18. Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection.

    PubMed

    Gu, Quan; Ding, Yong-Sheng; Jiang, Xiao-Ying; Zhang, Tong-Liang

    2010-04-01

    Apoptosis proteins have a central role in the development and the homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. The function of an apoptosis protein is closely related to its subcellular location. It is crucial to develop powerful tools to predict apoptosis protein locations for rapidly increasing gap between the number of known structural proteins and the number of known sequences in protein databank. In this study, amino acids pair compositions with different spaces are used to construct feature sets for representing sample of protein feature selection approach based on binary particle swarm optimization, which is applied to extract effective feature. Ensemble classifier is used as prediction engine, of which the basic classifier is the fuzzy K-nearest neighbor. Each basic classifier is trained with different feature sets. Two datasets often used in prior works are selected to validate the performance of proposed approach. The results obtained by jackknife test are quite encouraging, indicating that the proposed method might become a potentially useful tool for subcellular location of apoptosis protein, or at least can play a complimentary role to the existing methods in the relevant areas. The supplement information and software written in Matlab are available by contacting the corresponding author.

  19. Perturbative approach to covariance matrix of the matter power spectrum

    SciTech Connect

    Mohammed, Irshad; Seljak, Uros; Vlah, Zvonimir

    2016-06-30

    We evaluate the covariance matrix of the matter power spectrum using perturbation theory up to dominant terms at 1-loop order and compare it to numerical simulations. We decompose the covariance matrix into the disconnected (Gaussian) part, trispectrum from the modes outside the survey (beat coupling or super-sample variance), and trispectrum from the modes inside the survey, and show how the different components contribute to the overall covariance matrix. We find the agreement with the simulations is at a 10\\% level up to $k \\sim 1 h {\\rm Mpc^{-1}}$. We show that all the connected components are dominated by the large-scale modes ($k<0.1 h {\\rm Mpc^{-1}}$), regardless of the value of the wavevectors $k,\\, k'$ of the covariance matrix, suggesting that one must be careful in applying the jackknife or bootstrap methods to the covariance matrix. We perform an eigenmode decomposition of the connected part of the covariance matrix, showing that at higher $k$ it is dominated by a single eigenmode. The full covariance matrix can be approximated as the disconnected part only, with the connected part being treated as an external nuisance parameter with a known scale dependence, and a known prior on its variance for a given survey volume. Finally, we provide a prescription for how to evaluate the covariance matrix from small box simulations without the need to simulate large volumes.

  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. The potential distribution of Phlebotomus papatasi (Diptera: Psychodidae) in Libya based on ecological niche model.

    PubMed

    Abdel-Dayem, M S; Annajar, B B; Hanafi, H A; Obenauer, P J

    2012-05-01

    The increased cases of cutaneous leishmaniasis vectored by Phlebotomus papatasi (Scopoli) in Libya have driven considerable effort to develop a predictive model for the potential geographical distribution of this disease. We collected adult P. papatasi from 17 sites in Musrata and Yefern regions of Libya using four different attraction traps. Our trap results and literature records describing the distribution of P. papatasi were incorporated into a MaxEnt algorithm prediction model that used 22 environmental variables. The model showed a high performance (AUC = 0.992 and 0.990 for training and test data, respectively). High suitability for P. papatasi was predicted to be largely confined to the coast at altitudes <600 m. Regions south of 300 degrees N latitude were calculated as unsuitable for this species. Jackknife analysis identified precipitation as having the most significant predictive power, while temperature and elevation variables were less influential. The National Leishmaniasis Control Program in Libya may find this information useful in their efforts to control zoonotic cutaneous leishmaniasis. Existing records are strongly biased toward a few geographical regions, and therefore, further sand fly collections are warranted that should include documentation of such factors as soil texture and humidity, land cover, and normalized difference vegetation index (NDVI) data to increase the model's predictive power.

  2. Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition.

    PubMed

    Chen, Xin-Xin; Tang, Hua; Li, Wen-Chao; Wu, Hao; Chen, Wei; Ding, Hui; Lin, Hao

    2016-01-01

    Owing to the abuse of antibiotics, drug resistance of pathogenic bacteria becomes more and more serious. Therefore, it is interesting to develop a more reasonable way to solve this issue. Because they can destroy the bacterial cell structure and then kill the infectious bacterium, the bacterial cell wall lyases are suitable candidates of antibacteria sources. Thus, it is urgent to develop an accurate and efficient computational method to predict the lyases. Based on the consideration, in this paper, a set of objective and rigorous data was collected by searching through the Universal Protein Resource (the UniProt database), whereafter a feature selection technique based on the analysis of variance (ANOVA) was used to acquire optimal feature subset. Finally, the support vector machine (SVM) was used to perform prediction. The jackknife cross-validated results showed that the optimal average accuracy of 84.82% was achieved with the sensitivity of 76.47% and the specificity of 93.16%. For the convenience of other scholars, we built a free online server called Lypred. We believe that Lypred will become a practical tool for the research of cell wall lyases and development of antimicrobial agents.

  3. 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.

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

    PubMed Central

    Cameron, Kenneth M.

    2009-01-01

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

  5. Mapping the climatic suitable habitat of oriental arborvitae (Platycladus orientalis) for introduction and cultivation at a global scale

    PubMed Central

    Li, Guoqing; Du, Sheng; Wen, Zhongming

    2016-01-01

    Oriental arborvitae (Platycladus orientalis) is an important afforestation and ornamental tree species, which is native in eastern Asian. Therefore, a global suitable habitat map for oriental arborvitae is urgently needed for global promotion and cultivation. Here, the potential habitat and climatic requirements of oriental arborvitae at global scale were simulated using herbariums data and 13 thermal-moisture variables as input data for maximum entropy model (MaxEnt). The simulation performance of MaxEnt is evaluated by ten-fold cross-validation and a jackknife procedure. Results show that the potential habitat and climate envelop of oriental arborvitae can be successfully simulated by MaxEnt at global scale, with a mean test AUC value of 0.93 and mean training AUC value of 0.95. Thermal factors play more important roles than moisture factors in controlling the distribution boundary of oriental arborvitae’s potential ranges. There are about 50 countries suitable for introduction and cultivation of oriental arborvitae with an area of 2.0 × 107 km2, which occupied 13.8% of land area on the earth. This unique study will provide valuable information and insights needed to identify new regions with climatically suitable habitats for cultivation and introduction of oriental arborvitae around the world. PMID:27443221

  6. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

    PubMed Central

    Ragonnet-Cronin, Manon L.; Shilaih, Mohaned; Günthard, Huldrych F.; Hodcroft, Emma B.; Böni, Jürg; Fearnhill, Esther; Dunn, David; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Yang, Wan-Lin; Brown, Alison E.; Lycett, Samantha J.; Kouyos, Roger; Brown, Andrew J. Leigh

    2016-01-01

    Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes. PMID:27642070

  7. Analysis of secondary outcomes in nested case-control study designs.

    PubMed

    Kim, Ryung S; Kaplan, Robert C

    2014-10-30

    One of the main perceived advantages of using a case-cohort design compared with a nested case-control design in an epidemiologic study is the ability to evaluate with the same subcohort outcomes other than the primary outcome of interest. In this paper, we show that valid inferences about secondary outcomes can also be achieved in nested case-control studies by using the inclusion probability weighting method in combination with an approximate jackknife standard error that can be computed using existing software. Simulation studies demonstrate that when the sample size is sufficient, this approach yields valid type 1 error and coverage rates for the analysis of secondary outcomes in nested case-control designs. Interestingly, the statistical power of the nested case-control design was comparable with that of the case-cohort design when the primary and secondary outcomes were positively correlated. The proposed method is illustrated with the data from a cohort in Cardiovascular Health Study to study the association of C-reactive protein levels and the incidence of congestive heart failure.

  8. Population pharmacokinetics and limited sampling strategy for first-line tuberculosis drugs and moxifloxacin.

    PubMed

    Magis-Escurra, C; Later-Nijland, H M J; Alffenaar, J W C; Broeders, J; Burger, D M; van Crevel, R; Boeree, M J; Donders, A R T; van Altena, R; van der Werf, T S; Aarnoutse, R E

    2014-09-01

    Therapeutic drug monitoring (TDM) of tuberculosis (TB) drugs currently focuses on peak plasma concentrations, yet total exposure [area under the 24-h concentration-time curve (AUC₀₋₂₄)] is probably most relevant to the efficacy of these drugs. We therefore assessed population AUC₀₋₂₄ data for all four first-line TB drugs (rifampicin, isoniazid, pyrazinamide and ethambutol) as well as moxifloxacin and developed limited sampling strategies to estimate AUC₀₋₂₄ values conveniently. AUC₀₋₂₄ and other pharmacokinetic (PK) parameters were determined following intensive PK sampling in two Dutch TB referral centres. Best subset selection multiple linear regression was performed to derive limited sampling equations. Median percentage prediction error and median absolute percentage prediction error were calculated via jackknife analysis to evaluate bias and imprecision of the predictions. Geometric mean AUC₀₋₂₄ values for rifampicin, isoniazid, pyrazinamide, ethambutol and moxifloxacin were 41.1, 15.2, 380, 25.5 and 33.6 hmg/L, respectively. Limited sampling at various fixed sampling points enabled an accurate and precise prediction of AUC₀₋₂₄ values of all drugs separately and simultaneously. In the absence of clinically validated target values for AUC₀₋₂₄, average AUC₀₋₂₄ values can be used as reference values in TDM. Limited sampling of AUC₀₋₂₄ is feasible in many settings and allows for TDM to be performed at a larger scale.

  9. Trophic ecology of largemouth bass and northern pike in allopatric and sympatric assemblages in northern boreal lakes

    USGS Publications Warehouse

    Soupir, Craig A.; Brown, Michael L.; Kallemeyn, Larry W.

    2000-01-01

    Largemouth bass (Micropterus salmoides) and northern pike (Esox lucius) are top predators in the food chain in most aquatic environments that they occupy; however, limited information exists on species interactions in the northern reaches of largemouth bass distribution. We investigated the seasonal food habits of allopatric and sympatric assemblages of largemouth bass and northern pike in six interior lakes within Voyageurs National Park, Minnesota. Percentages of empty stomachs were variable for largemouth bass (38-54%) and northern pike (34.7-66.7%). Fishes (mainly yellow perch, Perca flavescens) comprised greater than 60% (mean percent mass, MPM) of the northern pike diet during all seasons in both allopatric and sympatric assemblages. Aquatic insects (primarily Odonata and Hemiptera) were important in the diets of largemouth bass in all communities (0.0-79.7 MPM). Although largemouth bass were observed in the diet of northern pike, largemouth bass apparently did not prey on northern pike. Seasonal differences were observed in the proportion of aquatic insects (P = 0.010) and fishes (P = 0.023) in the diets of northern pike and largemouth bass. Based on three food categories, jackknifed classifications correctly classified 77 and 92% of northern pike and largemouth bass values, respectively. Percent resource overlap values were biologically significant (greater than 60%) during at least one season in each sympatric assemblage, suggesting some diet overlap.

  10. Galaxy-galaxy lensing in the Dark Energy Survey Science Verification data

    NASA Astrophysics Data System (ADS)

    Clampitt, J.; Sánchez, C.; Kwan, J.; Krause, E.; MacCrann, N.; Park, Y.; Troxel, M. A.; Jain, B.; Rozo, E.; Rykoff, E. S.; Wechsler, R. H.; Blazek, J.; Bonnett, C.; Crocce, M.; Fang, Y.; Gaztanaga, E.; Gruen, D.; Jarvis, M.; Miquel, R.; Prat, J.; Ross, A. J.; Sheldon, E.; Zuntz, J.; Abbott, T. M. C.; Abdalla, F. B.; Armstrong, R.; Becker, M. R.; Benoit-Lévy, A.; Bernstein, G. M.; Bertin, E.; Brooks, D.; Burke, D. L.; Carnero Rosell, A.; Carrasco Kind, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Estrada, J.; Evrard, A. E.; Fausti Neto, A.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gruendl, R. A.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Lima, M.; March, M.; Marshall, J. L.; Martini, P.; Melchior, P.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Plazas, A. A.; Romer, A. K.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Vikram, V.; Walker, A. R.

    2017-03-01

    We present galaxy-galaxy lensing results from 139 deg2 of Dark Energy Survey (DES) Science Verification (SV) data. Our lens sample consists of red galaxies, known as redMaGiC, which are specifically selected to have a low photometric redshift error and outlier rate. The lensing measurement has a total signal-to-noise ratio of 29 over scales 0.09 < R < 15 Mpc h-1, including all lenses over a wide redshift range 0.2 < z < 0.8. Dividing the lenses into three redshift bins for this constant moving number density sample, we find no evidence for evolution in the halo mass with redshift. We obtain consistent results for the lensing measurement with two independent shear pipelines, NGMIX and IM3SHAPE. We perform a number of null tests on the shear and photometric redshift catalogues and quantify resulting systematic uncertainties. Covariances from jackknife subsamples of the data are validated with a suite of 50 mock surveys. The result and systematic checks in this work provide a critical input for future cosmological and galaxy evolution studies with the DES data and redMaGiC galaxy samples. We fit a halo occupation distribution (HOD) model, and demonstrate that our data constrain the mean halo mass of the lens galaxies, despite strong degeneracies between individual HOD parameters.

  11. Radiological technologists' performance for the detection of malignant microcalcifications in digital mammograms without and with a computer-aided detection system.

    PubMed

    Tanaka, Rie; Takamori, Miho; Uchiyama, Yoshikazu; Shiraishi, Junji

    2015-04-01

    The aim of this study was to investigate the diagnostic performance of radiological technologists (RTs) in the detection of malignant microcalcifications and to evaluate how much computer-aided detection (CADe) improved their performances compared with those by expert breast radiologists (BRs). Six board-certified breast RTs and four board-certified BRs participated in a free-response receiver operating characteristic observer study. The dataset consisted of 75 cases (25 malignant, 25 benign, and 25 normal cases) of digital mammograms, selected from the digital database for screening mammography provided by the University of South Florida. Average figure of merit (FOM) of the RTs' performances was statistically analyzed using jack-knife free-response receiver operating characteristic and compared with that of expert BRs. The detection performance of RTs was significantly improved by using CADe; average sensitivity was increased from 46.7% to 56.7%, with a decrease in the average number of false positives per case from 0.19 to 0.13. Detection accuracy of an average FOM was improved from 0.680 to 0.816 ([Formula: see text]) and the difference in FOMs between RTs and radiologists failed to reach statistical significance. RTs' performances for the identification of malignant microcalcifications on digital mammography were sufficiently high and comparable to those of radiologists by using CADe.

  12. 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).

  13. BICEP2 / Keck Array V: Measurements of B-mode polarization at degree angular scales and 150 GHz by the Keck Array

    DOE PAGES

    Ade, P. A. R.; Ahmed, Z.; Aikin, R. W.; ...

    2015-09-29

    Here, 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 spectralmore » 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.« less

  14. Regional frequency analysis at ungauged sites using a two-stage resampling generalized ensemble framework

    NASA Astrophysics Data System (ADS)

    Alobaidi, Mohammad H.; Marpu, Prashanth R.; Ouarda, Taha B. M. J.; Chebana, Fateh

    2015-10-01

    Regional frequency analysis (RFA) deals with the estimation of hydrological characteristics at sites where little or no data is available. Recently, machine learning applications to RFA have received considerable attention in terms of their flexibility in modeling as well as superior generalization ability compared to conventional approaches. The proper application of machine learning techniques, however, requires good understanding of the available information about system's dynamics, i.e. system variables. This paper presents two contributions to the literature. First, novel ensemble architecture, using a unique two-stage resampling approach, is proposed. The objective of the proposed ensemble model is to promote diversity within the individual learners and reduce over fitting. Second, the application of the proposed model is demonstrated in RFA case study to obtain improved regional flood quantile estimates at ungauged sites. A jackknife validation procedure is used for the evaluation of the model's performance. The method is applied to data from the province of Quebec, Canada. The model showed similar performance and generalization compared to major ensemble models in the literature, which were investigated in previous studies using the same data set. The proposed model confirmed the diversity requirement in ensemble modeling and, in the same time, validated the proposed model adherence to ensemble learning theory.

  15. iRNA-PseU: Identifying RNA pseudouridine sites

    PubMed Central

    Chen, Wei; Tang, Hua; Ye, Jing; Lin, Hao; Chou, Kuo-Chen

    2016-01-01

    As the most abundant RNA modification, pseudouridine plays important roles in many biological processes. Occurring at the uridine site and catalyzed by pseudouridine synthase, the modification has been observed in nearly all kinds of RNA, including transfer RNA, messenger RNA, small nuclear or nucleolar RNA, and ribosomal RNA. Accordingly, its importance to basic research and drug development is self-evident. Despite some experimental technologies have been developed to detect the pseudouridine sites, they are both time-consuming and expensive. Facing the explosive growth of RNA sequences in the postgenomic age, we are challenged to address the problem by computational approaches: For an uncharacterized RNA sequence, can we predict which of its uridine sites can be modified as pseudouridine and which ones cannot? Here a predictor called “iRNA-PseU” was proposed by incorporating the chemical properties of nucleotides and their occurrence frequency density distributions into the general form of pseudo nucleotide composition (PseKNC). It has been demonstrated via the rigorous jackknife test, independent dataset test, and practical genome-wide analysis that the proposed predictor remarkably outperforms its counterpart. For the convenience of most experimental scientists, the web-server for iRNA-PseU was established at http://lin.uestc.edu.cn/server/iRNA-PseU, by which users can easily get their desired results without the need to go through the mathematical details.

  16. Potential Distribution Map of Culicoides insignis (Diptera: Ceratopogonidae), Vector of Bluetongue Virus, in Northwestern Argentina.

    PubMed

    Veggiani Aybar, Cecilia A; Díaz Gomez, Romina A; Dantur Juri, María J; Lizarralde de Grosso, Mercedes S; Spinelli, Gustavo R

    2016-01-01

    Culicoides insignis Lutz is incriminated as a vector of bluetongue virus (BTV) to ruminants in America. In South America, almost all countries have serological evidence of BTV infections, but only four outbreaks of the disease have been reported. Although clinical diseases have never been cited in Argentina, viral activity has been detected in cattle. In this study, we developed a potential distribution map of Culicoides insignis populations in northwestern Argentina using Maximum Entropy Modeling (Maxent). For the analyses, information regarding both data of specimen collections between 2003 and 2013, and climatic and environmental variables was used. Variables selection was based on the ecological relevance in relation to Culicoides spp. biology and distribution in the area. The best Maxent model according to the Jackknife test included 53 C. insignis presence records and precipitation of the warmest quarter, altitude, and precipitation of the wettest month. Accuracy was evaluated by the area under the curve (AUC = 0.97). These results provide an important analytical resource of high potential for both the development of suitable control strategies and the assessment of disease transmission risk in the region.

  17. Meteorological conditions and land cover as predictors for the prevalence of Bluetongue virus in the Inner Mongolia Autonomous Region of Mainland China.

    PubMed

    Gao, Xiang; Qin, Hongyu; Xiao, Jianhua; Wang, Hongbin

    2017-03-01

    Bluetongue is a major disease of economic importance that affects ruminants worldwide. It is transmitted by species of Culicoides midges (Diptera: Ceratopogonidae). The Inner Mongolia Autonomous Region is one of the main pastoral areas for farmed sheep in Mainland China and, because of its large area, represents an ideal candidate region for the study of Bluetongue virus (BTV) distribution and prevalence characteristics. The present study conducted a detailed investigation into the spatial patterns of BTV transmission in sheep in the Inner Mongolia Autonomous Region, and assessed the inter-relationships between meteorological factors, land cover and the transmission of the virus was conducted. Reverse-transcriptase polymerase chain reaction (RT-PCR) was used for the determination of BTV infection in the surveyed animals. Between June 2013 and February 2015, 6199 sheep were subjected to virus detection and 2199 sheep (35.47%) were determined to be positive for BTV. Subsequently, a maximum entropy model (MaxEnt) was used to investigate the relationship between land cover, meteorological factors and the prevalence of BTV infection. Jackknife analysis revealed that the mean monthly temperature, rainfall and average wind speed were associated with the occurrence of BTV infection and that BTV infection positivity was significantly higher among animals from districts with a high percentage of grassland and forest area. Our findings indicate that meteorological factors and land cover may be important variables affecting transmission of BTV and should be taken into account in the development of future surveillance programmes for BTV.

  18. Stability and Uncertainty of Full Moment Tensor Solutions for M < 3.5 Induced Earthquakes

    NASA Astrophysics Data System (ADS)

    Boyd, O. S.; Dreger, D. S.

    2014-12-01

    The increase in earthquakes associated with industrial activities has created a need to investigate and characterize the source physics of induced seismicity. Many techniques and approaches are available to determine representative source parameters of these events. For M > 3.5 events, high quality seismic data from regional networks can be used to provide reasonable estimates of moment tensor solutions. In this investigation we explore various techniques and datasets to constrain full moment tensor solutions of M < 3.5 induced events, expanding upon the approach developed by Guilhem et al., 2014. Small magnitude events recorded by local seismic networks can yield good quality data with distinct body wave and converted phases depending upon the velocity structure and frequency range. Generating synthetic seismograms or Green's functions to accurately model these high frequency phases can be challenging. To investigate the variability associated with the choice of Green's functions, we test available codes to see how well they capture body wave phases. Other stability and uncertainty measures include the F-test, Jackknife test, residual bootstrap, and Network Sensitivity Solution, (Ford et al., 2009; Ford et al., 2010). Additional datasets to constrain the full moment tensor solution include P-wave first motions and amplitude ratios.

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

    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.

  20. 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.

  1. Discriminating lysosomal membrane protein types using dynamic neural network.

    PubMed

    Tripathi, Vijay; Gupta, Dwijendra Kumar

    2014-01-01

    This work presents a dynamic artificial neural network methodology, which classifies the proteins into their classes from their sequences alone: the lysosomal membrane protein classes and the various other membranes protein classes. In this paper, neural networks-based lysosomal-associated membrane protein type prediction system is proposed. Different protein sequence representations are fused to extract the features of a protein sequence, which includes seven feature sets; amino acid (AA) composition, sequence length, hydrophobic group, electronic group, sum of hydrophobicity, R-group, and dipeptide composition. To reduce the dimensionality of the large feature vector, we applied the principal component analysis. The probabilistic neural network, generalized regression neural network, and Elman regression neural network (RNN) are used as classifiers and compared with layer recurrent network (LRN), a dynamic network. The dynamic networks have memory, i.e. its output depends not only on the input but the previous outputs also. Thus, the accuracy of LRN classifier among all other artificial neural networks comes out to be the highest. The overall accuracy of jackknife cross-validation is 93.2% for the data-set. These predicted results suggest that the method can be effectively applied to discriminate lysosomal associated membrane proteins from other membrane proteins (Type-I, Outer membrane proteins, GPI-Anchored) and Globular proteins, and it also indicates that the protein sequence representation can better reflect the core feature of membrane proteins than the classical AA composition.

  2. 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.

  3. Comparison of two procedures for symptomatic hemorrhoidal disease: Ligation under Vision and Ferguson Hemorrhoidectomy - a retrospective cohort study

    PubMed Central

    Demir, Hakan; Karaman, Kerem; Ercan, Metin; Kocer, Havva Belma; Celebi, Fehmi

    2017-01-01

    Objective: To compare Ligation under Vision (LUV) with Ferguson Hemorrhoidectomy (FH) in patients with Grade II, III and IV hemorrhoidal diseases according to their postoperative outcomes. Methods: Between July 2008 and August 2014, 155 patients underwent FH and 120 patients LUV, in Sakarya University Teaching and Research Hospital. Our retrospective analysis focuses on postoperative complications, postoperative pain and rate of recurrence. In LUV procedure, submucosal tissue of the hemorrhoidal pile base was transfixed using absorbable sutures under direct vision through anoscope in the Jackknife position. Results: In a mean postoperative follow-up period of 51.76+/-22.3 months; ectropion, anal fissure, and anal incontinence were the most frequent complications. The overall complication rate was significantly less after LUV than FH, (6.7% vs. 14.2%, P=0.047). The complication rate and need for a second or third surgery did not significantly differ between the two procedures with the increase in affected quadrants (P>0.05). The visual analog scale (VAS) at 24 hours was similar in both groups (P=0.267). Conclusions: LUV is a safe, and practical procedure with similar outcomes compared to FH. LUV may be a better choice than excisional hemorrhoidectomies when three or four quadrants of the anal canal are involved with hemorrhoids as this reduces mucosal defect related possible complications such as ectropion and anal stenosis.

  4. BICEP2/KECK ARRAY V: MEASUREMENTS OF B-MODE POLARIZATION AT DEGREE ANGULAR SCALES AND 150 GHz BY THE KECK ARRAY

    SciTech Connect

    Ade, P. A. R.; Ahmed, Z.; Aikin, R. W.; Bock, J. J.; Brevik, J. A.; Crill, B. P.; Filippini, J. P.; Golwala, S. R.; Alexander, K. D.; Bischoff, C. A.; Buder, I.; Buza, V.; Connors, J.; Dvorkin, C.; Barkats, D.; Benton, S. J.; Bullock, E.; Dowell, C. D.; Duband, L.; Fliescher, S.; Collaboration: Keck Array and Bicep2 Collaborations; and others

    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 deg{sup 2} for an equivalent survey weight of 250,000 μK{sup −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.

  5. 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.

  6. 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.

  7. Statistics and frequency-domain moveout for multiple-taper receiver functions

    NASA Astrophysics Data System (ADS)

    Park, J.; Levin, V.

    2016-10-01

    The multiple-taper correlation (MTC) algorithm for the estimation of teleseismic receiver functions (RFs) has desirable statistical properties. This paper presents several adaptations to the MTC algorithm that exploit its frequency-domain uncertainty estimates to generate stable RFs that include moveout corrections for deeper interfaces. Narrow-band frequency averaging implicit in spectral cross-correlation restricts the MTC-based RF estimates to resolve Ps converted phases only at short delay times, appropriate to the upper 100 km of Earth's lithosphere. The Ps conversions from deeper interfaces can be reconstructed by the MTC algorithm in two ways. Event cross-correlation computes a cross-correlation of single-taper spectrum estimates for a cluster of events rather than for a set of eigenspectrum estimates of a single P coda. To extend the reach of the algorithm, pre-stack moveout corrections in the frequency domain preserves the formal uncertainties of the RF estimates, which are used to weight RF stacks. Moving-window migration retains the multiple-taper approach, but cross-correlates the P-polarized motion with time-delayed SH and SV motion to focus on a Ps phase of interest. The frequency-domain uncertainties of bin-averaged RFs do not translate directly into the time domain. A jackknife over data records in each bin stack offers uncertainty estimates in the time domain while preserving uncertainty weighting in the frequency-domain RF stack.

  8. Cosmic shear measurements with Dark Energy Survey Science Verification data

    NASA Astrophysics Data System (ADS)

    Becker, M. R.; Troxel, M. A.; MacCrann, N.; Krause, E.; Eifler, T. F.; Friedrich, O.; Nicola, A.; Refregier, A.; Amara, A.; Bacon, D.; Bernstein, G. M.; Bonnett, C.; Bridle, S. L.; Busha, M. T.; Chang, C.; Dodelson, S.; Erickson, B.; Evrard, A. E.; Frieman, J.; Gaztanaga, E.; Gruen, D.; Hartley, W.; Jain, B.; Jarvis, M.; Kacprzak, T.; Kirk, D.; Kravtsov, A.; Leistedt, B.; Peiris, H. V.; Rykoff, E. S.; Sabiu, C.; Sánchez, C.; Seo, H.; Sheldon, E.; Wechsler, R. H.; Zuntz, J.; Abbott, T.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Banerji, M.; Bauer, A. H.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Fausti Neto, A.; Fernandez, E.; Finley, D. A.; Flaugher, B.; Fosalba, P.; Gerdes, D. W.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; Maia, M. A. G.; March, M.; Martini, P.; Melchior, P.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Roodman, A.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, D.; Vikram, V.; Walker, A. R.; Dark Energy Survey Collaboration

    2016-07-01

    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 furthermore 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 compare the same jackknife procedure applied to the data and the simulations in order to search for additional sources of noise not captured by the simulations. We find no statistically significant extra sources of noise in the data. The overall detection significance with tomography for our highest source density catalog is 9.7 σ . Cosmological constraints from the measurements in this work are presented in a companion paper [DES et al., Phys. Rev. D 94, 022001 (2016).].

  9. Analysis of computer-aided detection techniques and signal characteristics for clustered microcalcifications on digital mammography and digital breast tomosynthesis

    NASA Astrophysics Data System (ADS)

    Samala, Ravi K.; Chan, Heang-Ping; Hadjiiski, Lubomir M.; Helvie, Mark A.

    2016-10-01

    With IRB approval, digital breast tomosynthesis (DBT) images of human subjects were collected using a GE GEN2 DBT prototype system. Corresponding digital mammograms (DMs) of the same subjects were collected retrospectively from patient files. The data set contained a total of 237 views of DBT and equal number of DM views from 120 human subjects, each included 163 views with microcalcification clusters (MCs) and 74 views without MCs. The data set was separated into training and independent test sets. The pre-processing, object prescreening and segmentation, false positive reduction and clustering strategies for MC detection by three computer-aided detection (CADe) systems designed for DM, DBT, and a planar projection image generated from DBT were analyzed. Receiver operating characteristic (ROC) curves based on features extracted from microcalcifications and free-response ROC (FROC) curves based on scores from MCs were used to quantify the performance of the systems. Jackknife FROC (JAFROC) and non-parametric analysis methods were used to determine the statistical difference between the FROC curves. The difference between the CADDM and CADDBT systems when the false positive rate was estimated from cases without MCs did not reach statistical significance. The study indicates that the large search space in DBT may not be a limiting factor for CADe to achieve similar performance as that observed in DM.

  10. Estimating temporal changes in extreme rainfall in Sicily Region (Italy)

    NASA Astrophysics Data System (ADS)

    Bonaccorso, Brunella; Aronica, Giuseppe

    2016-04-01

    An intensification of extreme rainfall events have characterized several areas of peninsular and insular Italy since the early 2000s, suggesting an upward ongoing trend likely driven by climate change. In the present study temporal changes in 1-, 3-, 6-, 12- and 24-hour annual maxima rainfall series from more than 200 sites in Sicily region (Italy) are examined. A regional study is performed in order to reduce the uncertainty in change detection related to the limited length of the available records of extreme rainfall series. More specifically, annual maxima series are treated according to a regional flood index - type approach to frequency analysis, by assuming stationarity on a decadal time scale. First a cluster analysis using at-site characteristics is used to determine homogeneous rainfall regions. Then, potential changes in regional L-moment ratios are analyzed using a 10-year moving window. Furthermore, the shapes of regional growth curves, derived by splitting the records into separate decades, are compared. In addition, a jackknife procedure is used to assess uncertainty in the fitted growth curves and to identify significant trends in quantile estimates. Results reveal that, despite L-moment ratios show a general decreasing trend and that growth curves corresponding to the last decade (2000-2009) are usually less steep than the ones of the previous periods, rainfall quantile estimates have increased during the 2000s due to a large increase in regional average median, mainly in Western Sicily.

  11. Landslide occurrences and recurrence intervals of heavy rainfalls in Japan

    NASA Astrophysics Data System (ADS)

    Saito, H.; Uchida, T.; Matsuyama, H.; Korup, O.

    2015-12-01

    Dealing with predicted increases in extreme weather conditions due to climate change requires robust knowledge about controls on rainfall-triggered landslides. This study developed the probable rainfall database from weather radar data, and analyzed the potential correlation between the landslide magnitude-frequency and the recurrence interval of the heavy rainfall across Japan. We analyzed 4,744 rainfall-induced landslides (Saito et al., 2014, Geology), 1 to 72 h rainfalls, and soil water index (SWI). We then estimated recurrence intervals for these rainfall parameters using a Gumbel distribution with jackknife fitting. Results showed that the recurrence intervals of rainfall events which caused landslides (<10^3 m^3) were less than 10 yr across Japan. The recurrence intervals increased with increases in landslide volumes. With regard to the landslides larger than 10^5 m^3, recurrence intervals of the rainfall events were more than 100 yr. These results suggest that recurrence intervals of heavy rainfalls are important for assessing regional landslide hazard in Japan.

  12. Mapping the climatic suitable habitat of oriental arborvitae (Platycladus orientalis) for introduction and cultivation at a global scale

    NASA Astrophysics Data System (ADS)

    Li, Guoqing; Du, Sheng; Wen, Zhongming

    2016-07-01

    Oriental arborvitae (Platycladus orientalis) is an important afforestation and ornamental tree species, which is native in eastern Asian. Therefore, a global suitable habitat map for oriental arborvitae is urgently needed for global promotion and cultivation. Here, the potential habitat and climatic requirements of oriental arborvitae at global scale were simulated using herbariums data and 13 thermal-moisture variables as input data for maximum entropy model (MaxEnt). The simulation performance of MaxEnt is evaluated by ten-fold cross-validation and a jackknife procedure. Results show that the potential habitat and climate envelop of oriental arborvitae can be successfully simulated by MaxEnt at global scale, with a mean test AUC value of 0.93 and mean training AUC value of 0.95. Thermal factors play more important roles than moisture factors in controlling the distribution boundary of oriental arborvitae’s potential ranges. There are about 50 countries suitable for introduction and cultivation of oriental arborvitae with an area of 2.0 × 107 km2, which occupied 13.8% of land area on the earth. This unique study will provide valuable information and insights needed to identify new regions with climatically suitable habitats for cultivation and introduction of oriental arborvitae around the world.

  13. 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

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

    PubMed

    Wang, Xiaofeng; Yan, Renxiang; Song, Jiangning

    2016-03-22

    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.

  15. Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils.

    PubMed

    Antweiler, Kai; Schreiter, Susanne; Keilwagen, Jens; Baldrian, Petr; Kropf, Siegfried; Smalla, Kornelia; Grosch, Rita; Heuer, Holger

    2017-03-01

    A statistical method was developed to test for equivalence of microbial communities analysed by next-generation sequencing of amplicons. The test uses Bray-Curtis distances between the microbial community structures and is based on a two-sample jackknife procedure. This approach was applied to investigate putative effects of the antifungal biocontrol strain RU47 on fungal communities in three arable soils which were analysed by high-throughput ITS amplicon sequencing. Two contrasting workflows to produce abundance tables of operational taxonomic units from sequence data were applied. For both, the developed test indicated highly significant equivalence of the fungal communities with or without previous exposure to RU47 for all soil types, with reference to fungal community differences in conjunction with field site or cropping history. However, minor effects of RU47 on fungal communities were statistically significant using highly sensitive multivariate tests. Nearly all fungal taxa responding to RU47 increased in relative abundance indicating the absence of ecotoxicological effects. Use of the developed equivalence test is not restricted to evaluate effects on soil microbial communities by inoculants for biocontrol, bioremediation or other purposes, but could also be applied for biosafety assessment of compounds like pesticides, or genetically engineered plants.

  16. BICEP2 / Keck Array V: Measurements of B-mode polarization at degree angular scales and 150 GHz by the Keck Array

    SciTech Connect

    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 IV, 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.; Thompson, K. L.; Tolan, J. E.; Turner, A. D.; Vieregg, A. G.; Weber, A. C.; Willmert, J.; Wong, C. L.; Yoon, K. W.

    2015-09-29

    Here, 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.

  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. Predicting the Potential Distribution of Polygala tenuifolia Willd. under Climate Change in China

    PubMed Central

    Li, Lin; Zhao, Yao; Pei, Lin; Zhao, Jiancheng

    2016-01-01

    Global warming has created opportunities and challenges for the survival and development of species. Determining how climate change may impact multiple ecosystem levels and lead to various species adaptations is necessary for both biodiversity conservation and sustainable biological resource utilization. In this study, we employed Maxent to predict changes in the habitat range and altitude of Polygala tenuifolia Willd. under current and future climate scenarios in China. Four representative concentration pathways (RCP2.6, RCP4.5, RCP6.0, and RCP8.5) were modeled for two time periods (2050 and 2070). The model inputs included 732 presence points and nine sets of environmental variables under the current conditions and the four RCPs in 2050 and 2070. The area under the receiver-operating characteristic (ROC) curve (AUC) was used to evaluate model performance. All of the AUCs were greater than 0.80, thereby placing these models in the “very good” category. Using a jackknife analysis, the precipitation in the warmest quarter, annual mean temperature, and altitude were found to be the top three variables that affect the range of P. tenuifolia. Additionally, we found that the predicted highly suitable habitat was in reasonable agreement with its actual distribution. Furthermore, the highly suitable habitat area was slowly reduced over time. PMID:27661983

  19. Identifying 2'-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions.

    PubMed

    Chen, Wei; Feng, Pengmian; Tang, Hua; Ding, Hui; Lin, Hao

    2016-06-01

    2'-O-methylationation is an important post-transcriptional modification and plays important roles in many biological processes. Although experimental technologies have been proposed to detect 2'-O-methylationation sites, they are cost-ineffective. As complements to experimental techniques, computational methods will facilitate the identification of 2'-O-methylationation sites. In the present study, we proposed a support vector machine-based method to identify 2'-O-methylationation sites. In this method, RNA sequences were formulated by nucleotide chemical properties and nucleotide compositions. In the jackknife cross-validation test, the proposed method obtained an accuracy of 95.58% for identifying 2'-O-methylationation sites in the human genome. Moreover, the model was also validated by identifying 2'-O-methylation sites in the Mus musculus and Saccharomyces cerevisiae genomes, and the obtained accuracies are also satisfactory. These results indicate that the proposed method will become a useful tool for the research on 2'-O-methylation.

  20. Angiosperm phylogeny based on matK sequence information.

    PubMed

    Hilu, Khidir W; Borsch, Thomas; Müller, Kai; Soltis, Douglas E; Soltis, Pamela S; Savolainen, Vincent; Chase, Mark W; Powell, Martyn P; Alice, Lawrence A; Evans, Rodger; Sauquet, Hervé; Neinhuis, Christoph; Slotta, Tracey A B; Rohwer, Jens G; Campbell, Christopher S; Chatrou, Lars W

    2003-12-01

    Plastid matK gene sequences for 374 genera representing all angiosperm orders and 12 genera of gymnosperms were analyzed using parsimony (MP) and Bayesian inference (BI) approaches. Traditionally, slowly evolving genomic regions have been preferred for deep-level phylogenetic inference in angiosperms. The matK gene evolves approximately three times faster than the widely used plastid genes rbcL and atpB. The MP and BI trees are highly congruent. The robustness of the strict consensus tree supercedes all individual gene analyses and is comparable only to multigene-based phylogenies. Of the 385 nodes resolved, 79% are supported by high jackknife values, averaging 88%. Amborella is sister to the remaining angiosperms, followed by a grade of Nymphaeaceae and Austrobaileyales. Bayesian inference resolves Amborella + Nymphaeaceae as sister to the rest, but with weak (0.42) posterior probability. The MP analysis shows a trichotomy sister to the Austrobaileyales representing eumagnoliids, monocots + Chloranthales, and Ceratophyllum + eudicots. The matK gene produces the highest internal support yet for basal eudicots and, within core eudicots, resolves a crown group comprising Berberidopsidaceae/Aextoxicaceae, Santalales, and Caryophyllales + asterids. Moreover, matK sequences provide good resolution within many angiosperm orders. Combined analyses of matK and other rapidly evolving DNA regions with available multigene data sets have strong potential to enhance resolution and internal support in deep level angiosperm phylogenetics and provide additional insights into angiosperm evolution.

  1. 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.

  2. A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%.

    PubMed Central

    Mehta, P. K.; Heringa, J.; Argos, P.

    1995-01-01

    To improve secondary structure predictions in protein sequences, the information residing in multiple sequence alignments of substituted but structurally related proteins is exploited. A database comprised of 70 protein families and a total of 2,500 sequences, some of which were aligned by tertiary structural superpositions, was used to calculate residue exchange weight matrices within alpha-helical, beta-strand, and coil substructures, respectively. Secondary structure predictions were made based on the observed residue substitutions in local regions of the multiple alignments and the largest possible associated exchange weights in each of the three matrix types. Comparison of the observed and predicted secondary structure on a per-residue basis yielded a mean accuracy of 72.2%. Individual alpha-helix, beta-strand, and coil states were respectively predicted at 66.7, and 75.8% correctness, representing a well-balanced three-state prediction. The accuracy level, verified by cross-validation through jack-knife tests on all protein families, dropped, on average, to only 70.9%, indicating the rigor of the prediction procedure. On the basis of robustness, conceptual clarity, accuracy, and executable efficiency, the method has considerable advantage, especially with its sole reliance on amino acid substitutions within structurally related proteins. PMID:8580842

  3. Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition

    PubMed Central

    Tang, Hua; Li, Wen-Chao; Wu, Hao; Ding, Hui

    2016-01-01

    Owing to the abuse of antibiotics, drug resistance of pathogenic bacteria becomes more and more serious. Therefore, it is interesting to develop a more reasonable way to solve this issue. Because they can destroy the bacterial cell structure and then kill the infectious bacterium, the bacterial cell wall lyases are suitable candidates of antibacteria sources. Thus, it is urgent to develop an accurate and efficient computational method to predict the lyases. Based on the consideration, in this paper, a set of objective and rigorous data was collected by searching through the Universal Protein Resource (the UniProt database), whereafter a feature selection technique based on the analysis of variance (ANOVA) was used to acquire optimal feature subset. Finally, the support vector machine (SVM) was used to perform prediction. The jackknife cross-validated results showed that the optimal average accuracy of 84.82% was achieved with the sensitivity of 76.47% and the specificity of 93.16%. For the convenience of other scholars, we built a free online server called Lypred. We believe that Lypred will become a practical tool for the research of cell wall lyases and development of antimicrobial agents. PMID:27437396

  4. Technical note: comparing von Luschan skin color tiles and modern spectrophotometry for measuring human skin pigmentation.

    PubMed

    Swiatoniowski, Anna K; Quillen, Ellen E; Shriver, Mark D; Jablonski, Nina G

    2013-06-01

    Prior to the introduction of reflectance spectrophotometry into anthropological field research during the 1950s, human skin color was most commonly classified by visual skin color matching using the von Luschan tiles, a set of 36 standardized, opaque glass tiles arranged in a chromatic scale. Our goal was to establish a conversion formula between the tile-based color matching method and modern reflectance spectrophotometry to make historical and contemporary data comparable. Skin pigmentation measurements were taken on the forehead, inner upper arms, and backs of the hands using both the tiles and a spectrophotometer on 246 participants showing a broad range of skin pigmentation. From these data, a second-order polynomial conversion formula was derived by jackknife analysis to estimate melanin index (M-index) based on tile values. This conversion formula provides a means for comparing modern data to von Luschan tile measurements recorded in historical reports. This is particularly important for populations now extinct, extirpated, or admixed for which tile-based measures of skin pigmentation are the only data available.

  5. HyspIRI Measurements of Agricultural Systems in California: 2013-2015

    NASA Astrophysics Data System (ADS)

    Townsend, P. A.; Kruger, E. L.; Singh, A.; Jablonski, A. D.; Kochaver, S.; Serbin, S.

    2015-12-01

    During 2013-2015, NASA collected high-altitude AVIRIS hyperspectral and MASTER thermal infrared imagery across large swaths of California in support of the HyspIRI planning and prototyping activities. During these campaigns, we made extensive measurements of photosynthetic capacity—Vcmax and Jmax—and their temperature sensitivities across a range of sites, crop types and environmental conditions. Our objectives were to characterize the physiological diversity of agricultural vegetation in California and develop generalizable algorithms to map these physiological parameters across several image acquisitions, regardless of crop type and canopy temperatures. We employed AVIRIS imagery to scale and estimate the vegetation parameters and MASTER surface temperature to provide context, since physiology responds exponentially to leaf temperature. We demonstrate a segmentation approach to disentangling leaf and background soil temperature, and then illustrate our retrievals of Vcmax and Jmax during overflight conditions across a large number of the 2013-2015 HyspIRI acquisitions. Our results show >80% repeatability (R2) across split sample jack-knifing, with RMSEs within 15% of the range of our data. The approach was robust across crop types (e.g., grape, almond, pistachio, avocado, pomegranate, oats, peppers, citrus, date palm, alfalfa, melons, beets) and leaf temperatures. A global imaging spectroscopy system such as HyspIRI will offer unprecedented ability to monitor agricultural crop performance under widely varying surface conditions.

  6. Japan unified hIgh-resolution relocated catalog for earthquakes (JUICE): Crustal seismicity beneath the Japanese Islands

    NASA Astrophysics Data System (ADS)

    Yano, Tomoko E.; Takeda, Tetsuya; Matsubara, Makoto; Shiomi, Katsuhiko

    2017-04-01

    We have generated a high-resolution catalog called the ;Japan Unified hIgh-resolution relocated Catalog for Earthquakes; (JUICE), which can be used to evaluate the geometry and seismogenic depth of active faults in Japan. We relocated > 1.1 million hypocenters from the NIED Hi-net catalog for events which occurred between January 2001 and December 2012, to a depth of 40 km. We apply a relative hypocenter determination method to the data in each grid square, in which entire Japan is divided into 1257 grid squares to parallelize the relocation procedure. We used a double-difference method, incorporating cross-correlating differential times as well as catalog differential times. This allows us to resolve, in detail, a seismicity distribution for the entire Japanese Islands. We estimated location uncertainty by a statistical resampling method, using Jackknife samples, and show that the uncertainty can be within 0.37 km in the horizontal and 0.85 km in the vertical direction with a 90% confidence interval for areas with good station coverage. Our seismogenic depth estimate agrees with the lower limit of the hypocenter distribution for a recent earthquake on the Kamishiro fault (2014, Mj 6.7), which suggests that the new catalog should be useful for estimating the size of future earthquakes for inland active faults.

  7. Identifying Antioxidant Proteins by Using Optimal Dipeptide Compositions.

    PubMed

    Feng, Pengmian; Chen, Wei; Lin, Hao

    2016-06-01

    Antioxidant proteins are a kind of molecules that can terminate cellular and DNA damages caused by free radical intermediates. The use of antioxidant proteins for prevention of diseases has been intensively studied in recent years. Thus, accurate identification of antioxidant proteins is essential for understanding their roles in pharmacology. In this study, a support vector machine-based predictor called AodPred was developed for identifying antioxidant proteins. In this predictor, the sequence was formulated by using the optimal 3-gap dipeptides obtained by using feature selection method. It was observed by jackknife cross-validation test that AodPred can achieve an overall accuracy of 74.79 % in identifying antioxidant proteins. As a user-friendly tool, AodPred is freely accessible at http://lin.uestc.edu.cn/server/AntioxiPred . To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results.

  8. A sedimentary paleomagnetic record of the Matuyama chron from the Western Antarctic margin (ODP Site 1101)

    NASA Astrophysics Data System (ADS)

    Guyodo, Yohan; Acton, Gary D.; Brachfeld, Stefanie; Channell, James E. T.

    2001-08-01

    A high-resolution paleomagnetic record for part of the Matuyama chron (0.7-2.1 Ma) is reported for Ocean Drilling Program Site 1101 (Leg 178), off the Antarctic Peninsula Pacific margin. A rock-magnetic investigation of 62 discrete samples revealed that the natural remanent magnetization (NRM) is carried by pseudo-single domain magnetite. Progressive alternating field demagnetization of 83 m of U-channels provided a polarity stratigraphy down to the Olduvai subchron. Two geomagnetic events preceding the Jaramillo subchron were identified, including the Cobb Mountain polarity interval. The bulk magnetic parameters vary by more than a factor of 20 over the entire time interval, but by less than a factor of 6 over the 0.7-1.1 Ma interval. This latter interval was selected for paleointensity determinations, which were carried out by normalizing the NRM by the anhysteretic remanent magnetization (ARM). Direct comparison of the Site 1101 paleointensity record with other curves available for the same time interval suggests a geomagnetic origin for features present in the record. A more quantitative comparison was achieved by means of a jackknife test performed on nine records of relative paleointensity over the 0.95-1.1 Ma interval. This test yielded no outlier for the period considered, confirming the geomagnetic character of the records. We have constructed a low-resolution stack revealing some of the characteristic paleointensity features of the Jaramillo subchron.

  9. [The genera of Bethylidae (Hymenoptera: Chrysidoidea) in four areas of Atlantic Rain Forest from Espírito Santo, Brazil].

    PubMed

    Mugrabi, Daniele F; Alencar, Isabel D C C; Barreto, Francisco C C; Azevedo, Celso O

    2008-01-01

    The generic richness and abundance of Bethylidae collected in four different hillside areas of Atlantic rain forest from Espírito Santo, Brazil were studied. The sites are Santa Maria de Jetibá (SMJ), Domingos Martins (DM), Pancas (P) and Atílio Vivacqua (AV). A total of 2,840 specimens of 12 genera were collected. Lepidosternopsis Ogloblin and Bakeriella Kieffer are first recorded from the State. Richness of taxa was calculated using first-order Jackknife richness with EstimateS program. Genera accumulation curves were ran to evaluate the samples. Abundance data were adjusted to the geometric distribution. Parameter k was used to compare areas. The generic profile was not equal for the sites we studied. The areas were considered disturbed. SMJ and DM presented genera richness bigger than in P and AV. The differences in the sites reflect the different preservation of each environment. Pseudisobrachium Kieffer and Dissomphalus Ashmead are most dominant genera in SMJ, DM and P, and Anisepyris Kieffer in AV. This study emphasizes the fact of Dissomphalus as the most abundant genus in rain forests. The generic profile found in AV is similar to that of some areas of Brazilian savannah.

  10. Fast estimation of motion from selected populations of retinal ganglion cells.

    PubMed

    Cerquera, Alexander; Freund, Jan

    2011-02-01

    We explore how the reconstruction efficiency of fast spike population codes varies with population size, population composition and code complexity. Our study is based on experiments with moving light patterns which are projected onto the isolated retina of a turtle Pseudemys scripta elegans. The stimulus features to reconstruct are sequences of velocities kept constant throughout segments of 500 ms. The reconstruction is based on the spikes of a retinal ganglion cell (RGC) population recorded extracellularly via a multielectrode array. Subsequent spike sorting yields the parallel spike trains of 107 RGCs as input to the reconstruction method, here a discriminant analysis trained and tested in jack-knife fashion. Motivated by behavioral response times, we concentrate on fast reconstruction, i.e., within 150 ms following a trigger event defined via significant changes of the population spike rate. Therefore, valid codes involve only few (≤3) spikes per cell. Using only the latency t(1) of each cell (with reference to the trigger event) corresponds to the most parsimonious population code considered. We evaluate the gain in reconstruction efficiency when supplementing t(1) by spike times t(2) and t(3). Furthermore, we investigate whether sub-populations of smaller size benefit significantly from a selection process or whether random compilations are equally efficient. As selection criteria we try different concepts (directionality, reliability, and discriminability). Finally, we discuss the implications of a selection process and its inter-relation with code complexity for optimized reconstruction.

  11. Separation of malignant and benign masses using image and segmentation features

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

    The purpose of this study is to investigate the efficacy of image features versus likelihood features of tumor boundaries for differentiating benign and malignant tumors and to compare the effectiveness of two neural networks in the classification study: (1) circular processing-based neural network and (2) conventional Multilayer Perceptron (MLP). The segmentation method used is an adaptive region growing technique coupled with a fuzzy shadow approach and maximum likelihood analyzer. Intensity, shape, texture, and likelihood features were calculated for the extracted Region of Interest (ROI). We performed these studies: experiment number 1 utilized image features used as inputs and the MLP for classification, experiment number 2 utilized image features used as inputs and the neural net with circular processing for classification, and experiment number 3 used likelihood values as inputs and the MLP for classification. The experiments were validated using an ROC methodology. We have tested these methods on 51 mammograms using a leave-one-case-out experiment (i.e., Jackknife procedure). The Az values for the four experiments were as follows: 0.66 in experiment number 1, 0.71 in experiment number 2, and 0.84 in experiment number 3.

  12. Construction of Abdominal Probabilistic Atlases and Their Value in Segmentation of Normal Organs in Abdominal CT Scans

    NASA Astrophysics Data System (ADS)

    Park, Hyunjin; Hero, Alfred; Bland, Peyton; Kessler, Marc; Seo, Jongbum; Meyer, Charles

    A good abdominal probabilistic atlas can provide important information to guide segmentation and registration applications in the abdomen. Here we build and test probabilistic atlases using 24 abdominal CT scans with available expert manual segmentations. Atlases are built by picking a target and mapping other training scans onto that target and then summing the results into one probabilistic atlas. We improve our previous abdominal atlas by 1) choosing a least biased target as determined by a statistical tool, i.e. multidimensional scaling operating on bending energy, 2) using a better set of control points to model the deformation, and 3) using higher information content CT scans with visible internal liver structures. One atlas is built in the least biased target space and two atlases are built in other target spaces for performance comparisons. The value of an atlas is assessed based on the resulting segmentations; whichever atlas yields the best segmentation performance is considered the better atlas. We consider two segmentation methods of abdominal volumes after registration with the probabilistic atlas: 1) simple segmentation by atlas thresholding and 2) application of a Bayesian maximum a posteriori method. Using jackknifing we measure the atlas-augmented segmentation performance with respect to manual expert segmentation and show that the atlas built in the least biased target space yields better segmentation performance than atlases built in other target spaces.

  13. Estimation of Distribution Overlap of Urn Models

    PubMed Central

    Hampton, Jerrad; Lladser, Manuel E.

    2012-01-01

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

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

    PubMed

    Tang, Hua; Chen, Wei; Lin, Hao

    2016-04-01

    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.

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

    PubMed

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

    2014-08-01

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

  16. Cosmic shear measurements with Dark Energy Survey Science Verification data

    SciTech Connect

    Becker, M. R.

    2016-07-06

    Here, 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.

  17. Improvement of Source Number Estimation Method for Single Channel Signal

    PubMed Central

    Du, Bolun; He, Yunze

    2016-01-01

    Source number estimation methods for single channel signal have been investigated and the improvements for each method are suggested in this work. Firstly, the single channel data is converted to multi-channel form by delay process. Then, algorithms used in the array signal processing, such as Gerschgorin’s disk estimation (GDE) and minimum description length (MDL), are introduced to estimate the source number of the received signal. The previous results have shown that the MDL based on information theoretic criteria (ITC) obtains a superior performance than GDE at low SNR. However it has no ability to handle the signals containing colored noise. On the contrary, the GDE method can eliminate the influence of colored noise. Nevertheless, its performance at low SNR is not satisfactory. In order to solve these problems and contradictions, the work makes remarkable improvements on these two methods on account of the above consideration. A diagonal loading technique is employed to ameliorate the MDL method and a jackknife technique is referenced to optimize the data covariance matrix in order to improve the performance of the GDE method. The results of simulation have illustrated that the performance of original methods have been promoted largely. PMID:27736959

  18. 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.

  19. Land use and soil contamination with Toxoplasma gondii oocysts in urban areas.

    PubMed

    Gao, Xiang; Wang, Hongbin; Wang, Huan; Qin, Hongyu; Xiao, Jianhua

    2016-10-15

    Because soil contaminated with Toxoplasma gondii oocysts is increasingly recognized as a major source of infection for humans, in this study, we investigated the spatial pattern of soil contamination with T. gondii oocysts in urban area of northeastern Mainland China. From April 2014 to May 2015, more than 9000 soil samples were collected. Detection of T. gondii oocysts was performed applying real-time quantitative PCR. Sensitivity was improved by analyzing four replicates for each sampling point. T. gondii was detected in 30.3% of all samples. Subsequently, a maximum entropy model was used to evaluate the effect of land use and intrinsic soil properties on the risk of contamination with oocysts. Jackknife analysis revealed that the likelihood for positive results is significantly enhanced in soil originating from foci of human habitation, wood land and grass land. Furthermore, soil temperature and humidity significantly influence the probability of contamination with T. gondii oocysts. Our findings indicate that land use may affect distribution of T. gondii oocysts in urban areas.

  20. Inference of hazel grouse population structure using multilocus data: a landscape genetic approach.

    PubMed

    Sahlsten, J; Thörngren, H; Höglund, J

    2008-12-01

    In conservation and management of species it is important to make inferences about gene flow, dispersal and population structure. In this study, we used 613 georeferenced tissue samples from hazel grouse (Bonasa bonasia) where each individual was genotyped at 12 microsatellite loci to make inference on population genetic structure, gene flow and dispersal in northern Sweden. Observed levels of genetic diversity suggest that Swedish hazel grouse do not suffer loss of genetic diversity compared with other grouse species. We found significant F(IS) (deviation from Hardy-Weinberg expectations) over the entire sample using jack-knifed estimators over loci, which is most likely explained by a Wahlund effect. With the use of spatial autocorrelation methods, we detected significant isolation by distance among individuals. Neighbourhood size was estimated in the order of 62-158 individuals corresponding to a dispersal distance of 950-1500 m. Using a spatial statistical model for landscape genetics to infer the number of populations and the spatial location of genetic discontinuities between these populations we found indications that Swedish hazel grouse are divided into a northern and a southern population. We could not find a sharp border between these two populations and none of the observed borders appeared to coincide with any potential geographical barriers.These results imply that gene flow appears somewhat unrestricted in the boreal taiga forests of northern Sweden and that the two populations of hazel grouse in Sweden may be explained by the post-glacial reinvasion history of the Scandinavian Peninsula.

  1. 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.

  2. 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.

  3. Adjusting for unmeasured confounding due to either of two crossed factors with a logistic regression model.

    PubMed

    Li, Li; Brumback, Babette A; Weppelmann, Thomas A; Morris, J Glenn; Ali, Afsar

    2016-08-15

    Motivated by an investigation of the effect of surface water temperature on the presence of Vibrio cholerae in water samples collected from different fixed surface water monitoring sites in Haiti in different months, we investigated methods to adjust for unmeasured confounding due to either of the two crossed factors site and month. In the process, we extended previous methods that adjust for unmeasured confounding due to one nesting factor (such as site, which nests the water samples from different months) to the case of two crossed factors. First, we developed a conditional pseudolikelihood estimator that eliminates fixed effects for the levels of each of the crossed factors from the estimating equation. Using the theory of U-Statistics for independent but non-identically distributed vectors, we show that our estimator is consistent and asymptotically normal, but that its variance depends on the nuisance parameters and thus cannot be easily estimated. Consequently, we apply our estimator in conjunction with a permutation test, and we investigate use of the pigeonhole bootstrap and the jackknife for constructing confidence intervals. We also incorporate our estimator into a diagnostic test for a logistic mixed model with crossed random effects and no unmeasured confounding. For comparison, we investigate between-within models extended to two crossed factors. These generalized linear mixed models include covariate means for each level of each factor in order to adjust for the unmeasured confounding. We conduct simulation studies, and we apply the methods to the Haitian data. Copyright © 2016 John Wiley & Sons, Ltd.

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

    PubMed

    Gao, Yu-Fei; Yuan, Fei; 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.

  5. Galaxy-galaxy lensing in the Dark Energy Survey science verification data

    SciTech Connect

    Clampitt, J.; Sánchez, C.; Kwan, J.; Krause, E.; MacCrann, N.; Park, Y.; Troxel, M. A.; Jain, B.; Rozo, E.; Rykoff, E. S.; Wechsler, R. H.; Blazek, J.; Bonnett, C.; Crocce, M.; Fang, Y.; Gaztanaga, E.; Gruen, D.; Jarvis, M.; Prat, R. Miquel J.; Ross, A. J.; Sheldon, E.; Zuntz, J.; Abbott, T. M. C.; Abdalla, F. B.; Armstrong, R.; Becker, M. R.; Benoit-Lévy, A.; Bernstein, G. M.; Bertin, E.; Brooks, D.; Burke, D. L.; Carnero Rosell, A.; Carrasco Kind, M.; Cunha, C. E.; D’Andrea, C. B.; da Costa, L. N.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Estrada, J.; Evrard, A. E.; Neto, A. Fausti; Flaugher, B.; Fosalba, P.; Frieman, J.; Gruendl, R. A.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Lima, M.; March, M.; Marshall, J. L.; Martini, P.; Melchior, P.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Plazas, A. A.; Romer, A. K.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Vikram, V.; Walker, A. R.

    2016-11-22

    Here, we present galaxy-galaxy lensing results from 139 square degrees of Dark Energy Survey (DES) Science Verification (SV) data. Our lens sample consists of red galaxies, known as redMaGiC, which are specifically selected to have a low photometric redshift error and outlier rate. The lensing measurement has a total signal-to-noise of 29 over scales 0.09 < R < 15 Mpc/h, including all lenses over a wide redshift range 0.2 < z < 0.8. Dividing the lenses into three redshift bins for this constant moving number density sample, we find no evidence for evolution in the halo mass with redshift. We also obtain consistent results for the lensing measurement with two independent shear pipelines, ngmix and im3shape. We perform a number of null tests on the shear and photometric redshift catalogs and quantify resulting systematic uncertainties. Covariances from jackknife subsamples of the data are validated with a suite of 50 mock surveys. Our results and systematics checks in this work provide a critical input for future cosmological and galaxy evolution studies with the DES data and redMaGiC galaxy samples. We fit a Halo Occupation Distribution (HOD) model, and demonstrate that our data constrains the mean halo mass of the lens galaxies, despite strong degeneracies between individual HOD parameters.

  6. Galaxy-Galaxy Lensing in the DES Science Verification Data

    SciTech Connect

    Clampitt, J.; et al.

    2016-03-18

    We present galaxy-galaxy lensing results from 139 square degrees of Dark Energy Survey (DES) Science Verification (SV) data. Our lens sample consists of red galaxies, known as redMaGiC, which are specifically selected to have a low photometric redshift error and outlier rate. The lensing measurement has a total signal-to-noise of 29, including all lenses over a wide redshift range $0.2 < z < 0.8$. Dividing the lenses into three redshift bins, we find no evidence for evolution in the halo mass with redshift. We obtain consistent results for the lensing measurement with two independent shear pipelines, ngmix and im3shape. We perform a number of null tests on the shear and photometric redshift catalogs and quantify resulting systematic errors. Covariances from jackknife subsamples of the data are validated with a suite of 50 mock surveys. The results and systematics checks in this work provide a critical input for future cosmological and galaxy evolution studies with the DES data and redMaGiC galaxy samples. We fit a Halo Occupation Distribution (HOD) model, and demonstrate that our data constrains the mean halo mass of the lens galaxies, despite strong degeneracies between individual HOD parameters.

  7. 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.

  8. Galaxy-galaxy lensing in the Dark Energy Survey science verification data

    DOE PAGES

    Clampitt, J.; Sánchez, C.; Kwan, J.; ...

    2016-11-22

    Here, we present galaxy-galaxy lensing results from 139 square degrees of Dark Energy Survey (DES) Science Verification (SV) data. Our lens sample consists of red galaxies, known as redMaGiC, which are specifically selected to have a low photometric redshift error and outlier rate. The lensing measurement has a total signal-to-noise of 29 over scales 0.09 < R < 15 Mpc/h, including all lenses over a wide redshift range 0.2 < z < 0.8. Dividing the lenses into three redshift bins for this constant moving number density sample, we find no evidence for evolution in the halo mass with redshift. Wemore » also obtain consistent results for the lensing measurement with two independent shear pipelines, ngmix and im3shape. We perform a number of null tests on the shear and photometric redshift catalogs and quantify resulting systematic uncertainties. Covariances from jackknife subsamples of the data are validated with a suite of 50 mock surveys. Our results and systematics checks in this work provide a critical input for future cosmological and galaxy evolution studies with the DES data and redMaGiC galaxy samples. We fit a Halo Occupation Distribution (HOD) model, and demonstrate that our data constrains the mean halo mass of the lens galaxies, despite strong degeneracies between individual HOD parameters.« less

  9. AUTO-IK: a 2D indicator kriging program for the automated non-parametric modeling of local uncertainty in earth sciences

    PubMed Central

    Goovaerts, P.

    2008-01-01

    Indicator kriging provides a flexible interpolation approach that is well suited for datasets where: 1) many observations are below the detection limit, 2) the histogram is strongly skewed, or 3) specific classes of attribute values are better connected in space than others (e.g. low pollutant concentrations). To apply indicator kriging at its full potential requires, however, the tedious inference and modeling of multiple indicator semivariograms, as well as the post-processing of the results to retrieve attribute estimates and associated measures of uncertainty. This paper presents a computer code that performs automatically the following tasks: selection of thresholds for binary coding of continuous data, computation and modeling of indicator semivariograms, modeling of probability distributions at unmonitored locations (regular or irregular grids), and estimation of the mean and variance of these distributions. The program also offers tools for quantifying the goodness of the model of uncertainty within a cross-validation and jack-knife frameworks. The different functionalities are illustrated using heavy metal concentrations from the well-known soil Jura dataset. A sensitivity analysis demonstrates the benefit of using more thresholds when indicator kriging is implemented with a linear interpolation model, in particular for variables with positively skewed histograms. PMID:20161335

  10. AUTO-IK: a 2D indicator kriging program for the automated non-parametric modeling of local uncertainty in earth sciences.

    PubMed

    Goovaerts, P

    2009-06-01

    Indicator kriging provides a flexible interpolation approach that is well suited for datasets where: 1) many observations are below the detection limit, 2) the histogram is strongly skewed, or 3) specific classes of attribute values are better connected in space than others (e.g. low pollutant concentrations). To apply indicator kriging at its full potential requires, however, the tedious inference and modeling of multiple indicator semivariograms, as well as the post-processing of the results to retrieve attribute estimates and associated measures of uncertainty. This paper presents a computer code that performs automatically the following tasks: selection of thresholds for binary coding of continuous data, computation and modeling of indicator semivariograms, modeling of probability distributions at unmonitored locations (regular or irregular grids), and estimation of the mean and variance of these distributions. The program also offers tools for quantifying the goodness of the model of uncertainty within a cross-validation and jack-knife frameworks. The different functionalities are illustrated using heavy metal concentrations from the well-known soil Jura dataset. A sensitivity analysis demonstrates the benefit of using more thresholds when indicator kriging is implemented with a linear interpolation model, in particular for variables with positively skewed histograms.

  11. Identify submitochondria and subchloroplast locations with pseudo amino acid composition: approach from the strategy of discrete wavelet transform feature extraction.

    PubMed

    Shi, Shao-Ping; Qiu, Jian-Ding; Sun, Xing-Yu; Huang, Jian-Hua; Huang, Shu-Yun; Suo, Sheng-Bao; Liang, Ru-Ping; Zhang, Li

    2011-03-01

    It is very challenging and complicated to predict protein locations at the sub-subcellular level. The key to enhancing the prediction quality for protein sub-subcellular locations is to grasp the core features of a protein that can discriminate among proteins with different subcompartment locations. In this study, a different formulation of pseudoamino acid composition by the approach of discrete wavelet transform feature extraction was developed to predict submitochondria and subchloroplast locations. As a result of jackknife cross-validation, with our method, it can efficiently distinguish mitochondrial proteins from chloroplast proteins with total accuracy of 98.8% and obtained a promising total accuracy of 93.38% for predicting submitochondria locations. Especially the predictive accuracy for mitochondrial outer membrane and chloroplast thylakoid lumen were 82.93% and 82.22%, respectively, showing an improvement of 4.88% and 27.22% when other existing methods were compared. The results indicated that the proposed method might be employed as a useful assistant technique for identifying sub-subcellular locations. We have implemented our algorithm as an online service called SubIdent (http://bioinfo.ncu.edu.cn/services.aspx).

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

    PubMed

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

    2010-03-17

    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 5-15 years), 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. Volume reductions were observed in both exposure groups relative to controls in striatal and thalamic regions bilaterally and in 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 intelligence quotient (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. Furthermore, 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.

  13. Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states.

    PubMed

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

    2010-07-27

    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.

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

    PubMed

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

    2009-10-01

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

  15. Using logistic regression to estimate delay-discounting functions.

    PubMed

    Wileyto, E Paul; Audrain-McGovern, Janet; Epstein, Leonard H; Lerman, Caryn

    2004-02-01

    The monetary choice questionnaire (MCQ) and similar computer tasks ask preference questions in order to ascertain indifference, the perceived equivalence of immediate versus larger delayed rewards. Indifference data are then fitted with a hyperbolic function, summarizing the decline in perceived value with delay time. We present a fitting method that estimates the hyperbolic parameter k directly from survey responses. Binary preferences are modeled as a function of time (X2) and a transformed reward ratio (X1), yielding logistic regression coefficients beta 2 and beta 1. The hyperbolic parameter emerges as k = beta 2/beta 1, where the logistic predicted p = .5 (the definition of indifference). The MCQ was administered to 1,073 adolescents and was scored using both standard and logistic methods. The means for In(k) were similar (standard, -4.53; logistic, -4.51), and the results were highly correlated (rho = .973). Simulated MCQ data showed that k was unbiased, except where beta 1 > or = -1, indicating a vague survey response. Jackknife standard errors provided excellent coverage.

  16. Prediction of membrane protein types using maximum variance projection

    NASA Astrophysics Data System (ADS)

    Wang, Tong; Yang, Jie

    2011-05-01

    Predicting membrane protein types has a positive influence on further biological function analysis. To quickly and efficiently annotate the type of an uncharacterized membrane protein is a challenge. In this work, a system based on maximum variance projection (MVP) is proposed to improve the prediction performance of membrane protein types. The feature extraction step is based on a hybridization representation approach by fusing Position-Specific Score Matrix composition. The protein sequences are quantized in a high-dimensional space using this representation strategy. Some problems will be brought when analysing these high-dimensional feature vectors such as high computing time and high classifier complexity. To solve this issue, MVP, a novel dimensionality reduction algorithm is introduced by extracting the essential features from the high-dimensional feature space. Then, a K-nearest neighbour classifier is employed to identify the types of membrane proteins based on their reduced low-dimensional features. As a result, the jackknife and independent dataset test success rates of this model reach 86.1 and 88.4%, respectively, and suggest that the proposed approach is very promising for predicting membrane proteins types.

  17. Prediction of subcellular location of apoptosis proteins combining tri-gram encoding based on PSSM and recursive feature elimination.

    PubMed

    Liu, Taigang; Tao, Peiying; Li, Xiaowei; Qin, Yufang; Wang, Chunhua

    2015-02-07

    Knowledge of apoptosis proteins plays an important role in understanding the mechanism of programmed cell death. Obtaining information on subcellular location of apoptosis proteins is very helpful to reveal the apoptosis mechanism and understand the function of apoptosis proteins. Because of the cost in time and labor associated with large-scale wet-bench experiments, computational prediction of apoptosis proteins subcellular location becomes very important and many computational tools have been developed in the recent decades. Existing methods differ in the protein sequence representation techniques and classification algorithms adopted. In this study, we firstly introduce a sequence encoding scheme based on tri-grams computed directly from position-specific score matrices, which incorporates evolution information represented in the PSI-BLAST profile and sequence-order information. Then SVM-RFE algorithm is applied for feature selection and reduced vectors are input to a support vector machine classifier to predict subcellular location of apoptosis proteins. Jackknife tests on three widely used datasets show that our method provides the state-of-the-art performance in comparison with other existing methods.

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

    PubMed

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

    2015-12-24

    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.

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

    PubMed

    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.

  20. Identifying the Types of Ion Channel-Targeted Conotoxins by Incorporating New Properties of Residues into Pseudo Amino Acid Composition

    PubMed Central

    Wu, Yun

    2016-01-01

    Conotoxins are a kind of neurotoxin which can specifically interact with potassium, sodium type, and calcium channels. They have become potential drug candidates to treat diseases such as chronic pain, epilepsy, and cardiovascular diseases. Thus, correctly identifying the types of ion channel-targeted conotoxins will provide important clue to understand their function and find potential drugs. Based on this consideration, we developed a new computational method to rapidly and accurately predict the types of ion-targeted conotoxins. Three kinds of new properties of residues were proposed to use in pseudo amino acid composition to formulate conotoxins samples. The support vector machine was utilized as classifier. A feature selection technique based on F-score was used to optimize features. Jackknife cross-validated results showed that the overall accuracy of 94.6% was achieved, which is higher than other published results, demonstrating that the proposed method is superior to published methods. Hence the current method may play a complementary role to other existing methods for recognizing the types of ion-target conotoxins. PMID:27631006

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

    PubMed

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

    2014-09-01

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

  2. Modeling Surface Winds in Mountainous Catchments as a Function of Topography and Vegetation

    NASA Astrophysics Data System (ADS)

    Winstral, A.; Marks, D.

    2006-12-01

    In order to develop accurate distributed hydrological models, spatially accurate meteorological forcing fields are required. In mountainous basins, elevation and topography strongly influence temperature, precipitation, vapor pressure, and wind. At the watershed scale, temperature, precipitation, and vapor pressure are largely dependent on elevation and receive adequate representation via lapse rates. Wind speed and its consequent effects on the redistribution of snow however, are also strongly dependent on proximal upstream physiography and strong gradients are often present within defined elevation bands. This study used wind data from a unique set of wind monitoring sites located across a gradient of exposures within the 0.36 km2 Reynolds Mountain East (RME) research basin in southwestern Idaho, USA to examine relationships between wind speeds, upstream topography, and vegetation. Following a one-year calibration period an optimal relationship between topography, vegetation cover, and hourly averaged wind speeds was developed. Using a jack-knife procedure the topography-vegetation-wind speed relationship was then validated in successive years at RME. The developed procedure for spatially distributing wind speeds accurately simulated the observed wind gradients, had extrapolation capabilities such that end-members could be reasonably predicted when not available, and was computationally efficient.

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

    PubMed

    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

    2014-08-01

    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 (NH4+ and NO3-). 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.

  4. Perturbative approach to covariance matrix of the matter power spectrum

    NASA Astrophysics Data System (ADS)

    Mohammed, Irshad; Seljak, Uroš; Vlah, Zvonimir

    2017-04-01

    We evaluate the covariance matrix of the matter power spectrum using perturbation theory up to dominant terms at 1-loop order and compare it to numerical simulations. We decompose the covariance matrix into the disconnected (Gaussian) part, trispectrum from the modes outside the survey (supersample variance) and trispectrum from the modes inside the survey, and show how the different components contribute to the overall covariance matrix. We find the agreement with the simulations is at a 10 per cent level up to k ∼ 1 h Mpc-1. We show that all the connected components are dominated by the large-scale modes (k < 0.1 h Mpc-1), regardless of the value of the wave vectors k, k΄ of the covariance matrix, suggesting that one must be careful in applying the jackknife or bootstrap methods to the covariance matrix. We perform an eigenmode decomposition of the connected part of the covariance matrix, showing that at higher k, it is dominated by a single eigenmode. The full covariance matrix can be approximated as the disconnected part only, with the connected part being treated as an external nuisance parameter with a known scale dependence, and a known prior on its variance for a given survey volume. Finally, we provide a prescription for how to evaluate the covariance matrix from small box simulations without the need to simulate large volumes.

  5. Estimation of ROC Curve with Complex Survey Data

    PubMed Central

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

    2015-01-01

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

  6. Influence of land use and meteorological factors on the spatial distribution of Toxocara canis and Toxocara cati eggs in soil in urban areas.

    PubMed

    Gao, Xiang; Wang, Hongbin; Li, Jianxin; Qin, Hongyu; Xiao, Jianhua

    2017-01-15

    Soil which has been contaminated by Toxocara spp. eggs is considered as one of the main infection sources of Toxocariasis in animals and humans. The present study conducted a detailed investigation into the spatial patterns of Toxocara canis (T. canis) and Toxocara cati (T. cati) eggs in soil in urban area of northeastern Mainland China, and assessed the inter-relationships between meteorological factors, land use and the distribution of the Toxocara spp. eggs. Polymerase chain reaction (PCR) was used for the determination of T. canis and T. cati eggs contamination in soil samples. Between April 2014 and May 2015, 9420 soil samples were subjected to PCR examination and 7027 sheep (74.6%) were determined to be positive for T. canis and T. cati eggs. Subsequently, we evaluated the effect of land use, and meteorological factors on the spatial distribution of T. canis and T. cati eggs based on a maximum entropy model. Jackknife analysis revealed that the area of residential land, wood and grass land and precipitation may influence the occurrence of T. canis and T. cati eggs in soil. Our findings indicate that land use and meteorological factors may be important variables affecting transmission of Toxocariasis and should be taken into account in the development of future surveillance programmes for Toxocariasis.

  7. Concomitant repair of stress urinary incontinence with proximal urethrovaginal fistula: Our experience

    PubMed Central

    Chodisetti, Subbarao; Boddepalli, Yogesh; Kota, Malakonda Reddy

    2016-01-01

    Introduction: Proximal urethrovaginal fistula (UVF) located close to the bladder neck may cause extensive sphincter damage and is usually associated with continuous incontinence, which may mask the associated stress urinary incontinence (SUI). Simultaneous correction of SUI avoids a second surgery for SUI, which needs dissection in ischemic fields and carries a high risk of failure. The aim of this study is to describe our technique of concomitant repair of SUI with proximal UVF and our results. Methods: Between July 2010 and August 2014, 14 patients underwent UVF repair in Jackknife position by the interposition of a Martius flap and simultaneous correction of SUI by modified McGuire pubovaginal autologous fascial sling. The procedure was carried out a minimum of 3 months of presentation and after detailed preoperative evaluation. Results: After a mean follow-up of 28 months, all 14 patients were continent. None of the patients developed recurrence of the UVF. Two patients presented with retention immediately after catheter removal and clean intermittent catheterization training was given to both of them. Two patients became pregnant during the follow-up period and were advised cesarean section near term. Conclusions: Repair of proximal UVF and correction of SUI can be performed in the same session to avoid the operation in an ischemic field. PMID:27555683

  8. 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

  9. Transanal Minimally Invasive Surgery (TAMIS) to Treat Vesicorectal Fistula: A New Approach

    PubMed Central

    Tobias-Machado, Marcos; Mattos, Pablo Aloisio Lima; Reis, Leonardo Oliveira; Juliano, César Augusto Braz; Pompeo, Antonio Carlos Lima

    2015-01-01

    ABSTRACT Purpose: Vesicorectal fistula is one of the most devastating postoperative complications after radical prostatectomy. Definitive treatment is difficult due to morbidity and recurrence. Despite many options, there is not an unanimous accepted approach. This article aimed to report a new minimally invasive approach as an option to reconstructive surgery. Materials and Methods: We report on Transanal Minimally Invasive Surgery (TAMIS) with miniLap devices for instrumentation in a 65 year old patient presenting with vesicorectal fistula after radical prostatectomy. We used Alexis® device for transanal access and 3, 5 and 11 mm triangulated ports for the procedure. The surgical steps were as follows: cystoscopy and implant of guide wire through fistula; patient at jack-knife position; transanal access; Identification of the fistula; dissection; vesical wall closure; injection of fibrin glue in defect; rectal wall closure. Results: The operative time was 240 minutes, with 120 minutes for reconstruction. No perioperative complications or conversion were observed. Hospital stay was two days and catheters were removed at four weeks. No recurrence was observed. Conclusions: This approach has low morbidity and is feasible. The main difficulties consisted in maintaining luminal dilation, instrumental manipulation and suturing. PMID:26689530

  10. Detection of the pairwise kinematic Sunyaev-Zel'dovich effect with BOSS DR11 and the Atacama Cosmology Telescope

    NASA Astrophysics Data System (ADS)

    De Bernardis, F.; Aiola, S.; Vavagiakis, E. M.; Battaglia, N.; Niemack, M. D.; Beall, J.; Becker, D. T.; Bond, J. R.; Calabrese, E.; Cho, H.; Coughlin, K.; Datta, R.; Devlin, M.; Dunkley, J.; Dunner, R.; Ferraro, S.; Fox, A.; Gallardo, P. A.; Halpern, M.; Hand, N.; Hasselfield, M.; Henderson, S. W.; Hill, J. C.; Hilton, G. C.; Hilton, M.; Hincks, A. D.; Hlozek, R.; Hubmayr, J.; Huffenberger, K.; Hughes, J. P.; Irwin, K. D.; Koopman, B. J.; Kosowsky, A.; Li, D.; Louis, T.; Lungu, M.; Madhavacheril, M. S.; Maurin, L.; McMahon, J.; Moodley, K.; Naess, S.; Nati, F.; Newburgh, L.; Nibarger, J. P.; Page, L. A.; Partridge, B.; Schaan, E.; Schmitt, B. L.; Sehgal, N.; Sievers, J.; Simon, S. M.; Spergel, D. N.; Staggs, S. T.; Stevens, J. R.; Thornton, R. J.; van Engelen, A.; Van Lanen, J.; Wollack, E. J.

    2017-03-01

    We present a new measurement of the kinematic Sunyaev-Zel'dovich effect using data from the Atacama Cosmology Telescope (ACT) and the Baryon Oscillation Spectroscopic Survey (BOSS). Using 600 square degrees of overlapping sky area, we evaluate the mean pairwise baryon momentum associated with the positions of 50,000 bright galaxies in the BOSS DR11 Large Scale Structure catalog. A non-zero signal arises from the large-scale motions of halos containing the sample galaxies. The data fits an analytical signal model well, with the optical depth to microwave photon scattering as a free parameter determining the overall signal amplitude. We estimate the covariance matrix of the mean pairwise momentum as a function of galaxy separation, using microwave sky simulations, jackknife evaluation, and bootstrap estimates. The most conservative simulation-based errors give signal-to-noise estimates between 3.6 and 4.1 for varying galaxy luminosity cuts. We discuss how the other error determinations can lead to higher signal-to-noise values, and consider the impact of several possible systematic errors. Estimates of the optical depth from the average thermal Sunyaev-Zel'dovich signal at the sample galaxy positions are broadly consistent with those obtained from the mean pairwise momentum signal.

  11. 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.

  12. GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis.

    PubMed

    Lin, Wei-Zhong; Xiao, Xuan; Chou, Kuo-Chen

    2009-11-01

    G-protein-coupled receptors (GPCRs) play fundamental roles in regulating various physiological processes as well as the activity of virtually all cells. Different GPCR families are responsible for different functions. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop an automated method to address the two problems: given the sequence of a query protein, can we identify whether it is a GPCR? If it is, what family class does it belong to? Here, a two-layer ensemble classifier called GPCR-GIA was proposed by introducing a novel scale called 'grey incident degree'. The overall success rate by GPCR-GIA in identifying GPCR and non-GPCR was about 95%, and that in identifying the GPCRs among their nine family classes was about 80%. These rates were obtained by the jackknife cross-validation tests on the stringent benchmark data sets where none of the proteins has > or = 50% pairwise sequence identity to any other in a same class. Moreover, a user-friendly web-server was established at http://218.65.61.89:8080/bioinfo/GPCR-GIA. For user's convenience, a step-by-step guide on how to use the GPCR-GIA web server is provided. Generally speaking, one can get the desired two-level results in around 10 s for a query protein sequence of 300-400 amino acids; the longer the sequence is, the more time that is needed.

  13. 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).

  14. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

    NASA Astrophysics Data System (ADS)

    Ragonnet-Cronin, Manon L.; Shilaih, Mohaned; Günthard, Huldrych F.; Hodcroft, Emma B.; Böni, Jürg; Fearnhill, Esther; Dunn, David; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Yang, Wan-Lin; Brown, Alison E.; Lycett, Samantha J.; Kouyos, Roger; Brown, Andrew J. Leigh

    2016-09-01

    Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes.

  15. Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks.

    PubMed

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

    2014-01-01

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

  16. Constructing large-scale genetic maps using an evolutionary strategy algorithm.

    PubMed Central

    Mester, D; Ronin, Y; Minkov, D; Nevo, E; Korol, A

    2003-01-01

    This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with approximately 50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology. PMID:14704202

  17. Identification of Secretory Proteins in Mycobacterium tuberculosis Using Pseudo Amino Acid Composition

    PubMed Central

    Yang, Huan; Tang, Hua; Chen, Xin-Xin; Zhang, Chang-Jian; Zhu, Pan-Pan; Ding, Hui

    2016-01-01

    Tuberculosis is killing millions of lives every year and on the blacklist of the most appalling public health problems. Recent findings suggest that secretory protein of Mycobacterium tuberculosis may serve the purpose of developing specific vaccines and drugs due to their antigenicity. Responding to global infectious disease, we focused on the identification of secretory proteins in Mycobacterium tuberculosis. A novel method called MycoSec was designed by incorporating g-gap dipeptide compositions into pseudo amino acid composition. Analysis of variance-based technique was applied in the process of feature selection and a total of 374 optimal features were obtained and used for constructing the final predicting model. In the jackknife test, MycoSec yielded a good performance with the area under the receiver operating characteristic curve of 0.93, demonstrating that the proposed system is powerful and robust. For user's convenience, the web server MycoSec was established and an obliging manual on how to use it was provided for getting around any trouble unnecessary. PMID:27597968

  18. Predicting red wolf release success in the southeastern United States

    USGS Publications Warehouse

    van Manen, Frank T.; Crawford, Barron A.; Clark, Joseph D.

    2000-01-01

    Although the red wolf (Canis rufus) was once found throughout the southeastern United States, indiscriminate killing and habitat destruction reduced its range to a small section of coastal Texas and Louisiana. Wolves trapped from 1973 to 1980 were taken to establish a captive breeding program that was used to repatriate 2 mainland and 3 island red wolf populations. We collected data from 320 red wolf releases in these areas and classified each as a success or failure based on survival and reproductive criteria, and whether recaptures were necessary to resolve conflicts with humans. We evaluated the relations between release success and conditions at the release sites, characteristics of released wolves, and release procedures. Although <44% of the variation in release success was explained, model performance based on jackknife tests indicated a 72-80% correct prediction rate for the 4 operational models we developed. The models indicated that success was associated with human influences on the landscape and the level of wolf habituation to humans prior to release. We applied the models to 31 prospective areas for wolf repatriation and calculated an index of release success for each area. Decision-makers can use these models to objectively rank prospective release areas and compare strengths and weaknesses of each.

  19. 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.

  20. Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines

    PubMed Central

    Chen, Wei; Xing, Pengwei; Zou, Quan

    2017-01-01

    As one of the most abundant RNA post-transcriptional modifications, N6-methyladenosine (m6A) involves in a broad spectrum of biological and physiological processes ranging from mRNA splicing and stability to cell differentiation and reprogramming. However, experimental identification of m6A sites is expensive and laborious. Therefore, it is urgent to develop computational methods for reliable prediction of m6A sites from primary RNA sequences. In the current study, a new method called RAM-ESVM was developed for detecting m6A sites from Saccharomyces cerevisiae transcriptome, which employed ensemble support vector machine classifiers and novel sequence features. The jackknife test results show that RAM-ESVM outperforms single support vector machine classifiers and other existing methods, indicating that it would be a useful computational tool for detecting m6A sites in S. cerevisiae. Furthermore, a web server named RAM-ESVM was constructed and could be freely accessible at http://server.malab.cn/RAM-ESVM/. PMID:28079126

  1. Different effects of ERβ and TROP2 expression in Chinese patients with early-stage colon cancer.

    PubMed

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

    2012-12-01

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

  2. Potential use of ionic species for identifying source land-uses of stormwater runoff.

    PubMed

    Lee, Dong Hoon; Kim, Jin Hwi; Mendoza, Joseph A; Lee, Chang-Hee; Kang, Joo-Hyon

    2017-02-01

    Identifying critical land-uses or source areas is important to prioritize resources for cost-effective stormwater management. This study investigated the use of information on ionic composition as a fingerprint to identify the source land-use of stormwater runoff. We used 12 ionic species in stormwater runoff monitored for a total of 20 storm events at five sites with different land-use compositions during the 2012-2014 wet seasons. A stepwise forward discriminant function analysis (DFA) with the jack-knifed cross validation approach was used to select ionic species that better discriminate the land-use of its source. Of the 12 ionic species, 9 species (K(+), Mg(2+), Na(+), NH4(+), Br(-), Cl(-), F(-), NO2(-), and SO4(2-)) were selected for better performance of the DFA. The DFA successfully differentiated stormwater samples from urban, rural, and construction sites using concentrations of the ionic species (70%, 95%, and 91% of correct classification, respectively). Over 80% of the new data cases were correctly classified by the trained DFA model. When applied to data cases from a mixed land-use catchment and downstream, the DFA model showed the greater impact of urban areas and rural areas respectively in the earlier and later parts of a storm event.

  3. KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.

    PubMed

    Wong, Yung-Hao; Lee, Tzong-Yi; Liang, Han-Kuen; Huang, Chia-Mao; Wang, Ting-Yuan; Yang, Yi-Huan; Chu, Chia-Huei; Huang, Hsien-Da; Ko, Ming-Tat; Hwang, Jenn-Kang

    2007-07-01

    Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. Herein, a new web server, KinasePhos 2.0, incorporates support vector machines (SVM) with the protein sequence profile and protein coupling pattern, which is a novel feature used for identifying phosphorylation sites. The coupling pattern [XdZ] denotes the amino acid coupling-pattern of amino acid types X and Z that are separated by d amino acids. The differences or quotients of coupling strength C(XdZ) between the positive set of phosphorylation sites and the background set of whole protein sequences from Swiss-Prot are computed to determine the number of coupling patterns for training SVM models. After the evaluation based on k-fold cross-validation and Jackknife cross-validation, the average predictive accuracy of phosphorylated serine, threonine, tyrosine and histidine are 90, 93, 88 and 93%, respectively. KinasePhos 2.0 performs better than other tools previously developed. The proposed web server is freely available at http://KinasePhos2.mbc.nctu.edu.tw/.

  4. Predicting the Distribution of Phlebotomus papatasi (Diptera: Psychodidae), the Primary Vector of Zoonotic Cutaneous Leishmaniasis, in Golestan Province of Iran Using Ecological Niche Modeling: Comparison of MaxEnt and GARP Models.

    PubMed

    Sofizadeh, Aioub; Rassi, Yavar; Vatandoost, Hassan; Hanafi-Bojd, Ahmad Ali; Mollalo, Abolfazl; Rafizadeh, Sayena; Akhavan, Amir Ahmad

    2017-03-01

    Zoonotic cutaneous leishmaniasis (ZCL) is a prevalent vector-borne disease in the Golestan province of Iran, with Phlebotomus papatasi (Scopoli, 1786) serving as the main vector. The aim of this study was to model the probability of presence of this species in the study area, and to determine the underlying factors affecting its distribution. Three villages were selected from each county of the province and visited monthly for investigating ZCL. Sticky paper traps were used for collecting the sand flies to determine the species present. The presence of Ph. papatasi was modeled using genetic algorithm for rule-set production (GARP) and maximum entropy (MaxEnt) techniques. Both models showed the central and northern parts of the province with lowland areas were more vulnerable to Ph. papatasi propagation, in comparison with the southern parts with mountainous and forest areas. The area under curve (AUC) of MaxEnt model for the training points was calculated as 0.90, indicating excellent performance of the model in predicting Ph. papatasi distribution. Jackknife test showed that the factors with the greatest influence in vector distribution were slope, vegetation cover, annual mean temperature, and altitude. By using ecological niche models, it is possible to identify areas with higher probability of presence of Ph. papatasi, which guides public health policy makers for planning better vector control interventions.

  5. Cosmic shear measurements with Dark Energy Survey Science Verification data

    DOE PAGES

    Becker, M. R.

    2016-07-06

    Here, 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 simulationsmore » 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.« less

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

    USGS Publications Warehouse

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

    1999-01-01

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

  7. 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.

  8. 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.

  9. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  11. Predicting discovery rates of genomic features.

    PubMed

    Gravel, Simon

    2014-06-01

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

  12. 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

  13. 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.

  14. 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.

  15. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland.

    PubMed

    Ragonnet-Cronin, Manon L; Shilaih, Mohaned; Günthard, Huldrych F; Hodcroft, Emma B; Böni, Jürg; Fearnhill, Esther; Dunn, David; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Yang, Wan-Lin; Brown, Alison E; Lycett, Samantha J; Kouyos, Roger; Brown, Andrew J Leigh

    2016-09-19

    Phylogenetic clustering approaches can elucidate HIV transmission dynamics. Comparisons across countries are essential for evaluating public health policies. Here, we used a standardised approach to compare the UK HIV Drug Resistance Database and the Swiss HIV Cohort Study while maintaining data-protection requirements. Clusters were identified in subtype A1, B and C pol phylogenies. We generated degree distributions for each risk group and compared distributions between countries using Kolmogorov-Smirnov (KS) tests, Degree Distribution Quantification and Comparison (DDQC) and bootstrapping. We used logistic regression to predict cluster membership based on country, sampling date, risk group, ethnicity and sex. We analysed >8,000 Swiss and >30,000 UK subtype B sequences. At 4.5% genetic distance, the UK was more clustered and MSM and heterosexual degree distributions differed significantly by the KS test. The KS test is sensitive to variation in network scale, and jackknifing the UK MSM dataset to the size of the Swiss dataset removed the difference. Only heterosexuals varied based on the DDQC, due to UK male heterosexuals who clustered exclusively with MSM. Their removal eliminated this difference. In conclusion, the UK and Swiss HIV epidemics have similar underlying dynamics and observed differences in clustering are mainly due to different population sizes.

  16. Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.

    PubMed

    Gao, Yu-Fei; Chen, Lei; Cai, Yu-Dong; Feng, Kai-Yan; Huang, Tao; Jiang, Yang

    2012-01-01

    Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.

  17. 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 the 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 location 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.

  18. DNA hybridization, cladistics, and the phylogeny of phalangerid marsupials.

    PubMed

    Springer, M S; Kirsch, J A; Aplin, K; Flannery, T

    1990-03-01

    Single-copy DNA/DNA hybridization experiments and numerical cladistic analyses of anatomical characters were used to investigate relationships among nine phalangerid (Marsupialia) species from four different genera. Both rate-dependent and rate-independent analyses of molecular data indicate that species of Trichosurus from one clade and that Strigocuscus, Phalanger, and Spilocuscus form a second. Within the latter group, Spilocuscus is excluded from a Strigocuscus-Phalanger clade, which, in turn, is not fully resolved on a jackknife strict consensus tree. Minimum-length Dollo, Wagner, and Camin-Sokal parisomy trees based on 35 anatomical characters, in contrast, suggest placement of Strigocuscus with Trichosurus rather than with Spilocuscus and Phalanger. However, there are two derived characters that support the alternative arrange of Strigocuscus with Spilocuscus and Phalanger and one character that further unites Strigocuscus and Phalanger. Thus, DNA hybridization results are not inconsistent with the distribution of derived character states among anatomical characters, only with minimum-length trees based on character data.

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

    NASA Technical Reports Server (NTRS)

    Hall, Timothy; Yonekura, Emmi

    2013-01-01

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

  20. Bioequivalence evaluation of two formulations of pidotimod using a limited sampling strategy.

    PubMed

    Huang, Ji-Han; Huang, Xiao-Hui; Wang, Kun; Li, Jian-Chun; Xie, Xue-Feng; Shen, Chen-Lin; Li, Lu-Jin; Zheng, Qing-Shan

    2013-07-01

    The aim of this study was to develop a limited sampling strategy (LSS) to assess the bioequivalence of two formulations of pidotimod. A randomized, two-way, cross-over study was conducted in healthy Chinese volunteers to compare two formulations of pidotimod. A limited sampling model was established using regression models to estimate the pharmacokinetic parameters and assess the bioequivalence of pidotimod. The model was internally validated by the Jack-knife method and graphical methods. The traditional non-compartmental method was also used to analyze the data and compared with LSS method. The results indicate that following oral administration of a single 800 mg dose, the plasma AUC(0-12 h) and C(max) of pidotimod can be predicted accurately using only two to four plasma samples. The bioequivalence assessment based on the LSS models provided results very similar to that obtained using all the observed concentration-time data points and indicate that the two pidotimod formulations were bioequivalent. A LSS method for assessing the bioequivalence of pidotimod formulations was established and proved to be applicable and accurate. This LSS method could be considered appropriate for a pidotimod bioequivalence study, providing an inexpensive cost of sampling acquisition and analysis. And the methodology presented here may also be applicable to bioequivalence evaluation of other medications.

  1. 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.

  2. Predicting membrane protein types with bragging learner.

    PubMed

    Niu, Bing; Jin, Yu-Huan; Feng, Kai-Yan; Liu, Liang; Lu, Wen-Cong; Cai, Yu-Dong; Li, Guo-Zheng

    2008-01-01

    The membrane protein type is an important feature in characterizing the overall topological folding type of a protein or its domains therein. Many investigators have put their efforts to the prediction of membrane protein type. Here, we propose a new approach, the bootstrap aggregating method or bragging learner, to address this problem based on the protein amino acid composition. As a demonstration, the benchmark dataset constructed by K.C. Chou and D.W. Elrod was used to test the new method. The overall success rate thus obtained by jackknife cross-validation was over 84%, indicating that the bragging learner as presented in this paper holds a quite high potential in predicting the attributes of proteins, or at least can play a complementary role to many existing algorithms in this area. It is anticipated that the prediction quality can be further enhanced if the pseudo amino acid composition can be effectively incorporated into the current predictor. An online membrane protein type prediction web server developed in our lab is available at http://chemdata.shu.edu.cn/protein/protein.jsp.

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

    PubMed

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

    2015-12-09

    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.

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

    PubMed Central

    Yang, Ya; Smith, Stephen A.

    2014-01-01

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

  5. 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.

  6. 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.

  7. Using the concept of Chou's pseudo amino acid composition to predict apoptosis proteins subcellular location: an approach by approximate entropy.

    PubMed

    Jiang, Xiaoying; Wei, Rong; Zhang, Tongliang; Gu, Quan

    2008-01-01

    The function of protein is closely correlated with it subcellular location. Prediction of subcellular location of apoptosis proteins is an important research area in post-genetic era because the knowledge of apoptosis proteins is useful to understand the mechanism of programmed cell death. Compared with the conventional amino acid composition (AAC), the Pseudo Amino Acid composition (PseAA) as originally introduced by Chou can incorporate much more information of a protein sequence so as to remarkably enhance the power of using a discrete model to predict various attributes of a protein. In this study, a novel approach is presented to predict apoptosis protein solely from sequence based on the concept of Chou's PseAA composition. The concept of approximate entropy (ApEn), which is a parameter denoting complexity of time series, is used to construct PseAA composition as additional features. Fuzzy K-nearest neighbor (FKNN) classifier is selected as prediction engine. Particle swarm optimization (PSO) algorithm is adopted for optimizing the weight factors which are important in PseAA composition. Two datasets are used to validate the performance of the proposed approach, which incorporate six subcellular location and four subcellular locations, respectively. The results obtained by jackknife test are quite encouraging. It indicates that the ApEn of protein sequence could represent effectively the information of apoptosis proteins subcellular locations. It can at least play a complimentary role to many of the existing methods, and might become potentially useful tool for protein function prediction. The software in Matlab is available freely by contacting the corresponding author.

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

    PubMed

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

    2006-09-01

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

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

    PubMed

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

    2015-07-01

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

  10. Life history dependent morphometric variation in stream-dwelling Atlantic salmon

    USGS Publications Warehouse

    Letcher, B.H.

    2003-01-01

    The time course of morphometric variation among life histories for stream-dwelling Atlantic salmon (Salmo salar L.) parr (age-0+ to age-2+) was analyzed. Possible life histories were combinations of parr maturity status in the autumn (mature or immature) and age at outmigration (smolt at age-2+ or later age). Actual life histories expressed with enough fish for analysis in the 1997 cohort were immature/age-2+ smolt, mature/age-2 +smolt, and mature/age-2+ non-smolt. Tagged fish were assigned to one of the three life histories and digital pictures from the field were analyzed using landmark-based geometric morphometrics. Results indicated that successful grouping of fish according to life history varied with fish age, but that fish could be grouped before the actual expression of the life histories. By March (age-1+), fish were successfully grouped using a descriptive discriminant function and successful assignment ranged from 84 to 97% for the remainder of stream residence. A jackknife of the discriminant function revealed an average life history prediction success of 67% from age-1+ summer to smolting. Low sample numbers for one of the life histories may have limited prediction success. A MANOVA on the shape descriptors (relative warps) also indicated significant differences in shape among life histories from age-1+ summer through to smolting. Across all samples, shape varied significantly with size. Within samples, shape did not vary significantly with size for samples from December (age-0+) to May (age-1+). During the age-1+ summer however, shape varied significantly with size, but the relationship between shape and size was not different among life histories. In the autumn (age-1+) and winter (age-2+), life history differences explained a significant portion of the change in shape with size. Life history dependent morphometric variation may be useful to indicate the timing of early expressions of life history variation and as a tool to explore temporal and

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

    PubMed Central

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

    2013-01-01

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

  12. Mito-GSAAC: mitochondria prediction using genetic ensemble classifier and split amino acid composition.

    PubMed

    Afridi, Tariq Habib; Khan, Asifullah; Lee, Yeon Soo

    2012-04-01

    Mitochondria are all-important organelles of eukaryotic cells since they are involved in processes associated with cellular mortality and human diseases. Therefore, trustworthy techniques are highly required for the identification of new mitochondrial proteins. We propose Mito-GSAAC system for prediction of mitochondrial proteins. The aim of this work is to investigate an effective feature extraction strategy and to develop an ensemble approach that can better exploit the advantages of this feature extraction strategy for mitochondria classification. We investigate four kinds of protein representations for prediction of mitochondrial proteins: amino acid composition, dipeptide composition, pseudo amino acid composition, and split amino acid composition (SAAC). Individual classifiers such as support vector machine (SVM), k-nearest neighbor, multilayer perceptron, random forest, AdaBoost, and bagging are first trained. An ensemble classifier is then built using genetic programming (GP) for evolving a complex but effective decision space from the individual decision spaces of the trained classifiers. The highest prediction performance for Jackknife test is 92.62% using GP-based ensemble classifier on SAAC features, which is the highest accuracy, reported so far on the Mitochondria dataset being used. While on the Malaria Parasite Mitochondria dataset, the highest accuracy is obtained by SVM using SAAC and it is further enhanced to 93.21% using GP-based ensemble. It is observed that SAAC has better discrimination power for mitochondria prediction over the rest of the feature extraction strategies. Thus, the improved prediction performance is largely due to the better capability of SAAC for discriminating between mitochondria and non-mitochondria proteins at the N and C terminus and the effective combination capability of GP. Mito-GSAAC can be accessed at http://111.68.99.218/Mito-GSAAC . It is expected that the novel approach and the accompanied predictor will have a

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

    PubMed

    Li, Guoqing; Du, Sheng; Guo, Ke

    2015-01-01

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

  14. Demographic analysis of the fitness of Problepsis superans (Lepidoptera: Geometridae) feeding on three ligustrum (Lamiales: Oleaceae) species.

    PubMed

    Hu, Liang-Xiong; Chen, Ye; He, Zheng-Sheng; Zou, Zhi-Wen; Xia, Bin

    2014-06-01

    Using the age-stage, two-sex life table, the effects of three ligustrum species, Ligustrum x vicaryi Hort., Ligustrum quihoui Carrière, and Ligustrum lucidum Aiton, on the fitness of Problepsis superans (Butler, 1885) (Lepidoptera: Geometridae) were assayed by considering life table parameters of P. superans at 27 +/- 1 degrees C, 70 +/- 5% relative humidity, and a photoperiod of 16:8 (L: D) h. The means and SEs of population parameters were calculated using the jackknife and bootstrap methods. The total developmental time of larval stage of P. superans on L. x vicaryi was significantly shorter than that on L. x vicaryi and L. quihoui, whereas higher fecundity was observed on L. x vicaryi. The highest value of the finite rate of increase was observed on L. x vicaryi. The intrinsic rate of increase of P. superans on L. x vicaryi, L. quihoui, and L. lucidum, was 0.147 +/- 0.004, 0.130 +/- 0.004, and 0.112 +/- 0.005, respectively, which differed significantly among the three ligustrum species. The net reproductive rate varied from 122.8 +/- 24.7 female offspring on L. lucidum to 242.2 +/- 36.2 female offspring on L. x vicaryi. The lowest mean generation time was observed on L. x vicaryi. The gross reproductive rate of P. superans on the three ligustrum species did not significantly differ. Based on growth and population parameters, the suitability of the three ligustrum species to P. superans is ranked from high to low in the order as L. x vicaryi, L. quihoui, and L. lucidum.

  15. Fossils impact as hard as living taxa in parsimony analyses of morphology.

    PubMed

    Cobbett, Andrea; Wilkinson, Mark; Wills, Matthew A

    2007-10-01

    Systematists disagree whether data from fossils should be included in parsimony analyses. In a handful of well-documented cases, the addition of fossil data radically overturns a hypothesis of relationships based on extant taxa alone. Fossils can break up long branches and preserve character combinations closer in time to deep splitting events. However, fossils usually require more interpretation than extant taxa, introducing greater potential for spurious codings. Moreover, because fossils often have more "missing" codings, they are frequently accused of increasing numbers of MPTs, frustrating resolution and reducing support. Despite the controversy, remarkably little is known about the effects of fossils more generally. Here we provide the first systematic study, investigating empirically the behavior of fossil and extant taxa in 45 published morphological data sets. First-order jackknifing is used to determine the effects that each terminal has on inferred relationships, on the number of MPTs, and on CI' and RI as measures of homoplasy. Bootstrap leaf stabilities provide a proxy for the contribution of individual taxa to the branch support in the rest of the tree. There is no significant difference in the impact of fossil versus extant taxa on relationships, numbers of MPTs, and CI' or RI. However, adding individual fossil taxa is more likely to reduce the total branch support of the tree than adding extant taxa. This must be weighed against the superior taxon sampling afforded by including judiciously coded fossils, providing data from otherwise unsampled regions of the tree. We therefore recommend that investigators should include fossils, in the absence of compelling and case specific reasons for their exclusion.

  16. 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.

  17. 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.; Sherrod, David R.; Scott, William E.; Stauffer, Peter H.

    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.

  18. Prey stage preference and functional response of Euseius hibisci to Tetranychus urticae (Acari: Phytoseiidae, Tetranychidae).

    PubMed

    Badii, Mohammad H; Hernández-Ortiz, Emilio; Flores, Adriana E; Landeros, Jerónimo

    2004-01-01

    The aims of this study were: (a) determine the prey stage preference of female Euseius hibisci (Chant) (Phytoseiidae) at constant densities of different stages of Tetranychus urticae Koch (Tetranychidae), (b) assess the functional response of the predator females to the varying densities of eggs, larvae, or protonymphs of T. urticae, and (c) estimate the functional response of E. hibisci when pollen of Ligustrum ovalifolium was present as well. We conducted experiments on excised pieces of strawberry leaf arenas (Fragaria ananassa) under laboratory conditions of 25+/-2 degrees C, 60+/-5% RH and 12 h photophase. Our results indicated that the predator consumed significantly more prey eggs than other prey stages. Consumption of prey deutonymphs and adults was so low that they were excluded from the non-choice functional response experiments. The functional response on all food items was of type II. The two parameters of the functional response were estimated for each prey type by means of the adjusted non-linear regression model. The highest estimated value a' (instantaneous rate of discovery) and the lowest value of Th (handling time, including digestion) were found for the predator feeding on prey eggs, and a' was lowest and Th highest when fed protonymphs. Using the jack-knife method, the values for the functional response parameters were estimated. The values of a' and Th produced by the model were similar among all prey types except for the eggs, which were different. Using pollen simultaneously with prey larvae decreased the consumption of the latter over the full range of prey densities The suitability of this predator for biological control of T. urticae on strawberry is discussed.

  19. PhyPA: Phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences.

    PubMed

    Xia, Xuhua

    2016-09-01

    While pairwise sequence alignment (PSA) by dynamic programming is guaranteed to generate one of the optimal alignments, multiple sequence alignment (MSA) of highly divergent sequences often results in poorly aligned sequences, plaguing all subsequent phylogenetic analysis. One way to avoid this problem is to use only PSA to reconstruct phylogenetic trees, which can only be done with distance-based methods. I compared the accuracy of this new computational approach (named PhyPA for phylogenetics by pairwise alignment) against the maximum likelihood method using MSA (the ML+MSA approach), based on nucleotide, amino acid and codon sequences simulated with different topologies and tree lengths. I present a surprising discovery that the fast PhyPA method consistently outperforms the slow ML+MSA approach for highly diverged sequences even when all optimization options were turned on for the ML+MSA approach. Only when sequences are not highly diverged (i.e., when a reliable MSA can be obtained) does the ML+MSA approach outperforms PhyPA. The true topologies are always recovered by ML with the true alignment from the simulation. However, with MSA derived from alignment programs such as MAFFT or MUSCLE, the recovered topology consistently has higher likelihood than that for the true topology. Thus, the failure to recover the true topology by the ML+MSA is not because of insufficient search of tree space, but by the distortion of phylogenetic signal by MSA methods. I have implemented in DAMBE PhyPA and two approaches making use of multi-gene data sets to derive phylogenetic support for subtrees equivalent to resampling techniques such as bootstrapping and jackknifing.

  20. Geology of the Cooper Ridge NE Quadrangle, Sweetwater County, Wyoming

    USGS Publications Warehouse

    Roehler, Henry W.

    1979-01-01

    The Cooper Ridge NE 7?-minute quadrangle is 18 miles southeast of Rock Springs, Wyo., on the east flank of the Rock Springs uplift. Upper Cretaceous rocks composing the Rock Springs Formation, Ericson Sandstone, Almond Formation, Lewis Shale, Fox Hills Sandstone, and Lance Formation, Paleocene rocks composing the Fort Union Formation, and Eocene rocks composing the Wasatch Formation are exposed and dip 5?-8? southeast. Outcrops are unfaulted and generally homoclinal, but a minor cross-trending fold, the Jackknife Spring anticline, plunges southeastward and interrupts the northeast strike of beds. Older rocks in the subsurface are faulted and folded, especially near the Brady oil and gas field. Coal beds are present in the Almond, Lance, and Fort Union Formations. Coal resources are estimated to be more than 762 million short tons in 16 beds more than 2.5 feet thick, under less than 3,000 ft of overburden. Nearly 166 million tons are under less than 200 ft of overburden and are recoverable by strip mining. Unknown quantities of oil and gas are present in the Cretaceous Rock Springs, Blair, and Dakota Formations, Jurassic sandstone (Entrada Sandstone of drillers), Jurassic(?) and Triassic(?) Nugget Sandstone, Permian Park City Formation, and Pennsylvanian and Permian Weber Sandstone at the Brady field, part of which is in the southeast corner of the quadrangle, and in the Dakota Sandstone at the Prenalta Corp. Bluewater 33-32 well near the northern edge of the quadrangle. Other minerals include uranium in the Almond Formation and titanium in the Rock Springs Formation.

  1. 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

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

  4. Comparison of soil bacterial communities of Pinus patula of Nilgiris, western ghats with other biogeographically distant pine forest clone libraries.

    PubMed

    Rohini-Kumar, M; Osborne, Jabez W; Saravanan, V S

    2013-07-01

    The bacterial community structure of the rhizosphere and non-rhizosphere soil of Pinus patula, found in the Nilgiris region of Western Ghats, was studied by constructing 16S rRNA gene clone libraries. In the rhizosphere and non-rhizosphere soil clone libraries constructed, 13 and 15 bacterial phyla were identified, respectively. The clone libraries showed the predominance of members of culturally underrepresented phyla like Acidobacteria and Verrucomicrobia. The Alphaproteobacteria and Acidobacteria clones were predominant in rhizosphere and non-rhizosphere soil samples, respectively. In rhizosphere, amongst Alphaproteobacteria members, Bradyrhizobium formed the significant proportion, whereas in non-rhizosphere, members of subdivision-6 of phylum Acidobacteria were abundant. The diversity analysis of P. patula soil libraries showed that the phylotypes (16S rRNA gene similarity cutoff, ≥97 %) of Acidobacteria and Bacteroidetes were relatively predominant and diverse followed by Alphaproteobacteria and Verrucomicrobia. The diversity indices estimated higher richness and abundance of bacteria in P. patula soil clone libraries than the pine forest clone libraries retrieved from previous studies. The tools like principal co-ordinate analysis and Jackknife cluster analysis, which were under UniFrac analysis indicated that variations in soil bacterial communities were attributed to their respective geographical locations due to the phylogenetic divergence amongst the clone libraries. Overall, the P. patula rhizosphere and non-rhizosphere clone libraries were found significantly unique in composition, evenly distributed and highly rich in phylotypes, amongst the biogeographically distant clone libraries. It was finally hypothesised that the phylogenetic divergence amongst the bacterial phylotypes and natural selection plays a pivotal role in the variations of bacterial communities across the geographical distance.

  5. 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

  6. Understanding Spatial and Temporal Variations of Arctic Circulation Using Oxygen Isotopes of Seawater

    NASA Astrophysics Data System (ADS)

    Yin, L.; Kopans-Johnson, C. R.; LeGrande, A. N.; Kelly, S.

    2015-12-01

    The isotopic ratio of 18O to 16O in seawater (2005ppm in ocean water is defined as 𝛿18Oseawater≡0 permil or 0‰) is a fundamental ocean tracer due to its distinct linear relationship with salinity(𝛿18O -S) from regional inland freshwater sources. As opposed to salinity alone, 𝛿18O distinguishes river runoff from sea-ice melt and traces ocean circulation pathways from coastal to open waters and surface to deep waters. Observations from the past 60 years of 𝛿18O seawater were compiled into a database by Schimdt et al. (1999), and subsequently used to calculate a 3-dimensional 1°x1° 𝛿18O global gridded dataset by LeGrande and Schmidt (2006). Although the Schmidt et al. (1999) Global Seawater Oxygen-18 Database (𝛿18Oobs) contains 25,514 measurements used to calculate the global gridded dataset, LeGrande and Schmidt (2006) point out that, "data coverage varies greatly from region to region," with seasonal variability creating biases in areas where sea ice is present. Python Pandas is used to automate the addition of 2,942 records to the Schmidt et al. (1999) Global Seawater Oxygen-18 Database (𝛿18Oobs), and examine the spatial and temporal distributions of 18O in the Arctic Ocean. 10 initial water masses are defined using spatial and temporal trends, clusters of observations, and Arctic surface circulation. Jackknife slope analysis of water mass 𝛿18O -S is used to determine anomalous data points and regional hydrology, resulting in 4 distinct Arctic water masses. These techniques are used to improve the gridded 𝛿18Oseawater dataset by distinguishing unique water masses, and accounting for seasonal variability of complex high latitude areas.

  7. Stringent Evaluation of CMIP5 Precipitations and Development of Optimal Weighting Methods

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Control simulations of precipitation by 23 CMIP5 coupled ocean-atmosphere general circulation models (CGCMs) have been evaluated in comparison with the Global Precipitation Climatology Project (GPCP) monthly precipitation data for the period of 1979-2005. Instead of looking at the first two moment statistics, mean and standard deviation, the performance of the CMIP5 models in reproducing the physical evolutions in the GPCP data by employing cyclostationary EOF (CSEOF) analysis. Each CSEOF loading vector (CSLV) and corresponding principal component (PC) time series derived from individual CMIP5 models are compared with those of the GPCP data for the first 10 modes. Only the first CSEOF mode (the seasonal cycle) was simulated with a reasonable accuracy; the average pattern correlation is 0.675 (0.446-0.764) and the average temporal correlation is 0.999 (0.997-0.999). The performance of the model quickly diminishes as the mode number increases, with the best pattern correlation less than 0.2 for modes higher than 4. In an effort to improve the CMIP5 precipitation data for practical uses, optimal weighting scheme is developed in CSEOF space. In this new scheme, optimal weighting is conducted for each physical mode. For validation, the Jackknife method is used by filling a missing year in GPCP data using the 23 CMIP5 model datasets. This procedure is repeated until all of the 23 years are covered. Correlation and RMSE are significantly improved in comparison with those of the best CMIP5 models. A similar experiment is conducted using a conventional optimal weighting at each grid point; the performance of an optimal weighting scheme at each grid point is not better than that of the best CMIP5 models, suggesting that the multi-model optimal ensemble in CSEOF space is much better than that at each grid point.

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

    NASA Astrophysics Data System (ADS)

    Giot, Olivier; Termonia, Piet; Degrauwe, Daan; De Troch, Rozemien; Caluwaerts, Steven; Smet, Geert; Berckmans, Julie; Deckmyn, Alex; De Cruz, Lesley; De Meutter, Pieter; Duerinckx, Annelies; Gerard, Luc; Hamdi, Rafiq; Van den Bergh, Joris; Van Ginderachter, Michiel; Van Schaeybroeck, Bert

    2016-03-01

    Using the regional climate model ALARO-0, the Royal Meteorological Institute of Belgium and Ghent University have 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, meaning 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.

  9. Predicting radiologists' true and false positive decisions in reading mammograms by using gaze parameters and image-based features

    NASA Astrophysics Data System (ADS)

    Gandomkar, Ziba; Tay, Kevin; Ryder, Will; Brennan, Patrick C.; Mello-Thoms, Claudia

    2016-03-01

    Radiologists' gaze-related parameters combined with image-based features were utilized to classify suspicious mammographic areas ultimately scored as True Positives (TP) and False Positives (FP). Eight breast radiologists read 120 two-view digital mammograms of which 59 had biopsy proven cancer. Eye tracking data was collected and nearby fixations were clustered together. Suspicious areas on mammograms were independently identified based on thresholding an intensity saliency map followed by automatic segmentation and pruning steps. For each radiologist reported area, radiologist's fixation clusters in the area, as well as neighboring suspicious areas within 2.5° of the center of fixation, were found. A 45-dimensional feature vector containing gaze parameters of the corresponding cluster along with image-based characteristics was constructed. Gaze parameters included total number of fixations in the cluster, dwell time, time to hit the cluster for the first time, maximum number of consecutive fixations, and saccade magnitude of the first fixation in the cluster. Image-based features consisted of intensity, shape, and texture descriptors extracted from the region around the suspicious area, its surrounding tissue, and the entire breast. For each radiologist, a userspecific Support Vector Machine (SVM) model was built to classify the reported areas as TPs or FPs. Leave-one-out cross validation was utilized to avoid over-fitting. A feature selection step was embedded in the SVM training procedure by allowing radial basis function kernels to have 45 scaling factors. The proposed method was compared with the radiologists' performance using the jackknife alternative free-response receiver operating characteristic (JAFROC). The JAFROC figure of merit increased significantly for six radiologists.

  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

    2016-02-06

    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.

  11. Efficacy of digital breast tomosynthesis for breast cancer diagnosis

    NASA Astrophysics Data System (ADS)

    Alakhras, M.; Mello-Thoms, C.; Rickard, M.; Bourne, R.; Brennan, P. C.

    2014-03-01

    Purpose: To compare the diagnostic performance of digital breast tomosynthesis (DBT) in combination with digital mammography (DM) with that of digital mammography alone. Materials and Methods: Twenty six experienced radiologists who specialized in breast imaging read 50 cases (27 cancers and 23 non-cancer cases) of patients who underwent DM and DBT. Both exams included the craniocaudal (CC) and mediolateral oblique (MLO) views. Histopathologic examination established truth in all lesions. Each case was interpreted in two modes, once with DM alone followed by DM+DBT, and the observers were asked to mark the location of any lesions, if present, and give it a score based on a five-category assessment by the Royal Australian and New Zealand College of Radiologists (RANZCR). The diagnostic performance of DM compared with that of DM+DBT was evaluated in terms of the difference between areas under receiver-operating characteristic curves (AUCs), Jackknife free-response receiver operator characteristics (JAFROC) figure-of-merit, sensitivity, location sensitivity and specificity. Results: Average AUC and JAFROC for DM versus DM+DBT was significantly different (AUCs 0.690 vs 0.781, p=< 0.0001), (JAFROC 0.618 vs. 0.732, p=< 0.0001) respectively. In addition, the use of DM+DBT resulted in an improvement in sensitivity (0.629 vs. 0.701, p=0.0011), location sensitivity (0.548 vs. 0.690, p=< 0.0001) and specificity (0.656 vs. 0.758, p=0.0015) when compared to DM alone. Conclusion: Adding DBT to the standard DM significantly improved radiologists' performance in terms of AUCs, JAFROC figure of merit, sensitivity, location sensitivity and specificity values.

  12. 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.

  13. 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.

  14. 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.

  15. [Estimation of appropriate dose for computed radiography by the threshold value of the image quality figure].

    PubMed

    Mochizuki, Yasuo; Abe, Shinji; Yamaguchi, Kojirou

    2009-04-20

    We estimated the optimum dose for imaging with a computed radiography (CR) system at two different pixel sizes based on the area under curve (AUC) in receiver operating characteristic (ROC) analysis and image quality figure (IQF). Samples for ROC analysis were prepared as follows. Acryl beads, 2.0 mm in diameter, were placed on a 50.0 mm tough water phantom that was fitted with a 20.0 mm Al filter (SID 200 cm, tube voltage 80 kV). The dose level at which the film density of the screen-film system (SRO250/SRG) was 1.0+/-0.05 served as the reference dose (0.69microC/kg). Five samples were prepared by multiplying the reference dose by 1/4, 1/2, 1, 2, and 4. The samples for image quality evaluation on the basis of IQF were prepared under identical conditions. A contrast-detail (C-D) phantom was placed on a 50.0 mm tough water phantom and images were taken. The contrast threshold of these samples was determined by 10 film readers, the same as those for the ROC analysis. When the significance of differences in the AUC was tested by the paired t-test (two-sided) and the Jackknife method, significant differences were noted between the reference dose and the 1/4 or 4-times dose at the standard pixel size (0.175 mm) and smaller pixel size (0.0875 mm) size, while no significant difference was noted between the reference dose and the 1/2 or 2-times dose. In terms of IQF, no significant difference was noted between standard and smaller pixel sizes (paired t-test). The IQF data indicate that the dose level for imaging with CR can be reduced by about 30% from the reference dose.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  17. The osmotic tolerance of boar spermatozoa and its usefulness as sperm quality parameter.

    PubMed

    Yeste, Marc; Briz, Mailo; Pinart, Elisabeth; Sancho, Sílvia; Bussalleu, Eva; Bonet, Sergi

    2010-06-01

    Predicting the fertility outcome of ejaculates is very important in the field of porcine reproduction. The aims of this study were to determine the effects of different osmotic treatments on boar spermatozoa and to correlate them with fertility and prolificacy, assessed as non-return rates within 60 days (NRR(60d)) of the first inseminations, and litter size (LS), respectively. Sperm samples (n=100) from one hundred healthy Piétrain boars were used to assess 48 treatments combining different osmolalities (ranged between 100 and 4000 mOsm kg(-1)), different compounds used to prepare anisotonic solutions, and two different modalities: return and non-return to isotonic conditions. Sperm quality was evaluated before and after applying the treatments on the basis of analyses of sperm viability, motility, morphology and percentages of acrosome-intact spermatozoa. Statistical analyses were performed using a one-way ANOVA and post hoc Tukey's test, linear regression analyses (Pearson correlation and multiple regression) and Jackknife cross-validation. Although three conventional parameters: sperm viability, sperm morphology and the percentages of acrosome-intact spermatozoa were significantly correlated with NRR(60d) and with LS, their respective osmotic tolerance parameters (defined for each parameter and treatment regarding with negative control) presented a higher Pearson coefficient with both fertility and prolificacy in three treatments (150 mOsm kg(-1) with non-return to isotonic conditions, 200 mOsm kg(-1) with return and 500 mOsm kg(-1) using sodium citrate and non-return to isotonic conditions). We conclude that osmotic resistance in sperm viability, sperm morphology and acrosome-intactness in the treatments mentioned above could be assessed along with classical parameters to better predict the fertilising ability of a given ejaculate.

  18. 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.

  19. Using non-linear methods to investigate the criterion validity of traffic-psychological test batteries.

    PubMed

    Risser, R; Chaloupka, Ch; Grundler, W; Sommer, M; Häusler, J; Kaufmann, C

    2008-01-01

    In several countries in Europe (among others Germany and Austria) persons who have lost their drivers licence have to undergo a psychological test in order to regain their licence. The article discusses the validity of two test batteries of the Expert System Traffic using standardized driving tests [Schuhfried, G., 2005. Manual Expert System Traffic (XPSV). Schuhfried GmbH, Mödling]. A global evaluation of the respondents' performance in a standardized driving test was used as criterion measure in order to divide the subjects into drivers, who were classified as relatively safe or unsafe according to their performance in a standardized driving test. Artificial neural networks were used to calculate the criterion validity. This yielded superior classification rates and validity coefficients compared to classical multivariate methods such as a logistic regression. The stability and generalizability of the results was empirically demonstrated using a jack-knife validation, an internal bootstrap validation and an independent validation sample which completed the test batteries and the standardized driving test as part of a so-called traffic-psychological assessment which is compulsory in Austria in all cases, where the driver's licence has been withdrawn, e.g., when caught driving under the influence of alcohol. Moreover, the procedure allows calculating incremental validities which enable the assessment of the relative importance of the individual predictor variables. This contributes to the transparency of the results obtained with artificial neural networks. In summary it can be said that the results provide empirical evidence of the validity of the traffic-psychological tests batteries used in this study. The practical implications of the results for traffic-psychological assessment are described.

  20. Effects of JPEG2000 data compression on an automated system for detecting clustered microcalcifications in digital mammograms.

    PubMed

    Penedo, Mónica; Lado, María J; Tahoces, Pablo G; Souto, Miguel; Vidal, Juan J

    2006-04-01

    The functionalities of the JPEG2000 standard have led to its incorporation into digital imaging and communications in medicine (DICOM), which makes this compression method available for medical systems. In this study, we evaluated the compression of mammographic images with JPEG2000 (16 : 1, 20 : 1, 40 : 1, 60.4 : 1, 80: 1, and 106 : 1) for applications with a computer-aided detection (CAD) system for clusters of microcalcifications. Jackknife free-response receiver operating characteristic (JAFROC) analysis indicated that differences in the detection of clusters of microcalcifications were not statistically significant for uncompressed versus 16: 1 (T = -0.7780; p = 0.4370), 20 : 1 (T = 1.0361; p = 0.3007), and 40 : 1 (T = 1.6966; p = 0.0904); and statistically significant for uncompressed versus 60.4 : 1 (T = 5.8883; p < 0.008), 80 : 1 (T = 7.8414; p < 0.008), and 106 : 1 (T = 17.5034; p = < 0.008). Although there is a small difference in peak signal-to-noise ratio (PSNR) between compression ratios, the true-positive (TP) and false-positive (FP) rates, and the free-response receiver operating characteristic (FROC), figure of merit values considerably decreased from a 60 : 1 compression ratio. The performance of the CAD system is significantly reduced when using images compressed at ratios greater than 40 : 1 with JPEG2000 compared to uncompressed images. Mammographic images compressed up to 20 : 1 provide a percentage of correct detections by our CAD system similar to uncompressed images, regardless of the characteristics of the cluster. Further investigation is required to determine how JPEG2000 affects the detectability of clusters of microcalcifications as a function of their characteristics.

  1. 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.

  2. Phylogenetic diversity and ecological pattern of ammonia-oxidizing archaea in the surface sediments of the western Pacific.

    PubMed

    Cao, Huiluo; Hong, Yiguo; Li, Meng; Gu, Ji-Dong

    2011-11-01

    The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the distribution pattern and diversities of AOA in the western Pacific. Under these different conditions, the distinct community composition between shallow and deep-sea sediments was clearly delineated based on the UniFrac PCoA and Jackknife Environmental Cluster analyses. Phylogenetic analyses showed that a few ammonia-oxidizing archaeal subclades in the marine water column/sediment clade and endemic lineages were indicative phylotypes for some environments. Higher phylogenetic diversity was observed in the Philippines while lower diversity in the hydrothermal vent habitat. Water depth and possibly with other environmental factors could be the main driving forces to shape the phylogenetic diversity of AOA observed, not only in the SCS but also in the whole western Pacific. The multivariate regression tree analysis also supported this observation consistently. Moreover, the functions of current and other climate factors were also discussed in comparison of phylogenetic diversity. The information collectively provides important insights into the ecophysiological requirements of uncultured ammonia-oxidizing archaeal lineages in the western Pacific Ocean.

  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. Integrating USArray and Cooperative New Madrid Seismic Network Data to Establish Central US Catalog Location and Magnitude Sensitivities

    NASA Astrophysics Data System (ADS)

    DeShon, H. R.

    2012-12-01

    The Cooperative New Madrid Seismic Network (CNMSN) monitors earthquake activity in the central US. The network provides excellent coverage of the New Madrid seismic zone (NMSZ) but has fewer regional stations located outside of the Mississippi embayment. The Earthscope Transportable Array (TA), however, temporarily expands earthquake identification and location ability as it marches through this region and in particular, adds valuable information for earthquakes located at the edges of the current network. Prior to the CNMSN, the Central Missouri Valley network reported locations for the central US using a more diffuse regional station spacing, and, in fact, that catalog reported many more earthquakes outside of the embayment and along the northern stretches of the NMSZ. Here, I have integrated TA waveform and phase data of central US earthquakes provided by the ANF with like data from the CNMSN. All waveform data of reported events from both networks is reviewed and phases combined. The integrated data is used to relocate central US seismicity, with analysis to date focused on activity in and north of the NMSZ. Events are relocated using HYPOELLIPSE and HYPOINVERSE following current CNMSN location and magnitude procedures, which are undergoing a transition during 2012. I test earthquake location and magnitude sensitivity to station distribution inside and outside of the embayment via jackknife testing. I will present results for events recorded from July 2011 through mid-November 2012. The study will allow us to 1) understand if the differences in seismicity pattern between the Central Missouri Valley catalog (1974-1994) and the CNMSN catalog (1995-present) are a function of station distribution, 2) provide more accurate estimates of earthquake locations outside of the Mississippi embayment, and 3) assess how changes in CNMSN processing effect catalog location and magnitude estimates in the central US.

  5. 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

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

    PubMed

    Ruschin, Mark; Timberg, Pontus; Båth, Magnus; Hemdal, Bengt; Svahn, Tony; Saunders, Rob S; Samei, Ehsan; Andersson, Ingvar; Mattsson, Soren; Chakrabort, Dev P; Tingber, Anders

    2007-02-01

    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 (JA-FROC) 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.

  7. 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.

  8. Addition of Digital Breast Tomosynthesis to Full-Field Digital Mammography in the Diagnostic Setting: Additional Value and Cancer Detectability

    PubMed Central

    Seo, Mirinae; Kim, Sun Ah; Kim, Won Hwa; Lim, Ji He; Lee, Su Hyun; Bae, Min Sun; Koo, Hye Ryoung; Cho, Nariya; Moon, Woo Kyung

    2016-01-01

    Purpose The purpose of this study was to assess the value of adding digital breast tomosynthesis (DBT) to full-field digital mammography (FFDM) in the diagnostic workup of breast cancer and to determine which lesion variables affect cancer detectability in the combined modality. Methods Between March and May 2012, paired FFDM and DBT images were obtained from 203 women as part of a diagnostic workup for breast cancer. Images from FFDM alone, DBT alone, and DBT combined with FFDM were reviewed in separate sessions by six blinded readers. Jackknife alternative free-response receiver operating characteristic (JAFROC) figure of merit (FOM), sensitivity, and specificity were compared between the modalities. Lesion characteristics affecting the cancer detection rate when using the combined modality were also analyzed. Results Among the 203 women, 126 women had a total of 129 malignancies and 77 women had total of 77 benign lesions. The overall JAFROC FOM of the combined modality was higher than that of FFDM alone (0.827 vs. 0.775, p<0.001) and that of DBT alone was higher than that of FFDM alone (0.807 vs. 0.775, p=0.027). The overall sensitivity of the combined modality was higher than that of FFDM alone (80.0% vs. 73.2%, p<0.001) and that of DBT alone was higher than that of FFDM alone (78.3% vs. 73.2%, p=0.007). Compared to FFDM alone, the combined modality detected an additional 48 cancers. Using the combined modality, the presence of masses or microcalcifications was significantly associated with the cancer detection rate (p<0.001). Conclusion The combination of DBT with FFDM results in a higher diagnostic yield than FFDM alone. Additionally, DBT alone performs better than FFDM alone. However, even when DBT is combined with FFDM, breast cancers with no discernible masses and those lacking calcifications are difficult to detect. PMID:28053633

  9. 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.

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

    PubMed

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

    1997-03-01

    The spectacular evolutionary radiation of hummingbirds (Trochilidae) has served as a model system for many biological studies. To begin to provide a historical context for these investigations, we generated a complete matrix of DNA hybridization distances among 26 hummingbirds and an outgroup swift (Chaetura pelagica) to determine the principal hummingbird lineages. FITCH topologies estimated from symmetrized delta TmH-C values and subjected to various validation methods (bootstrapping, weighted jackknifing, branch length significance) indicated a fundamental split between hermit (Eutoxeres aquila, Threnetes ruckeri; Phaethornithinae) and nonhermit (Trochilinae) hummingbirds, and provided strong support for six principal nonhermit clades with the following branching order: (1) a predominantly lowland group comprising caribs (Eulampis holosericeus) and relatives (Androdon aequatorialis and Heliothryx barroti) with violet-ears (Colibri coruscans) and relatives (Doryfera ludovicae); (2) an Andean-associated clade of highly polytypic taxa (Eriocnemis, Heliodoxa, and Coeligena); (3) a second endemic Andean clade (Oreotrochilus chimborazo, Aglaiocercus coelestis, and Lesbia victoriae) paired with thorntails (Popelairia conversii); (4) emeralds and relatives (Chlorostilbon mellisugus, Amazilia tzacatl, Thalurania colombica, Orthorhyncus cristatus and Campylopterus villaviscensio); (5) mountain-gems (Lampornis clemenciae and Eugenes fulgens); and (6) tiny bee-like forms (Archilochus colubris, Myrtis fanny, Acestrura mulsant, and Philodice mitchellii). Corresponding analyses on a matrix of unsymmetrized delta values gave similar support for these relationships except that the branching order of the two Andean clades (2, 3 above) was unresolved. In general, subsidiary relationships were consistent and well supported by both matrices, sometimes revealing surprising associations between forms that differ dramatically in plumage and bill morphology. Our results also reveal some

  11. 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

  12. 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).

  13. 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.

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

    PubMed

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

    2014-04-07

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

    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

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

    PubMed

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

    2012-03-01

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

  18. Clinical validation of a medical grade color monitor for chest radiology

    NASA Astrophysics Data System (ADS)

    Jacobs, J.; Zanca, F.; Verschakelen, J.; Marchal, G.; Bosmans, H.

    2009-02-01

    Until recently, the specifications of medical grade monochrome LCD monitors outperformed those of color LCD monitors. New generations of color LCD monitors, however, show specifications that are in many respects similar to those of monochrome monitors typically used in diagnostic workstations. The aim of present study was to evaluate the impact of different medical grade monitors in terms of detection of simulated lung nodules in chest x-ray images. Specifically, we wanted to compare a new medical grade color monitor (Barco Coronis 6MP color) to a medical grade grayscale monitor (Barco Coronis 3MP monochrome) and a consumer color monitor (Philips 200VW 1.7MP color) by means of an observer performance experiment. Using the free-response acquisition data paradigm, seven radiologists were asked to detect and locate lung nodules (170 in total), simulated in half of the 200 chest X-ray images used in the experiment. The jackknife free-response receiver operating characteristic (JAFROC) analysis of the data showed a statistically significant difference between at least two monitors, F-value=3.77 and p-value =0.0481. The different Figure of Merit values were 0.727, 0.723 and 0.697 for the new color LCD monitor, the medical grade monitor and the consumer color monitor respectively. There was no difference between the needed reading times but there was a difference between the mean calculated Euclidian distances between the position marked by the observers and the center of the simulated nodule, indicating a better accuracy with both medical grade monitors. Present data suggests that the new generation of medical grade color monitors could be used as diagnostic workstations.

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

    USGS Publications Warehouse

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

    2005-01-01

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

  20. Evaluating the statistical conclusion validity of weighted mean results in meta-analysis by analysing funnel graph diagrams.

    PubMed

    Elvik, R

    1998-03-01

    The validity of weighted mean results estimated in meta-analysis has been criticized. This paper presents a set of simple statistical and graphical techniques that can be used in meta-analysis to evaluate common points of criticism. The graphical techniques are based on funnel graph diagrams. Problems and techniques for dealing with them that are discussed include: (1) the so-called 'apples and oranges' problem, stating that mean results in meta-analysis tend to gloss over important differences that should be highlighted. A test of the homogeneity of results is described for testing the presence of this problem. If results are highly heterogeneous, a random effects model of meta-analysis is more appropriate than the fixed effects model of analysis. (2) The possible presence of skewness in a sample of results. This can be tested by comparing the mode, median and mean of the results in the sample. (3) The possible presence of more than one mode in a sample of results. This can be tested by forming a frequency distribution of the results and examining the shape of this distribution. (4) The sensitivity of the mean to the possible presence of atypical results (outliers) can be tested by comparing the overall mean to the mean of all results except the one suspected of being atypical. (5) The possible presence of publication bias can be tested by visual inspection of funnel graph diagrams in which data points have been sorted according to statistical significance and direction of effect. (6) The possibility of underestimating the standard error of the mean in meta-analyses by using multiple, correlated results from the same study as the unit of analysis can be addressed by using the jack-knife technique for estimating the uncertainty of the mean. Brief examples, taken from road safety research, are given of all these techniques.

  1. Rainfall variability drives interannual variation in N₂O emissions from a humid, subtropical pasture.

    PubMed

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

    2015-04-15

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

  2. Effect of sampling frequency on estimates of cumulative nitrous oxide emissions.

    PubMed

    Parkin, Timothy B

    2008-01-01

    It is generally recognized that soil N(2)O emissions can exhibit pronounced day-to-day variations; however, measurements of soil N(2)O flux with soil chambers typically are done only at discrete points in time. This study evaluated the impact of sampling frequency on the precision of cumulative N(2)O flux estimates calculated from field measurements. Automated chambers were deployed in a corn/soybean field and used to measure soil N(2)O fluxes every 6 h from 25 Feb. 2006 through 11 Oct. 2006. The chambers were located in two positions relative to the fertilizer bands-directly over a band or between fertilizer bands. Sampling frequency effects on cumulative N(2)O-N flux estimation were assessed using a jackknife technique where populations of N(2)O fluxes were constructed from the average daily fluxes measured in each chamber. These test populations were generated by selecting measured flux values at regular time intervals ranging from 1 to 21 d. It was observed that as sampling interval increased from 7 to 21 d, variances associated with cumulative flux estimates increased. At relatively frequent sampling intensities (i.e., once every 3 d) N(2)O-N flux estimates were within +/-10% of the expected value at both sampling positions. As the time interval between sampling was increased, the deviation in estimated cumulative N(2)O flux increased, such that sampling once every 21 d yielded estimates within +60% and -40% of the actual cumulative N(2)O flux. The variance of potential fluxes associated with the between-band positions was less than the over-band position, indicating that the underlying temporal variability impacts the efficacy of a given sampling protocol.

  3. MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM.

    PubMed

    Chou, Kuo-Chen; Shen, Hong-Bin

    2007-08-24

    Given an uncharacterized protein sequence, how can we identify whether it is a membrane protein or not? If it is, which membrane protein type it belongs to? These questions are important because they are closely relevant to the biological function of the query protein and to its interaction process with other molecules in a biological system. Particularly, with the avalanche of protein sequences generated in the Post-Genomic Age and the relatively much slower progress in using biochemical experiments to determine their functions, it is highly desired to develop an automated method that can be used to help address these questions. In this study, a 2-layer predictor, called MemType-2L, has been developed: the 1st layer prediction engine is to identify a query protein as membrane or non-membrane; if it is a membrane protein, the process will be automatically continued with the 2nd-layer prediction engine to further identify its type among the following eight categories: (1) type I, (2) type II, (3) type III, (4) type IV, (5) multipass, (6) lipid-chain-anchored, (7) GPI-anchored, and (8) peripheral. MemType-2L is featured by incorporating the evolution information through representing the protein samples with the Pse-PSSM (Pseudo Position-Specific Score Matrix) vectors, and by containing an ensemble classifier formed by fusing many powerful individual OET-KNN (Optimized Evidence-Theoretic K-Nearest Neighbor) classifiers. The success rates obtained by MemType-2L on a new-constructed stringent dataset by both the jackknife test and the independent dataset test are quite high, indicating that MemType-2L may become a very useful high throughput tool. As a Web server, MemType-2L is freely accessible to the public at http://chou.med.harvard.edu/bioinf/MemType.

  4. 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.

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

    PubMed

    Princé, Karine; Zuckerberg, Benjamin

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  7. Reader characteristics linked to detection of pulmonary nodules on radiographs: ROC vs. JAFROC analyses of performance

    NASA Astrophysics Data System (ADS)

    Kohli, Akshay; Robinson, John W.; Ryan, John; McEntee, Mark F.; Brennan, Patrick C.

    2011-03-01

    The purpose of this study is to explore whether reader characteristics are linked to heightened levels of diagnostic performance in chest radiology using receiver operating characteristic (ROC) and jackknife free response ROC (JAFROC) methodologies. A set of 40 postero-anterior chest radiographs was developed, of which 20 were abnormal containing one or more simulated nodules, of varying subtlety. Images were independently reviewed by 12 boardcertified radiologists including six chest specialists. The observer performance was measured in terms of ROC and JAFROC scores. For the ROC analysis, readers were asked to rate their degree of suspicion for the presence of nodules by using a confidence rating scale (1-6). JAFROC analysis required the readers to locate and rate as many suspicious areas as they wished using the same scale and resultant data were used to generate Az and FOM scores for ROC and JAFROC analyses respectively. Using Pearson methods, scores of performance were correlated with 7 reader characteristics recorded using a questionnaire. JAFROC analysis showed that improved reader performance was significantly (p<=0.05) linked with chest specialty (p<0.03), hours per week reading chest radiographs (p<0.03) and chest readings per year (p<0.04). ROC analyses demonstrated only one significant relationship, hours per week reading chest radiographs (p<0.02).The results of this study have shown that radiologist's performance in the detection of pulmonary nodules on radiographs is significantly linked to chest specialty, hours reading per week and number of radiographs read per year. Also, JAFROC is a more powerful predictor of performance as compared to ROC.

  8. 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

  9. Biology of Diaphorina citri (Homoptera: Psyllidae) on four host plants.

    PubMed

    Tsai, J H; Liu, Y H

    2000-12-01

    The biology of the citrus psyllid Diaphorina citri Kuwayama was studied at 25 degrees C on four commonly grown citrus and related plants [rough lemon, Citrus jambhiri Lush; sour orange, C aurantium L.; grapefruit, C. paradisi Macfadyen; and orange jessamine, Murraya paniculata (L.) Jack] in the laboratory. The biological characteristics of each life stage are described. The average egg incubation periods on orange jessamine, grapefruit, rough lemon, and sour orange varied very little (4.1-4.2 d). The average nymphal developmental periods on these four host plants were essentially the same except the fifth stadium. Survival of immatures on orange jessamine, grapefruit, rough lemon, and sour orange was 75.4, 84.6, 78.3, and 68.6%, respectively. Female adults lived an average of 39.7, 39.7, 47.6, and 43.7 d on these respective host plants. The average number of eggs laid per female on grapefruit (858 eggs) was significantly more than those on other hosts (P < 0.05). The intrinsic rate of natural increase (r(m)) for D. citri on grapefruit was highest. Jackknife estimates of r(m) varied from 0.188 on grapefruit to 0.162 on orange jessamine and rough lemon. The mean population generation time on these hosts ranged from 31.6 to 34.1 d. The continuous flushes produced by orange jessamine could play an important role in maintaining high populations of this vector when the new flushes are not available in the commercial citrus groves.

  10. Mathematical Modeling of Intestinal Iron Absorption Using Genetic Programming

    PubMed Central

    Colins, Andrea; Gerdtzen, Ziomara P.; Nuñez, Marco T.; Salgado, J. Cristian

    2017-01-01

    Iron is a trace metal, key for the development of living organisms. Its absorption process is complex and highly regulated at the transcriptional, translational and systemic levels. Recently, the internalization of the DMT1 transporter has been proposed as an additional regulatory mechanism at the intestinal level, associated to the mucosal block phenomenon. The short-term effect of iron exposure in apical uptake and initial absorption rates was studied in Caco-2 cells at different apical iron concentrations, using both an experimental approach and a mathematical modeling framework. This is the first report of short-term studies for this system. A non-linear behavior in the apical uptake dynamics was observed, which does not follow the classic saturation dynamics of traditional biochemical models. We propose a method for developing mathematical models for complex systems, based on a genetic programming algorithm. The algorithm is aimed at obtaining models with a high predictive capacity, and considers an additional parameter fitting stage and an additional Jackknife stage for estimating the generalization error. We developed a model for the iron uptake system with a higher predictive capacity than classic biochemical models. This was observed both with the apical uptake dataset used for generating the model and with an independent initial rates dataset used to test the predictive capacity of the model. The model obtained is a function of time and the initial apical iron concentration, with a linear component that captures the global tendency of the system, and a non-linear component that can be associated to the movement of DMT1 transporters. The model presented in this paper allows the detailed analysis, interpretation of experimental data, and identification of key relevant components for this complex biological process. This general method holds great potential for application to the elucidation of biological mechanisms and their key components in other complex

  11. 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.

  12. 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.

  13. The Internal Pudendal Artery Perforator Thigh Flap: A New Freestyle Pedicle Flap for the Ischial Region

    PubMed Central

    Goishi, Keiichi; Abe, Yoshiro; Takaku, Mitsuru; Seike, Takuya; Harada, Hiroshi; Nakanishi, Hideki

    2014-01-01

    Background: Recurrence and complication rates of pressure sores are highest in the ischial region, and other donor sites are needed for recurrent pressure sores. The potential of a new freestyle pedicle flap for ischial lesions, an internal pudendal artery perforator (iPap) thigh flap, was examined through anatomical and theoretical analyses and a case series using computed tomography angiography. Methods: The skin flap was designed in the thigh region based on an iPap. The skin perforators were marked with a Doppler probe. One patient underwent computed tomography angiography with fistulography to identify the damage to or effects on the pedicle vessels of the flap. Debridement of ischial lesions and flap elevation were performed in the jackknife position. Results: The iPap thigh flaps were performed in 5 patients, 4 with ischial pressure sores and 1 with calcinosis cutis of the ischial region. The width and length of the flaps ranged from 5 to 8 cm (mean, 6.6 cm) and 10 to 17 cm (mean, 12.6 cm), respectively. Three patients underwent partial osteotomy of the ischial bone. No complications, including flap necrosis or wound dehiscence of the donor and reconstructed sites, were observed. Conclusions: The perforator vessels of the internal pudendal artery are very close to the ischial tuberosity. Blood flow to the flap is reliable when careful debridement of the pressure sore is performed. The iPap thigh flap is a new option for soft-tissue defects in the ischial region, including ischial pressure sores. PMID:25289335

  14. 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

  15. [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.

  16. 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.

  17. Demographic history and rare allele sharing among human populations

    PubMed Central

    Gravel, Simon; Henn, Brenna M.; Gutenkunst, Ryan N.; Indap, Amit R.; Marth, Gabor T.; Clark, Andrew G.; Yu, Fuli; Gibbs, Richard A.; Bustamante, Carlos D.; Altshuler, David L.; Durbin, Richard M.; Abecasis, Gonçalo R.; Bentley, David R.; Chakravarti, Aravinda; Clark, Andrew G.; Collins, Francis S.; De La Vega, Francisco M.; Donnelly, Peter; Egholm, Michael; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Knoppers, Bartha M.; Lander, Eric S.; Lehrach, Hans; Mardis, Elaine R.; McVean, Gil A.; Nickerson, Debbie A.; Peltonen, Leena; Schafer, Alan J.; Sherry, Stephen T.; Wang, Jun; Wilson, Richard K.; Gibbs, Richard A.; Deiros, David; Metzker, Mike; Muzny, Donna; Reid, Jeff; Wheeler, David; Wang, Jun; Li, Jingxiang; Jian, Min; Li, Guoqing; Li, Ruiqiang; Liang, Huiqing; Tian, Geng; Wang, Bo; Wang, Jian; Wang, Wei; Yang, Huanming; Zhang, Xiuqing; Zheng, Huisong; Lander, Eric S.; Altshuler, David L.; Ambrogio, Lauren; Bloom, Toby; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Jaffe, David B.; Shefler, Erica; Sougnez, Carrie L.; Bentley, David R.; Gormley, Niall; Humphray, Sean; Kingsbury, Zoya; Koko-Gonzales, Paula; Stone, Jennifer; McKernan, Kevin J.; Costa, Gina L.; Ichikawa, Jeffry K.; Lee, Clarence C.; Sudbrak, Ralf; Lehrach, Hans; Borodina, Tatiana A.; Dahl, Andreas; Davydov, Alexey N.; Marquardt, Peter; Mertes, Florian; Nietfeld, Wilfiried; Rosenstiel, Philip; Schreiber, Stefan; Soldatov, Aleksey V.; Timmermann, Bernd; Tolzmann, Marius; Egholm, Michael; Affourtit, Jason; Ashworth, Dana; Attiya, Said; Bachorski, Melissa; Buglione, Eli; Burke, Adam; Caprio, Amanda; Celone, Christopher; Clark, Shauna; Conners, David; Desany, Brian; Gu, Lisa; Guccione, Lorri; Kao, Kalvin; Kebbel, Andrew; Knowlton, Jennifer; Labrecque, Matthew; McDade, Louise; Mealmaker, Craig; Minderman, Melissa; Nawrocki, Anne; Niazi, Faheem; Pareja, Kristen; Ramenani, Ravi; Riches, David; Song, Wanmin; Turcotte, Cynthia; Wang, Shally; Mardis, Elaine R.; Wilson, Richard K.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Weinstock, George; Durbin, Richard M.; Burton, John; Carter, David M.; Churcher, Carol; Coffey, Alison; Cox, Anthony; Palotie, Aarno; Quail, Michael; Skelly, Tom; Stalker, James; Swerdlow, Harold P.; Turner, Daniel; De Witte, Anniek; Giles, Shane; Gibbs, Richard A.; Wheeler, David; Bainbridge, Matthew; Challis, Danny; Sabo, Aniko; Yu, Fuli; Yu, Jin; Wang, Jun; Fang, Xiaodong; Guo, Xiaosen; Li, Ruiqiang; Li, Yingrui; Luo, Ruibang; Tai, Shuaishuai; Wu, Honglong; Zheng, Hancheng; Zheng, Xiaole; Zhou, Yan; Li, Guoqing; Wang, Jian; Yang, Huanming; Marth, Gabor T.; Garrison, Erik P.; Huang, Weichun; Indap, Amit; Kural, Deniz; Lee, Wan-Ping; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; Daly, Mark J.; DePristo, Mark A.; Altshuler, David L.; Ball, Aaron D.; Banks, Eric; Bloom, Toby; Browning, Brian L.; Cibulskis, Kristian; Fennell, Tim J.; Garimella, Kiran V.; Grossman, Sharon R.; Handsaker, Robert E.; Hanna, Matt; Hartl, Chris; Jaffe, David B.; Kernytsky, Andrew M.; Korn, Joshua M.; Li, Heng; Maguire, Jared R.; McCarroll, Steven A.; McKenna, Aaron; Nemesh, James C.; Philippakis, Anthony A.; Poplin, Ryan E.; Price, Alkes; Rivas, Manuel A.; Sabeti, Pardis C.; Schaffner, Stephen F.; Shefler, Erica; Shlyakhter, Ilya A.; Cooper, David N.; Ball, Edward V.; Mort, Matthew; Phillips, Andrew D.; Stenson, Peter D.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Bustamante, Carlos D.; Clark, Andrew G.; Boyko, Adam; Degenhardt, Jeremiah; Gravel, Simon; Gutenkunst, Ryan N.; Kaganovich, Mark; Keinan, Alon; Lacroute, Phil; Ma, Xin; Reynolds, Andy; Clarke, Laura; Flicek, Paul; Cunningham, Fiona; Herrero, Javier; Keenen, Stephen; Kulesha, Eugene; Leinonen, Rasko; McLaren, William M.; Radhakrishnan, Rajesh; Smith, Richard E.; Zalunin, Vadim; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Stütz, Adrian M.; Humphray, Sean; Bauer, Markus; Cheetham, R. Keira; Cox, Tony; Eberle, Michael; James, Terena; Kahn, Scott; Murray, Lisa; Chakravarti, Aravinda; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Hyland, Fiona C. L.; Manning, Jonathan M.; McLaughlin, Stephen F.; Peckham, Heather E.; Sakarya, Onur; Sun, Yongming A.; Tsung, Eric F.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Sudbrak, Ralf; Albrecht, Marcus W.; Amstislavskiy, Vyacheslav S.; Herwig, Ralf; Parkhomchuk, Dimitri V.; Sherry, Stephen T.; Agarwala, Richa; Khouri, Hoda M.; Morgulis, Aleksandr O.; Paschall, Justin E.; Phan, Lon D.; Rotmistrovsky, Kirill E.; Sanders, Robert D.; Shumway, Martin F.; Xiao, Chunlin; McVean, Gil A.; Auton, Adam; Iqbal, Zamin; Lunter, Gerton; Marchini, Jonathan L.; Moutsianas, Loukas; Myers, Simon; Tumian, Afidalina; Desany, Brian; Knight, James; Winer, Roger; Craig, David W.; Beckstrom-Sternberg, Steve M.; Christoforides, Alexis; Kurdoglu, Ahmet A.; Pearson, John V.; Sinari, Shripad A.; Tembe, Waibhav D.; Haussler, David; Hinrichs, Angie S.; Katzman, Sol J.; Kern, Andrew; Kuhn, Robert M.; Przeworski, Molly; Hernandez, Ryan D.; Howie, Bryan; Kelley, Joanna L.; Melton, S. Cord; Abecasis, Gonçalo R.; Li, Yun; Anderson, Paul; Blackwell, Tom; Chen, Wei; Cookson, William O.; Ding, Jun; Kang, Hyun Min; Lathrop, Mark; Liang, Liming; Moffatt, Miriam F.; Scheet, Paul; Sidore, Carlo; Snyder, Matthew; Zhan, Xiaowei; Zöllner, Sebastian; Awadalla, Philip; Casals, Ferran; Idaghdour, Youssef; Keebler, John; Stone, Eric A.; Zilversmit, Martine; Jorde, Lynn; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; Sahinalp, S. Cenk; Sudmant, Peter H.; Mardis, Elaine R.; Chen, Ken; Chinwalla, Asif; Ding, Li; Koboldt, Daniel C.; McLellan, Mike D.; Dooling, David; Weinstock, George; Wallis, John W.; Wendl, Michael C.; Zhang, Qunyuan; Durbin, Richard M.; Albers, Cornelis A.; Ayub, Qasim; Balasubramaniam, Senduran; Barrett, Jeffrey C.; Carter, David M.; Chen, Yuan; Conrad, Donald F.; Danecek, Petr; Dermitzakis, Emmanouil T.; Hu, Min; Huang, Ni; Hurles, Matt E.; Jin, Hanjun; Jostins, Luke; Keane, Thomas M.; Le, Si Quang; Lindsay, Sarah; Long, Quan; MacArthur, Daniel G.; Montgomery, Stephen B.; Parts, Leopold; Stalker, James; Tyler-Smith, Chris; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Balasubramanian, Suganthi; Bjornson, Robert; Du, Jiang; Grubert, Fabian; Habegger, Lukas; Haraksingh, Rajini; Jee, Justin; Khurana, Ekta; Lam, Hugo Y. K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; Li, Yingrui; Luo, Ruibang; Marth, Gabor T.; Garrison, Erik P.; Kural, Deniz; Quinlan, Aaron R.; Stewart, Chip; Stromberg, Michael P.; Ward, Alistair N.; Wu, Jiantao; Lee, Charles; Mills, Ryan E.; Shi, Xinghua; McCarroll, Steven A.; Banks, Eric; DePristo, Mark A.; Handsaker, Robert E.; Hartl, Chris; Korn, Joshua M.; Li, Heng; Nemesh, James C.; Sebat, Jonathan; Makarov, Vladimir; Ye, Kenny; Yoon, Seungtai C.; Degenhardt, Jeremiah; Kaganovich, Mark; Clarke, Laura; Smith, Richard E.; Zheng-Bradley, Xiangqun; Korbel, Jan O.; Humphray, Sean; Cheetham, R. Keira; Eberle, Michael; Kahn, Scott; Murray, Lisa; Ye, Kai; De La Vega, Francisco M.; Fu, Yutao; Peckham, Heather E.; Sun, Yongming A.; Batzer, Mark A.; Konkel, Miriam K.; Walker, Jerilyn A.; Xiao, Chunlin; Iqbal, Zamin; Desany, Brian; Blackwell, Tom; Snyder, Matthew; Xing, Jinchuan; Eichler, Evan E.; Aksay, Gozde; Alkan, Can; Hajirasouliha, Iman; Hormozdiari, Fereydoun; Kidd, Jeffrey M.; Chen, Ken; Chinwalla, Asif; Ding, Li; McLellan, Mike D.; Wallis, John W.; Hurles, Matt E.; Conrad, Donald F.; Walter, Klaudia; Zhang, Yujun; Gerstein, Mark B.; Snyder, Michael; Abyzov, Alexej; Du, Jiang; Grubert, Fabian; Haraksingh, Rajini; Jee, Justin; Khurana, Ekta; Lam, Hugo Y. K.; Leng, Jing; Mu, Xinmeng Jasmine; Urban, Alexander E.; Zhang, Zhengdong; Gibbs, Richard A.; Bainbridge, Matthew; Challis, Danny; Coafra, Cristian; Dinh, Huyen; Kovar, Christie; Lee, Sandy; Muzny, Donna; Nazareth, Lynne; Reid, Jeff; Sabo, Aniko; Yu, Fuli; Yu, Jin; Marth, Gabor T.; Garrison, Erik P.; Indap, Amit; Leong, Wen Fung; Quinlan, Aaron R.; Stewart, Chip; Ward, Alistair N.; Wu, Jiantao; Cibulskis, Kristian; Fennell, Tim J.; Gabriel, Stacey B.; Garimella, Kiran V.; Hartl, Chris; Shefler, Erica; Sougnez, Carrie L.; Wilkinson, Jane; Clark, Andrew G.; Gravel, Simon; Grubert, Fabian; Clarke, Laura; Flicek, Paul; Smith, Richard E.; Zheng-Bradley, Xiangqun; Sherry, Stephen T.; Khouri, Hoda M.; Paschall, Justin E.; Shumway, Martin F.; Xiao, Chunlin; McVean, Gil A.; Katzman, Sol J.; Abecasis, Gonçalo R.; Blackwell, Tom; Mardis, Elaine R.; Dooling, David; Fulton, Lucinda; Fulton, Robert; Koboldt, Daniel C.; Durbin, Richard M.; Balasubramaniam, Senduran; Coffey, Allison; Keane, Thomas M.; MacArthur, Daniel G.; Palotie, Aarno; Scott, Carol; Stalker, James; Tyler-Smith, Chris; Gerstein, Mark B.; Balasubramanian, Suganthi; Chakravarti, Aravinda; Knoppers, Bartha M.; Abecasis, Gonçalo R.; Bustamante, Carlos D.; Gharani, Neda; Gibbs, Richard A.; Jorde, Lynn; Kaye, Jane S.; Kent, Alastair; Li, Taosha; McGuire, Amy L.; McVean, Gil A.; Ossorio, Pilar N.; Rotimi, Charles N.; Su, Yeyang; Toji, Lorraine H.; TylerSmith, Chris; Brooks, Lisa D.; Felsenfeld, Adam L.; McEwen, Jean E.; Abdallah, Assya; Juenger, Christopher R.; Clemm, Nicholas C.; Collins, Francis S.; Duncanson, Audrey; Green, Eric D.; Guyer, Mark S.; Peterson, Jane L.; Schafer, Alan J.; Abecasis, Gonçalo R.; Altshuler, David L.; Auton, Adam; Brooks, Lisa D.; Durbin, Richard M.; Gibbs, Richard A.; Hurles, Matt E.; McVean, Gil A.

    2011-01-01

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

  18. 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.

  19. 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

  20. 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.

  1. A comparison of methods for limited-sampling strategy design using data from a phase I trial of the anthrapyrazole DuP-941.

    PubMed

    Jodrell, D I; Murray, L S; Hawtof, J; Graham, M A; Egorin, M J

    1996-01-01

    The pharmacokinetics of a drug in individual patients can be estimated using plasma samples collected at a limited number of time points. However, different methods for a limited-sampling strategy (LSS) design exist and the optimal method has not yet been defined. Plasma concentration data were available from 27 of 74 courses in a phase I study (dose range, 5-55 mg m-2) of the novel anthrapyrazole DuP-941. Three approaches to LSS development were compared. Firstly, forward stepwise regression (FSR) was used to derive equations to predict the DuP-941 area under the concentration-time curve (AUC) based on plasma concentrations measured at specified times. LSSs were developed using 14 randomly chosen data sets and were validated using the remaining 13 data sets. Secondly, "all subsets" regression (ASR) was used to develop LSSs. A jack-knife technique was also used to allow model development utilising 26 data sets and validation on the 27th data set. Thirdly, an LSS was developed using optimal sampling theory (OST), and the LSS was used in conjunction with a Bavesian algorithm. Selected sampling times for four-point LSSs were 10, 65, 185 and 485 min (FSR) and 10, 45, 200 and 480 min (OST). Ten candidate LSSs were developed using the ASR approach. ASR- and OST/Bayesian-derived four-point LSSs gave more precise (P < 0.05) estimates of AUC [mean absolute percentage of difference (MAD%) +/- SD: ASR, 6.4 +/- 3.7%; OST/Bayesian, 6.8 +/- 4.6%] than did FSR (MAD% = 15.1 +/- 9.9%). The OST/Bayesian approach is recommended because it allows estimation of all model parameters and is more flexible with regard to sample collection time and design variables.

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

    PubMed

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

    2005-01-01

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

  3. 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

  4. 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

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

    PubMed Central

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

    2011-01-01

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

  6. Non-parametric frequency analysis of extreme values for integrated disaster management considering probable maximum events

    NASA Astrophysics Data System (ADS)

    Takara, K. T.

    2015-12-01

    This paper describes a non-parametric frequency analysis method for hydrological extreme-value samples with a size larger than 100, verifying the estimation accuracy with a computer intensive statistics (CIS) resampling such as the bootstrap. Probable maximum values are also incorporated into the analysis for extreme events larger than a design level of flood control. Traditional parametric frequency analysis methods of extreme values include the following steps: Step 1: Collecting and checking extreme-value data; Step 2: Enumerating probability distributions that would be fitted well to the data; Step 3: Parameter estimation; Step 4: Testing goodness of fit; Step 5: Checking the variability of quantile (T-year event) estimates by the jackknife resampling method; and Step_6: Selection of the best distribution (final model). The non-parametric method (NPM) proposed here can skip Steps 2, 3, 4 and 6. Comparing traditional parameter methods (PM) with the NPM, this paper shows that PM often underestimates 100-year quantiles for annual maximum rainfall samples with records of more than 100 years. Overestimation examples are also demonstrated. The bootstrap resampling can do bias correction for the NPM and can also give the estimation accuracy as the bootstrap standard error. This NPM has advantages to avoid various difficulties in above-mentioned steps in the traditional PM. Probable maximum events are also incorporated into the NPM as an upper bound of the hydrological variable. Probable maximum precipitation (PMP) and probable maximum flood (PMF) can be a new parameter value combined with the NPM. An idea how to incorporate these values into frequency analysis is proposed for better management of disasters that exceed the design level. The idea stimulates more integrated approach by geoscientists and statisticians as well as encourages practitioners to consider the worst cases of disasters in their disaster management planning and practices.

  7. 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

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

    PubMed Central

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

    2008-01-01

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

  9. 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.

  10. Reliability of information-based integration of EEG and fMRI data: a simulation study.

    PubMed

    Assecondi, Sara; Ostwald, Dirk; Bagshaw, Andrew P

    2015-02-01

    Most studies involving simultaneous electroencephalographic (EEG) and functional magnetic resonance imaging (fMRI) data rely on the first-order, affine-linear correlation of EEG and fMRI features within the framework of the general linear model. An alternative is the use of information-based measures such as mutual information and entropy, which can also detect higher-order correlations present in the data. The estimate of information-theoretic quantities might be influenced by several parameters, such as the numerosity of the sample, the amount of correlation between variables, and the discretization (or binning) strategy of choice. While these issues have been investigated for invasive neurophysiological data and a number of bias-correction estimates have been developed, there has been no attempt to systematically examine the accuracy of information estimates for the multivariate distributions arising in the context of EEG-fMRI recordings. This is especially important given the differences between electrophysiological and EEG-fMRI recordings. In this study, we drew random samples from simulated bivariate and trivariate distributions, mimicking the statistical properties of EEG-fMRI data. We compared the estimated information shared by simulated random variables with its numerical value and found that the interaction between the binning strategy and the estimation method influences the accuracy of the estimate. Conditional on the simulation assumptions, we found that the equipopulated binning strategy yields the best and most consistent results across distributions and bias correction methods. We also found that within bias correction techniques, the asymptotically debiased (TPMC), the jackknife debiased (JD), and the best upper bound (BUB) approach give similar results, and those are consistent across distributions.

  11. 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

  12. 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.

  13. Mapping landscape scale variations of forest structure, biomass, and productivity in Amazonia

    NASA Astrophysics Data System (ADS)

    Saatchi, S.; Malhi, Y.; Zutta, B.; Buermann, W.; Anderson, L. O.; Araujo, A. M.; Phillips, O. L.; Peacock, J.; Ter Steege, H.; Lopez Gonzalez, G.; Baker, T.; Arroyo, L.; Almeida, S.; Higuchi, N.; Killeen, T.; Monteagudo, A.; Neill, D.; Pitman, N.; Prieto, A.; Salomão, R.; Silva, N.; Vásquez Martínez, R.; Laurance, W.; Ramírez, H. A.

    2009-06-01

    Landscape and environmental variables such as topography, geomorphology, soil types, and climate are important factors affecting forest composition, structure, productivity, and biomass. Here, we combine a network of forest inventories with recently developed global data products from satellite observations in modeling the potential distributions of forest structure and productivity in Amazonia and examine how geomorphology, soil, and precipitation control these distributions. We use the RAINFOR network of forest plots distributed in lowland forests across Amazonia, and satellite observations of tree cover, leaf area index, phenology, moisture, and topographical variations. A maximum entropy estimation (Maxent) model is employed to predict the spatial distribution of several key forest structure parameters: basal area, fraction of large trees, fraction of palms, wood density, productivity, and above-ground biomass at 5 km spatial resolution. A series of statistical tests at selected thresholds as well as across all thresholds and jackknife analysis are used to examine the accuracy of distribution maps and the relative contributions of environmental variables. The final maps were interpreted using soil, precipitation, and geomorphological features of Amazonia and it was found that the length of dry season played a key role in impacting the distribution of all forest variables except the wood density. Soil type had a significant impact on the wood productivity. Most high productivity forests were distributed either on less infertile soils of western Amazonia and Andean foothills, on crystalline shields, and younger alluvial deposits. Areas of low elevation and high density of small rivers of Central Amazonia showed distinct features, hosting mainly forests with low productivity and smaller trees.

  14. PRIMUS: Galaxy Clustering as a Function of Luminosity and Color at 0.2 < z < 1

    NASA Astrophysics Data System (ADS)

    Skibba, Ramin A.; Smith, M. Stephen M.; Coil, Alison L.; Moustakas, John; Aird, James; Blanton, Michael R.; Bray, Aaron D.; Cool, Richard J.; Eisenstein, Daniel J.; Mendez, Alexander 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, ξ(rp , π) and wp (rp ), using volume-limited samples constructed from a parent sample of over ~130, 000 galaxies with robust redshifts in seven independent fields covering 9 deg2 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 -1 < rp < 1 Mpc h -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 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.

  15. Uncertainty Analysis of the Variable Parameter McCarthy-Muskingum (VPMM) Method with Presence of Lateral Flow

    NASA Astrophysics Data System (ADS)

    Yadav, B.; Bardossy, A.; Perumal, M.

    2014-12-01

    Uncertainty analysis of the estimate of a hydrological model is a required exercise for the risk management linked to the variable of interest. This study subjects the Variable Parameter McCarthy-Muskingum (VPMM) method recently proposed by Perumal and Price (2013) to uncertainty analysis. The VPMM method has been developed based on the assumption that there exists no lateral flow in the river stretch where it is employed for routing. But in this study this method is applied for the study of flood wave movement in a 24.2 km stretch between Rottweil and Oberndorf of Neckar River in Germany in the presence of lateral inflow. The study also proposes a general procedure for simulating flood events with the consideration of lateral flow in the reach. The cross sectioned information of the considered river stretch is estimated by the Robust Parameter Estimation (ROPE) algorithm. ROPE algorithm is used to get the best performing parameters set of bed width (Trapezoidal section) and side slope. As the evaluation of VPMM is done with the help of Nash-Sutcliffe efficiency criterion, this study uses it as an objective function to check the performance of the method with different data sets obtained using the ROPE algorithm. The uncertainty associated with parameter K and due to the presence of lateral flow is checked by the Jackknife method. All the 26 flood events observed from the Neckar catchment from 1999 to 2004 have been used for the analysis of the VPMM method. When inflow and outflow hydrographs for lateral flow estimation are used, performance of the VPMM method as per N-S efficiency criterion can be up to 97.061 %. By the analysis of all 27 available flood events, a relationship between total rainfall and total loss is obtained, and the value of loss obtained from the developed relationship can be used to simulate outflow hydrograph with the maximum N-S efficiency of 93.812 %.

  16. Ammonia- and methane-oxidizing microorganisms in high-altitude wetland sediments and adjacent agricultural soils.

    PubMed

    Yang, Yuyin; Shan, Jingwen; Zhang, Jingxu; Zhang, Xiaoling; Xie, Shuguang; Liu, Yong

    2014-12-01

    Ammonia oxidation is known to be carried out by ammonia-oxidizing bacteria (AOB) and archaea (AOA), while methanotrophs (methane-oxidizing bacteria (MOB)) play an important role in mitigating methane emissions from the environment. However, the difference of AOA, AOB, and MOB distribution in wetland sediment and adjacent upland soil remains unclear. The present study investigated the abundances and community structures of AOA, AOB, and MOB in sediments of a high-altitude freshwater wetland in Yunnan Province (China) and adjacent agricultural soils. Variations of AOA, AOB, and MOB community sizes and structures were found in water lily-vegetated and Acorus calamus-vegetated sediments and agricultural soils (unflooded rice soil, cabbage soil, and garlic soil and flooded rice soil). AOB community size was higher than AOA in agricultural soils and lily-vegetated sediment, but lower in A. calamus-vegetated sediment. MOB showed a much higher abundance than AOA and AOB. Flooded rice soil had the largest AOA, AOB, and MOB community sizes. Principal coordinate analyses and Jackknife Environment Clusters analyses suggested that unflooded and flooded rice soils had relatively similar AOA, AOB, and MOB structures. Cabbage soil and A. calamus-vegetated sediment had relatively similar AOA and AOB structures, but their MOB structures showed a large difference. Nitrososphaera-like microorganisms were the predominant AOA species in garlic soil but were present with a low abundance in unflooded rice soil and cabbage soil. Nitrosospira-like AOB were dominant in wetland sediments and agricultural soils. Type I MOB Methylocaldum and type II MOB Methylocystis were dominant in wetland sediments and agricultural soils. Moreover, Pearson's correlation analysis indicated that AOA Shannon diversity was positively correlated with the ratio of organic carbon to nitrogen (p < 0.05). This work could provide some new insights toward ammonia and methane oxidation in soil and wetland sediment

  17. A new method for post Genome-Wide Association Study (GWAS) analysis of colorectal cancer in Taiwan.

    PubMed

    Wang, Hwei-Ming; Chang, Tzu-Hao; Lin, Feng-Mao; Chao, Te-Hsin; Huang, Wei-Chih; Liang, Chao; Chu, Chao-Fang; Chiu, Chih-Min; Wu, Wei-Yun; Chen, Ming-Cheng; Weng, Chen-Tsung; Weng, Shun-Long; Chiang, Feng-Fan; Huang, Hsien-Da

    2013-04-10

    Recently, single nucleotide polymorphisms (SNPs) located in specific loci or genes have been identified associated with susceptibility to colorectal cancer (CRC) in Genome-Wide Association Studies (GWAS). However, in different ethnicities and regions, the genetic variations and the environmental factors can widely vary. Therefore, here we propose a post-GWAS analysis method to investigate the CRC susceptibility SNPs in Taiwan by conducting a replication analysis and bioinformatics analysis. One hundred and forty-four significant SNPs from published GWAS results were collected by a literature survey, and two hundred and eighteen CRC samples and 385 normal samples were collected for post-GWAS analysis. Finally, twenty-six significant SNPs were identified and reported as associated with susceptibility to colorectal cancer, other cancers, obesity, and celiac disease in a previous GWAS study. Functional analysis results of 26 SNPs indicate that most biological processes identified are involved in regulating immune responses and apoptosis. In addition, an efficient prediction model was constructed by applying Jackknife feature selection and ANOVA testing. As compared to another risk prediction model of CRC for European Caucasians population, which performs 0.616 of AUC by using 54 SNPs, the proposed model shows good performance in predicting CRC risk within the Taiwanese population, i.e., 0.724 AUC by using 16 SNPs. We believe that the proposed risk prediction model is highly promising for predicting CRC risk within the Taiwanese population. In addition, the functional analysis results could be helpful to explore the potential associated regulatory mechanisms that may be involved in CRC development.

  18. 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.

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

    PubMed

    Morais, Gisele Cavalcante; Lee, James Tony

    2014-03-01

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

  20. Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers.

    PubMed

    Chou, Kuo-Chen; Shen, Hong-Bin

    2006-08-01

    Facing the explosion of newly generated protein sequences in the post genomic era, we are challenged to develop an automated method for fast and reliably annotating their subcellular locations. Knowledge of subcellular locations of proteins can provide useful hints for revealing their functions and understanding how they interact with each other in cellular networking. Unfortunately, it is both expensive and time-consuming to determine the localization of an uncharacterized protein in a living cell purely based on experiments. To tackle the challenge, a novel hybridization classifier was developed by fusing many basic individual classifiers through a voting system. The "engine" of these basic classifiers was operated by the OET-KNN (Optimized Evidence-Theoretic K-Nearest Neighbor) rule. As a demonstration, predictions were performed with the fusion classifier for proteins among the following 16 localizations: (1) cell wall, (2) centriole, (3) chloroplast, (4) cyanelle, (5) cytoplasm, (6) cytoskeleton, (7) endoplasmic reticulum, (8) extracell, (9) Golgi apparatus, (10) lysosome, (11) mitochondria, (12) nucleus, (13) peroxisome, (14) plasma membrane, (15) plastid, and (16) vacuole. To get rid of redundancy and homology bias, none of the proteins investigated here had >/=25% sequence identity to any other in a same subcellular location. The overall success rates thus obtained via the jack-knife cross-validation test and independent dataset test were 81.6% and 83.7%, respectively, which were 46 approximately 63% higher than those performed by the other existing methods on the same benchmark datasets. Also, it is clearly elucidated that the overwhelmingly high success rates obtained by the fusion classifier is by no means a trivial utilization of the GO annotations as prone to be misinterpreted because there is a huge number of proteins with given accession numbers and the corresponding GO numbers, but their subcellular locations are still unknown, and that the

  1. Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization.

    PubMed

    Chou, Kuo-Chen; Shen, Hong-Bin

    2006-08-18

    Predicting subcellular localization of human proteins is a challenging problem, especially when unknown query proteins do not have significant homology to proteins of known subcellular locations and when more locations need to be covered. To tackle the challenge, protein samples are expressed by hybridizing the gene ontology (GO) database and amphiphilic pseudo amino acid composition (PseAA). Based on such a representation frame, a novel ensemble classifier, called "Hum-PLoc", was developed by fusing many basic individual classifiers through a voting system. The "engine" of these basic classifiers was operated by the KNN (K-nearest neighbor) rule. As a demonstration, tests were performed with the ensemble classifier for human proteins among the following 12 locations: (1) centriole; (2) cytoplasm; (3) cytoskeleton; (4) endoplasmic reticulum; (5) extracell; (6) Golgi apparatus; (7) lysosome; (8) microsome; (9) mitochondrion; (10) nucleus; (11) peroxisome; (12) plasma membrane. To get rid of redundancy and homology bias, none of the proteins investigated here had > or = 25% sequence identity to any other in a same subcellular location. The overall success rates thus obtained via the jackknife cross-validation test and independent dataset test were 81.1% and 85.0%, respectively, which are more than 50% higher than those obtained by the other existing methods on the same stringent datasets. Furthermore, an incisive and compelling analysis was given to elucidate that the overwhelmingly high success rate obtained by the new predictor is by no means due to a trivial utilization of the GO annotations. This is because, for those proteins with "subcellular location unknown" annotation in Swiss-Prot database, most (more than 99%) of their corresponding GO numbers in GO database are also annotated with "cellular component unknown". The information and clues for predicting subcellular locations of proteins are actually buried into a series of tedious GO numbers, just like they

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

    PubMed Central

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

    2015-01-01

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

  3. A sequence alignment-independent method for protein classification.

    PubMed

    Vries, John K; Munshi, Rajan; Tobi, Dror; Klein-Seetharaman, Judith; Benos, Panayiotis V; Bahar, Ivet

    2004-01-01

    Annotation of the rapidly accumulating body of sequence data relies heavily on the detection of remote homologues and functional motifs in protein families. The most popular methods rely on sequence alignment. These include programs that use a scoring matrix to compare the probability of a potential alignment with random chance and programs that use curated multiple alignments to train profile hidden Markov models (HMMs). Related approaches depend on bootstrapping multiple alignments from a single sequence. However, alignment-based programs have limitations. They make the assumption that contiguity is conserved between homologous segments, which may not be true in genetic recombination or horizontal transfer. Alignments also become ambiguous when sequence similarity drops below 40%. This has kindled interest in classification methods that do not rely on alignment. An approach to classification without alignment based on the distribution of contiguous sequences of four amino acids (4-grams) was developed. Interest in 4-grams stemmed from the observation that almost all theoretically possible 4-grams (20(4)) occur in natural sequences and the majority of 4-grams are uniformly distributed. This implies that the probability of finding identical 4-grams by random chance in unrelated sequences is low. A Bayesian probabilistic model was developed to test this hypothesis. For each protein family in Pfam-A and PIR-PSD, a feature vector called a probe was constructed from the set of 4-grams that best characterised the family. In rigorous jackknife tests, unknown sequences from Pfam-A and PIR-PSD were compared with the probes for each family. A classification result was deemed a true positive if the probe match with the highest probability was in first place in a rank-ordered list. This was achieved in 70% of cases. Analysis of false positives suggested that the precision might approach 85% if selected families were clustered into subsets. Case studies indicated that the 4

  4. Causes of death in children younger than five years in China in 2015: an updated analysis

    PubMed Central

    Song, Peige; Theodoratou, Evropi; Li, Xue; Liu, Li; Chu, Yue; Black, Robert E.; Campbell, Harry; Rudan, Igor; Chan, Kit Yee

    2016-01-01

    Background Substantial progress in reducing the child mortality rate has been made globally in the last two decades. However, for China, the number of children dying from preventable diseases is still very large. It is important to have regularly updated information on the distribution of causes of death (COD) in children to inform policy and research. In this study, we aim to estimate the COD spectrum in children younger than five years old from 2009 to 2015 with a focus on the year 2015 and to provide an updated COD prediction model for China. Methods Updated data of under–five mortality rates (U5MRs) and the number of live births at national and provincial levels were obtained from United Nation's Inter–agency Group for Child Mortality Estimation (UN IGME), Institute for Health Metrics and Evaluation (IHME), and United Nations Population Division (UNPD). Then, we conducted a systematic review across four Chinese and English bibliographic databases and identified high–quality community–based longitudinal studies of COD in children younger than five years in China. We developed a number of single–cause models to predict the number of child death for main COD in different age groups at both national and provincial levels. The jackknife procedure was applied to construct the 95% Uncertainty Ranges (URs). Results From 2009 to 2015, the under–five mortality rates have declined by 37.1%. The leading causes of death in 2015 were preterm birth complications (17.4%), birth asphyxia (15.2%), congenital abnormalities (14.1%), accidents (13.5%) and pneumonia (12.4%) for children under five years old. The COD spectrum varied substantially across Chinese provinces with different development levels. The leading cause in children under five years in the wealthier provinces (with lower U5MRs) was congenital abnormalities (up to 18.9%), while in the poorer provinces (with higher U5MRs), pneumonia was the dominant COD (up to 23.4%). Conclusions This study updates and

  5. Digital Mapping of Soil Salinity and Crop Yield across a Coastal Agricultural Landscape Using Repeated Electromagnetic Induction (EMI) Surveys.

    PubMed

    Yao, Rongjiang; Yang, Jingsong; Wu, Danhua; Xie, Wenping; Gao, Peng; Jin, Wenhui

    2016-01-01

    Reliable and real-time information on soil and crop properties is important for the development of management practices in accordance with the requirements of a specific soil and crop within individual field units. This is particularly the case in salt-affected agricultural landscape where managing the spatial variability of soil salinity is essential to minimize salinization and maximize crop output. The primary objectives were to use linear mixed-effects model for soil salinity and crop yield calibration with horizontal and vertical electromagnetic induction (EMI) measurements as ancillary data, to characterize the spatial distribution of soil salinity and crop yield and to verify the accuracy of spatial estimation. Horizontal and vertical EMI (type EM38) measurements at 252 locations were made during each survey, and root zone soil samples and crop samples at 64 sampling sites were collected. This work was periodically conducted on eight dates from June 2012 to May 2013 in a coastal salt-affected mud farmland. Multiple linear regression (MLR) and restricted maximum likelihood (REML) were applied to calibrate root zone soil salinity (ECe) and crop annual output (CAO) using ancillary data, and spatial distribution of soil ECe and CAO was generated using digital soil mapping (DSM) and the precision of spatial estimation was examined using the collected meteorological and groundwater data. Results indicated that a reduced model with EMh as a predictor was satisfactory for root zone ECe calibration, whereas a full model with both EMh and EMv as predictors met the requirement of CAO calibration. The obtained distribution maps of ECe showed consistency with those of EMI measurements at the corresponding time, and the spatial distribution of CAO generated from ancillary data showed agreement with that derived from raw crop data. Statistics of jackknifing procedure confirmed that the spatial estimation of ECe and CAO exhibited reliability and high accuracy. A general

  6. 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

  7. Two-phase analysis in consensus genetic mapping.

    PubMed

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

    2012-05-01

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

  8. A model to predict bladder shapes from changes in bladder and rectal filling.

    PubMed

    Lotz, Heidi T; Remeijer, Peter; van Herk, Marcel; Lebesque, Joos V; de Bois, Josien A; Zijp, Lambert J; Moonen, Luc M

    2004-06-01

    The purpose of this study is to develop a model that quantifies in three dimensions changes in bladder shape due to changes in bladder and/or rectal volume. The new technique enables us to predict changes in bladder shape over a short period of time, based on known urinary inflow. Shortly prior to the treatment, the patient will be scanned using a cone beam CT scanner (x-ray volume imager) that is integrated with the linear accelerator. After (automated) delineation of the bladder, the model will be used to predict the short-term shape changes of the bladder for the time interval between image acquisition and dose delivery. The model was developed using multiple daily CT scans of the pelvic area of 19 patients. For each patient, the rigid bony structure in follow-up scans was matched to that of the planning CT scan, and the outer bladder and rectal wall were delineated. Each bladder wall was subdivided in 2500 domains. A fixed reference point inside the bladder was used to calculate for each bladder structure a "Mercator-like" 2D scalar map (similar to a height map of the globe), containing the distances from this reference point to each domain on the bladder wall. Subsequently, for all bladder shapes of a patient and for all domains on the wall individually, the distance to the reference point was fitted by a linear function of both bladder and rectal volume. The model uses an existing bladder structure to create a new structure via expansion (or contraction), until the expressed volume is reached. To evaluate the predictive power of the model, the jack-knife method was used. The errors in the fitting procedure depended on the part of the bladder and range from 0 to 0.5 cm (0.2 cm on average). It was found that a volume increase of 150 cc can lead to a displacement up to about 2.5 cm of the cranial part of the bladder. With the model, the uncertainty in the position of the bladder wall can be reduced down to a maximum value of about 0.5 cm in case the bladder

  9. Diagnosing Lung Nodules on Oncologic MR/PET Imaging: Comparison of Fast T1-Weighted Sequences and Influence of Image Acquisition in Inspiration and Expiration Breath-Hold

    PubMed Central

    Schwenzer, Nina F.; Seith, Ferdinand; Gatidis, Sergios; Brendle, Cornelia; Schmidt, Holger; Pfannenberg, Christina A.; laFougère, Christian; Nikolaou, Konstantin

    2016-01-01

    Objective First, to investigate the diagnostic performance of fast T1-weighted sequences for lung nodule evaluation in oncologic magnetic resonance (MR)/positron emission tomography (PET). Second, to evaluate the influence of image acquisition in inspiration and expiration breath-hold on diagnostic performance. Materials and Methods The study was approved by the local Institutional Review Board. PET/CT and MR/PET of 44 cancer patients were evaluated by 2 readers. PET/CT included lung computed tomography (CT) scans in inspiration and expiration (CTin, CTex). MR/PET included Dixon sequence for attenuation correction and fast T1-weighted volumetric interpolated breath-hold examination (VIBE) sequences (volume interpolated breath-hold examination acquired in inspiration [VIBEin], volume interpolated breath-hold examination acquired in expiration [VIBEex]). Diagnostic performance was analyzed for lesion-, lobe-, and size-dependence. Diagnostic confidence was evaluated (4-point Likert-scale; 1 = high). Jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Results Seventy-six pulmonary lesions were evaluated. Lesion-based detection rates were: CTex, 77.6%; VIBEin, 53.3%; VIBEex, 51.3%; and Dixon, 22.4%. Lobe-based detection rates were: CTex, 89.6%; VIBEin, 58.3%; VIBEex, 60.4%; and Dixon, 31.3%. In contrast to CT, inspiration versus expiration did not alter diagnostic performance in VIBE sequences. Diagnostic confidence was best for VIBEin and CTex and decreased in VIBEex and Dixon (1.2 ± 0.6; 1.2 ± 0.7; 1.5 ± 0.9; 1.7 ± 1.1, respectively). The JAFROC figure-of-merit of Dixon was significantly lower. All patients with malignant lesions were identified by CTex, VIBEin, and VIBEex, while 3 patients were false-negative in Dixon. Conclusion Fast T1-weighted VIBE sequences allow for identification of patients with malignant pulmonary lesions. The Dixon sequence is not recommended for lung nodule evaluation in oncologic MR

  10. Landslide triggering-thickness susceptibility, a simple proxy for landslide hazard? A test in the Mili catchment (North-Eastern Sicily, Italy)

    NASA Astrophysics Data System (ADS)

    Lombardo, Luigi; Fubelli, Giandomenico; Amato, Gabriele; Bonasera, Mauro; Mai, Martin

    2016-04-01

    This study implements a landslide triggering-thickness susceptibility approach in order to investigate the landslide scenario in the catchment of Mili, this being located in the north-easternmost sector of Sicily (Italy). From a detailed geomorphological campaign, thicknesses of mobilised materials at the triggering zone of each mass movement were collected and subsequently used as a dependent variable to be analysed in the framework of spatial predictive models. The adopted modelling methodology consisted of a presence-only learning algorithm which differently from classic presence-absence methods does not rely on stable conditions in order to derive functional relationships between dependent and independent variables. The dependent was pre-processed by reclassifying the crown thickness spectrum into a binary condition expressing thick (values equal or greater than 1m) and thin (values less than 1m) landslide crown classes. The explanatory variables were selected to express triggering-thickness dependency at different scales, these being in close proximity to the triggering point through primary and secondary attributes from a 2m-cell side Lidar HRDEM, at a medium scale through vegetation indexes from multispectral satellite images (ASTER) and a coarser scale through a geological, land use and tectonic maps. The choice of a presence-only approach allowed to effectively discriminate between the two types of landslide thicknesses at the triggering zone, producing excellent prediction skills associated with relatively low variances across a set of 50 randomly generated replicates. In addition, the role of each predictor was assessed for the two considered classes as relevant differences arose in terms of their contribution to the final models. In this regard, predictor importance, Jack-knife tests and response curves were used to assess the reliability of the models together with their geomorphological reasonability. This work attempts to capitalize on fieldwork data

  11. From Gaged to Ungaged- Predicting Long-term Environmental Flows, and Ecosystems Responses.

    NASA Astrophysics Data System (ADS)

    Sengupta, A.; Adams, S. K.; Stein, E. D.; Mazor, R.; Bledsoe, B. P.

    2015-12-01

    Modern management needs, such as water supply, quality, and ecosystem protection place numerous demands on instream flows. Many regions are interested in developing numeric flow criteria as a way of ensuring maintenance of flow patterns that protect biological resources while meeting other demands. Developing flow criteria requires the capacity to generate reliable time series of the daily flow at any stream reach of interest and to relate flow patterns to biological indicators of stream health. Most stream reaches are not gaged, and it is impractical to develop detailed models for all reaches where flow alteration needs to be evaluated. We present a novel mechanistic approach to efficiently predict flows and flow alteration at all ungaged stream locations within a region of interest. We used an "ensemble approach" whereby a series of regionally representative models were developed and calibrated. New sites of interest are assigned to one of the ensemble models based on similarity of catchment properties. For southern California, we selected 43 gaged sites representing the range of geomorphology, and watershed characteristics of streams in the region. For each gaged site, we developed a hydrologic model (HEC-HMS) to predict daily flows for a period representing dry, wet and normal precipitation. The final goal is to relate flow alterations to ecological responses, the models were calibrated to three separate performance metrics that reflect conditions important for instream biological communities- proportion of low flow days, flashiness and Nash Sutcliffe efficiency for overall model performance. We cross-validated the models using a "jack-knife" approach. Models were assigned to novel 840 bioassessment sites based on the results of a Random Forest model that identified catchment properties that most affected the runoff patterns. Daily flow data for existing and "reference conditions" was simulated for a 23-year period for current and reference (undeveloped

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

    PubMed Central

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

    2015-01-01

    Long-term morphine treatment leads to tolerance which attenuates analgesic effect and hampers clinical utilization. Recent studies have sought to reveal the mechanism of opioid receptors and neuroinflammation by observing morphological changes of cells in the rat spinal cord. This work proposes a high-content screening (HCS) based computational method, HCS-Morph, for predicting neuroinflammation in morphine tolerance to facilitate the development of tolerance therapy using immunostaining images for astrocytes, microglia, and neurons in the spinal cord. HCS-Morph first extracts numerous HCS-based features of cellular phenotypes. Next, an inheritable bi-objective genetic algorithm is used to identify a minimal set of features by maximizing the prediction accuracy of neuroinflammation. Finally, a mathematic model using a support vector machine with the identified features is established to predict drug-treated images to assess the effects of tolerance therapy. The dataset consists of 15 saline controls (1 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    thicknesses. In addition, the role of each predictor within the whole modelling procedure was assessed by applying Jackknife tests. These analyses focussed on evaluating the variation of AUC values across replicates comparing single variable models with models based on the full set of predictors iteratively deprived of one covariate. As a result, relevant differences among main contributors between the two considered classes were also quantitatively derived and geomorphologically interpreted. This work can be considered as an example for creating specific landslide susceptibility maps to be used in master planning in order to establish proportional countermeasures to different activation mechanisms. Keywords: statistical analysis, shallow landslide, landslide susceptibility, triggering factors, presence-only approach

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

    NASA Astrophysics Data System (ADS)

    Caporali, E.; Petrucci, A.

    2009-09-01

    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. 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

  16. Digital Mapping of Soil Salinity and Crop Yield across a Coastal Agricultural Landscape Using Repeated Electromagnetic Induction (EMI) Surveys

    PubMed Central

    Yao, Rongjiang; Yang, Jingsong; Wu, Danhua; Xie, Wenping; Gao, Peng; Jin, Wenhui

    2016-01-01

    Reliable and real-time information on soil and crop properties is important for the development of management practices in accordance with the requirements of a specific soil and crop within individual field units. This is particularly the case in salt-affected agricultural landscape where managing the spatial variability of soil salinity is essential to minimize salinization and maximize crop output. The primary objectives were to use linear mixed-effects model for soil salinity and crop yield calibration with horizontal and vertical electromagnetic induction (EMI) measurements as ancillary data, to characterize the spatial distribution of soil salinity and crop yield and to verify the accuracy of spatial estimation. Horizontal and vertical EMI (type EM38) measurements at 252 locations were made during each survey, and root zone soil samples and crop samples at 64 sampling sites were collected. This work was periodically conducted on eight dates from June 2012 to May 2013 in a coastal salt-affected mud farmland. Multiple linear regression (MLR) and restricted maximum likelihood (REML) were applied to calibrate root zone soil salinity (ECe) and crop annual output (CAO) using ancillary data, and spatial distribution of soil ECe and CAO was generated using digital soil mapping (DSM) and the precision of spatial estimation was examined using the collected meteorological and groundwater data. Results indicated that a reduced model with EMh as a predictor was satisfactory for root zone ECe calibration, whereas a full model with both EMh and EMv as predictors met the requirement of CAO calibration. The obtained distribution maps of ECe showed consistency with those of EMI measurements at the corresponding time, and the spatial distribution of CAO generated from ancillary data showed agreement with that derived from raw crop data. Statistics of jackknifing procedure confirmed that the spatial estimation of ECe and CAO exhibited reliability and high accuracy. A general

  17. 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.

  18. Fossil calibrations and molecular divergence time estimates in centrarchid fishes (Teleostei: Centrarchidae).

    PubMed

    Near, Thomas J; Bolnick, Daniel I; Wainwright, Peter C

    2005-08-01

    Molecular clock methods allow biologists to estimate divergence times, which in turn play an important role in comparative studies of many evolutionary processes. It is well known that molecular age estimates can be biased by heterogeneity in rates of molecular evolution, but less attention has been paid to the issue of potentially erroneous fossil calibrations. In this study we estimate the timing of diversification in Centrarchidae, an endemic major lineage of the diverse North American freshwater fish fauna, through a new approach to fossil calibration and molecular evolutionary model selection. Given a completely resolved multi-gene molecular phylogeny and a set of multiple fossil-inferred age estimates, we tested for potentially erroneous fossil calibrations using a recently developed fossil cross-validation. We also used fossil information to guide the selection of the optimal molecular evolutionary model with a new fossil jackknife method in a fossil-based model cross-validation. The centrarchid phylogeny resulted from a mixed-model Bayesian strategy that included 14 separate data partitions sampled from three mtDNA and four nuclear genes. Ten of the 31 interspecific nodes in the centrarchid phylogeny were assigned a minimal age estimate from the centrarchid fossil record. Our analyses identified four fossil dates that were inconsistent with the other fossils, and we removed them from the molecular dating analysis. Using fossil-based model cross-validation to determine the optimal smoothing value in penalized likelihood analysis, and six mutually consistent fossil calibrations, the age of the most recent common ancestor of Centrarchidae was 33.59 million years ago (mya). Penalized likelihood analyses of individual data partitions all converged on a very similar age estimate for this node, indicating that rate heterogeneity among data partitions is not confounding our analyses. These results place the origin of the centrarchid radiation at a time of major

  19. 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

  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

  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

    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. 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, ξ(r{sub p} , π) 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.

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

    PubMed Central

    2014-01-01

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

  4. GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions.

    PubMed

    Xiao, Xuan; Wang, Pu; Chou, Kuo-Chen

    2011-03-01

    G protein-coupled receptors (GPCRs) are among the most frequent targets of therapeutic drugs. With the avalanche of newly generated protein sequences in the post genomic age, to expedite the process of drug discovery, it is highly desirable to develop an automated method to rapidly identify GPCRs and their types. A new predictor was developed by hybridizing two different modes of pseudo-amino acid composition (PseAAC): the functional domain PseAAC and the low-frequency Fourier spectrum PseAAC. The new predictor is called GPCR-2L, where "2L" means that it is a two-layer predictor: the 1st layer prediction engine is to identify a query protein as GPCR or not; if it is, the prediction will be automatically continued to further identify it as belonging to one of the following six types: (1) rhodopsin-like (Class A), (2) secretin-like (Class B), (3) metabotropic glutamate/pheromone (Class C), (4) fungal pheromone (Class D), (5) cAMP receptor (Class E), or (6) frizzled/smoothened family (Class F). The overall success rate of GPCR-2L in identifying proteins as GPCRs or non-GPCRs is over 97.2%, while identifying GPCRs among their six types is over 97.8%. Such high success rates were derived by the rigorous jackknife cross-validation on a stringent benchmark dataset, in which none of the included proteins had ≥40% pairwise sequence identity to any other protein in a same subset. As a user-friendly web-server, GPCR-2L is freely accessible to the public at http://icpr.jci.edu.cn/, by which one can obtain the 2-level results in about 20 s for a query protein sequence of 500 amino acids. The longer the sequence is, the more time it may usually need. The high success rates reported here indicate that it is a quite effective approach to identify GPCRs and their types with the functional domain information and the low-frequency Fourier spectrum analysis. It is anticipated that GPCR-2L may become a useful tool for both basic research and drug development in the areas related to

  5. 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

    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.

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

    PubMed Central

    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 jackknife free-response receiver operating characteristic figure of merit (FOM) was calculated on a per–malignant nodule or per-mass basis. Noninferiority was defined by the lower limit of the 95% confidence interval (CI) of the difference between lower-dose and routine-dose FOMs being less than −0.10. Results Twenty-nine patients had 62 malignant hepatic nodules and masses. Estimated FOM differences between lower-dose FBP and lower-dose ANLM versus routine-dose FBP were noninferior (difference: −0.041 [95% CI: −0.090, 0.009] and −0.003 [95% CI: −0.052, 0.047], respectively). In patients with dedicated liver scans, lower-dose ANLM images were noninferior (difference: +0.015 [95% CI: −0.077, 0.106]), whereas lower-dose FBP images were not (difference −0.049 [95% CI:

  7. Power laws for heavy-tailed distributions: modeling allele and haplotype diversity for the national marrow donor program.

    PubMed

    Slater, Noa; Louzoun, Yoram; Gragert, Loren; Maiers, Martin; Chatterjee, Ansu; Albrecht, Mark

    2015-04-01

    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

  8. 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

  9. 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

    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

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

    PubMed

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

    2012-01-15

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    A transfer-function based on chironomids was created to reconstruct past summer temperatures from a training set comprised of 33 south eastern Australian lakes. Statistical analyses show that mean February temperature (MFT) is the most robust and independent variable explaining chironomid species variability. The best MFT transfer function was a partial least squares (PLS) model with a coefficient of determination (r2Jackknifed) of 0.69, a root mean squared error of prediction (RMSEP) of 2.33˚C, and maximum bias of 2.15°C. The transfer function was tested by applying it to a Late Glacial to Holocene record from Blue Lake, New South Wales using published data. The reconstruction displays an overall pattern very similar to the Milankovitch driven summer insolation curve for 30°S and to the chironomid based summer temperature reconstruction from Eagle Tarn, Tasmania (Rees and Cwynar 2010) suggesting that the model is robust. The transfer function was also applied to reconstruct the Last Glacial Maxium (LGM) summer temperature from Welsby Lagoon, North Stradbroke Island (Queensland). Preliminary results show a c. 4.2~8.6˚C of cooling in summer temperatures during the LGM from south east Australia. Stable oxygen and deuterium isotope composition (δ18O and δD) 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 δ18O 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 δ18O to modern lake temperatures has been investigated. Deuterium (δD) on the head capsules has been measured concurrently and the relationship to climate and environment will be explored based on the latest available

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    PubMed Central

    Kissling, Wilm Daniel; Dalby, Lars; Fløjgaard, Camilla; Lenoir, Jonathan; Sandel, Brody; Sandom, Christopher; Trøjelsgaard, 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

  14. 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

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

    PubMed

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

    2014-07-01

    Ecological trait data are essential for understanding the broad-scale distribution of biodiversity and its response to global change. For animals, diet represents a fundamental aspect of species' evolutionary adaptations, ecological and functional roles, and trophic interactions. However, the importance of diet for macroevolutionary and macroecological dynamics remains little explored, partly because of the lack of comprehensive trait datasets. We compiled and evaluated a comprehensive global dataset of diet preferences of mammals ("MammalDIET"). Diet information was digitized from two global and cladewide data sources and errors of data entry by multiple data recorders were assessed. We then developed a hierarchical extrapolation procedure to fill-in diet information for species with missing information. Missing data were extrapolated with information from other taxonomic levels (genus, other species within the same genus, or family) and this extrapolation was subsequently validated both internally (with a jack-knife approach applied to the compiled species-level diet data) and externally (using independent species-level diet information from a comprehensive continentwide data source). Finally, we grouped mammal species into trophic levels and dietary guilds, and their species richness as well as their proportion of total richness were mapped at a global scale for those diet categories with good validation results. The success rate of correctly digitizing data was 94%, indicating that the consistency in data entry among multiple recorders was high. Data sources provided species-level diet information for a total of 2033 species (38% of all 5364 terrestrial mammal species, based on the IUCN taxonomy). For the remaining 3331 species, diet information was mostly extrapolated from genus-level diet information (48% of all terrestrial mammal species), and only rarely from other species within the same genus (6%) or from family level (8%). Internal and external

  16. 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

  17. 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.

  18. Diagnostic Performance on Low Dose Computed Tomography For Acute Appendicitis Among Attending and Resident Radiologists

    PubMed Central

    Chang, Chih-Chen; Wong, Yon-Cheong; Wu, Cheng-Hsien; Chen, Huan-Wu; Wang, Li-Jen; Lee, Yu-Hsien; Wu, Patricia Wanping; Irama, Wiwan; Chen, Wei Yuan; Chang, Chee-Jen

    2016-01-01

    Background Low-dose computed tomography (LDCT) techniques can reduce exposure to radiation. Several previous studies have shown that radiation dose reduction in LDCT does not decrease the diagnostic performance for appendicitis among attending radiologists. But, the LDCT diagnostic performance for acute appendicitis in radiology residents with variable training levels has not been well discussed. Objectives To compare inter-observer and intra-observer differences of diagnostic performance on non-enhanced LDCT (NE-LDCT) and contrast-enhanced standard dose CT (CE-SDCT) for acute appendicitis among attending and resident radiologists. Patients and Methods This retrospective study included 101 patients with suspected acute appendicitis who underwent NE-LDCT and CE-SDCT. The CT examinations were interpreted and recorded on a five-point scale independently by three attending radiologists and three residents with 4, 1 and 1 years of training. Diagnostic performance for acute appendicitis of all readers on both examinations was represented by area under receiver operating characteristic (ROC) curves. Inter-observer and intra-observer AUC values were compared using Jackknife FROC software on both modalities. The diagnostic accuracy of each reader on NE-LDCT was compared with body mass index (BMI) subgroups and noise using independent T test. Results Diagnostic performances for acute appendicitis were not statistically different for attending radiologists at both examinations. Better performance was noted on the CE-SDCT with a borderline significant difference (P = 0.05) for senior radiology resident. No statistical difference of AUC values was observed between attending radiologists and fourth year resident on both examinations. Statistically significant differences of AUC values were observed between attending radiologists and first year residents (P = 0.001 ~ 0.018) on NE-LDCT. Diagnostic accuracies of acute appendicitis on NE-LDCT for each reader were not significantly

  19. A Designed Experiments Approach to Optimizing MALDI-TOF MS Spectrum Processing Parameters Enhances Detection of Antibiotic Resistance in Campylobacter jejuni

    PubMed Central

    Penny, Christian; Grothendick, Beau; Zhang, Lin; Borror, Connie M.; Barbano, Duane; Cornelius, Angela J.; Gilpin, Brent J.; Fagerquist, Clifton K.; Zaragoza, William J.; Jay-Russell, Michele T.; Lastovica, Albert J.; Ragimbeau, Catherine; Cauchie, Henry-Michel; Sandrin, Todd R.

    2016-01-01

    MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this study was to enhance strain level resolution for Campylobacter jejuni through the optimization of spectrum processing parameters using a series of designed experiments. A collection of 172 strains of C. jejuni were collected from Luxembourg, New Zealand, North America, and South Africa, consisting of four groups of antibiotic resistant isolates. The groups included: (1) 65 strains resistant to cefoperazone (2) 26 resistant to cefoperazone and beta-lactams (3) 5 strains resistant to cefoperazone, beta-lactams, and tetracycline, and (4) 76 strains resistant to cefoperazone, teicoplanin, amphotericin, B and cephalothin. Initially, a model set of 16 strains (three biological replicates and three technical replicates per isolate, yielding a total of 144 spectra) of C. jejuni was subjected to each designed experiment to enhance detection of antibiotic resistance. The most optimal parameters were applied to the larger collection of 172 isolates (two biological replicates and three technical replicates per isolate, yielding a total of 1,031 spectra). We observed an increase in antibiotic resistance detection whenever either a curve based similarity coefficient (Pearson or ranked Pearson) was applied rather than a peak based (Dice) and/or the optimized preprocessing parameters were applied. Increases in antimicrobial resistance detection were scored using the jackknife maximum similarity technique following cluster analysis. From the first four groups of antibiotic resistant isolates, the optimized preprocessing parameters increased detection respective to the aforementioned groups by: (1) 5% (2) 9% (3) 10%, and (4) 2%. An additional second categorization was created from the

  20. 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

  1. 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

  2. Estimating the spatial distribution of evapotranspiration using the water balance model WAVE and fine spatial resolution airborne remote sensing images from the DAIS-sensor: Experimental set-up

    NASA Astrophysics Data System (ADS)

    Verstraeten, W. W.; Veroustraete, F.; Feyen, J.

    2003-04-01

    -simulations of the water balance model WAVE on some specific locations (derived from Price, 1990 and Bastiaanssen et al., 1998) and; (2) determining the spatial input parameters of WAVE in order to simulate the spatial patterns of evapotranspiration (based on D'Urso); the Split-Data, Split-Window, Jack-knife, and cross-correlation techniques will take care of the temporal and spatial validation of the results.

  3. 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

  4. 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 = Q0 fη. 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

  5. Validation of a single-stage fixed-rate step test for the prediction of maximal oxygen uptake in healthy adults.

    PubMed

    Hansen, Dominique; Jacobs, Nele; Thijs, Herbert; Dendale, Paul; Claes, Neree

    2016-09-01

    Healthcare professionals with limited access to ergospirometry remain in need of valid and simple submaximal exercise tests to predict maximal oxygen uptake (VO2max ). Despite previous validation studies concerning fixed-rate step tests, accurate equations for the estimation of VO2max remain to be formulated from a large sample of healthy adults between age 18-75 years (n > 100). The aim of this study was to develop a valid equation to estimate VO2max from a fixed-rate step test in a larger sample of healthy adults. A maximal ergospirometry test, with assessment of cardiopulmonary parameters and VO2max , and a 5-min fixed-rate single-stage step test were executed in 112 healthy adults (age 18-75 years). During the step test and subsequent recovery, heart rate was monitored continuously. By linear regression analysis, an equation to predict VO2max from the step test was formulated. This equation was assessed for level of agreement by displaying Bland-Altman plots and calculation of intraclass correlations with measured VO2max . Validity further was assessed by employing a Jackknife procedure. The linear regression analysis generated the following equation to predict VO2max (l min(-1) ) from the step test: 0·054(BMI)+0·612(gender)+3·359(body height in m)+0·019(fitness index)-0·012(HRmax)-0·011(age)-3·475. This equation explained 78% of the variance in measured VO2max (F = 66·15, P<0·001). The level of agreement and intraclass correlation was high (ICC = 0·94, P<0·001) between measured and predicted VO2max . From this study, a valid fixed-rate single-stage step test equation has been developed to estimate VO2max in healthy adults. This tool could be employed by healthcare professionals with limited access to ergospirometry.

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

    PubMed

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

    2015-01-01

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

  7. 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.

  8. Effect of reconstruction methods and x-ray tube current–time product on nodule detection in an anthropomorphic thorax phantom: A crossed-modality JAFROC observer study

    PubMed Central

    Thompson, J. D.; Chakraborty, D. P.; Szczepura, K.; Tootell, A. K.; Vamvakas, I.; Manning, D. J.; Hogg, P.

    2016-01-01

    Purpose: To evaluate nodule detection in an anthropomorphic chest phantom in computed tomography (CT) images reconstructed with adaptive iterative dose reduction 3D (AIDR3D) and filtered back projection (FBP) over a range of tube current–time product (mAs). Methods: Two phantoms were used in this study: (i) an anthropomorphic chest phantom was loaded with spherical simulated nodules of 5, 8, 10, and 12 mm in diameter and +100, −630, and −800 Hounsfield units electron density; this would generate CT images for the observer study; (ii) a whole-body dosimetry verification phantom was used to ultimately estimate effective dose and risk according to the model of the BEIR VII committee. Both phantoms were scanned over a mAs range (10, 20, 30, and 40), while all other acquisition parameters remained constant. Images were reconstructed with both AIDR3D and FBP. For the observer study, 34 normal cases (no nodules) and 34 abnormal cases (containing 1–3 nodules, mean 1.35 ± 0.54) were chosen. Eleven observers evaluated images from all mAs and reconstruction methods under the free-response paradigm. A crossed-modality jackknife alternative free-response operating characteristic (JAFROC) analysis method was developed for data analysis, averaging data over the two factors influencing nodule detection in this study: mAs and image reconstruction (AIDR3D or FBP). A Bonferroni correction was applied and the threshold for declaring significance was set at 0.025 to maintain the overall probability of Type I error at α = 0.05. Contrast-to-noise (CNR) was also measured for all nodules and evaluated by a linear least squares analysis. Results: For random-reader fixed-case crossed-modality JAFROC analysis, there was no significant difference in nodule detection between AIDR3D and FBP when data were averaged over mAs [F(1, 10) = 0.08, p = 0.789]. However, when data were averaged over reconstruction methods, a significant difference was seen between multiple pairs of mAs settings

  9. 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

  10. 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

  11. 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 μS/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 μS/cm. To improve model sensitivity in freshwater lakes we expanded the calibration data set with 11 dilute (6-61 μS/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

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

    /Linux Operating system: UNIX/Linux Has the code been vectorised or parallelized?: Yes RAM: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 3.5M, SMP AMD opteron Classification: 2.3 External routines: OCTAVE ( http://www.gnu.org/software/octave/), GNU Scientific Library ( http://www.gnu.org/software/gsl/), OPENMP ( http://openmp.org/wp/) Nature of problem: The optimal simulation and modeling of multiple quantum magic angle spinning NMR spectra, for general systems, especially those with mild to significant disorder. The approach outlined and implemented in C and OCTAVE also produces model parameter error estimates. Solution method: A model for each distinct chemical site is first proposed, for the individual contribution of crystallite orientations to the spectrum. This model is averaged over all powder angles [1], as well as the (stochastic) parameters; isotropic chemical shift and quadrupole coupling constant. The latter is accomplished via sampling from a bi-variate Gaussian distribution, using the Box-Muller algorithm to transform Sobol (quasi) random numbers [2]. A simulated annealing optimization is performed, and finally the non-linear jackknife [3] is applied in developing model parameter error estimates. Additional comments: The distribution contains a script, mqmasOpt.m, which runs in the OCTAVE language workspace. Running time: Example: (1597 powder angles) × (200 Samples) × (81 F2 frequency pts) × (31 F1 frequency points) = 58.35 seconds, SMP AMD opteron. References:S.K. Zaremba, Annali di Matematica Pura ed Applicata 73 (1966) 293. H. Niederreiter, Random Number Generation and Quasi-Monte Carlo Methods, SIAM, 1992. T. Fox, D. Hinkley, K. Larntz, Technometrics 22 (1980) 29.

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

    NASA Astrophysics Data System (ADS)

    Lisowski, M.; Battaglia, M.

    2011-12-01

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

  14. Assessment of NHTSA’s Report “Relationships Between Fatality Risk, Mass, and Footprint in Model Year 2003-2010 Passenger Cars and LTVs”

    SciTech Connect

    Wenzel, Tom

    2016-06-01

    NHTSA recently completed a logistic regression analysis updating its 2003, 2010, and 2012 studies of the relationship between vehicle mass and US fatality risk per vehicle mile traveled (VMT; Kahane 2010, Kahane 2012, Puckett 2016). The new study updates the 2012 analysis using FARS data from 2005 to 2011 for model year 2003 to 2010. Using the updated databases, NHTSA estimates that reducing vehicle mass by 100 pounds while holding footprint fixed would increase fatality risk per VMT by 1.49% for lighter-than-average cars and by 0.50% for heavierthan- average cars, but reduce risk by 0.10% for lighter-than-average light-duty trucks, by 0.71% for heavier-than-average light-duty trucks, and by 0.99% for CUVs/minivans. Using a jack knife method to estimate the statistical uncertainty of these point estimates, NHTSA finds that none of these estimates are statistically significant at the 95% confidence level; however, the 1.49% increase in risk associated with mass reduction in lighter-than-average cars, and the 0.71% and 0.99% decreases in risk associated with mass reduction in heavier-than-average light trucks and CUVs/minivans, are statistically significant at the 90% confidence interval. The effect of mass reduction on risk that NHTSA estimated in 2016 is more beneficial than in its 2012 study, particularly for light trucks and CUVs/minivans. The 2016 NHTSA analysis estimates that reducing vehicle footprint by one square foot while holding mass constant would increase fatality risk per VMT by 0.28% in cars, by 0.38% in light trucks, and by 1.18% in CUVs and minivans.This report replicates the 2016 NHTSA analysis, and reproduces their main results. This report uses the confidence intervals output by the logistic regression models, which are smaller than the intervals NHTSA estimated using a jack-knife technique that accounts for the sampling error in the FARS fatality and state crash data. In addition to reproducing the NHTSA results, this report also examines the

  15. 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

    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

  16. 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

  17. Milankovitch rhythms in the Cretaceous: A GCM modelling study

    NASA Astrophysics Data System (ADS)

    Park, Jeffrey; Oglesby, Robert J.

    1991-10-01

    A major feature of the Cretaceous sedimentary record is the presence of cyclical bedding in carbonate sequences, many of which have periodicities similar to those of the Milankovitch rhythms of the earth-sun orbit. We used an atmospheric general circulation model, the NCAR CCM1, to investigate changes in the modeled Cretaceous atmospheric climate resulting from imposed Milankovitch orbital insolation changes. We extend a previous study using a 100 Ma mid-Cretaceous reconstruction to include perpetual-season (January and July) effects due to changes in obliquity as well as changes in precession. A total of eighteen pairs of insolation states have been examined. We perform a regression for linear sensitivity coefficients appropriate to precession and obliquity insolation changes, as well as compute a jackknife estimate of the coefficient uncertainty. Comparison of the regression residual to inherent model variability allows an estimate of any systematic but nonlinear model response to orbital insolation changes. Of particular importance is the response of the atmospheric hydrologic cycle. Changes in this cycle are consistent with at least three examples of Cretaceous bedding cycles: (1) The South Atlantic, where cyclical changes in the E- P balance with precession and, to a lesser extent, obliquity may account for regional oxic versus anoxic cycles observed in Cretaceous marine sediments cored from this region. (2) Regional changes in E- P over the east Tethys and adjacent continents with changes in insolation, which could induce changes in the production of oceanic deep water, possibly accounting for global occurrences of cyclic anoxic conditions. (3) Our simulations show a significant response of the hydrologic cycle to obliquity in July over western North America. This response, however, is smaller and more localized than those observed in low-latitude regions, and may not be robust to small changes in model boundary conditions. For most regions and modeled

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

    SciTech Connect

    A. Hassan; J. Chapman

    2008-11-01

    -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.

  19. 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

    %, 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