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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

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…

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

2012-01-01

3

Bootstrap Methods: Another Look at the Jackknife  

Microsoft Academic Search

We discuss the following problem: given a random sample $\\\\mathbf{X} = (X_1, X_2, \\\\cdots, X_n)$ from an unknown probability distribution $F$, estimate the sampling distribution of some prespecified random variable $R(\\\\mathbf{X}, F)$, on the basis of the observed data $\\\\mathbf{x}$. (Standard jackknife theory gives an approximate mean and variance in the case $R(\\\\mathbf{X}, F) = \\\\theta(\\\\hat{F}) - \\\\theta(F), \\\\theta$ some

B. Efron

1979-01-01

4

Tests for the Jackknife Autocorrelation Estimator "r(Q2)."  

ERIC Educational Resources Information Center

Two tests for the jackknife autocorrelation estimator r(Q2) are evaluated. It is shown that a test based on the conventional approach for estimating the standard error of a jackknife estimator leads to unacceptable Type I error. An alternative approach is proposed that leads to a more satisfactory test when n>20. (Author/SLD)

Huitema, Bradley E.; McKean, Joseph W.

1996-01-01

5

The Jackknife and Multilevel Modeling: A New Application of an Old Trick  

ERIC Educational Resources Information Center

In this article the authors demonstrate two instances where the jackknife can be used to enhance hierarchical linear model (HLM) analyses. The jackknife was used to improve the HLM estimates of composite measures by jackknifing over items. The first study examined fixed-effects and variance component estimation. The jackknife appeared to reduce…

Wolfe, Richard G.; Dunn, Jennifer L.

2003-01-01

6

A unified jackknife theory for empirical best prediction with M-estimation  

Microsoft Academic Search

The paper presents a unified jackknife theory for a fairly general class of mixed models which includes some of the widely used mixed linear models and generalized linear mixed models as special cases. The paper develops jackknife theory for the important, but so far neglected, prediction problem for the general mixed model. For estimation of fixed parameters, a jackknife method

Jiming Jiang; P. Lahiri; Shu-Mei Wan

2002-01-01

7

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

ERIC Educational Resources Information Center

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

Pandey, Tej N.; Hubert, Lawrence J.

8

Jackknife-based selection of Gram-Schmidt orthogonalized descriptors in QSAR.  

PubMed

This study is an implementation of a robust jackknife-based descriptor selection procedure assisted with Gram-Schmidt orthogonalization. Selwood data including 31 molecules and 53 descriptors was considered in this study. Both multiple linear regression (MLR) and partial least squares (PLS) regression methods were applied during the jackknife procedures, and the desired results were obtained when using PLS regression on both autoscaled and orthogonalized data sets. Having used the Gram-Schmidt technique, descriptors were all orthogonalized, and their number was reduced to 30. A reproducible set of descriptors was obtained when PLS-jackknife was applied to the Gram-Schmidt orthogonalized data. The simple statistical t-test was applied to determine the significance of the obtained regression coefficients from jackknife resampling.Increasing the sample size, descriptors, based on their information content, were introduced into the model one by one and were sorted. The number of validated descriptors was in proportion with the sample size in the jackknife. The PLS-jackknife parameters, such as sample size and number and number of latent variables in PLS, and the starting descriptor in Gram-Schmidt orthogonalization were investigated and optimized.Applying PLS-jackknife to orthogonalized data in the optimized condition, five descriptors were validated with q²TOT2 ) 0.693 and R² ) 0.811. Compared to the previous reports, the obtained results are satisfactory. PMID:21069957

Kompany-Zareh, Mohsen; Omidikia, Nematollah

2010-12-27

9

Spatial Interpolation and its Uncertainty Using Automated Anisotropic Inverse Distance Weighting (IDW) - Cross-Validation\\/Jackknife Approach  

Microsoft Academic Search

In order to estimate rainfall magnitude at unmeasured locations, this entry to the Spatial Interpolation Comparison of 1997 (SIC'97) used 2-dimensional, anisotropic, inverse-distance weighting interpolator (IDW), with cross-validation as a method of optimizing the interpolator's parameters. A jackknife resampling was then used to reduce bias of the predictions and estimate their uncertainty. The method is easy to programme, \\

Maciej Tomczak

1998-01-01

10

Recent advances in observer performance methodology: jackknife free-response ROC (JAFROC).  

PubMed

The jackknife free-response receiver operating characteristic (JAFROC) method allows quantitative analysis of observer data such as that observed when radiologists interpret images, which could contain more than one lesion and a location can be reported for each perceived lesion. The method was recently validated with a perception-based simulation model that incorporated the detectability parameter of the standard binormal ROC model, and in addition allowed simultaneous samples from both noise and signal distributions. The total number of noise samples is an important new parameter that measures reader expertise. The new sampling model incorporates search, which is an integral part of lesion detection that has not been possible to model until now. The model was used to generate simulated FROC ratings data, which was used to assess the statistical validity of JAFROC analysis. We found that JAFROC analysis is a statistically valid approach for analysing FROC data and that JAFROC analysis exhibited significantly greater statistical power than the existing ROC approach. PMID:15933077

Chakraborty, Dev P

2005-01-01

11

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

PubMed

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

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

2015-02-10

12

Water-soluble jack-knife prawn extract inhibits 5-hydroxytryptamine-induced vasoconstriction and platelet aggregation in humans.  

PubMed

Coronary artery spasm plays an important role in the pathogenesis of various ischemic heart diseases or serious arrhythmia. The aim of this study is to look for functional foods which have physiologically active substances preventing 5-hydroxytryptamine (5-HT)-related vasospastic diseases including peri- and postoperative ischemic complications of coronary artery bypass grafting (CABG) from ocean resources in Japanese coastal waters. First, we evaluated the effect of water-soluble ocean resource extracts on the response to 5-HT in HEK293 cells which have forcibly expressed cyan fluorescent protein-fused 5-HT2A receptors (5-HT2A-CFP). Among 5 different water-soluble extracts of ocean resources, the crude water-soluble jack-knife prawn extract (WJPE) significantly reduced maximal Ca(2+) influx induced by 0.1 ?M 5-HT in a concentration-dependent manner. The Crude WJPE significantly inhibited, in a concentration-dependent manner, 5-HT-induced constriction of human saphenous vein. 5-HT released from activated platelets plays a crucial roles in the constriction of coronary artery. Next the WJPE was purified for applying the experiment of 5-HT-induced human platelet aggregation. The purified WJPE significantly inhibited 5-HT-induced human platelet aggregation also in a concentration-dependent manner. Based on our findings, jack-knife prawn could be one of a functional food with health-promoting benefits for most people with vasospastic diseases including patients who have gone CABG. PMID:25464143

Gamoh, Shuji; Kanai, Tasuku; Tanaka-Totoribe, Naoko; Ohkura, Masamichi; Kuwabara, Masachika; Nakamura, Eisaku; Yokota, Atsuko; Yamasaki, Tetsuo; Watanabe, Akiko; Hayashi, Masahiro; Fujimoto, Shouichi; Yamamoto, Ryuichi

2015-02-11

13

Receiver Functions From Multiple-Taper Spectral Correlation: Backazimuthal Stacking, Single-Station Migration, and Jackknife Uncertainty  

NASA Astrophysics Data System (ADS)

The multiple-taper correlation (MTC) algorithm (Park & Levin, 2000) for the estimation of teleseismic receiver functions (RFs) has desirable statistical properties, but needs enhancement to exploit its potential. In particular, theory predicts that a P-S conversion at an interface between anisotropic media will generate conjugate patterns of P-SV and P-SH converted waves with the backazimuth of the incoming wave. Using a weighted back-azimuthal stack of MTC RFs, one can evaluate whether the radial and transverse RF follow the anisotropic pattern, follow an independent pattern predicted for a dipping interface, or exhibit random behavior that suggests scattering by 3-D structure. Frequency averaging implicit in spectral cross-correlation restricts the MTC RF estimates to resolve Ps converted phases only at short delay times, appropriate to the upper 100 km of Earth's lithosphere. Ps conversions from deeper interfaces can be reconstructed by the MTC algorithm in two ways. Event cross-correlation (ECC) 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. Moving-window migration (MWM) retains the multiple-taper approach, but cross-correlates the P-polarized motion with SH or SV component motion that is time delayed to focus on a Ps phase of interest. An alternative error-propagation based on the jackknife offers uncertainty estimates in the time domain.

Park, J.; Levin, V.

2005-12-01

14

Power spectral estimates using two-dimensional Morlet-fan wavelets with emphasis on the long wavelengths: jackknife errors, bandwidth resolution and orthogonality properties  

NASA Astrophysics Data System (ADS)

We present a method for estimating the errors on local and global wavelet power spectra using the jackknife approach to error estimation, and compare results with jackknifed multitaper (MT) spectrum estimates. We test the methods on both synthetic and real data, the latter being free air gravity over the Congo Basin. To satisfy the independence requirement of the jackknife we investigate the orthogonality properties of the 2-D Morlet wavelet. Although Morlet wavelets are non-orthogonal, we show that careful selection of parameters can yield approximate orthogonality in space and azimuth. We also find that, when computed via the Fourier transform, the continuous wavelet transform (CWT) contains errors at very long wavelengths due to the discretization of large-scale wavelets in the Fourier domain. We hence recommend the use of convolution in the space-domain at these scales, even though this is computationally more expensive. Finally, in providing an investigation into the bandwidth resolution of CWT and MT spectra and errors at long wavelengths, we show that the Morlet wavelet is superior in this regard to Slepian tapers. Wavelets with higher bandwidth resolution deliver smaller spectral error estimates, in contrast to the MT method, where tapers with higher bandwidth resolution deliver larger errors. This results in the fan-WT having better spectral estimation properties at long wavelengths than Slepian MTs.

Kirby, J. F.; Swain, C. J.

2013-07-01

15

Jackknife-blockwise empirical likelihood methods under dependence  

Microsoft Academic Search

Empirical likelihood for general estimating equations is a method for testing hypothesis or constructing confidence regions on parameters of interest. If the number of parameters of interest is smaller than that of estimating equations, a profile empirical likelihood has to be employed. In case of dependent data, a profile blockwise empirical likelihood method can be used. However, if too many

Rongmao Zhang; Liang Peng; Yongcheng Qi

2012-01-01

16

Determinants of Health Expenditure Growth of the OECD Countries: Jackknife Resampling Plan Estimates  

Microsoft Academic Search

Due to the lack of internal consistency across unit root and cointegration test methods for short time-series data, past research findings conflict on whether the OECD health expenditure data are stationary. Stationarity reasonably guarantees that the estimated OLS relationship is nonspurious. This paper departs from past investigations that applied asymptotic statistical tests of unit root to insufficient time-series lengths. Instead,

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

2004-01-01

17

log-normal model agree with predictions from the nonparametric jackknife estimator, which  

E-print Network

, Species Coexistence: Ecological and Evolu- tionary Perspectives (Blackwell, Oxford, 1999). 14. S. Engen, R. Lande, J. Theor. Biol. 178, 325 (1996). 15. S. Engen, R. Lande, Math. Biosci. 132, 169 (1996). 16. R. V

Myers, Ransom A.

18

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

Microsoft Academic Search

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

Gail Gong

1986-01-01

19

Testing the significance of interobserver agreement measures in the presence of autocorrelation: The jackknife procedure  

Microsoft Academic Search

Users of interobserver agreement statistics have heretofore ignored the problem of autocorrelation in behavior sequences when testing the statistical significance of agreement measures. Due to autocorrelation traditional reliability tests based on the 2 × 2 contingency-table model (e.g., kappa, phi) are incorrect. Correct tests can be developed by using the bivariate time series as a statistical model. Seen from this

Stephen V. Faraone; Donald D. Dorfman

1988-01-01

20

ASYMPTOTIC DISTRIBUTION OF JIVE IN A HETEROSKEDASTIC IV REGRESSION WITH MANY INSTRUMENTS  

E-print Network

This paper derives the limiting distributions of alternative jackknife instrumental variables (JIV) estimators and gives formulas for accompanying consistent standard errors in the presence of heteroskedasticity and many ...

Chao, John C.

21

An Empirical Comparison of Several Interval Estimation Procedures for Coefficient Alpha  

ERIC Educational Resources Information Center

Use of Tukey's Jackknife in establishing a confidence interval around the population coefficient alpha is explored and the robustness of Feldt's procedure along with ten variants of the Jackknife when the data do not conform to the necessary normality requirements are evaluated. Only two of the variants compared to Feldt's approach. (RC)

Pandey, Tej N.; Hubert, Lawrence

1975-01-01

22

International Journal of Systematic and Evolutionary Microbiology (2001), 51, 731735 Printed in Great Britain Construction and bootstrap analysis of DNA  

E-print Network

International Journal of Systematic and Evolutionary Microbiology (2001), 51, 731­735 Printed by bootstrap, jackknife or operational taxonomic unit-jackknife analysis. Moreover, the program can be also, is the so-called `gene tree', the topology of 01753 # 2001 IUMS 731 #12;V. Hampl, A. Pavli!c) ek and J

Flegr, Jaroslav

23

16 CFR 1632.1 - Definitions.  

Code of Federal Regulations, 2011 CFR

...beds (including jackknife sofa beds), sofa lounges (including glide-outs), studio couches and studio divans (including twin studio divans and studio beds), and juvenile product pads such as car bed pads, carriage pads, basket pads, infant...

2011-01-01

24

16 CFR 1632.1 - Definitions.  

Code of Federal Regulations, 2013 CFR

...beds (including jackknife sofa beds), sofa lounges (including glide-outs), studio couches and studio divans (including twin studio divans and studio beds), and juvenile product pads such as car bed pads, carriage pads, basket pads, infant...

2013-01-01

25

16 CFR 1632.1 - Definitions.  

Code of Federal Regulations, 2014 CFR

...beds (including jackknife sofa beds), sofa lounges (including glide-outs), studio couches and studio divans (including twin studio divans and studio beds), and juvenile product pads such as car bed pads, carriage pads, basket pads, infant...

2014-01-01

26

16 CFR 1632.1 - Definitions.  

Code of Federal Regulations, 2010 CFR

...beds (including jackknife sofa beds), sofa lounges (including glide-outs), studio couches and studio divans (including twin studio divans and studio beds), and juvenile product pads such as car bed pads, carriage pads, basket pads, infant...

2010-01-01

27

16 CFR 1632.1 - Definitions.  

Code of Federal Regulations, 2012 CFR

...beds (including jackknife sofa beds), sofa lounges (including glide-outs), studio couches and studio divans (including twin studio divans and studio beds), and juvenile product pads such as car bed pads, carriage pads, basket pads, infant...

2012-01-01

28

MOLECULAR PHYLOGENY OF THE LICHEN FAMILIES CLADONIACEAE , SPHAEROPHORACEAE , AND STEREOCAULACEAE (LECANORALES, ASCOMYCOTINA)  

Microsoft Academic Search

Abstract: Maximum parsimony analysis of nuclear SSU rDNA sequences was utilized to infer the phylogenetic relationships of representatives of the macrolichen families Cladoniaceae, Sphaerophoraceae, andStereocaulaceae (Lecanorales subord. Cladoniineae, Ascomycotina). Farris' parsimony jackknifing, and a similar jackknife strategy with branch-swapping and multiple addition sequences in PAUP*, were performed to assess branch support. The results indicate that the Sphaerophoraceae should be emended

Mats Wedin; Heidi Döring; Stefan Ekman

2000-01-01

29

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

NASA Astrophysics Data System (ADS)

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.

Mobberley, M. P.

2010-02-01

30

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

ERIC Educational Resources Information Center

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…

Larwin, Karen; Harvey, Milton

2012-01-01

31

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

E-print Network

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

Mazumder, Asit

2008-01-01

32

ESTIMATION OF THE COANCESTRY COEFFICIENT: BASIS FOR A SHORT-TERM GENETIC DISTANCE  

Microsoft Academic Search

A distance measure for populations diverging by drift only is based on the coancestry coefficient 0, and three estimators of the distance Si@= -h(l - 0) are constructed for multiallelic, multilocus data. Simulations of a monoecious population mating at random showed that a weighted ratio of single-locus estimators performed better than an unweighted average or a least squares estimator. Jackknifing

JOHN REYNOLDS; B. S. WEIR; C. CLARK COCKERHAM

1983-01-01

33

Estimated genotype error rates from bowhead whale microsatellite data  

Microsoft Academic Search

We calculate error rates using opportunistic replicate samples in the microsatellite data for bowhead whales. The estimated rate (1%\\/genotype) falls within normal ranges reviewed in this paper. The results of a jackknife analysis identified five individuals that were highly influential on estimates of Hardy-Weinberg equilibrium for four different markers. In each case, the influential individual was homozygous for a rare

Phillip A Morin; Richard G LeDuc; Eric Archer; Karen K Martien; Barbara L Taylor; Ryan Huebinger; John W. Bickham

34

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

Microsoft Academic Search

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

Derrick Nguyen; Bernard Widrow

1989-01-01

35

Model-Based Methods for Analysis of Data from 1990 NAEP Trial State Assessment. Research and Development Report.  

ERIC Educational Resources Information Center

Model-based methods for estimating the population mean in stratified clustered sampling are described. The importance of adjusting the weights is assessed by an approach considering the sampling variation of the adjusted weights and its (variance) components. The resulting estimators are more efficient than the jackknife estimators for a variety…

Longford, N. T.

36

46 CFR 160.043-6 - Marking and packing.  

Code of Federal Regulations, 2010 CFR

...can opener. (c) Packing. Each jackknife, complete with lanyard attached, shall be packed in a heat-sealed bag of waterproof vinyl resin or polyethylene film not less than 0.004 inch in thickness. The bag shall be marked in a clear and...

2010-10-01

37

46 CFR 160.043-6 - Marking and packing.  

Code of Federal Regulations, 2011 CFR

...can opener. (c) Packing. Each jackknife, complete with lanyard attached, shall be packed in a heat-sealed bag of waterproof vinyl resin or polyethylene film not less than 0.004 inch in thickness. The bag shall be marked in a clear and...

2011-10-01

38

Interannual variability and intraannual stability of the otolith shape in European anchovy Engraulis encrasicolus (L.) in the Bay of Biscay  

Microsoft Academic Search

recruitment of 2000. The classification success of the discriminant analysis indicated a strong separation between year groups (P < 0? 001), overall, 98% of individuals were correctly classified. Results from both jackknife and Cohen's kappa procedures confirmed the high rates of classification success obtained by the discriminant analysis (99 and 97%, respectively). Stability in the intraannual shape analysis leads to

C. Gonzalez-Salas; P. Lenfant

2007-01-01

39

MAPPING BALD EAGLE COMMUNAL NIGHT ROOST HABITAT IN NORTHWEST WASHINGTON USING SATELLITE IMAGERY  

E-print Network

of the species as endangered under the Endangered Species Act in 1978, appears to have ended. While, and standard deviation of aspect. I assessed model classification accuracy using a jackknife procedure. The model had an overall classification accuracy of 83.2%, with roosts correctly classified at 82

Wallin, David O.

40

Statistical Genetics of an Annual Plant, Impatiens capensis. I. Genetic Basis of Quantitative Variation  

Microsoft Academic Search

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 quanti- tative characters in Impatiens capensis. Early life cycle characters showed evidence of dominance and\\/ or maternal effects, while later characters

Thomas Mitchell-Olds; Joy Bergelson

1990-01-01

41

Anova Tests for Homogeneity of Variance: Nonnormality and Unequal Samples  

Microsoft Academic Search

This paper presents an exposition and an empirical comparison of two potentially useful tests for homogeneity of variance. Control of Type I error rate, P(EI), and power are investigated for three forms of the Box test and for two forms of the jackknife test with equal and unequal n's under conditions of normality and nonnormality. The Box test is shown

Charles G. Martin; Paul A. Games

1977-01-01

42

Delsuc et al. Additional support for the new chordate phylogeny Additional Molecular Support for the New  

E-print Network

for the new chordate phylogeny 2 SUMMARY Recent phylogenomic analyses have suggested tunicates instead tunicates and vertebrates (Olfactores). Chordates were recovered as monophyletic with cephalochordates ­ Chordates ­ Tunicates ­ Cephalochordates ­ Olfactores ­ Ribosomal RNA ­ Jackknife ­ Evolution. halsde

Paris-Sud XI, Université de

43

Bradley Efron: A Conversation with Good Friends  

Microsoft Academic Search

Bradley Efron is Professor of Statistics and Biostatistics at Stanford University. He works on a combination of theoretical and applied topics, including empirical Bayes, survival analysis, exponential families, bootstrap and jackknife methods and confidence intervals. Most of his applied work has originated in biomedical consulting projects at the Stanford Medical School, mixed in with a few papers concerning astronomy and

Susan Holmes

2003-01-01

44

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

ERIC Educational Resources Information Center

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…

White, David J.; Williver, S. Todd

2014-01-01

45

Volume and biomass for curlleaf cercocarpus in Nevada. Research paper  

SciTech Connect

Volume and biomass equations were developed for curlleaf cercocarpus (Cercocarpus ledifolius) in the Egan and Schell Mountains near Ely, NV. The equations predict cubic foot volume of wood and bark for variable minimum branch diameters. Wood density factors are given to convert volume predictions to pounds of fiber biomass. The reliability of the equations was assessed using the jackknife technique to construct confidence intervals.

Chojnacky, D.C.

1984-11-01

46

Volume and biomass for curlleaf cercocarpus in Nevada. Research paper  

Microsoft Academic Search

Volume and biomass equations were developed for curlleaf cercocarpus (Cercocarpus ledifolius) in the Egan and Schell Mountains near Ely, NV. The equations predict cubic foot volume of wood and bark for variable minimum branch diameters. Wood density factors are given to convert volume predictions to pounds of fiber biomass. The reliability of the equations was assessed using the jackknife technique

Chojnacky

1984-01-01

47

Resampling methods for evaluating classification accuracy of wildlife habitat models  

Microsoft Academic Search

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

David L. Verbyla; John A. Litvaitis

1989-01-01

48

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

Microsoft Academic Search

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

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

2004-01-01

49

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

PubMed Central

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

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

2014-01-01

50

First season QUaD CMB temperature and polarization power spectra  

E-print Network

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

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

2007-05-16

51

A note on bias and mean squared error in steady-state quantile estimation  

NASA Astrophysics Data System (ADS)

When using a batch means methodology for estimation of a nonlinear function of a steady-state mean from the output of simulation experiments, it has been shown that a jackknife estimator may reduce the bias and mean squared error (mse) compared to the classical estimator, whereas the average of the classical estimators from the batches (the batch means estimator) has a worse performance from the point of view of bias and mse. In this paper we show that, under reasonable assumptions, the performance of the jackknife, classical and batch means estimators for the estimation of quantiles of the steady-state distribution exhibit similar properties as in the case of the estimation of a nonlinear function of a steady-state mean. We present some experimental results from the simulation of the waiting time in queue for an M/M/1 system under heavy traffic.

Muñoz, David F.; Ramírez-López, Adán

2013-10-01

52

HIV-1 protease cleavage site prediction based on two-stage feature selection method.  

PubMed

Knowledge of the mechanism of HIV protease cleavage specificity is critical to the design of specific and effective HIV inhibitors. Searching for an accurate, robust, and rapid method to correctly predict the cleavage sites in proteins is crucial when searching for possible HIV inhibitors. In this article, HIV-1 protease specificity was studied using the correlation-based feature subset (CfsSubset) selection method combined with Genetic Algorithms method. Thirty important biochemical features were found based on a jackknife test from the original data set containing 4,248 features. By using the AdaBoost method with the thirty selected features the prediction model yields an accuracy of 96.7% for the jackknife test and 92.1% for an independent set test, with increased accuracy over the original dataset by 6.7% and 77.4%, respectively. Our feature selection scheme could be a useful technique for finding effective competitive inhibitors of HIV protease. PMID:22591479

Niu, Bing; Yuan, Xiao-Cheng; Roeper, Preston; Su, Qiang; Peng, Chun-Rong; Yin, Jing-Yuan; Ding, Juan; Li, HaiPeng; Lu, Wen-Cong

2013-03-01

53

Resampling Methods: Concepts, Applications, and Justification  

NSDL National Science Digital Library

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

Yu, Chong Hu

54

Changes in aquatic plant communitieson the island of Valaam due to invasion by the muskrat Ondatra zibethicus L.(Rodentia, Mammalia)  

Microsoft Academic Search

Muskrat invaded Valaam Island (Northern part of European Russia) in the 1970s. Aquatic plant communities of 1962 and 1993 were compared on the same plots. Quantitative changes were tested with the help of jack-knifing estimates of most known inventory (a-) diversity indicators. Qualitative transformations were assessed using ß-diversity values. The results demonstrated substantially more discriminant ability of diversity measures than

Vladimir V. Smirnov; Kirill Tretyakov

1998-01-01

55

Robust finite-intersection tests for homogeneity of ordered variances  

Microsoft Academic Search

The finite-intersection approach, a special case of the well-known union-intersection method, often yields reasonable solutions to intricate, analytically intractable problems of testing hypotheses. In this paper we address the famous robust inference problem of testing homoscedasticity, but for the case where the variances are subject to order restrictions. Specifically, we propose some jackknife tests for this purpose which use finite-intersection

Govind S. Mudholkar; Michael P. McDermott; Anil Mudholkar

1995-01-01

56

Generalized Sobol' Indices 1 New results for the functional ANOVA and  

E-print Network

Simplified Saint-Venant flood model Overflow in meters (Lamboni, Iooss, Popelin, Gamboa, 2012) at a dyke Seminar #12;Generalized Sobol' Indices 4 The cost model Cp = 1S>0m (flood cost) + 1S 0m(0.2 + 0.8(1 - e-statistics (skillful reading may be required) & Efron & Stein (1981) for jackknife f(x) = f()() + d j=1 f(j)(xj) + j

Owen, Art

57

Phylogeny of the Prolecithophora (Platyhelminthes) Inferred from 18S rDNA Sequences  

Microsoft Academic Search

Complete nuclear 18S rDNA sequences from 14 species of the Prolecithophora were obtained and used, in combination with literature data, to generate the first parsimony-based hypothesis of the phylogeny of the order Prolecithophora (Platyhelminthes). Bootstrap, parsimony jack-knife, and Bremer support values were computed and compared. The monophyly of the Prolecithophora sensu stricto and the family Plagiostomidae is strongly supported. The

Michael Norén; Ulf Jondelius

1999-01-01

58

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

USGS Publications Warehouse

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.

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

2006-01-01

59

Prediction of DNase I Hypersensitive Sites by Using Pseudo Nucleotide Compositions  

PubMed Central

DNase I hypersensitive sites (DHS) associated with a wide variety of regulatory DNA elements. Knowledge about the locations of DHS is helpful for deciphering the function of noncoding genomic regions. With the acceleration of genome sequences in the postgenomic age, it is highly desired to develop cost-effective computational methods to identify DHS. In the present work, a support vector machine based model was proposed to identify DHS by using the pseudo dinucleotide composition. In the jackknife test, the proposed model obtained an accuracy of 83%, which is competitive with that of the existing method. This result suggests that the proposed model may become a useful tool for DHS identifications. PMID:25215331

Jiang, Ning; Liu, Nan

2014-01-01

60

New Statistical Insights of Globular Cluster Systems  

NASA Astrophysics Data System (ADS)

Globular clusters are cosmological fossils, revealing the history of the universe and galaxies. Some galaxies are found to have multiple generations of globular clusters. Traditionally, these multiple epochs of cluster formation have been detected through graphical methods. In this presentation, we discuss statistical model selection to determine the number of components in globular cluster systems. In addition to the popular Akaike Information Criterion (AIC) and Bayes Information Criterion (BIC), we introduce Jackknife Information Criterion (JIC). We compare the results from statistical model selection methods to graphical methods in previous globular cluster bimodality studies. The data for our presentation were obtained from the VizieR catalog service.

Lee, H.

2006-07-01

61

Prediction of rat protein subcellular localization with pseudo amino acid composition based on multiple sequential features.  

PubMed

The study of rat proteins is an indispensable task in experimental medicine and drug development. The function of a rat protein is closely related to its subcellular location. Based on the above concept, we construct the benchmark rat proteins dataset and develop a combined approach for predicting the subcellular localization of rat proteins. From protein primary sequence, the multiple sequential features are obtained by using of discrete Fourier analysis, position conservation scoring function and increment of diversity, and these sequential features are selected as input parameters of the support vector machine. By the jackknife test, the overall success rate of prediction is 95.6% on the rat proteins dataset. Our method are performed on the apoptosis proteins dataset and the Gram-negative bacterial proteins dataset with the jackknife test, the overall success rates are 89.9% and 96.4%, respectively. The above results indicate that our proposed method is quite promising and may play a complementary role to the existing predictors in this area. PMID:21309740

Shi, Ruijia; Xu, Cunshuan

2011-06-01

62

Phylogenetic relationships among New Caledonian Sapotaceae (Ericales): molecular evidence for generic polyphyly and repeated dispersal.  

PubMed

The phylogeny of a representative group of genera and species from the Sapotaceae tribe Chrysophylleae, mainly from Australia and New Caledonia, was studied by jackknife analyses of sequences of nuclear ribosomal DNA. The phylogeny conflicts with current opinions on generic delimitation in Sapotaceae. Pouteria and Niemeyera, as presently circumscribed, are both shown to be nonmonophyletic. In contrast, all species currently assigned to these and other segregate genera confined to Australia, New Caledonia, or neighboring islands, form a supported clade. Earlier classifications in which more genera are recognized may better reflect relationships among New Caledonian taxa. Hence, there is need for a revision of generic boundaries in Chrysophylleae, and particularly within the Pouteria complex, including Leptostylis, Niemeyera, Pichonia, Pouteria pro parte (the main part of section Oligotheca), and Pycnandra. Section Oligotheca have been recognized as the separate genus Planchonella, a monophyletic group that needs to be resurrected. Three clades with strong support in our jackknife analysis have one Australian species that is sister to a relatively large group of New Caledonian endemics, suggesting multiple dispersal events between this small and isolated tropical island and Australia. The phylogeny also suggests an interesting case of a relatively recent and rapid radiation of several lineages of Sapotaceae within New Caledonia. PMID:21652444

Bartish, Igor V; Swenson, Ulf; Munzinger, Jérôme; Anderberg, Arne A

2005-04-01

63

Variance estimation for clustered recurrent event data with a small number of clusters.  

PubMed

Often in biomedical studies, the event of interest is recurrent and within-subject events cannot usually be assumed independent. In semi-parametric estimation of the proportional rates model, a working independence assumption leads to an estimating equation for the regression parameter vector, with within-subject correlation accounted for through a robust (sandwich) variance estimator; these methods have been extended to the case of clustered subjects. We consider variance estimation in the setting where subjects are clustered and the study consists of a small number of moderate-to-large-sized clusters. We demonstrate through simulation that the robust estimator is quite inaccurate in this setting. We propose a corrected version of the robust variance estimator, as well as jackknife and bootstrap estimators. Simulation studies reveal that the corrected variance is considerably more accurate than the robust estimator, and slightly more accurate than the jackknife and bootstrap variance. The proposed methods are used to compare hospitalization rates between Canada and the U.S. in a multi-centre dialysis study. PMID:16149126

Schaubel, Douglas E

2005-10-15

64

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

PubMed Central

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

Shahrudin, Shahriza

2015-01-01

65

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

PubMed Central

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

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

2015-01-01

66

Linear regression in astronomy. II  

NASA Technical Reports Server (NTRS)

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

Feigelson, Eric D.; Babu, Gutti J.

1992-01-01

67

Otolith elemental signatures indicate population separation in deep-sea rockfish, Helicolenus dactylopterus and Pontinus kuhlii, from the Azores  

NASA Astrophysics Data System (ADS)

Deep sea rockfish, Helicolenus dactylopterus and Pontinus kuhlii from the Azores archipelago were used to study population structuring using the trace element composition of the otolith. Through solution-based inductively coupled plasma mass spectrometry we identified elemental profiles that adequately identified fish from different island groups in the region (East, West and Central). Mg:Ca, Pb:Ca and Li:Ca ratios combined to distinguish H. dactylopterus with 67% overall success. Sr:Ca, Ba:Ca, Li:Ca and Cu:Ca provided adequate distinction in P. kuhlii with a mean jack-knifed classification success of 75%. This was a first attempt at determining the distinguishability of fish aggregations from this oceanic island setting, where suitable habitat for these species is limited and fragmented. Results of our study corroborate with previous research pointing to constrained home ranges for these species. Implications for fisheries management are important since these commercial resources should be managed locally rather than regionally.

Higgins, Ruth; Isidro, Eduardo; Menezes, Gui; Correia, Alberto

2013-10-01

68

Indian Ocean sea surface temperature and Eritrean highlands rainfall  

NASA Astrophysics Data System (ADS)

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

Mebrhatu, Mehari Tesfazgi; Walker, Sue

69

Prediction of CpG island methylation status by integrating DNA physicochemical properties.  

PubMed

As an inheritable epigenetic modification, DNA methylation plays important roles in many biological processes. The non-uniform distribution of DNA methylation across the genome implies that characterizing genome-wide DNA methylation patterns is necessary to better understand the regulatory mechanisms of DNA methylation. Although a series of experimental technologies have been proposed, they are cost-ineffective for DNA methylation status detection. As complements to experimental techniques, computational methods will facilitate the identification of DNA methylation status. In the present study, we proposed a Naïve Bayes model to predict CpG island methylation status. In this model, DNA sequences are formulated by "pseudo trinucleotide composition" into which three DNA physicochemical properties were incorporated. It was observed by the jack-knife test that the overall success rate achieved by the proposed model in predicting the DNA methylation status was 88.22%. This result indicates that the proposed model is a useful tool for DNA methylation status prediction. PMID:25172426

Feng, Pengmian; Chen, Wei; Lin, Hao

2014-10-01

70

Dirichlet Component Regression and its Applications to Psychiatric Data.  

PubMed

We describe a Dirichlet multivariable regression method useful for modeling data representing components as a percentage of a total. This model is motivated by the unmet need in psychiatry and other areas to simultaneously assess the effects of covariates on the relative contributions of different components of a measure. The model is illustrated using the Positive and Negative Syndrome Scale (PANSS) for assessment of schizophrenia symptoms which, like many other metrics in psychiatry, is composed of a sum of scores on several components, each in turn, made up of sums of evaluations on several questions. We simultaneously examine the effects of baseline socio-demographic and co-morbid correlates on all of the components of the total PANSS score of patients from a schizophrenia clinical trial and identify variables associated with increasing or decreasing relative contributions of each component. Several definitions of residuals are provided. Diagnostics include measures of overdispersion, Cook's distance, and a local jackknife influence metric. PMID:22058582

Gueorguieva, Ralitza; Rosenheck, Robert; Zelterman, Daniel

2008-08-15

71

Prediction of Cancer Drugs by Chemical-Chemical Interactions  

PubMed Central

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

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

2014-01-01

72

Avian community response to small-scale habitat disturbance in Maine  

USGS Publications Warehouse

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.

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

1989-01-01

73

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

SciTech Connect

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.

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

1980-05-29

74

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

SciTech Connect

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.

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

1981-01-01

75

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

PubMed

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

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

2014-02-01

76

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

PubMed

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

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

2014-09-01

77

Weak redshift discretisation in the Local Group of Galaxies?  

E-print Network

We discuss the distribution of radial velocities of galaxies belonging to the Local Group. Two independent samples of galaxies as well as several methods of reduction from the heliocentric to the galactocentric radial velocities are explored. We applied the power spectrum analysis using the Hann function as a weighting method, together with the jackknife error estimation. We performed a detailed analysis of this approach. The distribution of galaxy redshifts seems to be non-random. An excess of galaxies with radial velocities of $\\sim 24 {km} \\cdot {s}^{-1}$ and $\\sim 36 {km} \\cdot {s}^{-1}$ is detected, but the effect is statistically weak. Only one peak for radial velocities of $\\sim 24 {km} \\cdot {s}^{-1}$ seems to be confirmed at the confidence level of 95%.

Wlodzimierz Godlowski; Katarzyna Bajan; Piotr Flin

2005-11-09

78

Support Vector Machines for Predicting Membrane Protein Types by Using Functional Domain Composition  

PubMed Central

Membrane proteins are generally classified into the following five types: 1), type I membrane protein; 2), type II membrane protein; 3), multipass transmembrane proteins; 4), lipid chain-anchored membrane proteins; and 5), GPI-anchored membrane proteins. In this article, based on the concept of using the functional domain composition to define a protein, the Support Vector Machine algorithm is developed for predicting the membrane protein type. High success rates are obtained by both the self-consistency and jackknife tests. The current approach, complemented with the powerful covariant discriminant algorithm based on the pseudo-amino acid composition that has incorporated quasi-sequence-order effect as recently proposed by K. C. Chou (2001), may become a very useful high-throughput tool in the area of bioinformatics and proteomics. PMID:12719255

Cai, Yu-Dong; Zhou, Guo-Ping; Chou, Kuo-Chen

2003-01-01

79

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)

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.

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

2003-05-01

80

Prediction of mitochondrial proteins based on genetic algorithm - partial least squares and support vector machine.  

PubMed

Mitochondria are essential cell organelles of eukaryotes. Hence, it is vitally important to develop an automated and reliable method for timely identification of novel mitochondrial proteins. In this study, mitochondrial proteins were encoded by dipeptide composition technology; then, the genetic algorithm-partial least square (GA-PLS) method was used to evaluate the dipeptide composition elements which are more important in recognizing mitochondrial proteins; further, these selected dipeptide composition elements were applied to support vector machine (SVM)-based classifiers to predict the mitochondrial proteins. All the models were trained and validated by the jackknife cross-validation test. The prediction accuracy is 85%, suggesting that it performs reasonably well in predicting the mitochondrial proteins. Our results strongly imply that not all the dipeptide compositions are informative and indispensable for predicting proteins. The source code of MATLAB and the dataset are available on request under liml@scu.edu.cn. PMID:17701100

Tan, F; Feng, X; Fang, Z; Li, M; Guo, Y; Jiang, L

2007-11-01

81

Absence of significant cross-correlation between WMAP and SDSS  

NASA Astrophysics Data System (ADS)

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

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

2010-04-01

82

Pine Hollow Watershed Project : FY 2000 Projects.  

SciTech Connect

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

Sherman County Soil and Water Conservation District

2001-06-01

83

PACo: A Novel Procrustes Application to Cophylogenetic Analysis  

PubMed Central

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

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

2013-01-01

84

Spectral estimation for geophysical time-series with inconvenient gaps  

NASA Astrophysics Data System (ADS)

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

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

2012-09-01

85

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

USGS Publications Warehouse

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

Kery, M.; Royle, J.A.

2008-01-01

86

Prediction of bacterial protein subcellular localization by incorporating various features into Chou's PseAAC and a backward feature selection approach.  

PubMed

Information on the subcellular localization of bacterial proteins is essential for protein function prediction, genome annotation and drug design. Here we proposed a novel approach to predict the subcellular localization of bacterial proteins by fusing features from position-specific score matrix (PSSM), Gene Ontology (GO) and PROFEAT. A backward feature selection approach by linear kennel of SVM was then used to rank the integrated feature vectors and extract optimal features. Finally, SVM was applied for predicting protein subcellular locations based on these optimal features. To validate the performance of our method, we employed jackknife cross-validation tests on three low similarity datasets, i.e., M638, Gneg1456 and Gpos523. The overall accuracies of 94.98%, 93.21%, and 94.57% were achieved for these three datasets, which are higher (from 1.8% to 10.9%) than those by state-of-the-art tools. Comparison results suggest that our method could serve as a very useful vehicle for expediting the prediction of bacterial protein subcellular localization. PMID:24929100

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

2014-09-01

87

Predictability of Zimbabwe summer rainfall  

NASA Astrophysics Data System (ADS)

Predictors of Zimbabwe summer rainfall are investigated with a view to improved long-range forecasts. Teleconnectivity is assessed in respect of sea-surface temperatures, the Southern Oscillation index, the Quasi-biennial Oscillation (QBO), outgoing longwave radiation (OLR) and wind. Spectral analyses of historical rainfall gives an indication of cycles in the range 2.3, 18 and 3.8 years, possibly associated with the QBO, the luni-solar tide and the El No-Southern Oscillation (ENSO), respectively. Pair-wise correlations are found between Zimbabwe summer rainfall and SST in the central Indian Ocean (r<-0.5) in austral spring. Below normal OLR values in September over southern Africa corresponds with good rains in the following summer. Rainfall-upper-wind correlations are optimum (r<-0.7) over the equatorial Atlantic in spring. Comparatively weak correlation with the QBO may also reflect biennial adjustment of monsoon and global ENSO teleconnections. Additional predictor variables are utilized and multivariate models are formulated for early and late summer rainfall and maize yield in Zimbabwe. The models use three to five predictors, are trained over a 22-year period and perform well in jack-knife skill tests. Summer rainfall forecasts with one season lead times are viable and could ameliorate hardship caused by drought.

Makarau, Amos; Jury, Mark R.

1997-11-01

88

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

PubMed Central

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

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

2015-01-01

89

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

PubMed

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

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

2012-10-01

90

PredHydroxy: computational prediction of protein hydroxylation site locations based on the primary structure.  

PubMed

Compared to well-known and extensively studied protein phosphorylation, protein hydroxylation attracts much less attention and the molecular mechanism of the hydroxylation is still incompletely understood. And yet annotation of hydroxylation in proteomes is a first-critical step toward decoding protein function and understanding their physiological roles that have been implicated in the pathological processes and providing useful information for the drug designs of various diseases related with hydroxylation. In this work, we present a novel method called PredHydroxy to automate the prediction of the proline and lysine hydroxylation sites based on position weight amino acids composition, 8 high-quality amino acid indices and support vector machines. The PredHydroxy achieved a promising performance with an area under the receiver operating characteristic curve (AUC) of 82.72% and a Matthew's correlation coefficient (MCC) of 69.03% for hydroxyproline as well as an AUC of 87.41% and a MCC of 66.68% for hydroxylysine in jackknife cross-validation. The results obtained from both the cross validation and independent tests suggest that the PredHydroxy might be a powerful and complementary tool for further experimental investigation of protein hydroxylation. Feature analyses demonstrate that hydroxylation and non-hydroxylation have distinct location-specific differences; alpha and turn propensity is of importance for the hydroxylation of proline and lysine residues. A user-friendly server is freely available on the web at: . PMID:25534958

Shi, Shao-Ping; Chen, Xiang; Xu, Hao-Dong; Qiu, Jian-Ding

2015-03-17

91

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

PubMed

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

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

2007-01-01

92

Newest mobile drilling rig  

SciTech Connect

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

Not Available

1981-01-01

93

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

USGS Publications Warehouse

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

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

2006-01-01

94

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

USGS Publications Warehouse

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

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

1999-01-01

95

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

NASA Astrophysics Data System (ADS)

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

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

2008-04-01

96

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

USGS Publications Warehouse

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.

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

1999-01-01

97

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

NASA Technical Reports Server (NTRS)

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.

Hall, Timothy; Yonekura, Emmi

2013-01-01

98

Differentiation of fecal Escherichia coli from poultry and free-living birds by (GTG)5-PCR genomic fingerprinting.  

PubMed

Determination of the non-point sources of fecal pollution is essential for the assessment of potential public health risk and development of appropriate management practices for prevention of further contamination. Repetitive extragenic palindromic-PCR coupled with (GTG)(5) primer [(GTG)(5)-PCR] was performed on 573 Escherichia coli isolates obtained from the feces of poultry (chicken, duck and turkey) and free-living (Canada goose, hawk, magpie, seagull and songbird) birds to evaluate the efficacy of (GTG)(5)-PCR genomic fingerprinting in the prediction of the correct source of fecal pollution. A discriminant analysis with the jack-knife algorithm of (GTG)(5)-PCR DNA fingerprints revealed that 95%, 94.1%, 93.2%, 84.6%, 79.7%, 76.7%, 75.3% and 70.7% of magpie, hawk, turkey, seagull, Canada goose, chicken, duck and songbird fecal E. coli isolates classified into the correct host source, respectively. The results of this study indicate that (GTG)(5)-PCR can be considered to be a complementary molecular tool for the rapid determination of E. coli isolates identity and tracking the non-point sources of fecal pollution. PMID:17572150

Mohapatra, Bidyut R; Broersma, Klaas; Mazumder, Asit

2008-04-01

99

Interpolation of Global Monthly Rain-Gauge Observations for Climate Change Analysis  

NASA Astrophysics Data System (ADS)

Monthly precipitation sums are observed at thousands of meteorological stations worldwide. Different institutes (e.g. the Global Precipitation Climatology Centre, GPCC, and the Climatic Research Unit, CRU, of the University of East Anglia) interpolate these observations to regular grids. These data are used widely in climate research, e.g. for the investigation of the hydrological cycle and climate change. Results of the interpolation depend on the station density, which varies considerably around the globe. It also depends on the interpolation method used (e.g. Ordinary Kriging and Shepard's Method). These methods are general interpolation methods that do not take into account the specifics of precipitation. The question discussed in this presentation is whether we can do better by using an interpolation strategy especially designed for monthly precipitation observations. Based on a dense local dataset (one station per 109 km2) and a less dense global dataset (one station per 27,000 km2) of 50 years of monthly precipitation observations, various interpolation strategies are compared. This includes the interpolation of transformed variables, the consideration of local spatial correlation of precipitation as well as data quality. The Jack-knife error is used to compare the different strategies. The major result is that some strategies used so far are far from optimal.

Grieser, Jürgen

2014-05-01

100

Estimating survival probabilities by exposure levels: utilizing vital statistics and complex survey data with mortality follow-up.  

PubMed

We present a two-step approach for estimating hazard rates and, consequently, survival probabilities, by levels of general categorical exposure. The resulting estimator utilizes three sources of data: vital statistics data and census data are used at the first step to estimate the overall hazard rate for a given combination of gender and age group, and cohort data constructed from a nationally representative complex survey with linked mortality records, are used at the second step to divide the overall hazard rate by exposure levels. We present an explicit expression for the resulting estimator and consider two methods for variance estimation that account for complex multistage sample design: (1) the leaving-one-out jackknife method, and (2) the Taylor linearization method, which provides an analytic formula for the variance estimator. The methods are illustrated with smoking and all-cause mortality data from the US National Health Interview Survey Linked Mortality Files, and the proposed estimator is compared with a previously studied crude hazard rate estimator that uses survey data only. The advantages of a two-step approach and possible extensions of the proposed estimator are discussed. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25656596

Landsman, V; Lou, W Y W; Graubard, B I

2015-05-20

101

Conotoxin superfamily prediction using diffusion maps dimensionality reduction and subspace classifier.  

PubMed

Conotoxins are disulfide-rich small peptides that are invaluable channel-targeted peptides and target neuronal receptors, which have been demonstrated to be potent pharmaceuticals in the treatment of Alzheimer's disease, Parkinson's disease, and epilepsy. Accurate prediction of conotoxin superfamily would have many important applications towards the understanding of its biological and pharmacological functions. In this study, a novel method, named dHKNN, is developed to predict conotoxin superfamily. Firstly, we extract the protein's sequential features composed of physicochemical properties, evolutionary information, predicted secondary structures and amino acid composition. Secondly, we use the diffusion maps for dimensionality reduction, which interpret the eigenfunctions of Markov matrices as a system of coordinates on the original data set in order to obtain efficient representation of data geometric descriptions. Finally, an improved K-local hyperplane distance nearest neighbor subspace classifier method called dHKNN is proposed for predicting conotoxin superfamilies by considering the local density information in the diffusion space. The overall accuracy of 91.90% is obtained through the jackknife cross-validation test on a benchmark dataset, indicating the proposed dHKNN is promising. PMID:21787305

Yin, Jiang-Bo; Fan, Yong-Xian; Shen, Hong-Bin

2011-09-01

102

Predicting Protein Phenotypes Based on Protein-Protein Interaction Network  

PubMed Central

Background Identifying associated phenotypes of proteins is a challenge of the modern genetics since the multifactorial trait often results from contributions of many proteins. Besides the high-through phenotype assays, the computational methods are alternative ways to identify the phenotypes of proteins. Methodology/Principal Findings Here, we proposed a new method for predicting protein phenotypes in yeast based on protein-protein interaction network. Instead of only the most likely phenotype, a series of possible phenotypes for the query protein were generated and ranked acording to the tethering potential score. As a result, the first order prediction accuracy of our method achieved 65.4% evaluated by Jackknife test of 1,267 proteins in budding yeast, much higher than the success rate (15.4%) of a random guess. And the likelihood of the first 3 predicted phenotypes including all the real phenotypes of the proteins was 70.6%. Conclusions/Significance The candidate phenotypes predicted by our method provided useful clues for the further validation. In addition, the method can be easily applied to the prediction of protein associated phenotypes in other organisms. PMID:21423698

Liu, Xiao-Jun; Cai, Yu-Dong

2011-01-01

103

Prediction of Antimicrobial Peptides Based on Sequence Alignment and Feature Selection Methods  

PubMed Central

Antimicrobial peptides (AMPs) represent a class of natural peptides that form a part of the innate immune system, and this kind of ‘nature's antibiotics’ is quite promising for solving the problem of increasing antibiotic resistance. In view of this, it is highly desired to develop an effective computational method for accurately predicting novel AMPs because it can provide us with more candidates and useful insights for drug design. In this study, a new method for predicting AMPs was implemented by integrating the sequence alignment method and the feature selection method. It was observed that, the overall jackknife success rate by the new predictor on a newly constructed benchmark dataset was over 80.23%, and the Mathews correlation coefficient is 0.73, indicating a good prediction. Moreover, it is indicated by an in-depth feature analysis that the results are quite consistent with the previously known knowledge that some amino acids are preferential in AMPs and that these amino acids do play an important role for the antimicrobial activity. For the convenience of most experimental scientists who want to use the prediction method without the interest to follow the mathematical details, a user-friendly web-server is provided at http://amp.biosino.org/. PMID:21533231

Wang, Ping; Hu, Lele; Liu, Guiyou; Jiang, Nan; Chen, Xiaoyun; Xu, Jianyong; Zheng, Wen; Li, Li; Tan, Ming; Chen, Zugen; Song, Hui; Cai, Yu-Dong; Chou, Kuo-Chen

2011-01-01

104

Analysis and Prediction of Translation Rate Based on Sequence and Functional Features of the mRNA  

PubMed Central

Protein concentrations depend not only on the mRNA level, but also on the translation rate and the degradation rate. Prediction of mRNA's translation rate would provide valuable information for in-depth understanding of the translation mechanism and dynamic proteome. In this study, we developed a new computational model to predict the translation rate, featured by (1) integrating various sequence-derived and functional features, (2) applying the maximum relevance & minimum redundancy method and incremental feature selection to select features to optimize the prediction model, and (3) being able to predict the translation rate of RNA into high or low translation rate category. The prediction accuracies under rich and starvation condition were 68.8% and 70.0%, respectively, evaluated by jackknife cross-validation. It was found that the following features were correlated with translation rate: codon usage frequency, some gene ontology enrichment scores, number of RNA binding proteins known to bind its mRNA product, coding sequence length, protein abundance and 5?UTR free energy. These findings might provide useful information for understanding the mechanisms of translation and dynamic proteome. Our translation rate prediction model might become a high throughput tool for annotating the translation rate of mRNAs in large-scale. PMID:21253596

Xu, Zhongping; Zheng, Yufang; Feng, Kai-Yan; Li, Hai-Peng; Kong, Xiangyin; Cai, Yu-Dong

2011-01-01

105

Predicting Metabolic Pathways of Small Molecules and Enzymes Based on Interaction Information of Chemicals and Proteins  

PubMed Central

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. PMID:23029334

Feng, Kai-Yan; Huang, Tao; Jiang, Yang

2012-01-01

106

Prediction and Analysis of Protein Hydroxyproline and Hydroxylysine  

PubMed Central

Background Hydroxylation is an important post-translational modification and closely related to various diseases. Besides the biotechnology experiments, in silico prediction methods are alternative ways to identify the potential hydroxylation sites. Methodology/Principal Findings In this study, we developed a novel sequence-based method for identifying the two main types of hydroxylation sites – hydroxyproline and hydroxylysine. First, feature selection was made on three kinds of features consisting of amino acid indices (AAindex) which includes various physicochemical properties and biochemical properties of amino acids, Position-Specific Scoring Matrices (PSSM) which represent evolution information of amino acids and structural disorder of amino acids in the sliding window with length of 13 amino acids, then the prediction model were built using incremental feature selection method. As a result, the prediction accuracies are 76.0% and 82.1%, evaluated by jackknife cross-validation on the hydroxyproline dataset and hydroxylysine dataset, respectively. Feature analysis suggested that physicochemical properties and biochemical properties and evolution information of amino acids contribute much to the identification of the protein hydroxylation sites, while structural disorder had little relation to protein hydroxylation. It was also found that the amino acid adjacent to the hydroxylation site tends to exert more influence than other sites on hydroxylation determination. Conclusions/Significance These findings may provide useful insights for exploiting the mechanisms of hydroxylation. PMID:21209839

Hu, Le-Le; Niu, Shen; Huang, Tao; Wang, Kai; Shi, Xiao-He; Cai, Yu-Dong

2010-01-01

107

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

SciTech Connect

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

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

1992-09-30

108

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

PubMed Central

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

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

2014-01-01

109

Estimation of finite seismic source parameters for selected events of the West Bohemia year 2008 seismic swarm  

NASA Astrophysics Data System (ADS)

Finite seismic source parameters were determined for a set of 91 selected events of the West Bohemia year 2008 earthquake swarm ( M L from 0.6 to 3.7) using the stopping phases method. According to the theory, two stopping phases are generated along the source border where the rupture process terminates. These two phases form a Hilbert transform pair; it is also a criterion for their identification. Circular and elliptical source models were considered and their parameters were recovered using the differences in arrival times between the identified stopping phases. Generalization of the circular to elliptical model was found to be statistically significant only for a minority of the events; consequently, only circular source models were investigated in detail. Individual source parameter errors were estimated with the use of the jackknife method. Our results are in good agreement with a previously published theoretical formula relating source radius and magnitude and also with the relation derived in the year 2000 swarm. Our results also confirm rather well the general theoretical assumption about the constant stress drop (with median value of 2.4 MPa and with the majority of values ranging from 1 to 10 MPa).

Kolá?, Petr; R?žek, Bohuslav

2015-04-01

110

Transabdominal Extralevator Abdominoperineal Excision (eLAPE) Performed by Laparoscopic Approach with No Position Change.  

PubMed

As a new surgical technique, extralevator abdominoperineal excision (eLAPE) is recommended for the treatment of low rectal cancer. The patient's position is changed to a prone jackknife position before extralevator excision is performed via the perineal approach. Whether the extralevator excision can be completed through a transabdominal route under laparoscopy is controversial. This study was designed to introduce a modified technique of laparoscopic-assisted eLAPE and to evaluate the feasibility and safety of this technique. With no change of position, laparoscopic eLAPE was performed in 12 patients with low rectal cancer through a transabdominal route between February 2012 and August 2013. There was no case with bowel perforation and positive circumferential resection margins among these 12 patients. The mean operative time was 177.1 minutes, and the mean intraoperative blood loss was 92.5?mL. The mean time to passing of first flatus was 2.3 days, and the mean postoperative hospital stay was 7.5 days. There was no case with bladder dysfunction. No patients suffered from sexual dysfunction during the follow-up period. Without the change of the patient's position, eLAPE can be performed through a transabdominal route by the laparoscopic approach. The procedure of the former eLAPE is simplified without compromising oncologic outcome. PMID:25658808

Zhang, Xingmao; Wang, Zheng; Liang, Jianwei; Zhou, Zhixiang

2015-03-01

111

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

PubMed

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. PMID:24893754

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

112

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

PubMed Central

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

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

2015-01-01

113

The k-sample problem in a multi-state model and testing transition probability matrices.  

PubMed

The choice of multi-state models is natural in analysis of survival data, e.g., when the subjects in a study pass through different states like 'healthy', 'in a state of remission', 'relapse' or 'dead' in a health related quality of life study. Competing risks is another common instance of the use of multi-state models. Statistical inference for such event history data can be carried out by assuming a stochastic process model. Under such a setting, comparison of the event history data generated by two different treatments calls for testing equality of the corresponding transition probability matrices. The present paper proposes solution to this class of problems by assuming a non-homogeneous Markov process to describe the transitions among the health states. A class of test statistics are derived for comparison of [Formula: see text] treatments by using a 'weight process'. This class, in particular, yields generalisations of the log-rank, Gehan, Peto-Peto and Harrington-Fleming tests. For an intrinsic comparison of the treatments, the 'leave-one-out' jackknife method is employed for identifying influential observations. The proposed methods are then used to develop the Kolmogorov-Smirnov type supremum tests corresponding to the various extended tests. To demonstrate the usefulness of the test procedures developed, a simulation study was carried out and an application to the Trial V data provided by International Breast Cancer Study Group is discussed. PMID:23722306

Tattar, Prabhanjan N; Vaman, H J

2014-07-01

114

Identification of core T cell network based on immunome interactome  

PubMed Central

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

2014-01-01

115

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

PubMed

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

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

2009-10-01

116

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

PubMed Central

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

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

2014-01-01

117

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

PubMed

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

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

2014-12-01

118

Predicting the Types of J-Proteins Using Clustered Amino Acids  

PubMed Central

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

Feng, Pengmian; Zuo, Yongchun

2014-01-01

119

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

PubMed Central

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

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

2014-01-01

120

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

PubMed

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. PMID:22679884

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

2012-05-01

121

Effects of Taxon Sampling in Reconstructions of Intron Evolution  

PubMed Central

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

Nikitin, Mikhail A.; Aleoshin, Vladimir V.

2013-01-01

122

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

NASA Astrophysics Data System (ADS)

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.

Rahman, Atiqur

123

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

PubMed

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. PMID:19048186

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

2010-04-01

124

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

PubMed

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. PMID:18506293

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

2008-01-01

125

Forecasting natural aquifer discharge using a numerical model and convolution.  

PubMed

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. PMID:23914881

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

2014-01-01

126

O-GlcNAcPRED: a sensitive predictor to capture protein O-GlcNAcylation sites.  

PubMed

O-GlcNAcylation is a ubiquitous post-translational modification of proteins that is involved in the majority of cellular processes and is associated with many diseases. To reduce the workload and increase the relevance of experimental identification of protein O-GlcNAcylation sites, O-GlcNAcPRED, a support vector machine (SVM)-based model, was developed to capture potential O-GlcNAcylation sites. By virtue of the novel adapted normal distribution bi-profile Bayes (ANBPB) feature extraction method, O-GlcNAcPRED yielded a sensitivity of 80.83%, a specificity of 78.17% and an accuracy of 79.50% in jackknife cross-validation experiments. In an independent test on 38 recently experimentally identified human O-GlcNAcylated proteins with 67 O-GlcNAcylation sites, O-GlcNAcPRED captured 26 proteins and 39 sites, clearly outperforming the existing predictors, YinOYang and O-GlcNAcscan. PMID:24056994

Jia, Cang-Zhi; Liu, Tian; Wang, Zhi-Ping

2013-11-01

127

Estimation of ROC curve with complex survey data.  

PubMed

The receiver operating characteristic (ROC) curve can be utilized to evaluate the performance of diagnostic tests. The area under the ROC curve (AUC) is a widely used summary index for comparing multiple ROC curves. Both parametric and nonparametric methods have been developed to estimate and compare the AUCs. However, these methods are usually only applicable to data collected from simple random samples and not surveys and epidemiologic studies that use complex sample designs such as stratified and/or multistage cluster sampling with sample weighting. Such complex samples can inflate variances from intra-cluster correlation and alter the expectations of test statistics because of the use of sample weights that account for differential sampling rates. In this paper, we modify the nonparametric method to incorporate sampling weights to estimate the AUC and employ leaving-one-out jackknife methods along with the balanced repeated replication method to account for the effects of the complex sampling in the variance estimation of our proposed estimators of the AUC. The finite sample properties of our methods are evaluated using simulations, and our methods are illustrated by comparing the estimated AUC for predicting overweight/obesity using different measures of body weight and adiposity among sampled children and adults in the US Hispanic Health and Nutrition Examination Survey. Copyright © 2014 John Wiley & Sons, Ltd. PMID:25546290

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

2015-04-15

128

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

PubMed

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

Aoki, Yuta; Cortese, Samuele; Tansella, Michele

2014-09-29

129

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

PubMed Central

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

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

2014-01-01

130

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

SciTech Connect

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.

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

2010-09-13

131

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

SciTech Connect

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

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

2010-01-22

132

Distinguishing centrarchid genera by use of lateral line scales  

USGS Publications Warehouse

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.

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

2007-01-01

133

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

PubMed Central

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

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

2013-01-01

134

A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction.  

PubMed

During last few decades accurate determination of protein structural class using a fast and suitable computational method has been a challenging problem in protein science. In this context a meaningful representation of a protein sample plays a key role in achieving higher prediction accuracy. In this paper based on the concept of Chou's pseudo amino acid composition (Chou, K.C., 2001. Proteins 43, 246-255), a new feature representation method is introduced which is composed of the amino acid composition information, the amphiphilic correlation factors and the spectral characteristics of the protein. Thus the sample of a protein is represented by a set of discrete components which incorporate both the sequence order and the length effect. On the basis of such a statistical framework a simple radial basis function network based classifier is introduced to predict protein structural class. A set of exhaustive simulation studies demonstrates high success rate of classification using the self-consistency and jackknife test on the benchmark datasets. PMID:21106461

Sahu, Sitanshu Sekhar; Panda, Ganapati

2010-12-01

135

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

PubMed

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

Barrett, Craig F; Freudenstein, John V

2008-05-01

136

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

PubMed Central

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

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

2014-01-01

137

Prediction of success for polymerase chain reactions using the Markov maximal order model and support vector machine.  

PubMed

Polymerase chain reaction (PCR) is hailed as one of the monumental scientific techniques of the twentieth century, and has become a common and often indispensable technique in many areas. However, researchers still frequently find some DNA templates very hard to amplify with PCR, although many kinds of endeavors were introduced to optimize the amplification. In fact, during the past decades, the experimental procedure of PCR was always the focus of attention, while the analysis of a DNA template, the PCR experimental subject itself, was almost neglected. Up to now, nobody can certainly identify whether a fragment of DNA can be simply amplified using conventional Taq DNA polymerase-based PCR protocol. Characterizing a DNA template and then developing a reliable and efficient method to predict the success of PCR reactions is thus urgently needed. In this study, by means of the Markov maximal order model, we construct a 48-D feature vector to represent a DNA template. Support vector machine (SVM) is then employed to help evaluate PCR result. To examine the anticipated success rates of our predictor, jackknife cross-validation test is adopted. The overall accuracy of our approach arrives at 93.12%, with the sensitivity, specificity, and MCC of 94.68%, 91.58%, and 0.863%, respectively. PMID:25636491

Li, Chun; Yang, Yan; Fei, Wenchao; He, Ping-An; Yu, Xiaoqing; Zhang, Defu; Yi, Shumin; Li, Xuepeng; Zhu, Jin; Wang, Changzhong; Wang, Zhifu

2015-03-21

138

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

NASA Astrophysics Data System (ADS)

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.

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

2012-09-01

139

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

NASA Astrophysics Data System (ADS)

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.

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

2012-03-01

140

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

PubMed

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 (AUC????)] is probably most relevant to the efficacy of these drugs. We therefore assessed population AUC???? data for all four first-line TB drugs (rifampicin, isoniazid, pyrazinamide and ethambutol) as well as moxifloxacin and developed limited sampling strategies to estimate AUC???? values conveniently. AUC???? 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 AUC???? 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 AUC???? values of all drugs separately and simultaneously. In the absence of clinically validated target values for AUC????, average AUC???? values can be used as reference values in TDM. Limited sampling of AUC???? is feasible in many settings and allows for TDM to be performed at a larger scale. PMID:24985091

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

141

Patterns of connectivity among populations of a coral reef fish  

NASA Astrophysics Data System (ADS)

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.

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

2013-06-01

142

Demography and randomized life table statistics for peach twig borer Anarsia lineatella (Lepidoptera: Gelechiidae).  

PubMed

This work studies for first time the effect of constant temperatures (15, 20, 25, 30 and 3 degrees C) on the demography of Anarsia lineatella Zeller (Lepidoptera: Gelechiidae) based on jackknife and bootstrap randomization methods. Male and female longevity was substantially reduced at the higher temperatures in contrast to intermediate and lower temperatures. According to a second order polynomial regression function, high correlations were observed between temperatures and the age of first reproduction as well as temperature and oviposition times. Net reproductive rate was highest at 25 degrees C and 74.172, while the intrinsic rate of increase displayed its highest values at 30 degrees C and was estimated to be 0.238. Birth rate and finite capacity of increase were higher at 30 degrees C and estimated to be 0.235 and 1.268, respectively. Mean generation time and doubling time varied significantly with temperature and the shortest mean generation and doubling time was obtained at 30 degrees C (25.566 and 2.909 d respectively). Life expectancy had its lowest value 10.3 d at 25 degrees C, whereas cohorts that were maintained at 20 and 15 degrees C increased their life expectation approximately three to sixfold. PMID:23786054

Damos, Petros

2013-04-01

143

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

NASA Astrophysics Data System (ADS)

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

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

2012-01-01

144

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

PubMed Central

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

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

2014-01-01

145

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

PubMed

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

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

2010-06-01

146

Estimation of age at death from the pubic symphysis and the auricular surface of the ilium using a smoothing procedure.  

PubMed

We discuss here the estimation of age at death from two indicators (pubic symphysis and the sacro-pelvic surface of the ilium) based on four different osteological series from Portugal, Great-Britain, South Africa or USA (European origin). These samples and the scoring system of the two indicators were used by Schmitt et al. (2002), applying the methodology proposed by Lucy et al. (1996). In the present work, the same data was processed using a modification of the empirical method proposed by Lucy et al. (2002). The various probability distributions are estimated from training data by using kernel density procedures and Jackknife methodology. Bayes's theorem is then used to produce the posterior distribution from which point and interval estimates may be made. This statistical approach reduces the bias of the estimates to less than 70% of what was obtained by the initial method. This reduction going up to 52% if knowledge of sex of the individual is available, and produces an age for all the individuals that improves age at death assessment. PMID:22206714

Martins, Rui; Oliveira, Paulo Eduardo; Schmitt, Aurore

2012-06-10

147

Clustering of Supernova Ia Host Galaxies  

NASA Astrophysics Data System (ADS)

For the first time the cross-correlation between Type Ia supernova host galaxies and surrounding field galaxies is measured using the Supernova Legacy Survey sample. Over the z=0.2-0.9 redshift range we find that supernova hosts are correlated an average of 60% more strongly than similarly selected field galaxies over the 3"-100" range and about a factor of 3 more strongly below 10''. The correlation errors are empirically established with a jackknife analysis of the four SNLS fields. The hosts are more correlated than the field at a significance of 99% in the fitted amplitude and slope, with the point-by-point difference of the two correlation functions having a reduced ?2 for 8 degrees of freedom of 4.3, which has a probability of random occurrence of less than 3×10-5. The correlation angle is 1.5" +/- 0.5", which deprojects to a fixed comoving correlation length of approximately 6.5+/-2 h-1 Mpc. Weighting the field galaxies with the mass and star formation rate supernova frequencies of the simple A+B model produces good agreement with the observed clustering. We conclude that these supernova clustering differences are primarily the expected outcome of the dependence of supernova rates on galaxy masses and stellar populations with their clustering environment.

Carlberg, R. G.; Sullivan, M.; Le Borgne, D.; Conley, A.; Howell, D. A.; Perrett, K.; Astier, P.; Balam, D.; Balland, C.; Basa, S.; Hardin, D.; Fouchez, D.; Guy, J.; Hook, I.; Pain, R.; Pritchet, C. J.; Regnault, N.; Rich, J.; Perlmutter, S.

2008-07-01

148

Consistency of methods for analysing location-specific data.  

PubMed

Although the receiver operating characteristic (ROC) method is the acknowledged gold-standard for imaging system assessment, it ignores localisation information and differentiation between multiple abnormalities per case. As the free-response ROC (FROC) method uses localisation information and more closely resembles the clinical reporting process, it is being increasingly used. A number of methods have been proposed to analyse the data that result from an FROC study: jackknife alternative FROC (JAFROC) and a variant termed JAFROC1, initial detection and candidate analysis (IDCA) and ROC analysis via the reduction of the multiple ratings on a case to a single rating. The focus of this paper was to compare JAFROC1, IDCA and the ROC analysis methods using a clinical FROC human data set. All methods agreed on the ordering of the modalities and all yielded statistically significant differences of the figures-of-merit, i.e. p < 0.05. Both IDCA and JAFROC1 yielded much smaller p-values than ROC. The results are consistent with a recent simulation-based validation study comparing these and other methods. In conclusion, IDCA or JAFROC1 analysis of FROC human data may be superior at detecting modality differences than ROC analysis. PMID:20159917

Zanca, F; Chakraborty, D P; Marchal, G; Bosmans, H

2010-01-01

149

A quantitative method for evaluating the detectability of lesions in digital mammography.  

PubMed

This study presents a quantitative method for evaluating the detectability of microcalcifications in digital mammography. Four hundred and twenty microcalcifications (with various morphology, size and contrast), simulated with a previously validated method, were used for the creation of image datasets. Lesions were inserted into 163 regions of interests of 59 selected raw digital mammograms with various anatomical backgrounds and acquired with a Siemens Novation DR. After processing, these composite images were scored by experienced radiologists, who located multiple simulated lesions and rated them under conditions of free-search. For statistical analysis, free-response receiver-operating characteristic curves are plotted; the use of jackknife free-response receiver-operating characteristic method has also been investigated. The main advantage of this methodology is that the exact number of inserted microcalcifications is well known and that the lesions are fully characterised in terms of pathology, size, morphology and peak contrast. A first application has been the evaluation of the effect of anatomical background on microcalcifications detection. Preliminary findings in this study indicate that this method may be a promising tool to evaluate factors that have an influence on the detectability of lesions, such as the clinical processing or the viewing conditions. PMID:18319282

Zanca, F; Van Ongeval, C; Jacobs, J; Marchal, G; Bosmans, H

2008-01-01

150

Consistency of methods for analysing location-specific data  

PubMed Central

Although the receiver operating characteristic (ROC) method is the acknowledged gold-standard for imaging system assessment, it ignores localisation information and differentiation between multiple abnormalities per case. As the free-response ROC (FROC) method uses localisation information and more closely resembles the clinical reporting process, it is being increasingly used. A number of methods have been proposed to analyse the data that result from an FROC study: jackknife alternative FROC (JAFROC) and a variant termed JAFROC1, initial detection and candidate analysis (IDCA) and ROC analysis via the reduction of the multiple ratings on a case to a single rating. The focus of this paper was to compare JAFROC1, IDCA and the ROC analysis methods using a clinical FROC human data set. All methods agreed on the ordering of the modalities and all yielded statistically significant differences of the figures-of-merit, i.e. p < 0.05. Both IDCA and JAFROC1 yielded much smaller p-values than ROC. The results are consistent with a recent simulation-based validation study comparing these and other methods. In conclusion, IDCA or JAFROC1 analysis of FROC human data may be superior at detecting modality differences than ROC analysis. PMID:20159917

Zanca, F.; Chakraborty, D. P.; Marchal, G.; Bosmans, H.

2010-01-01

151

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

PubMed

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

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

2014-01-01

152

SCLAP: an adaptive boosting method for predicting subchloroplast localization of plant proteins.  

PubMed

Chloroplasts are organelles found in plant system and other photosynthetic eukaryotes. Since a large number of essential pathways take place in this organelle, proteins in the chloroplast are considered vital. Therefore, knowledge about the subchloroplast localization of the chloroplast proteins will provide precise information in understanding its interaction within the chloroplast. To address this, an AdaBoost-based prediction system to predict the subchloroplast localization of chloroplast proteins (SCLAP) was developed. It integrates three different sequence-based features for prediction, beside the addition of similarity-based module for significant improvement in prediction performance. SCLAP achieved an overall accuracy of 89.3% in jackknife cross-validation test against the benchmark dataset, which was considered highest among existing tools and equals the SubIdent, and 85.9% accuracy in new error-free dataset. Evaluation of SCLAP with the independent dataset, five-fold cross-validation, and their corresponding receiver operator characteristic curve analysis demonstrated the SCLAP's efficient performance. SCLAP is the webserver implementation of our algorithm written in PERL. The server can be used to predict the subchloroplast localization of chloroplast proteins ( http://sclap.bicpu.edu.in/predict.php ). PMID:23289782

Saravanan, Vijayakumar; Lakshmi, P T V

2013-02-01

153

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

PubMed Central

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

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

2003-01-01

154

The diagnostic accuracy of dual-view digital mammography, single-view breast tomosynthesis and a dual-view combination of breast tomosynthesis and digital mammography in a free-response observer performance study  

PubMed Central

The purpose of the present study was to compare the diagnostic accuracy of dual-view digital mammography (DM), single-view breast tomosynthesis (BT) and BT combined with the opposite DM view. Patients with subtle lesions were selected to undergo BT examinations. Two radiologists who are non-participants in the study and have experience in using DM and BT determined the locations and extents of lesions in the images. Five expert mammographers interpreted the cases using the free-response paradigm. The task was to mark and rate clinically reportable findings suspicious for malignancy and clinically relevant benign findings. The marks were scored with reference to the outlined regions into lesion localization or non-lesion localization, and analysed by the jackknife alternative free-response receiver operating characteristic method. The analysis yielded statistically significant differences between the combined modality and dual-view DM (p < 0.05). No differences were found between single-view BT and dual-view DM or between single-view BT and the combined modality. PMID:20228048

Svahn, T.; Andersson, I.; Chakraborty, D.; Svensson, S.; Ikeda, D.; Förnvik, D.; Mattsson, S.; Tingberg, A.; Zackrisson, S.

2010-01-01

155

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

PubMed Central

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

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

2012-01-01

156

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

PubMed

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

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

2007-01-01

157

Prediction of protein structural class using tri-gram probabilities of position-specific scoring matrix and recursive feature elimination.  

PubMed

Knowledge of structural class plays an important role in understanding protein folding patterns. As a transitional stage in recognition of three-dimensional structure of a protein, protein structural class prediction is considered to be an important and challenging task. In this study, we firstly introduce a feature extraction technique which is based on tri-grams computed directly from position-specific scoring matrix (PSSM). A total of 8,000 features are extracted to represent a protein. Then, support vector machine-recursive feature elimination (SVM-RFE) is applied for feature selection and reduced features are input to a support vector machine (SVM) classifier to predict structural class of a given protein. To examine the effectiveness of our method, jackknife tests are performed on six widely used benchmark datasets, i.e., Z277, Z498, 1189, 25PDB, D640, and D1185. The overall accuracies of 97.1, 98.6, 92.5, 93.5, 94.2, and 95.9 % are achieved on these datasets, respectively. Comparison of the proposed method with other prediction methods shows that our method is very promising to perform the prediction of protein structural class. PMID:25583603

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

2015-03-01

158

Computer-aided assessment of cardiac computed tomographic images  

NASA Astrophysics Data System (ADS)

The accurate interpretation of cardiac CT images is commonly hindered by the presence of motion artifacts. Since motion artifacts commonly can obscure the presence of coronary lesions, physicians must spend much effort analyzing images at multiple cardiac phases in order to determine which coronary structures are assessable for potential lesions. In this study, an artificial neural network (ANN) classifier was designed to assign assessability indices to calcified plaques in individual region-of-interest (ROI) images reconstructed at multiple cardiac phases from two cardiac scans obtained at heart rates of 66 bpm and 90 bpm. Six individual features (volume, circularity, mean intensity, margin gradient, velocity, and acceleration) were used for analyzing images. Visually-assigned assessability indices were used as a continuous truth, and jack-knife analysis with four testing sets was used to evaluate the performance of the ANN classifier. In a study in which all six features were inputted into the ANN classifier, correlation coefficients of 0.962 +/- 0.006 and 0.935 +/- 0.023 between true and ANN-assigned assessability indices were obtained for databases corresponding to 66 bpm and 90 bpm, respectively.

King, Martin; Giger, Maryellen; Suzuki, Kenji; Pan, Xiaochuan

2007-03-01

159

BICEP2 I: Detection Of B-mode Polarization at Degree Angular Scales  

E-print Network

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 (TES) 150 GHz bolometers each with temperature sensitivity of approx. 300 uk.sqrt(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 degrees was observed to a depth of 87 nK-degrees 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-LCDM expectation in the range 305\\sigma$. Through jackknife tests and simulations based on detailed calibration measurements we show that systematic contamination is much smaller than the observed excess. We also e...

Ade, P A R; 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

2014-01-01

160

Hyperdiversity of ectomycorrhizal fungus assemblages on oak seedlings in mixed forests in the southern Appalachian Mountains.  

PubMed

Diversity of ectotrophic mycobionts on outplanted seedlings of two oak species (Quercus rubra and Quercus prinus) was estimated at two sites in mature mixed forests in the southern Appalachian Mountains by sequencing nuclear 5.8S rRNA genes and the flanking internal transcribed spacer regions I and II (ITS). The seedlings captured a high diversity of mycorrhizal ITS-types and late-stage fungi were well represented. Total richness was 75 types, with 42 types having a frequency of only one. The first and second order jackknife estimates were 116 and 143 types, respectively. Among Basidiomycetes, tomentelloid/thelephoroid, russuloid, and cortinarioid groups were the richest. The ascomycete Cenococcum geophilum was ubiquitously present. Dominant fungi included a putative Tuber sp. (Ascomycetes), and Basidiomycetes including a putative Craterellus sp., and Laccaria cf. laccata. Diversity was lower at a drier high elevation oak forest site compared to a low elevation mesic cove--hardwood forest site. Fungal specificity for red oak vs. white oak seedlings was unresolved. The high degree of rarity in this system imposes limitations on the power of community analyses at finer scales. The high mycobiont diversity highlights the potential for seedlings to acquire carbon from mycelial networks and confirms the utility of using outplanted seedlings to estimate ectomycorrhizal diversity. PMID:15723674

Walker, John F; Miller, Orson K; Horton, Jonathan L

2005-03-01

161

Exploratory Structural Equation Modeling of Resting-state fMRI: applicability of group models to individual subjects  

PubMed Central

The extension of group-level connectivity methods to individual subjects remains a hurdle for statistical analyses of neuroimaging data. Previous group analyses of positron emission tomography data in clinically depressed patients, for example, have shown that resting-state connectivity prior to therapy predicts how patients eventually respond to pharmacological and cognitive-behavioral therapy. Such applications would be considerably more informative for clinical decision making if these connectivity methods could be extended into the individual subject domain. To test such an extension, 46 treatment-naïve depressed patients were enrolled in an fMRI study to model baseline resting-state functional connectivity. Resting-state fMRI scans were acquired and submitted to exploratory structural equation modeling (SEM) to derive the optimal group connectivity model. Jackknife and split sample tests confirm that group model was highly reproducible, and path weights were consistent across the best five group models. When this model was applied to data from individual subjects, 85% of patients fit the group model. Histogram analysis of individual subjects’ paths indicate that some paths are better representative of group membership. These results suggest that exploratory SEM is a viable technique for neuroimaging connectivity analyses of individual subjects’ resting-state fMRI data. PMID:19162206

James, G. Andrew; Kelley, Mary E.; Craddock, R. Cameron; Holtzheimer, Paul E.; Dunlop, Boadie; Nemeroff, Charles; Mayberg, Helen S.; Hu, Xiaoping P.

2009-01-01

162

Computer aided morphometry of the neonatal fetal alcohol syndrome face  

NASA Astrophysics Data System (ADS)

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).

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

1993-09-01

163

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

NASA Astrophysics Data System (ADS)

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.

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

164

APSLAP: an adaptive boosting technique for predicting subcellular localization of apoptosis protein.  

PubMed

Apoptotic proteins play key roles in understanding the mechanism of programmed cell death. Knowledge about the subcellular localization of apoptotic protein is constructive in understanding the mechanism of programmed cell death, determining the functional characterization of the protein, screening candidates in drug design, and selecting protein for relevant studies. It is also proclaimed that the information required for determining the subcellular localization of protein resides in their corresponding amino acid sequence. In this work, a new biological feature, class pattern frequency of physiochemical descriptor, was effectively used in accordance with the amino acid composition, protein similarity measure, CTD (composition, translation, and distribution) of physiochemical descriptors, and sequence similarity to predict the subcellular localization of apoptosis protein. AdaBoost with the weak learner as Random-Forest was designed for the five modules and prediction is made based on the weighted voting system. Bench mark dataset of 317 apoptosis proteins were subjected to prediction by our system and the accuracy was found to be 100.0 and 92.4 %, and 90.1 % for self-consistency test, jack-knife test, and tenfold cross validation test respectively, which is 0.9 % higher than that of other existing methods. Beside this, the independent data (N151 and ZW98) set prediction resulted in the accuracy of 90.7 and 87.7 %, respectively. These results show that the protein feature represented by a combined feature vector along with AdaBoost algorithm holds well in effective prediction of subcellular localization of apoptosis proteins. The user friendly web interface "APSLAP" has been constructed, which is freely available at http://apslap.bicpu.edu.in and it is anticipated that this tool will play a significant role in determining the specific role of apoptosis proteins with reliability. PMID:23982307

Saravanan, Vijayakumar; Lakshmi, P T V

2013-12-01

165

Clinical validation of a medical grade color monitor for chest radiology  

NASA Astrophysics Data System (ADS)

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.

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

2009-02-01

166

Evaluation of chest tomosynthesis for the detection of pulmonary nodules: effect of clinical experience and comparison with chest radiography  

NASA Astrophysics Data System (ADS)

Chest tomosynthesis refers to the technique of collecting low-dose projections of the chest at different angles and using these projections to reconstruct section images of the chest. In this study, a comparison of chest tomosynthesis and chest radiography in the detection of pulmonary nodules was performed and the effect of clinical experience of chest tomosynthesis was evaluated. Three senior thoracic radiologists, with more than ten years of experience of chest radiology and 6 months of clinical experience of chest tomosynthesis, acted as observers in a jackknife free-response receiver operating characteristics (JAFROC-1) study, performed on 42 patients with and 47 patients without pulmonary nodules examined with both chest tomosynthesis and chest radiography. MDCT was used as reference and the total number of nodules found using MDCT was 131. To investigate the effect of additional clinical experience of chest tomosynthesis, a second reading session of the tomosynthesis images was performed one year after the initial one. The JAFROC-1 figure of merit (FOM) was used as the principal measure of detectability. In comparison with chest radiography, chest tomosynthesis performed significantly better with regard to detectability. The observer-averaged JAFROC-1 FOM was 0.61 for tomosynthesis and 0.40 for radiography, giving a statistically significant difference between the techniques of 0.21 (p<0.0001). The observer-averaged JAFROC-1 FOM of the second reading of the tomosynthesis cases was not significantly higher than that of the first reading, indicating no improvement in detectability due to additional clinical experience of tomosynthesis.

Zachrisson, Sara; Vikgren, Jenny; Svalkvist, Angelica; Johnsson, Åse A.; Boijsen, Marianne; Flinck, Agneta; Månsson, Lars Gunnar; Kheddache, Susanne; Båth, Magnus

2009-02-01

167

JAFROC analysis revisited: figure-of-merit considerations for human observer studies  

NASA Astrophysics Data System (ADS)

Jackknife alternative free-response receiver operating characteristic (JAFROC) is a method for measuring human observer performance in localization tasks. JAFROC is being increasingly used to evaluate imaging modalities because it has been shown to have greater statistical power than conventional receiver operating characteristic (ROC) analysis, which neglects location information. JAFROC neglects the non-lesion localization marks ("false positives") on abnormal images. JAFROC1 is an alternative method that includes these marks. Both methods are lesion-centric in the sense that they assign equal importance to all lesions; an image with many lesions would tend to dominate the performance metric, and clinically less significant lesions are treated identically as more significant ones. In this paper weighted JAFROC and JAFROC1 analyses are described that treat each abnormal image (not each lesion) as a unit of measurement and account for different lesion clinical significances (weights). Lesion-centric and weighted methods were tested using a simulator that includes multiple-reader multiple-case multiple-modality location level correlations. For comparison, ROC analysis was also tested where the rating of the highest rated mark on an image was assumed to be its "ROC" rating. The testing involved random numbers of lesions per image, random weights, case-mixes (ratio of normal to abnormal images) and different correlation structures. We found that for either JAFROC or JAFROC1, both lesion-centric and weighted analyses had correct NH behavior and comparable statistical powers. For either lesion-centric or weighted analyses JAFROC1 yielded the highest power, followed by JAFROC and ROC yielded the least power, confirming a recent study using a less flexible single-reader dual-modality simulator. Provided the number of normal cases is not too small, JAFROC1 is the preferred method for analyzing human observer free-response data. For either JAFROC or JAFROC1 weighted analysis is preferable.

Chakraborty, D. P.; Yoon, Hong-Jun

2009-02-01

168

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

PubMed Central

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

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

2013-01-01

169

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

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.

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

2008-01-01

170

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

PubMed

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±199.9gN2O-Nha(-1)yr(-1) over the two year period, though emissions from 2008 (2148±273gN2O-Nha(-1)yr(-1)) were 42% higher than 2007 (1504±126gN2O-Nha(-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 30days. 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 24hour mean in the pasture, whereas sampling at noon proved the most accurate in the shaded rainforest and lychee orchard. PMID:25613765

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

2015-04-15

171

Demographic history and rare allele sharing among human populations.  

PubMed

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

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

172

Prediction of Protein S-Nitrosylation Sites Based on Adapted Normal Distribution Bi-Profile Bayes and Chou’s Pseudo Amino Acid Composition  

PubMed Central

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

Jia, Cangzhi; Lin, Xin; Wang, Zhiping

2014-01-01

173

Historical extension of operational NDVI products for livestock insurance in Kenya  

NASA Astrophysics Data System (ADS)

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

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

2014-05-01

174

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

PubMed Central

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

2013-01-01

175

Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data  

PubMed Central

A procedure is presented for refinement of a homology model of E.Coli tRNAVal, originally based on the X-ray structure of yeast tRNAPhe, using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N-HN RDCs measured with Pf1 phage alignment, and 20 imino N-HN RDCs obtained from magnetic field dependent alignment of tRNAVal. The refinement strategy aims to largely retain the local geometry of the 58% identical tRNAPhe by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Qfree = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNAPhe, in agreement with previous NMR-based tRNAVal models. PMID:18787959

Grishaev, Alexander; Ying, Jinfa; Canny, Marella D.; Pardi, Arthur; Bax, Ad

2008-01-01

176

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

PubMed

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

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

2006-09-01

177

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

NASA Astrophysics Data System (ADS)

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.

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

2013-12-01

178

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

NASA Astrophysics Data System (ADS)

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

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

2012-02-01

179

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

PubMed

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

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

2015-03-01

180

Predicting Anatomical Therapeutic Chemical (ATC) Classification of Drugs by Integrating Chemical-Chemical Interactions and Similarities  

PubMed Central

The Anatomical Therapeutic Chemical (ATC) classification system, recommended by the World Health Organization, categories drugs into different classes according to their therapeutic and chemical characteristics. For a set of query compounds, how can we identify which ATC-class (or classes) they belong to? It is an important and challenging problem because the information thus obtained would be quite useful for drug development and utilization. By hybridizing the informations of chemical-chemical interactions and chemical-chemical similarities, a novel method was developed for such purpose. It was observed by the jackknife test on a benchmark dataset of 3,883 drug compounds that the overall success rate achieved by the prediction method was about 73% in identifying the drugs among the following 14 main ATC-classes: (1) alimentary tract and metabolism; (2) blood and blood forming organs; (3) cardiovascular system; (4) dermatologicals; (5) genitourinary system and sex hormones; (6) systemic hormonal preparations, excluding sex hormones and insulins; (7) anti-infectives for systemic use; (8) antineoplastic and immunomodulating agents; (9) musculoskeletal system; (10) nervous system; (11) antiparasitic products, insecticides and repellents; (12) respiratory system; (13) sensory organs; (14) various. Such a success rate is substantially higher than 7% by the random guess. It has not escaped our notice that the current method can be straightforwardly extended to identify the drugs for their 2nd-level, 3rd-level, 4th-level, and 5th-level ATC-classifications once the statistically significant benchmark data are available for these lower levels. PMID:22514724

Chen, Lei; Zeng, Wei-Ming; Cai, Yu-Dong; Feng, Kai-Yan; Chou, Kuo-Chen

2012-01-01

181

Classification and Analysis of Regulatory Pathways Using Graph Property, Biochemical and Physicochemical Property, and Functional Property  

PubMed Central

Given a regulatory pathway system consisting of a set of proteins, can we predict which pathway class it belongs to? Such a problem is closely related to the biological function of the pathway in cells and hence is quite fundamental and essential in systems biology and proteomics. This is also an extremely difficult and challenging problem due to its complexity. To address this problem, a novel approach was developed that can be used to predict query pathways among the following six functional categories: (i) “Metabolism”, (ii) “Genetic Information Processing”, (iii) “Environmental Information Processing”, (iv) “Cellular Processes”, (v) “Organismal Systems”, and (vi) “Human Diseases”. The prediction method was established trough the following procedures: (i) according to the general form of pseudo amino acid composition (PseAAC), each of the pathways concerned is formulated as a 5570-D (dimensional) vector; (ii) each of components in the 5570-D vector was derived by a series of feature extractions from the pathway system according to its graphic property, biochemical and physicochemical property, as well as functional property; (iii) the minimum redundancy maximum relevance (mRMR) method was adopted to operate the prediction. A cross-validation by the jackknife test on a benchmark dataset consisting of 146 regulatory pathways indicated that an overall success rate of 78.8% was achieved by our method in identifying query pathways among the above six classes, indicating the outcome is quite promising and encouraging. To the best of our knowledge, the current study represents the first effort in attempting to identity the type of a pathway system or its biological function. It is anticipated that our report may stimulate a series of follow-up investigations in this new and challenging area. PMID:21980418

Cai, Yu-Dong; Chou, Kuo-Chen

2011-01-01

182

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

PubMed Central

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

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

2011-01-01

183

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

PubMed

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

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

2010-01-01

184

Hepatitis C Virus Network Based Classification of Hepatocellular Cirrhosis and Carcinoma  

PubMed Central

Hepatitis C virus (HCV) is a main risk factor for liver cirrhosis and hepatocellular carcinoma, particularly to those patients with chronic liver disease or injury. The similar etiology leads to a high correlation of the patients suffering from the disease of liver cirrhosis with those suffering from the disease of hepatocellular carcinoma. However, the biological mechanism for the relationship between these two kinds of diseases is not clear. The present study was initiated in an attempt to investigate into the HCV infection protein network, in hopes to find good biomarkers for diagnosing the two diseases as well as gain insights into their progression mechanisms. To realize this, two potential biomarker pools were defined: (i) the target genes of HCV, and (ii) the between genes on the shortest paths among the target genes of HCV. Meanwhile, a predictor was developed for identifying the liver tissue samples among the following three categories: (i) normal, (ii) cirrhosis, and (iii) hepatocellular carcinoma. Interestingly, it was observed that the identification accuracy was higher with the tissue samples defined by extracting the features from the second biomarker pool than that with the samples defined based on the first biomarker pool. The identification accuracy by the jackknife validation for the between-genes approach was 0.960, indicating that the novel approach holds a quite promising potential in helping find effective biomarkers for diagnosing the liver cirrhosis disease and the hepatocellular carcinoma disease. It may also provide useful insights for in-depth study of the biological mechanisms of HCV-induced cirrhosis and hepatocellular carcinoma. PMID:22493692

Huang, Tao; Wang, Junjie; Cai, Yu-Dong; Yu, Hanry; Chou, Kuo-Chen

2012-01-01

185

Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features  

PubMed Central

Background Adenosine-5?-triphosphate (ATP) is one of multifunctional nucleotides and plays an important role in cell biology as a coenzyme interacting with proteins. Revealing the binding sites between protein and ATP is significantly important to understand the functionality of the proteins and the mechanisms of protein-ATP complex. Results In this paper, we propose a novel framework for predicting the proteins’ functional residues, through which they can bind with ATP molecules. The new prediction protocol is achieved by combination of sequence evolutional information and bi-profile sampling of multi-view sequential features and the sequence derived structural features. The hypothesis for this strategy is single-view feature can only represent partial target’s knowledge and multiple sources of descriptors can be complementary. Conclusions Prediction performances evaluated by both 5-fold and leave-one-out jackknife cross-validation tests on two benchmark datasets consisting of 168 and 227 non-homologous ATP binding proteins respectively demonstrate the efficacy of the proposed protocol. Our experimental results also reveal that the residue structural characteristics of real protein-ATP binding sites are significant different from those normal ones, for example the binding residues do not show high solvent accessibility propensities, and the bindings prefer to occur at the conjoint points between different secondary structure segments. Furthermore, results also show that performance is affected by the imbalanced training datasets by testing multiple ratios between positive and negative samples in the experiments. Increasing the dataset scale is also demonstrated useful for improving the prediction performances. PMID:22651691

2012-01-01

186

Prediction of Deleterious Non-Synonymous SNPs Based on Protein Interaction Network and Hybrid Properties  

PubMed Central

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

Xu, Heng; He, Zhisong; Feng, Kai-Yan; Hu, LeLe; Cui, WeiRen; Wang, Kai; Dong, Xiao; Xie, Lu; Kong, Xiangyin; Cai, Yu-Dong; Li, Yixue

2010-01-01

187

Improved Classification of Lung Cancer Tumors Based on Structural and Physicochemical Properties of Proteins Using Data Mining Models  

PubMed Central

Detecting divergence between oncogenic tumors plays a pivotal role in cancer diagnosis and therapy. This research work was focused on designing a computational strategy to predict the class of lung cancer tumors from the structural and physicochemical properties (1497 attributes) of protein sequences obtained from genes defined by microarray analysis. The proposed methodology involved the use of hybrid feature selection techniques (gain ratio and correlation based subset evaluators with Incremental Feature Selection) followed by Bayesian Network prediction to discriminate lung cancer tumors as Small Cell Lung Cancer (SCLC), Non-Small Cell Lung Cancer (NSCLC) and the COMMON classes. Moreover, this methodology eliminated the need for extensive data cleansing strategies on the protein properties and revealed the optimal and minimal set of features that contributed to lung cancer tumor classification with an improved accuracy compared to previous work. We also attempted to predict via supervised clustering the possible clusters in the lung tumor data. Our results revealed that supervised clustering algorithms exhibited poor performance in differentiating the lung tumor classes. Hybrid feature selection identified the distribution of solvent accessibility, polarizability and hydrophobicity as the highest ranked features with Incremental feature selection and Bayesian Network prediction generating the optimal Jack-knife cross validation accuracy of 87.6%. Precise categorization of oncogenic genes causing SCLC and NSCLC based on the structural and physicochemical properties of their protein sequences is expected to unravel the functionality of proteins that are essential in maintaining the genomic integrity of a cell and also act as an informative source for drug design, targeting essential protein properties and their composition that are found to exist in lung cancer tumors. PMID:23505559

Ramani, R. Geetha; Jacob, Shomona Gracia

2013-01-01

188

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

PubMed

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

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

2014-09-01

189

Morphometric convergence and molecular divergence: the taxonomic status and evolutionary history of Gymnura crebripunctata and Gymnura marmorata in the eastern Pacific Ocean.  

PubMed

To clarify the taxonomic status of Gymnura crebripunctata and Gymnura marmorata, the extent of morphological and nucleotide variation between these nominal species was examined using multivariate morphological and mitochondrial DNA comparisons of the same characters with congeneric species. Discriminant analysis of 21 morphometric variables from four species (G. crebripunctata, G. marmorata, Gymnura micrura and Gymnura poecilura) successfully distinguished species groupings. Classification success of eastern Pacific species improved further when specimens were grouped by species and sex. Discriminant analysis of size-corrected data generated species assignments that were consistently accurate in separating the two species (100% jackknifed assignment success). Nasal curtain length was identified as the character which contributed the most to discrimination of the two species. Sexual dimorphism was evident in several characters that have previously been relied upon to distinguish G. crebripunctata from G. marmorata. A previously unreported feature, the absence of a tail spine in G. crebripunctata, provides an improved method of field identification between these species. Phylogenetic and genetic distance analyses based on 698 base pairs of the mitochondrial cytochrome b gene indicate that G. crebripunctata and G. marmorata form highly divergent lineages, supporting their validity as distinct species. The closely related batoid Aetoplatea zonura clustered within the Gymnura clade, indicating that it may not represent a valid genus. Strong population structuring (overall Phi(ST) = 0.81, P < 0.01) was evident between G. marmorata from the Pacific coast of the Baja California peninsula and the Gulf of California, supporting the designation of distinct management units in these regions. PMID:20738578

Smith, W D; Bizzarro, J J; Richards, V P; Nielsen, J; Márquez-Flarías, F; Shivji, M S

2009-09-01

190

Effect of volatile compounds in grass silage on voluntary intake by growing cattle.  

PubMed

Twenty-four low dry matter (DM) silages differing in fermentation quality were harvested at the same time from a crop that consisted mainly of timothy (Phleum pratense), and meadow fescue (Festuca pratensis). The silage samples were analysed by gas chromatography (GC) - mass spectrometry and gas chromatography - flame ionisation detection in order to determine and quantify volatiles present in silage. The voluntary intake of the 24 silages had been measured in a previous feeding trial with growing steers of Norwegian Red. Thirteen esters, five aldehydes, three alcohols, and one sulphide were identified and quantified. A total of 51 variables describing the chemical composition of the silages were included in a partial least-squares regression, and the relationship of silage fermentation quality to voluntary intake was elucidated. The importance of variables describing silage fermentation quality in relation to intake was judged from a best combination procedure, jack-knifing, and empirical correlations of the variables to intake. The GC-analysed compounds were mainly present in poorly fermented silages. However, compared with other explanatory chemical variables none of these compounds was of importance for the voluntary intake as evaluated by partial least-squares regression. A validated variance of 71% in silage DM intake was explained with the selected variables: total acids (TA), total volatile fatty acids (TVFA), lactic acid/total acid ratio and propionic acid. In this study extent (by the variable TA) and type of silage fermentation (by TVFA) influenced intake. Further, it is suggested that by restricting the fermentation in low DM grass silages the potential intake of silage DM is maximised. PMID:22444294

Krizsan, S J; Westad, F; Adnøy, T; Odden, E; Aakre, S E; Randby, A T

2007-03-01

191

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

PubMed Central

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

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

2009-01-01

192

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

PubMed

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

Buchanan, Patricia A; Vardaxis, Vassilios G

2009-03-01

193

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

194

Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops.  

PubMed

In protein structure prediction, a central problem is defining the structure of a loop connecting 2 secondary structures. This problem frequently occurs in homology modeling, fold recognition, and in several strategies in ab initio structure prediction. In our previous work, we developed a classification database of structural motifs, ArchDB. The database contains 12,665 clustered loops in 451 structural classes with information about phi-psi angles in the loops and 1492 structural subclasses with the relative locations of the bracing secondary structures. Here we evaluate the extent to which sequence information in the loop database can be used to predict loop structure. Two sequence profiles were used, a HMM profile and a PSSM derived from PSI-BLAST. A jack-knife test was made removing homologous loops using SCOP superfamily definition and predicting afterwards against recalculated profiles that only take into account the sequence information. Two scenarios were considered: (1) prediction of structural class with application in comparative modeling and (2) prediction of structural subclass with application in fold recognition and ab initio. For the first scenario, structural class prediction was made directly over loops with X-ray secondary structure assignment, and if we consider the top 20 classes out of 451 possible classes, the best accuracy of prediction is 78.5%. In the second scenario, structural subclass prediction was made over loops using PSI-PRED (Jones, J Mol Biol 1999;292:195-202) secondary structure prediction to define loop boundaries, and if we take into account the top 20 subclasses out of 1492, the best accuracy is 46.7%. Accuracy of loop prediction was also evaluated by means of RMSD calculations. PMID:16021623

Fernandez-Fuentes, Narcis; Querol, Enrique; Aviles, Francesc X; Sternberg, Michael J E; Oliva, Baldomero

2005-09-01

195

Asymmetric Constriction of Dividing Escherichia coli Cells Induced by Expression of a Fusion between Two Min Proteins  

PubMed Central

The Min system, consisting of MinC, MinD, and MinE, plays an important role in localizing the Escherichia coli cell division machinery to midcell by preventing FtsZ ring (Z ring) formation at cell poles. MinC has two domains, MinCn and MinCc, which both bind to FtsZ and act synergistically to inhibit FtsZ polymerization. Binary fission of E. coli usually proceeds symmetrically, with daughter cells at roughly 180° to each other. In contrast, we discovered that overproduction of an artificial MinCc-MinD fusion protein in the absence of other Min proteins induced frequent and dramatic jackknife-like bending of cells at division septa, with cell constriction predominantly on the outside of the bend. Mutations in the fusion known to disrupt MinCc-FtsZ, MinCc-MinD, or MinD-membrane interactions largely suppressed bending division. Imaging of FtsZ-green fluorescent protein (GFP) showed no obvious asymmetric localization of FtsZ during MinCc-MinD overproduction, suggesting that a downstream activity of the Z ring was inhibited asymmetrically. Consistent with this, MinCc-MinD fusions localized predominantly to segments of the Z ring at the inside of developing cell bends, while FtsA (but not ZipA) tended to localize to the outside. As FtsA is required for ring constriction, we propose that this asymmetric localization pattern blocks constriction of the inside of the septal ring while permitting continued constriction of the outside portion. PMID:24682325

Rowlett, Veronica Wells

2014-01-01

196

Flexible Meta-Regression to Assess the Shape of the Benzene–Leukemia Exposure–Response Curve  

PubMed Central

Background Previous evaluations of the shape of the benzene–leukemia exposure–response curve (ERC) were based on a single set or on small sets of human occupational studies. Integrating evidence from all available studies that are of sufficient quality combined with flexible meta-regression models is likely to provide better insight into the functional relation between benzene exposure and risk of leukemia. Objectives We used natural splines in a flexible meta-regression method to assess the shape of the benzene–leukemia ERC. Methods We fitted meta-regression models to 30 aggregated risk estimates extracted from nine human observational studies and performed sensitivity analyses to assess the impact of a priori assessed study characteristics on the predicted ERC. Results The natural spline showed a supralinear shape at cumulative exposures less than 100 ppm-years, although this model fitted the data only marginally better than a linear model (p = 0.06). Stratification based on study design and jackknifing indicated that the cohort studies had a considerable impact on the shape of the ERC at high exposure levels (> 100 ppm-years) but that predicted risks for the low exposure range (< 50 ppm-years) were robust. Conclusions Although limited by the small number of studies and the large heterogeneity between studies, the inclusion of all studies of sufficient quality combined with a flexible meta-regression method provides the most comprehensive evaluation of the benzene–leukemia ERC to date. The natural spline based on all data indicates a significantly increased risk of leukemia [relative risk (RR) = 1.14; 95% confidence interval (CI), 1.04–1.26] at an exposure level as low as 10 ppm-years. PMID:20064779

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

2010-01-01

197

Streamflow prediction in ungauged catchments using copula-based dissimilarity measures  

NASA Astrophysics Data System (ADS)

There are many procedures in the available literature to perform prediction in ungauged basins. Commonly, the Euclidean metric is used as a proxy of the hydrologic dissimilarity. Here we propose a procedure to find a metric on the basis of dissimilarity measures that are estimated from pairwise empirical copula densities of runoff. A metric is then defined in an transformed space of basin descriptors, whose parameterization is obtained with a variance reducing technique. A hydrologic model was run in an ungauged basin with sets of global parameters obtained from the k nearest neighboring donor basins using various metrics to take into account the uncertainty of its parameterization. Hydrologic model parameters were regionalized with a multiscale parameter regionalization technique whose transfer function parameters were found via calibration. The streamflow in an ungauged basin was found as an ensemble streamflow prediction to account for the uncertainties of the transfer function parameters as well as those to define the metric. This technique was applied in 38 German basins ranging in size from 70 to 4000 km2. For each basin, a number of catchment descriptors and several climatic indices were quantified, e.g., mean slope, aspect, shape factor, mean elevation, and mean monthly temperature in January, among others. Daily streamflow time series correspond to the period from 1961 to 2000. Simulated daily discharge was validated with a Jackknife cross-validation technique. Nash-Sutcliffe efficiencies obtained in this way ranged between 0.76 and 0.86. These results suggested that the proposed technique would produce reasonable results in ungauged basins.

Samaniego, Luis; BáRdossy, AndráS.; Kumar, Rohini

2010-02-01

198

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

NASA Astrophysics Data System (ADS)

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.

Dannheim, Jennifer; Rumohr, Heye

2012-09-01

199

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

PubMed

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

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

200

Population genetics of two rare perennials in isolated wetlands: Sagittaria isoetiformis and S. teres (Alismataceae).  

PubMed

We investigated genetic structure in two closely related perennial plants that occur in isolated wetlands: Sagittaria isoetiformis, restricted to the southeastern Coastal Plain of North America, and S. teres, endemic to the northeastern Coastal Plain. Using horizontal starch-gel electrophoresis, we screened 527 individuals from 11 populations of S. isoetiformis and 367 individuals from seven populations of S. teres. A high proportion of the 16 loci were polymorphic (%P(S) = 93.8% in S. isoetiformis and %P(S) = 75.0% in S. teres), with higher mean numbers of alleles per polymorphic locus and effective alleles per locus in S. isoetiformis (AP = 3.27, A(E) = 1.90) than in S. teres (AP = 2.58, A(E) = 1.30). Species- and population-level expected heterozygosities were higher in S. isoetiformis (H(ES) = 0.399, H(EP) = 0.218) than in S. teres (H(ES) = 0.177, H(EP) = 0.101). Jackknife estimates of F statistics indicated moderate levels of inbreeding in S. teres (F(IS) = 23.1%). Strong differentiation characterized these geographically isolated populations (G(ST) = 39.9% in S. isoetiformis, and G(ST) = 26.1% in S. teres). Genetic identities varied substantially within (? = 75%, range = 0.558-0.963 in S. isoetiformis; ? = 89%, range = 0.776-0.963 in S. teres) and among species (? = 81%, range = 0.506-0.882), leading to the discrimination of four regional population clusters using nonmetric multidimensional scaling (NMDS). It appears that S. isoetiformis and S. teres are a progenitor-derivative species pair. PMID:10947999

Edwards, A L; Sharitz, R R

2000-08-01

201

Asymmetric constriction of dividing Escherichia coli cells induced by expression of a fusion between two min proteins.  

PubMed

The Min system, consisting of MinC, MinD, and MinE, plays an important role in localizing the Escherichia coli cell division machinery to midcell by preventing FtsZ ring (Z ring) formation at cell poles. MinC has two domains, MinCn and MinCc, which both bind to FtsZ and act synergistically to inhibit FtsZ polymerization. Binary fission of E. coli usually proceeds symmetrically, with daughter cells at roughly 180° to each other. In contrast, we discovered that overproduction of an artificial MinCc-MinD fusion protein in the absence of other Min proteins induced frequent and dramatic jackknife-like bending of cells at division septa, with cell constriction predominantly on the outside of the bend. Mutations in the fusion known to disrupt MinCc-FtsZ, MinCc-MinD, or MinD-membrane interactions largely suppressed bending division. Imaging of FtsZ-green fluorescent protein (GFP) showed no obvious asymmetric localization of FtsZ during MinCc-MinD overproduction, suggesting that a downstream activity of the Z ring was inhibited asymmetrically. Consistent with this, MinCc-MinD fusions localized predominantly to segments of the Z ring at the inside of developing cell bends, while FtsA (but not ZipA) tended to localize to the outside. As FtsA is required for ring constriction, we propose that this asymmetric localization pattern blocks constriction of the inside of the septal ring while permitting continued constriction of the outside portion. PMID:24682325

Rowlett, Veronica Wells; Margolin, William

2014-06-01

202

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

NASA Astrophysics Data System (ADS)

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

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

2006-05-01

203

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

USGS Publications Warehouse

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.

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

2000-01-01

204

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

PubMed Central

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

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

2013-01-01

205

A comparison of ROC inferred from FROC and conventional ROC  

NASA Astrophysics Data System (ADS)

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.

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

2014-03-01

206

A genetic programming approach for Burkholderia Pseudomallei diagnostic pattern discovery  

PubMed Central

Motivation: Finding diagnostic patterns for fighting diseases like Burkholderia pseudomallei using biomarkers involves two key issues. First, exhausting all subsets of testable biomarkers (antigens in this context) to find a best one is computationally infeasible. Therefore, a proper optimization approach like evolutionary computation should be investigated. Second, a properly selected function of the antigens as the diagnostic pattern which is commonly unknown is a key to the diagnostic accuracy and the diagnostic effectiveness in clinical use. Results: A conversion function is proposed to convert serum tests of antigens on patients to binary values based on which Boolean functions as the diagnostic patterns are developed. A genetic programming approach is designed for optimizing the diagnostic patterns in terms of their accuracy and effectiveness. During optimization, it is aimed to maximize the coverage (the rate of positive response to antigens) in the infected patients and minimize the coverage in the non-infected patients while maintaining the fewest number of testable antigens used in the Boolean functions as possible. The final coverage in the infected patients is 96.55% using 17 of 215 (7.4%) antigens with zero coverage in the non-infected patients. Among these 17 antigens, BPSL2697 is the most frequently selected one for the diagnosis of Burkholderia Pseudomallei. The approach has been evaluated using both the cross-validation and the Jack–knife simulation methods with the prediction accuracy as 93% and 92%, respectively. A novel approach is also proposed in this study to evaluate a model with binary data using ROC analysis. Contact: z.r.yang@ex.ac.uk PMID:19561021

Yang, Zheng Rong; Lertmemongkolchai, Ganjana; Tan, Gladys; Felgner, Philip L.; Titball, Richard

2009-01-01

207

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

PubMed

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

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

2014-04-01

208

Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels.  

PubMed

Asterids comprise 1/4-1/3 of all flowering plants and are classified in 10 orders and >100 families. The phylogeny of asterids is here explored with jackknife parsimony analysis of chloroplast DNA from 132 genera representing 103 families and all higher groups of asterids. Six different markers were used, three of the markers represent protein coding genes, rbcL, ndhF, and matK, and three other represent non-coding DNA; a region including trnL exons and the intron and intergenic spacers between trnT (UGU) to trnF (GAA); another region including trnV exons and intron, trnM and intergenic spacers between trnV (UAC) and atpE, and the rps16 intron. The three non-coding markers proved almost equally useful as the three coding genes in phylogenetic reconstruction at the high level of orders and families in asterids, and in relation to the number of aligned positions the non-coding markers were even more effective. Basal interrelationships among Cornales, Ericales, lamiids (new name replacing euasterids I), and campanulids (new name replacing euasterids II) are resolved with strong support. Family interrelationships are fully or almost fully resolved with medium to strong support in Cornales, Garryales, Gentianales, Solanales, Aquifoliales, Apiales, and Dipsacales. Within the three large orders Ericales, Lamiales, and Asterales, family interrelationships remain partly unclear. The analysis has contributed to reclassification of several families, e.g., Tetrameristaceae, Ebenaceae, Styracaceae, Montiniaceae, Orobanchaceae, and Scrophulariaceae (by inclusion of Pellicieraceae, Lissocarpaceae, Halesiaceae, Kaliphoraceae, Cyclocheilaceae, and Myoporaceae+Buddlejaceae, respectively), and to the placement of families that were unplaced in the APG-system, e.g., Sladeniaceae, Pentaphylacaceae, Plocospermataceae, Cardiopteridaceae, and Adoxaceae (in Ericales, Ericales, Lamiales, Aquifoliales, and Dipsacales, respectively), and Paracryphiaceae among campanulids. Several families of euasterids remain unclassified to order. PMID:12144762

Bremer, Birgitta; Bremer, Kåre; Heidari, Nahid; Erixon, Per; Olmstead, Richard G; Anderberg, Arne A; Källersjö, Mari; Barkhordarian, Edit

2002-08-01

209

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

NASA Astrophysics Data System (ADS)

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

Blascheck, P.; Häge, M.; Joswig, M.

2012-04-01

210

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

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

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

2010-01-01

211

Validation and statistical power comparison of methods for analyzing free-response observer performance studies  

PubMed Central

Rationale and Objectives The aim of this work was to validate and compare the statistical powers of proposed methods for analyzing free-response data using a search-model based simulator. Materials and Methods A free-response data simulator is described that can model a single reader interpreting the same cases in two modalities, or two CAD algorithms, or two human observers, interpreting the same cases in one modality. A variance components model, analogous to the Roe and Metz receiver operating characteristic (ROC) data simulator, is described, that models intra-case and inter-modality correlations in free-response studies. Two generic observers were simulated: a quasi-human observer and a quasi-CAD algorithm. Null hypothesis (NH) validity and statistical powers of ROC, jackknife alternative free-response operating characteristic (JAFROC), a variant of JAFROC termed JAFROC-1, initial detection and candidate analysis (IDCA) and a non-parametric (NP) approach were investigated. Results All methods had valid NH behavior over a wide range of simulator parameters. For equal numbers of normal and abnormal cases, for the human observer, the statistical power ranking of the methods was JAFROC-1 > JAFROC > (IDCA ~ NP) > ROC. For the CAD algorithm the ranking was (NP ~ IDCA) > (JAFROC-1~JAFROC) > ROC. In either case the statistical power of the highest ranked method exceeded that of the lowest ranked method by about a factor of two. Dependence of statistical power on simulator parameters followed expected trends. For data sets with more abnormal cases than normal cases, JAFROC-1 power significantly exceeded JAFROC power. Conclusion Based on this work the recommendation is to use JAFROC-1 for human observers (including human-observers with CAD assist) and the NP method for evaluating CAD algorithms. PMID:19000872

Chakraborty, Dev P.

2009-01-01

212

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)

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

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

2012-10-01

213

Demographic history and rare allele sharing among human populations  

PubMed Central

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

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

2011-01-01

214

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

PubMed

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

Princé, Karine; Zuckerberg, Benjamin

2015-02-01

215

Use of selected chemical markers in combination with a multiple regression model to assess the contribution of domesticated animal sources of fecal pollution in the environment.  

PubMed

Human and animal wastes are major sources of environmental pollution. Reliable methods of identifying waste sources are necessary to specify the types and locations of measures that best prevent and mitigate pollution. This investigation demonstrates the use of chemical markers (fecal sterols and bile acids) to identify selected sources of fecal pollution in the environment. Fecal sterols and bile acids were determined for pig, horse, cow, and chicken feces (10-26 feces samples for each animal). Concentrations of major fecal sterols (coprostanol, epicoprostanol, cholesterol, cholestanol, stigmastanol, and stigmasterol) and bile acids (lithocholic acid, deoxycholic acid, cholic acid, chenodeoxycholic acid, ursodeoxycholic acid, and hyodeoxycholic acid) were determined using a gas chromatography and mass spectrometer (GC-MS) technique. The fecal sterol and bile acid concentration data were used to estimate parameters of a multiple linear regression model for fecal source identification. The regression model was calibrated using 75% of the available data validated against the remaining 25% of the data points in a jackknife process that was repeated 15 times. The regression results were very favorable in the validation data set, with an overall coefficient of determination between predicted and actual fecal source of 0.971. To check the potential of the proposed model, it was applied on a set of simulated runoff data in predicting the specific animal sources. Almost 100% accuracy was obtained between the actual and predicted fecal sources. While additional work using polluted water (as opposed to fresh fecal samples) as well as multiple pollution sources are needed, results of this study clearly indicate the potential of this model to be useful in identifying the individual sources of fecal pollution. PMID:17590407

Tyagi, Punam; Edwards, Dwayne R; Coyne, Mark S

2007-11-01

216

Testate Amoebae as Paleohydrological Proxies in the Florida Everglades  

NASA Astrophysics Data System (ADS)

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).

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

2011-12-01

217

A comparison of Australian and USA radiologists' performance in detection of breast cancer  

NASA Astrophysics Data System (ADS)

The aim of current work was to compare the performance of radiologists that read a higher number of cases to those that read a lower number, as well as examine the effect of number of years of experience on performance. This study compares Australian and USA radiologist with differing levels of experience when reading mammograms. Thirty mammographic cases were presented to 41 radiologists, 21 from Australia and 20 from the USA. Readers were asked to locate and visualize cancer and assign a mark-rating pair with confidence levels from 1 to 5. A jackknife free-response receiver operating characteristic (JAFROC), inferred receiver operating characteristic (ROC), sensitivity, specificity and location sensitivity were calculated. A Mann-Whitney test was used to compare the performance of Australian and USA radiologists using SPSS software. The results showed that the USA radiologists sampled had more years of experience (p?0.01) but read less mammograms per year (p?0.03). Significantly higher sensitivity and location sensitivity (p? 0.001) were found for the Australia radiologists when experience and the number of mammograms read per year were taken into account. There were no differences between the two countries in overall performance measured by JAFROC and inferred ROC. For the most experienced radiologists within the Australian sample experienced ROC and location sensitivity were higher when compared to the least experienced. The increased number of years experience of the USA radiologists did not result in an increase in any performance metrics. The number of cases per year is a better predictor of improved diagnostic performance.

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

2014-03-01

218

Efficacy of digital breast tomosynthesis for breast cancer diagnosis  

NASA Astrophysics Data System (ADS)

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.

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

2014-03-01

219

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

NASA Astrophysics Data System (ADS)

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, ?(rp , ?) 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.

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

220

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

PubMed

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

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

2004-07-01

221

Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties.  

PubMed

More than ten thousand coding variants are contained in each human genome; however, our knowledge of the way genetic variants underlie phenotypic differences is far from complete. Small insertions and deletions (indels) are one of the most common types of human genetic variants, and indels play a significant role in human inherited disease. To date, we still lack a comprehensive understanding of how indels cause diseases. Therefore, identification and analysis of such deleterious variants is a key challenge and has been of great interest in the current research in genome biology. Increasing numbers of computational methods have been developed for discriminating between deleterious indels and neutral indels. However, most of the existing methods are based on traditional sequential or structural features, which cannot completely explain the association between indels and the resulting induced inherited disease. In this study, we establish a novel method to predict deleterious non-frameshifting indels based on features extracted from both protein interaction networks and traditional hybrid properties. Each indel was coded by 1,246 features. Using the maximum relevance minimum redundancy method and the incremental feature selection method, we obtained an optimal feature set containing 42 features, of which 21 features were derived from protein interaction networks. Based on the optimal feature set, an 88 % accuracy and a 0.76 MCC value were achieved by a Random Forest as evaluated by the Jackknife cross-validation test. This method outperformed existing methods of predicting deleterious indels, and can be applied in practice for deleterious non-frameshifting indel predictions in genome research. The analysis of the optimal features selected in the model revealed that network interactions play more important roles and could be informative for better illustrating an indel's function and disease associations than traditional sequential or structural features. These results could shed some light on the genetic basis of human genetic variations and human inherited diseases. PMID:25248637

Zhang, Ning; Huang, Tao; Cai, Yu-Dong

2015-02-01

222

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

223

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

NASA Astrophysics Data System (ADS)

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

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

2014-03-01

224

H-ATLAS: estimating redshifts of Herschel sources from sub-mm fluxes  

NASA Astrophysics Data System (ADS)

Upon its completion, the Herschel Astrophysics Terahertz Large Area Survey (H-ATLAS) will be the largest sub-millimetre survey to date, detecting close to half-a-million sources. It will only be possible to measure spectroscopic redshifts for a small fraction of these sources. However, if the rest-frame spectral energy distribution (SED) of a typical H-ATLAS source is known, this SED and the observed Herschel fluxes can be used to estimate the redshifts of the H-ATLAS sources without spectroscopic redshifts. In this paper, we use a sub-set of 40 H-ATLAS sources with previously measured redshifts in the range 0.5 < z < 4.2 to derive a suitable average template for high-redshift H-ATLAS sources. We find that a template with two dust components (Tc = 23.9 K, Th = 46.9 K and ratio of mass of cold dust to mass of warm dust of 30.1) provides a good fit to the rest-frame fluxes of the sources in our calibration sample. We use a jackknife technique to estimate the accuracy of the redshifts estimated with this template, finding a root mean square of ?z/(1 + z) = 0.26. For sources for which there is prior information that they lie at z > 1, we estimate that the rms of ?z/(1 + z) = 0.12. We have used this template to estimate the redshift distribution for the sources detected in the H-ATLAS equatorial fields, finding a bimodal distribution with a mean redshift of 1.2, 1.9 and 2.5 for 250, 350 and 500 ?m selected sources, respectively.

Pearson, E. A.; Eales, S.; Dunne, L.; Gonzalez-Nuevo, J.; Maddox, S.; Aguirre, J. E.; Baes, M.; Baker, A. J.; Bourne, N.; Bradford, C. M.; Clark, C. J. R.; Cooray, A.; Dariush, A.; De Zotti, G.; Dye, S.; Frayer, D.; Gomez, H. L.; Harris, A. I.; Hopwood, R.; Ibar, E.; Ivison, R. J.; Jarvis, M.; Krips, M.; Lapi, A.; Lupu, R. E.; Micha?owski, M. J.; Rosenman, M.; Scott, D.; Valiante, E.; Valtchanov, I.; van der Werf, P.; Vieira, J. D.

2013-11-01

225

Remote Sensing of Miombo Woodland's Aboveground Biomass and LAI using RADARSAT and Landsat ETM+ Data  

NASA Astrophysics Data System (ADS)

Estimations of biomass are critical in Miombo Woodlands because they represent a primary source of food, fiber, and fuel for 340 million rural peoples and another 15 million urban dwellers in southern Africa. The purpose of this study is to estimate woody aboveground biomass and Leaf Area Index (LAI) in Niassa Reserve, northern Mozambique. The objective of this study is to use optical and microwave satellite data with contemporaneous field data to estimate biomass and LAI. Fifty field plots were surveyed across the Niassa Reserve for biomass and LAI in July and December 2004, respectively. Remote sensing data consisting of RADARSAT backscatter (C- band, ë=5.6 cm) and a June 2004 Landsat ETM+ were acquired. Normalized Difference Vegetation Index (NDVI), Simple Ratio (SR), and a land-cover map (72% total accuracy) were derived from the Landsat scene. Field measurements of biomass and LAI correlated with Radarsat backscatter (Rsqbiomass=0.45, RsqLAI = 0.35, P<0.0001 ), NDVI (Rsqbiomass =0.15, RsqLAI=0.14-, p <0.0001 ) and SR (Rsqbiomass=-0.14, RsqLAI= 0.17, p <0.0001). A jackknife stepwise regression technique was used to develop the best predictive models for biomass (biomass = -5.19 +0.074*radarsat+1.56*SR, Rsq=0.53) and LAI (LAI= -0.66+0.01*radarsat+0.22*SR, Rsq=0.45). The addition of NDVI did not improve the model. Forest biomass and LAI maps were then produced for Niassa Reserve with an estimated peak total biomass of 18 kg/hm2 and a mean LAI of 2.8 m2/m2. In the east both biomass and LAI are lower than the western Niassa Reserve.

Ribeiro, N. S.; Saatchi, S. S.; Shugart, H. H.; Wshington-Allen, R. A.

2007-05-01

226

The Effect of Large-Scale Structure on the SDSS Galaxy Three-Point Correlation Function  

E-print Network

We present measurements of the normalised redshift-space three-point correlation function (Q_z) of galaxies from the Sloan Digital Sky Survey (SDSS) main galaxy sample. We have applied our "npt" algorithm to both a volume-limited (36738 galaxies) and magnitude-limited sample (134741 galaxies) of SDSS galaxies, and find consistent results between the two samples, thus confirming the weak luminosity dependence of Q_z recently seen by other authors. We compare our results to other Q_z measurements in the literature and find it to be consistent within the full jack-knife error estimates. However, we find these errors are significantly increased by the presence of the ``Sloan Great Wall'' (at z ~ 0.08) within these two SDSS datasets, which changes the 3-point correlation function (3PCF) by 70% on large scales (s>=10h^-1 Mpc). If we exclude this supercluster, our observed Q_z is in better agreement with that obtained from the 2dFGRS by other authors, thus demonstrating the sensitivity of these higher-order correlation functions to large-scale structures in the Universe. This analysis highlights that the SDSS datasets used here are not ``fair samples'' of the Universe for the estimation of higher-order clustering statistics and larger volumes are required. We study the shape-dependence of Q_z(s,q,theta) as one expects this measurement to depend on scale if the large scale structure in the Universe has grown via gravitational instability from Gaussian initial conditions. On small scales (s 10h^-1 Mpc, we see considerable shape-dependence in Q_z.

R. C. Nichol; R. K. Sheth; Y. Suto; A. J. Gray; I. Kayo; R. H. Wechsler; F. Marin; G. Kulkarni; M. Blanton; A. J. Connolly; J. P. Gardner; B. Jain; C. J. Miller; A. W. Moore; A. Pope; J. Pun; D. Schneider; J. Schneider; A. Szalay; I. Szapudi; I. Zehavi; N. A. Bahcall; I. Csabai; J. Brinkmann

2006-02-24

227

Prediction of membrane proteins using split amino acid and ensemble classification.  

PubMed

Knowledge of the types of membrane protein provides useful clues in deducing the functions of uncharacterized membrane proteins. An automatic method for efficiently identifying uncharacterized proteins is thus highly desirable. In this work, we have developed a novel method for predicting membrane protein types by exploiting the discrimination capability of the difference in amino acid composition at the N and C terminus through split amino acid composition (SAAC). We also show that the ensemble classification can better exploit this discriminating capability of SAAC. In this study, membrane protein types are classified using three feature extraction and several classification strategies. An ensemble classifier Mem-EnsSAAC is then developed using the best feature extraction strategy. Pseudo amino acid (PseAA) composition, discrete wavelet analysis (DWT), SAAC, and a hybrid model are employed for feature extraction. The nearest neighbor, probabilistic neural network, support vector machine, random forest, and Adaboost are used as individual classifiers. The predicted results of the individual learners are combined using genetic algorithm to form an ensemble classifier, Mem-EnsSAAC yielding an accuracy of 92.4 and 92.2% for the Jackknife and independent dataset test, respectively. Performance measures such as MCC, sensitivity, specificity, F-measure, and Q-statistics show that SAAC-based prediction yields significantly higher performance compared to PseAA- and DWT-based systems, and is also the best reported so far. The proposed Mem-EnsSAAC is able to predict the membrane protein types with high accuracy and consequently, can be very helpful in drug discovery. It can be accessed at http://111.68.99.218/membrane. PMID:21850437

Hayat, Maqsood; Khan, Asifullah; Yeasin, Mohammed

2012-06-01

228

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

PubMed Central

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

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

2014-01-01

229

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

PubMed Central

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

Braun, Edward L.

2014-01-01

230

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

PubMed

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

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

2014-04-01

231

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

NASA Astrophysics Data System (ADS)

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

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

2008-09-01

232

Effect of herbicide combinations on Bt-maize rhizobacterial diversity.  

PubMed

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

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

2014-11-28

233

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

PubMed

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

Jia, Cangzhi; Lin, Xin; Wang, Zhiping

2014-01-01

234

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

PubMed

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

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

1997-03-01

235

Comparative quantitation of cytomegalovirus (CMV) DNA in solid organ transplant recipients with CMV infection by using two high-throughput automated systems.  

PubMed

Cytomegalovirus (CMV) DNA quantitation in clinical specimens is progressively becoming a cornerstone in the diagnosis and management of CMV infection in the immunocompromised host. We evaluated two automated and reproducible PCR tests, the LightCycler (Roche Molecular Biochemicals, Indianapolis, Ind.) and the COBAS AMPLICOR CMV Monitor (Roche Diagnostics, Pleasanton, Calif.), for the detection of CMV DNA in blood samples from transplant recipients with CMV infection as determined by shell vial culture. Following a log transformation analysis, the mean CMV DNA in plasma (PL), whole blood (WB), peripheral blood leukocytes (PBL), and peripheral blood mononuclear cells (PBMC) using the LightCycler was 6.79 copies per ml, 7.23 copies per ml, 6.38 copies per 2 x 10(6) cells, and 6.27 copies per 2 x 10(6) cells, respectively. This compares to 7.86 copies per ml, 8.37 copies per ml, 7.59 copies per 2 x 10(6) cells, and 7.44 copies per 2 x 10(6) cells, respectively, using COBAS AMPLICOR CMV Monitor. While higher CMV DNA levels were observed for the various blood compartments analyzed using COBAS AMPLICOR CMV Monitor, a high degree of correlation was evident between the two automated systems (jackknife correlation r = PL 0.77 [95% confidence interval (CI); 0.64, 0.90], WB 0.77 [95% CI; 0.62, 0.92], PBL 0.77 [95% CI; 0.67, 0.88], and PBMC 0.81 [95% CI; 0.72, 0.89], all P < 0.001). Therefore, we conclude that either automated diagnostic system is accurate for CMV DNA quantitation. PMID:11724864

Razonable, R R; Brown, R A; Espy, M J; Rivero, A; Kremers, W; Wilson, J; Groettum, C; Smith, T F; Paya, C V

2001-12-01

236

Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property.  

PubMed

Given a regulatory pathway system consisting of a set of proteins, can we predict which pathway class it belongs to? Such a problem is closely related to the biological function of the pathway in cells and hence is quite fundamental and essential in systems biology and proteomics. This is also an extremely difficult and challenging problem due to its complexity. To address this problem, a novel approach was developed that can be used to predict query pathways among the following six functional categories: (i) "Metabolism", (ii) "Genetic Information Processing", (iii) "Environmental Information Processing", (iv) "Cellular Processes", (v) "Organismal Systems", and (vi) "Human Diseases". The prediction method was established trough the following procedures: (i) according to the general form of pseudo amino acid composition (PseAAC), each of the pathways concerned is formulated as a 5570-D (dimensional) vector; (ii) each of components in the 5570-D vector was derived by a series of feature extractions from the pathway system according to its graphic property, biochemical and physicochemical property, as well as functional property; (iii) the minimum redundancy maximum relevance (mRMR) method was adopted to operate the prediction. A cross-validation by the jackknife test on a benchmark dataset consisting of 146 regulatory pathways indicated that an overall success rate of 78.8% was achieved by our method in identifying query pathways among the above six classes, indicating the outcome is quite promising and encouraging. To the best of our knowledge, the current study represents the first effort in attempting to identity the type of a pathway system or its biological function. It is anticipated that our report may stimulate a series of follow-up investigations in this new and challenging area. PMID:21980418

Huang, Tao; Chen, Lei; Cai, Yu-Dong; Chou, Kuo-Chen

2011-01-01

237

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

PubMed Central

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

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

2010-01-01

238

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

SciTech Connect

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.

Robert J. Englar

2000-06-19

239

Prediction and analysis of antibody amyloidogenesis from sequences.  

PubMed

Antibody amyloidogenesis is the aggregation of soluble proteins into amyloid fibrils that is one of major causes of the failures of humanized antibodies. The prediction and prevention of antibody amyloidogenesis are helpful for restoring and enhancing therapeutic effects. Due to a large number of possible germlines, the existing method is not practical to predict sequences of novel germlines, which establishes individual models for each known germline. This study proposes a first automatic and across-germline prediction method (named AbAmyloid) capable of predicting antibody amyloidogenesis from sequences. Since the amyloidogenesis is determined by a whole sequence of an antibody rather than germline-dependent properties such as mutated residues, this study assess three types of germline-independent sequence features (amino acid composition, dipeptide composition and physicochemical properties). AbAmyloid using a Random Forests classifier with dipeptide composition performs well on a data set of 12 germlines. The within- and across-germline prediction accuracies are 83.10% and 83.33% using Jackknife tests, respectively, and the novel-germline prediction accuracy using a leave-one-germline-out test is 72.22%. A thorough analysis of sequence features is conducted to identify informative properties for further providing insights to antibody amyloidogenesis. Some identified informative physicochemical properties are amphiphilicity, hydrophobicity, reverse turn, helical structure, isoelectric point, net charge, mutability, coil, turn, linker, nuclear protein, etc. Additionally, the numbers of ubiquitylation sites in amyloidogenic and non-amyloidogenic antibodies are found to be significantly different. It reveals that antibodies less likely to be ubiquitylated tend to be amyloidogenic. The method AbAmyloid capable of automatically predicting antibody amyloidogenesis of novel germlines is implemented as a publicly available web server at http://iclab.life.nctu.edu.tw/abamyloid. PMID:23308169

Liaw, Chyn; Tung, Chun-Wei; Ho, Shinn-Ying

2013-01-01

240

Uncertainty in Pedotransfer Functions from Soil Survey Data  

NASA Astrophysics Data System (ADS)

Pedotransfer functions (PTFs) are empirical relationships between hard-to-get soil parameters, i.e. hydraulic properties, and more easily obtainable basic soil properties, such as texture. Use of PTFs in large-scale projects and pilot studies relies on data of soil survey that provides soil basic data as a categorical information. Unlike numerical variables, categorical data cannot be directly used in statistical regressions or neural networks to develop PTFs. Objectives of this work were (a) to find and test techniques to develop PTFs for soil water retention and saturated hydraulic conductivity with soil categorical data as inputs, (b) to evaluate sources of uncertainty in results of such PTFs and to research opportunities of mitigating the uncertainty. We used a subset of about 12,000 samples from the US National Soil characterization database to estimate water retention, and the data set for circa 1000 hydraulic conductivity measurements done in the US. Regression trees and polynomial neural networks based on dummy coding were the techniques tried for the PTF development. The jackknife validation was used to prevent the over-parameterization. Both techniques were equally efficient in developing PTFs, but regression trees gave much more transparent results. Textural class was the leading predictor with RMSE values of about 6.5 and 4.1 vol.% for water retention at -33 and -1500 kPa, respectively. The RMSE values decreased 10% when the laboratory textural analysis was used to establish the textural class. Textural class in the field was determined correctly only in 41% of all cases. To mitigate this source of error, we added slopes, position on the slope classes, and land surface shape classes to the list of PTF inputs. Regression trees generated topotextural groups that encompassed several textural classes. Using topographic variables and soil horizon appeared to be the way to make up for errors made in field determination of texture. Adding field descriptors of soil structure to the field-determined textural class gave similar results. No large improvement was achieved probably because textural class, topographic descriptors and structure descriptors were correlated predictors in many cases. Both median values and uncertainty of the saturated hydraulic conductivity had a power-law decrease as clay content increased. Defining two classes of bulk density helped to estimate hydraulic conductivity within textural classes. We conclude that categorical field soil survey data can be used in PTF-based estimating soil water retention and saturated hydraulic conductivity with quantified uncertainty

Pachepsky, Y. A.; Rawls, W. J.

2002-05-01

241

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

SciTech Connect

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

Wei Jun; Chan Heangping; Zhou Chuan; Wu Yita; Sahiner, Berkman; Hadjiiski, Lubomir M.; Roubidoux, Marilyn A.; Helvie, Mark A. [Department of Radiology, University of Michigan, 1500 East Medical Center Drive, C478 Med-Inn Building, Ann Arbor, Michigan 48109-5842 (United States)

2011-04-15

242

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

243

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition  

PubMed Central

Meiotic recombination is an important biological process. As a main driving force of evolution, recombination provides natural new combinations of genetic variations. Rather than randomly occurring across a genome, meiotic recombination takes place in some genomic regions (the so-called ‘hotspots’) with higher frequencies, and in the other regions (the so-called ‘coldspots’) with lower frequencies. Therefore, the information of the hotspots and coldspots would provide useful insights for in-depth studying of the mechanism of recombination and the genome evolution process as well. So far, the recombination regions have been mainly determined by experiments, which are both expensive and time-consuming. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the recombination regions. In this study, a predictor, called ‘iRSpot-PseDNC’, was developed for identifying the recombination hotspots and coldspots. In the new predictor, the samples of DNA sequences are formulated by a novel feature vector, the so-called ‘pseudo dinucleotide composition’ (PseDNC), into which six local DNA structural properties, i.e. three angular parameters (twist, tilt and roll) and three translational parameters (shift, slide and rise), are incorporated. It was observed by the rigorous jackknife test that the overall success rate achieved by iRSpot-PseDNC was >82% in identifying recombination spots in Saccharomyces cerevisiae, indicating the new predictor is promising or at least may become a complementary tool to the existing methods in this area. Although the benchmark data set used to train and test the current method was from S. cerevisiae, the basic approaches can also be extended to deal with all the other genomes. Particularly, it has not escaped our notice that the PseDNC approach can be also used to study many other DNA-related problems. As a user-friendly web-server, iRSpot-PseDNC is freely accessible at http://lin.uestc.edu.cn/server/iRSpot-PseDNC. PMID:23303794

Chen, Wei; Feng, Peng-Mian; Lin, Hao; Chou, Kuo-Chen

2013-01-01

244

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

PubMed

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

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

2014-03-15

245

The Geomagnetic Field Over the Last 5 MYR from Lava Flows, and, Properties of the Venusian Lithosphere from Magellan Data.  

NASA Astrophysics Data System (ADS)

The dissertation consists of two unrelated parts. Chapters 2 and 3 investigate long-term properties of the geomagnetic field. Chapters 4-6 are studies of Venus using data from the Magellan mission. Chapter 2 presents a new database comprising palaeomagnetic directions from lava flows over the past 5 Myr. Existing palaeosecular variation models fail to take account of time-averaged field structure and do not adequately describe the properties of the database. In chapter 3 regularized models of the time-averaged field are constructed from Brunhes, normal and reverse polarity subsets of the new database. Non-zonal models are required to fit the data. Normal and reverse stable polarity field structures are significantly different. Normal polarity field models are similar to historical field maps; differences may be real or due to data quality and distribution. Jackknife estimates of the models suggest that data from a few sites contribute significant structure; removing these sites yields conservative estimates of the time-averaged field. Chapter 4 presents an investigation of polygonal fracture patterns observed in radar images of volcanic plains on Venus. The patterns are similar to jointing in lava flows on Earth, but the scale of the venusian networks is much larger than their terrestrial counterparts. The venusian networks may be the result of increased heat flux to the base of the lithosphere, during the formation of flood basalt provinces. Chapter 5 is a study of topographic flexural features on Venus. These are modeled using a thin-elastic plate model. Reliable estimates of mechanical lithospheric thickness are in the range 21-37 km. Dynamical models predict a thick viscous lithosphere. Numerical simulations are used to explore the validity of a 2-D cartesian approximation to an axisymmetric load geometry. Chapter 6 presents a preliminary resolution analysis of Magellan cycle 5 gravity data. Multi-taper spectral coherence estimates show the best resolution available from the Doppler residuals to be 450-500 km. Thus in some regions it should be possible to distinguish between local compensation, flexural or dynamic support of topography.

Johnson, Catherine Louise

1994-01-01

246

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

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

247

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

PubMed

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

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

2003-09-01

248

iNR-PhysChem: a sequence-based predictor for identifying nuclear receptors and their subfamilies via physical-chemical property matrix.  

PubMed

Nuclear receptors (NRs) form a family of ligand-activated transcription factors that regulate a wide variety of biological processes, such as homeostasis, reproduction, development, and metabolism. Human genome contains 48 genes encoding NRs. These receptors have become one of the most important targets for therapeutic drug development. According to their different action mechanisms or functions, NRs have been classified into seven subfamilies. With the avalanche of protein sequences generated in the postgenomic age, we are facing the following challenging problems. Given an uncharacterized protein sequence, how can we identify whether it is a nuclear receptor? If it is, what subfamily it belongs to? To address these problems, we developed a predictor called iNR-PhysChem in which the protein samples were expressed by a novel mode of pseudo amino acid composition (PseAAC) whose components were derived from a physical-chemical matrix via a series of auto-covariance and cross-covariance transformations. It was observed that the overall success rate achieved by iNR-PhysChem was over 98% in identifying NRs or non-NRs, and over 92% in identifying NRs among the following seven subfamilies: NR1--thyroid hormone like, NR2--HNF4-like, NR3--estrogen like, NR4--nerve growth factor IB-like, NR5--fushi tarazu-F1 like, NR6--germ cell nuclear factor like, and NR0--knirps like. These rates were derived by the jackknife tests on a stringent benchmark dataset in which none of protein sequences included has ?60% pairwise sequence identity to any other in a same subset. As a user-friendly web-server, iNR-PhysChem is freely accessible to the public at either http://www.jci-bioinfo.cn/iNR-PhysChem or http://icpr.jci.edu.cn/bioinfo/iNR-PhysChem. Also 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 mathematics involved in developing the predictor. It is anticipated that iNR-PhysChem may become a useful high throughput tool for both basic research and drug design. PMID:22363503

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

2012-01-01

249

NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features.  

PubMed

Nuclear receptors (NRs) are one of the most abundant classes of transcriptional regulators in animals. They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. Therefore, NRs are a very important target for drug development. Nuclear receptors form a superfamily of phylogenetically related proteins and have been subdivided into different subfamilies due to their domain diversity. In this study, a two-level predictor, called NR-2L, was developed that can be used to identify a query protein as a nuclear receptor or not based on its sequence information alone; if it is, the prediction will be automatically continued to further identify it among the following seven subfamilies: (1) thyroid hormone like (NR1), (2) HNF4-like (NR2), (3) estrogen like, (4) nerve growth factor IB-like (NR4), (5) fushi tarazu-F1 like (NR5), (6) germ cell nuclear factor like (NR6), and (7) knirps like (NR0). The identification was made by the Fuzzy K nearest neighbor (FK-NN) classifier based on the pseudo amino acid composition formed by incorporating various physicochemical and statistical features derived from the protein sequences, such as amino acid composition, dipeptide composition, complexity factor, and low-frequency Fourier spectrum components. As a demonstration, it was shown through some benchmark datasets derived from the NucleaRDB and UniProt with low redundancy that the overall success rates achieved by the jackknife test were about 93% and 89% in the first and second level, respectively. The high success rates indicate that the novel two-level predictor can be a useful vehicle for identifying NRs and their subfamilies. As a user-friendly web server, NR-2L is freely accessible at either http://icpr.jci.edu.cn/bioinfo/NR2L or http://www.jci-bioinfo.cn/NR2L. Each job submitted to NR-2L can contain up to 500 query protein sequences and be finished in less than 2 minutes. The less the number of query proteins is, the shorter the time will usually be. All the program codes for NR-2L are available for non-commercial purpose upon request. PMID:21858146

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

2011-01-01

250

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

SciTech Connect

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.

Viero, Marco P.; Martin, Peter G.; Netterfield, Calvin B. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, ON M5S 3H4 (Canada); Ade, Peter A. R.; Griffin, Matthew; Hargrave, Peter C.; Mauskopf, Philip; Moncelsi, Lorenzo; Pascale, Enzo [Department of Physics and Astronomy, Cardiff University, 5 The Parade, Cardiff, CF24 3AA (United Kingdom); Bock, James J. [Jet Propulsion Laboratory, Pasadena, CA 91109-8099 (United States); Chapin, Edward L.; Halpern, Mark; Marsden, Gaelen [Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, BC V6T 1Z1 (Canada); Devlin, Mark J.; Klein, Jeff [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Gundersen, Joshua O. [Department of Physics, University of Miami, 1320 Campo Sano Drive, Coral Gables, FL 33146 (United States); Hughes, David H. [Instituto Nacional de AstrofIsica Optica y Electronica (INAOE), Aptdo. Postal 51 y 72000 Puebla (Mexico); MacTavish, Carrie J. [Astrophysics Group, Imperial College London, Blackett Laboratory, Prince Consort Road, London SW7 2AZ (United Kingdom); Negrello, Mattia [Department of Physics and Astronomy, The Open University, Walton Hall, Milton Keynes, MK7 6AA (United Kingdom); Olmi, Luca, E-mail: viero@astro.utoronto.c [University of Puerto Rico, Rio Piedras Campus, Physics Department, Box 23343, UPR station, San Juan (Puerto Rico)

2009-12-20

251

Developing Pedotransfer Functions for Saline and Saline-Alkali Soils  

NASA Astrophysics Data System (ADS)

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

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

2010-05-01

252

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

253

Frequency-dependent Lg Q within the continental United States  

USGS Publications Warehouse

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

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

2004-01-01

254

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

PubMed

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

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

255

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

NASA Astrophysics Data System (ADS)

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

Guiot, Joel; Corona, Christophe

2010-05-01

256

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

PubMed Central

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

2015-01-01

257

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

PubMed Central

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

2014-01-01

258

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

PubMed Central

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

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

2015-01-01

259

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

PubMed Central

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

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

2014-01-01

260

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

NASA Astrophysics Data System (ADS)

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.

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

2015-02-01

261

Casimir interactions between magnetic flux tubes in a dense lattice  

NASA Astrophysics Data System (ADS)

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

Mazur, Dan; Heyl, Jeremy S.

2015-03-01

262

Evaluation of clinical image processing algorithms used in digital mammography.  

PubMed

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

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

2009-03-01

263

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

NASA Astrophysics Data System (ADS)

We present deep radio observations of four nearby dwarf spheroidal (dSph) galaxies, designed to detect extended synchrotron emission resulting from weakly interacting massive particle (WIMP) dark matter annihilations in their halos. Models by Colafrancesco et al. (CPU07) predict the existence of angularly large, smoothly distributed radio halos in such systems, which stem from electron and positron annihilation products spiraling in a turbulent magnetic field. We map a total of 40.5 deg2 around the Draco, Ursa Major II, Coma Berenices, and Willman 1 dSphs with the Green Bank Telescope (GBT) at 1.4 GHz to detect this annihilation signature, greatly reducing discrete-source confusion using the NVSS catalog. We achieve a sensitivity of ?sub <~ 7 mJy beam-1 in our discrete source-subtracted maps, implying that the NVSS is highly effective at removing background sources from GBT maps. For Draco we obtained approximately concurrent Very Large Array observations to quantify the variability of the discrete source background, and find it to have a negligible effect on our results. We construct radial surface brightness profiles from each of the subtracted maps, and jackknife the data to quantify the significance of the features therein. At the ~10' resolution of our observations, foregrounds contribute a standard deviation of 1.8 mJy beam-1 <= ?ast <= 5.7 mJy beam-1 to our high-latitude maps, with the emission in Draco and Coma dominated by foregrounds. On the other hand, we find no significant emission in the Ursa Major II and Willman 1 fields, and explore the implications of non-detections in these fields for particle dark matter using the fiducial models of CPU07. For a WIMP mass M ? = 100 GeV annihilating into b\\bar{b} final states and B = 1 ?G, upper limits on the annihilation cross-section for Ursa Major II and Willman I are log (lang?vrang?, cm3 s-1) <~ -25 for the preferred set of charged particle propagation parameters adopted by CPU07; this is comparable to that inferred at ?-ray energies from the two-year Fermi Large Area Telescope data. We discuss three avenues for improving the constraints on lang?vrang? presented here, and conclude that deep radio observations of dSphs are highly complementary to indirect WIMP searches at higher energies.

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

2013-08-01

264

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

NASA Astrophysics Data System (ADS)

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

Horálek, Josef; Šílený, Jan

2013-08-01

265

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

NASA Astrophysics Data System (ADS)

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

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

2013-12-01

266

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

SciTech Connect

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

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

2013-08-10

267

Tumor classification using phylogenetic methods on expression data.  

PubMed

Tumor classification is a well-studied problem in the field of bioinformatics. Developments in the field of DNA chip design have now made it possible to measure the expression levels of thousands of genes in sample tissue from healthy cell lines or tumors. A number of studies have examined the problems of tumor classification: class discovery, the problem of defining a number of classes of tumors using the data from a DNA chip, and class prediction, the problem of accurately classifying an unknown tumor, given expression data from the unknown tumor and from a learning set. The current work has applied phylogenetic methods to both problems. To solve the class discovery problem, we impose a metric on a set of tumors as a function of their gene expression levels, and impose a tree structure on this metric, using standard tree fitting methods borrowed from the field of phylogenetics. Phylogenetic methods provide a simple way of imposing a clear hierarchical relationship on the data, with branch lengths in the classification tree representing the degree of separation witnessed. We tested our method for class discovery on two data sets: a data set of 87 tissues, comprised mostly of small, round, blue-cell tumors (SRBCTs), and a data set of 22 breast tumors. We fit the 87 samples of the first set to a classification tree, which neatly separated into four major clusters corresponding exactly to the four groups of tumors, namely neuroblastomas, rhabdomyosarcomas, Burkitt's lymphomas, and the Ewing's family of tumors. The classification tree built using the breast cancer data separated tumors with BRCA1 mutations from those with BRCA2 mutations, with sporadic tumors separated from both groups and from each other. We also demonstrate the flexibility of the class discovery method with regard to standard resampling methodology such as jackknifing and noise perturbation. To solve the class prediction problem, we built a classification tree on the learning set, and then sought the optimal placement of each test sample within the classification tree. We tested this method on the SRBCT data set, and classified each tumor successfully. PMID:15178197

Desper, Richard; Khan, Javed; Schäffer, Alejandro A

2004-06-21

268

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

SciTech Connect

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

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

2009-02-15

269

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

PubMed Central

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

2013-01-01

270

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

SciTech Connect

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

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

2014-02-15

271

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

NASA Astrophysics Data System (ADS)

We report results from the BICEP2 experiment, a cosmic microwave background (CMB) polarimeter specifically designed to search for the signal of inflationary gravitational waves in the B-mode power spectrum around ?˜80. The telescope comprised a 26 cm aperture all-cold refracting optical system equipped with a focal plane of 512 antenna coupled transition edge sensor 150 GHz bolometers each with temperature sensitivity of ?300 ?KCMB?s . BICEP2 observed from the South Pole for three seasons from 2010 to 2012. A low-foreground region of sky with an effective area of 380 square deg was observed to a depth of 87 nK deg in Stokes Q and U. In this paper we describe the observations, data reduction, maps, simulations, and results. We find an excess of B-mode power over the base lensed-?CDM expectation in the range 305?. Through jackknife tests and simulations based on detailed calibration measurements we show that systematic contamination is much smaller than the observed excess. Cross correlating against WMAP 23 GHz maps we find that Galactic synchrotron makes a negligible contribution to the observed signal. We also examine a number of available models of polarized dust emission and find that at their default parameter values they predict power ˜(5-10)× smaller than the observed excess signal (with no significant cross-correlation with our maps). However, these models are not sufficiently constrained by external public data to exclude the possibility of dust emission bright enough to explain the entire excess signal. Cross correlating BICEP2 against 100 GHz maps from the BICEP1 experiment, the excess signal is confirmed with 3? significance and its spectral index is found to be consistent with that of the CMB, disfavoring dust at 1.7?. The observed B-mode power spectrum is well fit by a lensed-?CDM+tensor theoretical model with tensor-to-scalar ratio r =0.20-0.05+0.07, with r=0 disfavored at 7.0?. Accounting for the contribution of foreground, dust will shift this value downward by an amount which will be better constrained with upcoming data sets.

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.; Bicep2 Collaboration

2014-06-01

272

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

PubMed Central

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

Guiot, Joel; Corona, Christophe

2010-01-01

273

Milankovitch rhythms in the Cretaceous: A GCM modelling study  

NASA Astrophysics Data System (ADS)

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 quantities the response due to precessional changes is considerably larger than that due to obliquity changes. The response to obliquity, though generally small, can be important at low latitudes as well as at high latitudes. There is no clear indication of any significant nonlinear response to either orbital parameter. This means that the mean component of the plane fit to the model response to the two orbital parameters can serve the same purpose as the mean of an extended model control simulation. Zonal averages of the model response are typically small relative to zonal averages of the control simulations. This suggests that the net poleward transport of latent heat by the atmosphere in our set of simulations is only weakly sensitive to orbital cycles, and is instead dominated by the meridional sea-surface temperature gradient. A necessary next step will be the use of seasonal-cycle simulations with interactive soil moisture and beyond that the interactive computation of sea-surface temperatures.

Park, Jeffrey; Oglesby, Robert J.

1991-10-01

274

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

NASA Astrophysics Data System (ADS)

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

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

2010-05-01

275

Optimized multiple quantum MAS lineshape simulations in solid state NMR  

NASA Astrophysics Data System (ADS)

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

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

2009-10-01

276

Dynamics of interfaces and detergency  

NASA Astrophysics Data System (ADS)

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

Johnson, Edward George