Note: This page contains sample records for the topic jackknifing from Science.gov.
While these samples are representative of the content of Science.gov,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of Science.gov
to obtain the most current and comprehensive results.
Last update: November 12, 2013.
1

Jackknifing Multitaper Spectrum Estimates  

Microsoft Academic Search

This article discusses some examples of jackknifing multitaper estimates of spectra, coherences, and frequency estimates. Examples include barometric pressure data, where spectrum with an extremely large range plus many narrow-band processes are seen. Analysis of dropped-call rates in cellular phone systems and their coherence with solar radio data illustrates further uses of the jackknife and some of the complexities encountered

David J. Thomson; KARL HEINRICH HOFMANN

2007-01-01

2

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

3

PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING  

Microsoft Academic Search

Because they are designed to produced just one tree, neighbor-joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor-joining programs may give misleading bootstrap frequencies because they do not suppress zero-length branches and\\/or are sensitive to the order of terminals in the data. A new procedure, parsimony jackknifing, overcomes these problems while running hundreds

James S. Farris; Victor A. Albert; Mari Källersjö; Diana Lipscomb; Arnold G. Kluge

1996-01-01

4

Adjusted jackknife for imputation under unequal probability sampling without replacement  

Microsoft Academic Search

Imputation is commonly used to compensate for item non-response in sample surveys. If we treat the imputed values as if they are true values, and then compute the variance estimates by using standard methods, such as the jackknife, we can seriously underestimate the true variances. We propose a modified jackknife variance estimator which is defined for any without-replacement unequal probability

Yves G. Berger; J. N. K. Rao

2006-01-01

5

A jackknife variance estimator for unequal probability sampling  

Microsoft Academic Search

The jackknife method is often used for variance estimation in sample surveys but has only been developed for a limited class of sampling designs. We propose a jackknife variance estimator which is defined for any without-replacement unequal probability sampling design. We demonstrate design consistency of this estimator for a broad class of point estimators. A Monte Carlo study shows how

Yves G. Berger; Chris J. Skinner

2005-01-01

6

On the Generalized Jackknife and its Relation to Statistical Differentials.  

National Technical Information Service (NTIS)

The flexibility of the definition of the first-order generalized jackknife is exploited so that its relation to the method of statistical differentials can be seen. The estimators presented have the same bias reduction and asymptotic distributional proper...

H. L. Gray W. R. Schucany T. A. Watkins

1975-01-01

7

Neural Network Model Selection Using Asymptotic Jackknife Estimator and Cross-Validation Method.  

National Technical Information Service (NTIS)

Two theorems and a lemma are presented about the use of jackknife estimator and the cross-validation method for model selection. Theorem 1 gives the asymptotic form for the jackknife estimator. Combined with the model selection criterion, this asymptotic ...

Y. Liu

1993-01-01

8

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

National Technical Information Service (NTIS)

Properties of two alternative procedures to the Jackknife Point and Confidence Interval Estimation Procedure of Gaver and Chu have been studied. They are called the Log-Normal Likelihood Procedure (LNLJ) and the Moment Procedure (MP). These two procedures...

B. Aba

1981-01-01

9

Evaluating the Asymptotic Limits of the Delete-a-Group Jackknife for Model Analyses.  

National Technical Information Service (NTIS)

The delete-a-group jackknife can be effectively used when estimating the variances of statistics based on a large sample. The theory supporting its use is asymptotic, however. Consequently, analysts have questioned its effectiveness when estimating parame...

P. S. Kott S. T. Garren

2010-01-01

10

Consistency of the jackknife-after-bootstrap variance estimator for the bootstrap quantiles of a Studentized statistic  

Microsoft Academic Search

Efron [J. Roy. Statist. Soc. Ser. B 54 (1992) 83–111] proposed a computationally efficient method, called the jackknife-after-bootstrap, for estimating the variance of a bootstrap estimator for independent data. For dependent data, a version of the jackknife-after-bootstrap method has been recently proposed by Lahiri [Econometric Theory 18 (2002) 79–98]. In this paper it is shown that the jackknife-after-bootstrap estimators of

S. N. Lahiri

2005-01-01

11

The jackknife as an approach for uncertainty assessment in gamma spectrometric measurements of uranium isotope ratios  

NASA Astrophysics Data System (ADS)

The jackknife as an approach for uncertainty estimation in gamma spectrometric uranium isotope ratio measurements was evaluated. Five different materials ranging from depleted uranium (DU) to high enriched uranium (HEU) were measured using gamma spectrometry. High resolution inductively coupled plasma mass spectrometry (ICP-SFMS) was used as a reference method for comparing the results obtained with the gamma spectrometric method. The relative combined uncertainty in the gamma spectrometric measurements of the 238U/235U isotope ratio using the jackknife was about 10-20% (k = 2), which proved to be fit-for-purpose in order to distinguish between different uranium categories. Moreover, the enrichment of 235U in HEU could be measured with an uncertainty of 1-2%.

Ramebäck, H.; Vesterlund, A.; Tovedal, A.; Nygren, U.; Wallberg, L.; Holm, E.; Ekberg, C.; Skarnemark, G.

2010-08-01

12

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

PubMed

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

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

2004-08-01

13

Building a Better Delete-a-Group Jackknife for a Calibration Estimator (Like That Based on Data from the ARMS III).  

National Technical Information Service (NTIS)

This note summarizes much of the theory behind the use of the Delete-a- Group (DAG) jackknife with calibrated survey data like that coming from the third phase of the Agricultural Resources and Management Survey (ARMS III). A DAG jackknife employing 15 se...

P. S. Kott

2008-01-01

14

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

PubMed

The use of nontraditional exercise devices such as the Ab Lounge™ has been promoted as being as effective as the traditional abdominal crunch in strengthening the abdominal musculature. Evidence for this is lacking, however. The purpose of this study was to compare the degree of activation of the upper and lower rectus abdominis using electromyography (EMG) during a traditional crunch with the basic jackknife using the Ab Lounge™. Twenty-two subjects (6 men and 16 women) were randomly selected from the student population at the University of the West Indies (Mona Campus). The mean age of the participants was 20.5 ± 1.5 years, height 166.4 ± 6.2 cm, weight 64 ± 10.3 kg, and waist-hip ratio 0.7 ± 0.1. Surface EMG was used to assess the muscle activity from the upper and lower rectus abdominis while each exercise was performed. The EMG data were full-wave rectified and normalized using a mathematical model that was set up in Microsoft Excel for Windows XP. Statistical analysis was performed on the data using a univariate analysis of variance with gender as a covariate. Significance was determined by p < 0.05. The mean EMG data recorded for the upper rectus abdominis was significantly higher with the traditional crunch when compared with the basic jackknife performed on the Ab Lounge™ (F = 4.39, p = 0.04). The traditional crunch produced a higher level of activity in the lower rectus abdominis when compared with the basic jackknife, but this was not statistically significant (F = 0.249, p = 0.62). There was no significant interaction between gender and the effect of the type of exercise on upper and lower rectus abdominis activation. These results suggest that the traditional abdominal crunch is more effective than the basic jackknife is in activating the rectus abdominis musculature. PMID:21912295

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

2012-06-01

15

A jackknife-like method for classification and uncertainty assessment of multi-category tumor samples using gene expression information  

PubMed Central

Background The use of gene expression profiling for the classification of human cancer tumors has been widely investigated. Previous studies were successful in distinguishing several tumor types in binary problems. As there are over a hundred types of cancers, and potentially even more subtypes, it is essential to develop multi-category methodologies for molecular classification for any meaningful practical application. Results A jackknife-based supervised learning method called paired-samples test algorithm (PST), coupled with a binary classification model based on linear regression, was proposed and applied to two well known and challenging datasets consisting of 14 (GCM dataset) and 9 (NC160 dataset) tumor types. The results showed that the proposed method improved the prediction accuracy of the test samples for the GCM dataset, especially when t-statistic was used in the primary feature selection. For the NCI60 dataset, the application of PST improved prediction accuracy when the numbers of used genes were relatively small (100 or 200). These improvements made the binary classification method more robust to the gene selection mechanism and the size of genes to be used. The overall prediction accuracies were competitive in comparison to the most accurate results obtained by several previous studies on the same datasets and with other methods. Furthermore, the relative confidence R(T) provided a unique insight into the sources of the uncertainty shown in the statistical classification and the potential variants within the same tumor type. Conclusion We proposed a novel bagging method for the classification and uncertainty assessment of multi-category tumor samples using gene expression information. The strengths were demonstrated in the application to two bench datasets.

2010-01-01

16

Demographic analysis, a comparison of the jackknife and bootstrap methods, and predation projection: a case study of Chrysopa pallens (Neuroptera: Chrysopidae).  

PubMed

The life table of the green lacewing, Chrysopa pallens (Rambur), was studied at 22 degrees C, a photoperiod of 15:9 (L:D) h, and 80% relative humidity in the laboratory. The raw data were analyzed using the age-stage, two-sex life table. The intrinsic rate of increase (r), the finite rate of increase (lambda), the net reproduction rate (R0), and the mean generation time (T) of Ch. pallens were 0.1258 d(-1), 1.1340 d(-1), 241.4 offspring and 43.6 d, respectively. For the estimation of the means, variances, and SEs of the population parameters, we compared the jackknife and bootstrap techniques. Although similar values of the means and SEs were obtained with both techniques, significant differences were observed in the frequency distribution and variances of all parameters. The jackknife technique will result in a zero net reproductive rate upon the omission of a male, an immature death, or a nonreproductive female. This result represents, however, a contradiction because an intrinsic rate of increase exists in this situation. Therefore, we suggest that the jackknife technique should not be used for the estimation of population parameters. In predator-prey interactions, the nonpredatory egg and pupal stages of the predator are time refuges for the prey, and the pest population can grow during these times. In this study, a population projection based on the age-stage, two-sex life table is used to determine the optimal interval between releases to fill the predation gaps and maintain the predatory capacity of the control agent. PMID:23448008

Yu, Ling-Yuan; Chen, Zhen-Zhen; Zheng, Fang-Qiang; Shi, Ai-Ju; Guo, Ting-Ting; Yeh, Bao-Hua; Chi, Hsin; Xu, Yong-Yu

2013-02-01

17

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

PubMed

We investigated the effect of temperature and wing morphology on the quantitative genetic variances and covariances of five size-related traits in the sand cricket, Gryllus firmus. Micropterous and macropterous crickets were reared in the laboratory at 24, 28 and 32 degrees C. Quantitative genetic parameters were estimated using a nested full-sib family design, and (co)variance matrices were compared using the T method, Flury hierarchy and Jackknife-manova method. The results revealed that the mean phenotypic value of each trait varied significantly among temperatures and wing morphs, but temperature reaction norms were not similar across all traits. Micropterous individuals were always smaller than macropterous individuals while expressing more phenotypic variation, a finding discussed in terms of canalization and life-history trade-offs. We observed little variation between the matrices of among-family (co)variation corresponding to each combination of temperature and wing morphology, with only one matrix of six differing in structure from the others. The implications of this result are discussed with respect to the prediction of evolutionary trajectories. PMID:15525410

Bégin, M; Roff, D A; Debat, V

2004-11-01

18

An Iterative Jackknife Approach for Assessing Reliability and Power of fMRI Group Analyses  

PubMed Central

For functional magnetic resonance imaging (fMRI) group activation maps, so-called second-level random effect approaches are commonly used, which are intended to be generalizable to the population as a whole. However, reliability of a certain activation focus as a function of group composition or group size cannot directly be deduced from such maps. This question is of particular relevance when examining smaller groups (<20–27 subjects). The approach presented here tries to address this issue by iteratively excluding each subject from a group study and presenting the overlap of the resulting (reduced) second-level maps in a group percent overlap map. This allows to judge where activation is reliable even upon excluding one, two, or three (or more) subjects, thereby also demonstrating the inherent variability that is still present in second-level analyses. Moreover, when progressively decreasing group size, foci of activation will become smaller and/or disappear; hence, the group size at which a given activation disappears can be considered to reflect the power necessary to detect this particular activation. Systematically exploiting this effect allows to rank clusters according to their observable effect size. The approach is tested using different scenarios from a recent fMRI study (children performing a “dual-use” fMRI task, n?=?39), and the implications of this approach are discussed.

Wilke, Marko

2012-01-01

19

Estimating the variances of robust estimators of location: influence curve, jackknife and bootstrap  

Microsoft Academic Search

For an estimator of locations to be useful for inferential purposes, a reliable method of estimating its variance is needed. In this paper, three methods of variance estimation are compared for ten location estimaters across a variety of parent distributions both symmetric and skew. Recommendations are made for different situations based on the bias of the variance estimater as well

David M. Rocke; George W. Downs

1981-01-01

20

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

21

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

Microsoft Academic Search

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

Bradley Efron; Gail Gong

1983-01-01

22

ROCView: prototype software for data collection in jackknife alternative free-response receiver operating characteristic analysis  

PubMed Central

ROCView has been developed as an image display and response capture (IDRC) solution to image display and consistent recording of reader responses in relation to the free-response receiver operating characteristic paradigm. A web-based solution to IDRC for observer response studies allows observations to be completed from any location, assuming that display performance and viewing conditions are consistent with the study being completed. The simplistic functionality of the software allows observations to be completed without supervision. ROCView can display images from multiple modalities, in a randomised order if required. Following registration, observers are prompted to begin their image evaluation. All data are recorded via mouse clicks, one to localise (mark) and one to score confidence (rate) using either an ordinal or continuous rating scale. Up to nine “mark-rating” pairs can be made per image. Unmarked images are given a default score of zero. Upon completion of the study, both true-positive and false-positive reports can be downloaded and adapted for analysis. ROCView has the potential to be a useful tool in the assessment of modality performance difference for a range of imaging methods.

Thompson, J; Hogg, P; Thompson, S; Manning, D; Szczepura, K

2012-01-01

23

A Fortran IV Program for Estimating Parameters through Multiple Matrix Sampling with Standard Errors of Estimate Approximated by the Jackknife.  

ERIC Educational Resources Information Center

Described and listed herein with concomitant sample input and output is the Fortran IV program which estimates parameters and standard errors of estimate per parameters for parameters estimated through multiple matrix sampling. The specific program is an improved and expanded version of an earlier version. (Author/BJG)

Shoemaker, David M.

24

A Fortran IV Program for Estimating Parameters through Multiple Matrix Sampling with Standard Errors of Estimate Approximated by the Jackknife.  

ERIC Educational Resources Information Center

|Described and listed herein with concomitant sample input and output is the Fortran IV program which estimates parameters and standard errors of estimate per parameters for parameters estimated through multiple matrix sampling. The specific program is an improved and expanded version of an earlier version. (Author/BJG)|

Shoemaker, David M.

25

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

Microsoft Academic Search

We investigated the effect of temperature and wing morphology on the quantitative genetic variances and covariances of five size-related traits in the sand cricket, Gryllus firmus. Micropterous and macropterous crickets were reared in the laboratory at 24, 28 and 32 ? C. Quantitative genetic parameters were estimated using a nested full-sib family design, and (co)variance matrices were compared using the

M. Begin; D. A. Roff; V. Debat

2004-01-01

26

An Assessment of the Dunlop Maxaret Anti-Locking Braking System Fitted to an Articulated Vehicle.  

National Technical Information Service (NTIS)

Jack-knifing of articulated vehicles is usually caused by the locking of the tractor rear wheels when brakes are applied. A method of preventing jack-knifing is to use an anti-locking braking system to ensure that these wheels do not lock. This report des...

H. A. Wilkins

1968-01-01

27

16 CFR 1632.1 - Definitions.  

Code of Federal Regulations, 2013 CFR

...not contain a detachable mattress such as chaise lounges, drop-arm love seats, press-back lounges, push-back sofas, sleep lounges, sofa beds (including jackknife sofa beds), sofa lounges (including glide-outs), studio couches and...

2013-01-01

28

Comparison of several non-linear-regression methods for fitting the Michaelis-Menten equation.  

PubMed Central

The known jackknife methods (i.e. standard jackknife, weighted jackknife, linear jackknife and weighted linear jackknife) for the determination of the parameters (as well as of their confidence regions) were tested and compared with the simple Marquardt's technique (comprising the calculation of confidence intervals from the variance-co-variance matrix). The simulated data corresponding to the Michaelis-Menten equation with defined structure and magnitude of error of the dependent variable were used for fitting. There were no essential differences between the results of both point and interval parameter estimations by the tested methods. Marquardt's procedure yielded slightly better results than the jackknives for five scattered data points (the use of this method is advisable for routine analyses). The classical jackknife was slightly superior to the other methods for 20 data points (this method can be recommended for very precise calculations if great numbers of data are available). The weighting does not seem to be necessary in this type of equation because the parameter estimates obtained with all methods with the use of constant weights were comparable with those calculated with the weights corresponding exactly to the real error structure whereas the relative weighting led to rather worse results.

Matyska, L; Kovar, J

1985-01-01

29

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

ERIC Educational Resources Information Center

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

Stapleton, Laura M.

2008-01-01

30

Robust Tests for the Equality of Variances  

Microsoft Academic Search

Alternative formulations of Levene's test statistic for equality of variances are found to be robust under nonnormality. These statistics use more robust estimators of central location in place of the mean. They are compared with the unmodified Levene's statistic, a jackknife procedure, and a ? test suggested by Layard which are all found to be less robust under nonnormality.

Morton B. Brown; Alan B. Forsythe

1974-01-01

31

Resampling methods revisited: advancing the understanding and applications in educational research  

Microsoft Academic Search

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

Haiyan Bai; Wei Pan

2008-01-01

32

Computer-Intensive Randomization in Systematics  

Microsoft Academic Search

There has been a sort of cottage industry in the development of randomization routines in systematics beginning with the bootstrap and the jackknife and, in a sense, culminating with various Monte Carlo routines that have been used to assess the performance of phylogenetic methods in limiting circumstances. These methods can be segregated into three basic areas of interest: measures of

Mark E. Siddall

2001-01-01

33

Western US streamflow and atmospheric circulation patterns during El Niño-Southern Oscillation  

Microsoft Academic Search

Using principal component analysis (PCA), cluster analysis, and jackknife analysis, we investigated the spatial and temporal modes that dominate streamflow variability in the western US in response to El Niño-Southern Oscillation (ENSO) events. Spatial variability was investigated with data only from ENSO years and with rotated PCA on 79 streamflow stations in the western United States. Eight regions, or clusters,

Thomas C. Piechota; John A. Dracup; Robert G. Fovell

1997-01-01

34

ANOVA Tests of Homogeneity of Variance When n's Are Unequal.  

ERIC Educational Resources Information Center

Stability of Type I error rates and power are investigated for three forms of the Box test and two forms of the jackknife test with equal and unequal sample sizes under conditions of normality and nonnormality. The Box test is shown to be robust to violations of the assumption of normality when sampling is from leptokurtic populations. The…

Martin, Charles G.; Games, Paul A.

35

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

36

Examining the relationships among academic self-concept, instrumental motivation, and TIMSS 2007 science scores: a cross-cultural comparison of five East Asian countries\\/regions and the United States  

Microsoft Academic Search

Many American authors expressed their concern that US competitiveness in science, technology, engineering, and mathematics (STEM) is losing ground. Using the Trends in International Mathematics and Science Study (TIMSS) 2007 data, this study investigated how academic self-concept and instrumental motivation influence science test performance among East Asian and American students. Jackknife regression modelling indicated that in East Asia science competency

Chong Ho Yu

2012-01-01

37

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

38

An Empirical Investigation of Sampling Errors in Educational Survey Research.  

ERIC Educational Resources Information Center

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

Ross, Kenneth N.

1979-01-01

39

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

ERIC Educational Resources Information Center

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

Bai, Haiyan; Pan, Wei

2008-01-01

40

The bispectrum of the Lyman ? forest at z ? 2-2.4 from a large sample of UVES QSO absorption spectra (LUQAS)  

Microsoft Academic Search

We present a determination of the bispectrum of the flux in the Lyman ? forest of quasi- stellar object (QSO) absorption spectra obtained from a large sample of Ultraviolet Echelle Spectrograph (UVES) QSO absorption spectra (LUQAS), which consists of spectra observed with the high-resolution UVES. Typical errors on the observed bispectrum as obtained from a jack-knife estimator are ? 50

M. Viel; S. Matarrese; A. Heavens; M. G. Haehnelt; T.-S. Kim; V. Springel; L. Hernquist

41

Some properties of Kendall's partial rank correlation coefficient  

Microsoft Academic Search

We show through a simulation study that the approximate distribution of Kendall's partial rank correlation coefficient [tau]12.3 can be obtained by Jackknifing. We also present some examples which demonstrate that [tau]12.3 can be difficult to interpret.

Paul I. Nelson; Shie-Shien Yang

1988-01-01

42

Bootstrapping an Econometric Model: Some Empirical Results.  

National Technical Information Service (NTIS)

The bootstrap, like the jack-knife, is a technique for estimating standard errors. The idea is to use Monte-Carlo simulation, based on a non-parametric estimate of the underlying error distribution. The bootstrap will be applied to an econometric model de...

D. Freedman S. Peters

1983-01-01

43

VEHICLE DYNAMICS CONTROL WITH ROLLOVER PREVENTION FOR ARTICULATED HEAVY TRUCKS  

Microsoft Academic Search

Rollover and jack-knifing of articulated heavy trucks are serious threats for motorists. Active safety technologies have been demonstrated to have potential to reduce or prevent the occurrence of these types of accidents. The Vehicle Dynamics Control (VDC) system utilizes differential braking to affect vehicle response and has been shown to be quite effective in controlling vehicle yaw response. In this

Daniel D. Eisele; Huei Peng

2000-01-01

44

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).…

Larwin, Karen; Harvey, Milton

2012-01-01

45

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

46

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

47

Inferring Phylogenetic Networks from Gene Order Data  

PubMed Central

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

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

2013-01-01

48

Inferring phylogenetic networks from gene order data.  

PubMed

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

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

2013-08-28

49

Bootstrapping: applications to psychophysiology.  

PubMed

This paper presents the statistical technique known as the bootstrap to the general audience of psychophysiologists. The bootstrap, introduced by Efron (1979), allows data analysts to study the distribution of sample statistics that might otherwise be too complicated to consider. The technique, which requires simple calculations, involves drawing repeated samples (with replacement) from the empirical--or the actual--data distribution and then building a distribution for a statistic by calculating a value of the statistic for each sample. The bootstrap can be used to obtain confidence intervals, standard errors, and even higher moments for the statistic. It is similar to the well-known jackknife of Quenouille and Tukey. After discussing the history and theory of both the bootstrap and the jackknife, we illustrate the use of the bootstrap in the statistical analysis of correlation coefficients and the general linear model. PMID:2727223

Wasserman, S; Bockenholt, U

1989-03-01

50

Analyzing bankruptcy in the restaurant industry: A multiple discriminant model  

Microsoft Academic Search

This study estimated a multiple discriminant model for analyzing US restaurant firm bankruptcy. The model achieved a 92-percent accuracy rate in classifying the in-sample firms into bankrupt and non-bankrupt groups. The jackknife cross-validation accuracy rate was 89 percent. The ex-post classification of out-of-sample restaurants, mainly non-bankrupt firms, was 80 percent correct. The model suggests that restaurant firms with low earnings

Zheng Gu

2002-01-01

51

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 H.

2009-02-24

52

A predictor of transmembrane ?-helix domains of proteins based on neural networks  

Microsoft Academic Search

Back-propagation, feed-forward neural networks are used to predict a-helical transmembrane segments of proteins. The networks are trained on the few membrane proteins whose transmembrane a-helix domains are known to atomic or nearly atomic resolution. When testing is performed with a jackknife procedure on the proteins of the training set, the fraction of total correct assignments is as high as 0.87,

Rita Casadio; Piero Fariselli; Chiara Taroni; Mario Compiani

1996-01-01

53

Ability of the cognitive behavioral driver's inventory to distinguish malingerers from brain-damaged subjects  

Microsoft Academic Search

The Cognitive Behavioral Driver's Inventory (CBDI) was analyzed for its ability to discriminate brain-damaged patients from intact subjects who feigned brain-damage. In a sample of 251 neurologically impaired patients and 48 malingering volunteers, the computer-administered distinguished most malingerers from genuine patients. A jackknifed count revealed that the CBDI had 90% sensitivity for detecting malingerers, and 98% specificity for detecting non-malingering

Odie L. Bracy

1997-01-01

54

Optimisation du rééchantillonnage dans un logiciel d'Amélioration des Plantes  

Microsoft Academic Search

RÉSUMÉ. DIOGENE, un logiciel d'Amélioration des Plantes conçu et développé au sein du Département EFPA de l'INRA, fonctionne sous Solaris et Linux. C'est un logiciel libre (licence GPL), en évolution constante, qui traite de modèles de Biométrie générale, de Génétique Quantitative et de Génétique des Populations. Il fait largement appel aux techniques de rééchantillonnage (jackknife et bootstrap) pour tester des

Service Forêt-Bois; Unité EPHYSE

55

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

Microsoft Academic Search

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

Luc Denys

2006-01-01

56

Filters and templates: stonefly (Plecoptera) richness in Ouachita Mountains streams, U.S.A  

Microsoft Academic Search

SUMMARY 1. We collected adult stoneflies periodically over a 1-year period at 38 sites in two headwater catchments in the Ouachita Mountains, Arkansas, U.S.A. The 43 species collected were a subset of the Ozark-Ouachita fauna and the much larger fauna of the eastern U.S.A. We estimated 78-91% species coverage in the two catchments using jackknife extrapolation of species richness from

ANDREW L. S HELDON

2008-01-01

57

The bispectrum of the Lyman alpha forest at z~ 2-2.4 from a large sample of UVES QSO absorption spectra (LUQAS)  

Microsoft Academic Search

We present a determination of the bispectrum of the flux in the Lyman alpha forest of quasi-stellar object (QSO) absorption spectra obtained from a large sample of Ultraviolet Echelle Spectrograph (UVES) QSO absorption spectra (LUQAS), which consists of spectra observed with the high-resolution UVES. Typical errors on the observed bispectrum as obtained from a jack-knife estimator are ~ 50 per

M. Viel; S. Matarrese; A. Heavens; M. G. Haehnelt; T.-S. Kim; V. Springel; L. Hernquist

2004-01-01

58

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  

Microsoft Academic Search

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

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

2002-01-01

59

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

Microsoft Academic Search

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

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

2000-01-01

60

Statistical Tests for Comparison of Daily Variability in Observed and Simulated Climates.  

NASA Astrophysics Data System (ADS)

Tests for differences in daily variability based on the jackknife are presented. These tests properly account for the effect of autocorrelation in the data and are reasonably robust against departures from normality. Three measures for the daily variability are considered: process, within-month, and innovation variance. The jackknife statistic compares the logarithm of these measures. The standard errors of this logarithm are obtained by recomputing the variance estimates for all subsamples wherein one month is omitted from the complete simple. A simple extension of the jackknife procedure is given to obtain a powerful multivariate test in situations that the differences in variance have the same sign across the region considered or over the year.As an illustration the tests are applied to near-surface temperatures over Europe simulated by the coupled ECHAM/LSG model. It is shown that the control run of the model significantly overestimates the process variance in winter and spring and the within-month variance in all seasons. Significant differences are also found for the innovation variances of the daily temperatures, but the sign of the differences varies over the yew. In a perturbed run with enhanced atmospheric greenhouse gas concentrations the daily temperature variability over Europe significantly decreases in winter and spring compared with the control run.

Adri Buishand, T.; Beersma, Jules J.

1996-10-01

61

Ongoing Estimation of the Epidemic Parameters of a Stochastic, Spatial, Discrete-Time Model for a 1983-84 Avian Influenza Epidemic  

PubMed Central

SUMMARY We formulate a stochastic, spatial, discrete-time model of viral “Susceptible, Exposed, Infectious, Recovered” animal epidemics and apply it to an avian influenza epidemic in Pennsylvania in 1983–84. Using weekly data for the number of newly infectious cases collected during the epidemic, we find estimates for the latent period of the virus and the values of two parameters within the transmission kernel of the model. These data are then jackknifed on a progressive weekly basis to show how our estimates can be applied to an ongoing epidemic to generate continually improving values of certain epidemic parameters.

Rorres, C.; Pelletier, S. T. K.; Bruhn, M. C.; Smith, G.

2013-01-01

62

On population size estimators in the poisson mixture model.  

PubMed

Estimating population sizes via capture-recapture experiments has enormous applications. The Poisson mixture model can be adopted for those applications with a single list in which individuals appear one or more times. We compare several nonparametric estimators, including the Chao estimator, the Zelterman estimator, two jackknife estimators and the bootstrap estimator. The target parameter of the Chao estimator is a lower bound of the population size. Those of the other four estimators are not lower bounds, and they may produce lower confidence limits for the population size with poor coverage probabilities. A simulation study is reported and two examples are investigated. PMID:23865502

Mao, Chang Xuan; Yang, Nan; Zhong, Jinhua

2013-07-19

63

ldne: a program for estimating effective population size from data on linkage disequilibrium.  

PubMed

ldne is a program with a Visual Basic interface that implements a recently developed bias correction for estimates of effective population size (N(e) ) based on linkage disequilibrium data. The program reads genotypic data in standard formats and can accommodate an arbitrary number of samples, individuals, loci, and alleles, as well as two mating systems: random and lifetime monogamy. ldne calculates separate estimates using different criteria for excluding rare alleles, which facilitates evaluation of data for highly polymorphic markers such as microsatellites. The program also introduces a jackknife method for obtaining confidence intervals that appears to perform better than parametric methods currently in use. PMID:21585883

Waples, Robin S; DO, Chi

2008-07-01

64

Prediction of replication origins by calculating DNA structural properties.  

PubMed

In this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the Saccharomyces cerevisiae genome. We found that both DNA bendability and cleavage intensity in core replication regions were significantly lower than in the linker regions. By using these two DNA structural characteristics, we developed a computational model for ORI prediction and evaluated the model in a benchmark dataset. The predictive performance of the jackknife cross-validation indicates that DNA bendability and cleavage intensity have the ability to describe core replication regions and our model is effective in ORI prediction. PMID:22449982

Chen, Wei; Feng, Pengmian; Lin, Hao

2012-02-28

65

The Purley train crash mechanism: injuries and prevention.  

PubMed Central

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

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

1992-01-01

66

Identifying GPCRs and their types with Chou's pseudo amino acid composition: an approach from multi-scale energy representation and position specific scoring matrix.  

PubMed

G-protein coupled receptor (GPCR) is a membrane protein family, which serves as an interface between cell and the outside world. They are involved in various physiological processes and are the targets of more than 50% of the marketed drugs. The function of GPCRs can be known by conducting Biological experiments. However, the rapid increase of GPCR sequences entering into databanks, it is very time consuming and expensive to determine their function based only on experimental techniques. Hence, the computational prediction of GPCRs is very much demanding for both pharmaceutical and educational research. Feature extraction of GPCRs in the proposed research is performed using three techniques i.e. Pseudo amino acid composition, Wavelet based multi-scale energy and Evolutionary information based feature extraction by utilizing the position specific scoring matrices. For classification purpose, a majority voting based ensemble method is used; whose weights are optimized using genetic algorithm. Four classifiers are used in the ensemble i.e. Nearest Neighbor, Probabilistic Neural Network, Support Vector Machine and Grey Incidence Degree. The performance of the proposed method is assessed using Jackknife test for a number of datasets. First, the individual performances of classifiers are assessed for each dataset using Jackknife test. After that, the performance for each dataset is improved by using weighted ensemble classification. The weights of ensemble are optimized using various runs of Genetic Algorithm. We have compared our method with various other methods. The significance in performance of the proposed method depicts it to be useful for GPCRs classification. PMID:22316312

Zia-Ur-Rehman; Khan, Asifullah

2012-08-01

67

SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations  

PubMed Central

SoRT2 is a web server that allows the user to perform genome rearrangement analysis involving reversals, generalized transpositions and translocations (including fusions and fissions), and infer phylogenetic trees of genomes being considered based on their pairwise genome rearrangement distances. It takes as input two or more linear/circular multi-chromosomal gene (or synteny block) orders in FASTA-like format. When the input is two genomes, SoRT2 will quickly calculate their rearrangement distance, as well as a corresponding optimal scenario by highlighting the genes involved in each rearrangement operation. In the case of multiple genomes, SoRT2 will also construct phylogenetic trees of these genomes based on a matrix of their pairwise rearrangement distances using distance-based approaches, such as neighbor-joining (NJ), unweighted pair group method with arithmetic mean (UPGMA) and Fitch–Margoliash (FM) methods. In addition, if the function of computing jackknife support values is selected, SoRT2 will further perform the jackknife analysis to evaluate statistical reliability of the constructed NJ, UPGMA and FM trees. SoRT2 is available online at http://bioalgorithm.life.nctu.edu.tw/SORT2/.

Huang, Yen-Lin; Huang, Chen-Cheng; Tang, Chuan Yi; Lu, Chin Lung

2010-01-01

68

[Nonparametric methods for comparative assessment of species diversity as applied to riverine macrozoobenthic communities].  

PubMed

Models for relationship between sampling effort and estimates of species number and other characteristics of species diversity are considered and evaluated. In the analysis, different randomization algorithms and other statistical methods of monitoring data processing are used including jackknife and bootstrap procedures, algorithms ICE and Chao2, Colwell-Mao interpolation model, Mikhaelis-Menten curves, and others. A comparative analysis of overall species richness in macrozoobenthic communities using streams of the Lower Volga basin as a case study is performed with the aid of different extrapolation models, and the resulting estimates are discussed. The relationships are analyzed between sampling effort (number of hydrobiological samples) and cumulative estimates of species richness and basic indices of species diversity. The means towards improvement of conclusions substantiation when ranking riverine communities by species diversity are considered. PMID:20583636

Shitikov, V K; Zinchenko, T D; Abrosimova, E V

69

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

USGS Publications Warehouse

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

Cohn, T. A.

2005-01-01

70

Magnetic Moments of Odd-A Sb Isotopes to 133Sb: Significant Evidence for Mesonic Exchange Current Contributions and on Core Collective g Factors  

NASA Astrophysics Data System (ADS)

The magnetic moments of ( double magic+1 proton) nuclei having a ``jack-knife'' j = l-s configuration form crucial tests for the theoretical treatment of mesonic exchange currents and core polarization effects in finite nuclei. The reported precision measurement and analysis of the magnetic moment of 133Sb ( 132Sn+oneg7/2 proton) ? = 3.00\\(1\\)?N provides the first such test in medium-heavy nuclei. In addition, new data on the N dependence of the 7/2+ 123-133Sb ground state moments are presented. Analysis in terms of particle-core coupling indicates slightly negative collective g factors of heavy Sn core nuclei.

Stone, N. J.; Doran, D.; Lindroos, M.; Rikovska, J.; Veskovic, M.; White, G.; Williams, D. A.; Fogelberg, B.; Jacobsson, L.; Towner, I. S.; Heyde, K.

1997-02-01

71

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

72

Total removal of a falcotentorial junction meningioma by biparietooccipital craniotomy in the sea lion position: a case report.  

PubMed

The successful total removal of a huge falcotentorial junction meningioma in a 59-year-old woman by biparietooccipital craniotomy with the patient in the sea lion position (prone with a hyperextended neck and with 20 degrees elevation of the upper and lower halves of the body) is reported, with some comments on the advantages of this approach and position. Taking advantage of the exposure of the dural sinus, the confluens sinuum pressure was measured by direct catheterization with the patient in various positions. The pressure was 3.6 cm H2O in the sea lion position, 2.4 cm H2O in the reverse jackknife position (supine with 20 degrees elevation of the upper and lower halves of the body), and -12 cm H2O in the sitting position. PMID:6504289

Suzuki, M; Sobata, E; Hatanaka, M; Suzuki, S; Iwabuchi, T; Makiguchi, K

1984-11-01

73

Prediction of protein structural classes using hybrid properties.  

PubMed

In this paper, amino acid compositions are combined with some protein sequence properties (physiochemical properties) to predict protein structural classes. We are able to predict protein structural classes using a mathematical model that combines the nearest neighbor algorithm (NNA), mRMR (minimum redundancy, maximum relevance), and feature forward searching strategy. Jackknife cross-validation is used to evaluate the prediction accuracy. As a result, the prediction success rate improves to 68.8%, which is better than the 62.2% obtained when using only amino acid compositions. Therefore, we conclude that the physiochemical properties are factors that contribute to the protein folding phenomena and the most contributing features are found to be the amino acid composition. We expect that prediction accuracy will improve further as more sequence information comes to light. A web server for predicting the protein structural classes is available at http://app3.biosino.org:8080/liwenjin/index.jsp. PMID:18953662

Li, Wenjin; Lin, Kao; Feng, Kaiyan; Cai, Yudong

2008-10-25

74

Detecting thermophilic proteins through selecting amino acid and dipeptide composition features.  

PubMed

Detecting thermophilic proteins is an important task for designing stable protein engineering in interested temperatures. In this work, we develop a simple but efficient method to classify thermophilic proteins from mesophilic ones using the amino acid and dipeptide compositions. Since most of the amino acid and dipeptide compositions are redundant, we propose a new forward floating selection technique to select only a useful subset of these compositions as features for support vector machine-based classification. We test the proposed method on a benchmark data set of 915 thermophilic and 793 mesophilic proteins. The results show that our method using 28 amino acid and dipeptide compositions achieves an accuracy rate of 93.3% evaluated by the jackknife cross-validation test, which is higher not only than the existing methods but also than using all amino acid and dipeptide compositions. PMID:21547362

Nakariyakul, Songyot; Liu, Zhi-Ping; Chen, Luonan

2011-05-06

75

Identification of voltage-gated potassium channel subfamilies from sequence information using support vector machine.  

PubMed

Proteins belonging to different subfamilies of Voltage-gated K(+) channels (VKC) are functionally divergent. The traditional method to classify ion channels is more time consuming. Thus, it is highly desirable to develop novel computational methods for VKC subfamily classification. In this study, a support vector machine based method was proposed to predict VKC subfamilies using amino acid and dipeptide compositions. In order to remove redundant information, a novel feature selection technique was employed to single out optimized features. In the jackknife cross-validation, the proposed method (VKCPred) achieved an overall accuracy of 93.09% with 93.22% average sensitivity and 98.34% average specificity, which are superior to that of other two state-of-the-art classifiers. These results indicate that VKCPred can be efficiently used to identify and annotate voltage-gated K(+) channels' subfamilies. The VKCPred software and dataset are freely available at http://cobi.uestc.edu.cn/people/hlin/tools/VKCPred/. PMID:22297432

Chen, Wei; Lin, Hao

2012-01-31

76

Simultaneous quantitative analysis of three compounds using three-dimensional fluorescence spectra based on digital image techniques.  

PubMed

Digital image processing has been applied on various fields such as classification and qualitative analysis. In this work, a very simple quantitative approach was proposed for the first time. Based on the digital grayscale images of three-dimensional fluorescence spectra, several wavelet moment invariants were calculated, and used to establish the linear models for the quantitative analysis. This approach was applied to the quantitative analysis of Tryptophan, Tyrosine and Phenylalanine in mixture samples, and the correlation coefficients R(2) of the obtained linear models were more than 0.99, which were supported by the strict statistical parameters as well as leave-one-out and Jackknife cross-validations. Our study indicates that the selected wavelet moment invariants are immune from the noise and background signals, and the quantitative analysis can be performed accurately based on the overlapping peaks of compounds in mixture. This proposed approach provides a novel pathway for the analysis of three-dimensional spectra. PMID:22477062

Zhai, Hong Lin; Shan, Zhi Jie; Li, Rui Na; Yu, E

2012-04-03

77

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

PubMed

Computational prediction of protein structural class based on sequence data remains a challenging problem in current protein science. In this paper, a new feature extraction approach based on relative polypeptide composition is introduced. This approach could take into account the background distribution of a given k-mer under a Markov model of order k-2, and avoid the curse of dimensionality with the increase of k by using a T-statistic feature selection strategy. The selected features are then fed to a support vector machine to perform the prediction. To verify the performance of our method, jackknife cross-validation tests are performed on four widely used benchmark datasets. Comparison of our results with existing methods shows that our method provides satisfactory performance for structural class prediction. PMID:22316305

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

2012-04-01

78

Identification of Antioxidants from Sequence Information Using Na?ve Bayes  

PubMed Central

Antioxidant proteins are substances that protect cells from the damage caused by free radicals. Accurate identification of new antioxidant proteins is important in understanding their roles in delaying aging. Therefore, it is highly desirable to develop computational methods to identify antioxidant proteins. In this study, a Naïve Bayes-based method was proposed to predict antioxidant proteins using amino acid compositions and dipeptide compositions. In order to remove redundant information, a novel feature selection technique was employed to single out optimized features. In the jackknife test, the proposed method achieved an accuracy of 66.88% for the discrimination between antioxidant and nonantioxidant proteins, which is superior to that of other state-of-the-art classifiers. These results suggest that the proposed method could be an effective and promising high-throughput method for antioxidant protein identification.

Feng, Peng-Mian; Chen, Wei

2013-01-01

79

Comparative Analysis on Determinants of Self-Rated Health Among Non-Hispanic White, Hispanic, and Asian American Older Adults.  

PubMed

The purpose of the study is (1) to compare the effects of factors on self-rated health (SRH) among older non-Hispanic Whites (NHW), Hispanic, and Asian Californians and (2) to provide estimated influence size of each factor on SRH. This study analyzed secondary data drawn from the 2005 California Health Interview Survey. Binary logit regressions were used to analyze data with the Jackknife replication sampling weights. Significant differences were found in SRH among the three groups. Hispanics and Asians reported poorer health than NHW. Socioeconomic status, acculturation, and health access significantly accounted for an association between ethnicity and SRH. However, the magnitudes of their effects on SRH varied across the groups and by the factors examined. This study discusses and concludes with some recommendations on the opportunities presented by the Affordable Care Act and Healthy People 2020. PMID:23744285

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

2013-06-01

80

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

81

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

82

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

PubMed

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

Fattorini, Lorenzo; Franceschi, Sara; Maffei, Daniela

2013-09-11

83

A method for WD40 repeat detection and secondary structure prediction.  

PubMed

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

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

2013-06-11

84

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

85

A support vector machine based pharmacodynamic prediction model for searching active fraction and ingredients of herbal medicine: Naodesheng prescription as an example.  

PubMed

The complex chemical composition of herbal medicine leads to the lack of appropriate method for identifying active compounds and optimizing the formulation of herbal medicine. One of the most commonly used method is bioassay-guided fractionation. However, if the herbal medicine was divided into many fractions, it would cost much money and time in carrying out such a full bioassay. So, can we just perform the bioassay of a few fractions, and then develop a method to predict the bioactivities of other fractions? This study is designed to try to answer the question. In this work, a support vector machine (SVM) pharmacodynamic prediction model was introduced to search active fraction and ingredients of Naodesheng prescription. The prescription was first divided into five extracts, yielding a total of 2?=32 combinations. Anti-platelet aggregation experiment with SD rats was just carried out on 16 combinations. The effects of the remained 32-16=16 combinations were then predicted by the SVM model. The prediction quality was evaluated by both the rigorous jackknife test and the independent dataset validation test. Furthermore, the present method was compared with the frequently used MLR, PCR and PLSR. The present method outperforms the other 3 methods, yielding: RMSECV=2.40, R=0.895 by the jackknife test and RMSEP=7.41, R=0.910 by the independent dataset test. It indicates that the SVM prediction model has good accuracy and generalization ability. The active fraction and ingredients of Naodesheng prescription were then predicted by the model. It is believed that the present model can be extended to help search the active fraction and ingredients of other herbal medicines. PMID:21664786

Chen, Chao; Li, Shu-xian; Wang, Shu-mei; Liang, Sheng-wang

2011-05-17

86

Would species richness estimators change the observed species area relationship?  

NASA Astrophysics Data System (ADS)

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

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

2009-01-01

87

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

PubMed

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

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

2013-09-01

88

Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling  

PubMed Central

The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g., rbcL, matK, rDNA). In this paper we address scalability of Maximum-Likelihood-based phylogeny reconstruction with respect to the number of taxa by example of several large nested single-gene rbcL alignments comprising 400 up to 3,491 taxa. In order to test the effect of taxon sampling, we employ an appropriately adapted taxon jackknifing approach. In contrast to standard jackknifing, this taxon subsampling procedure is not conducted entirely at random, but based on drawing subsamples from empirical taxon-groups which can either be user-defined or determined by using taxonomic information from databases. Our results indicate that, despite an unfavorable number of sequences to number of base pairs ratio, i.e., many relatively short sequences, Maximum Likelihood tree searches and bootstrap analyses scale well on single-gene rbcL alignments with a dense taxon sampling up to several thousand sequences. Moreover, the newly implemented taxon subsampling procedure can be beneficial for inferring higher level relationships and interpreting bootstrap support from comprehensive analysis.

Stamatakis, Alexandros; Goker, Markus; Grimm, Guido W.

2010-01-01

89

Bootstrapping phylogenies inferred from rearrangement data  

PubMed Central

Background Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have been designed over the last few years and have found use in comparative genomics and phylogenetic inference. However, the assessment of phylogenies built from such data has not been properly addressed to date. The standard method used in sequence-based phylogenetic inference is the bootstrap, but it relies on a large number of homologous characters that can be resampled; yet in the case of rearrangements, the entire genome is a single character. Alternatives such as the jackknife suffer from the same problem, while likelihood tests cannot be applied in the absence of well established probabilistic models. Results We present a new approach to the assessment of distance-based phylogenetic inference from whole-genome data; our approach combines features of the jackknife and the bootstrap and remains nonparametric. For each feature of our method, we give an equivalent feature in the sequence-based framework; we also present the results of extensive experimental testing, in both sequence-based and genome-based frameworks. Through the feature-by-feature comparison and the experimental results, we show that our bootstrapping approach is on par with the classic phylogenetic bootstrap used in sequence-based reconstruction, and we establish the clear superiority of the classic bootstrap for sequence data and of our corresponding new approach for rearrangement data over proposed variants. Finally, we test our approach on a small dataset of mammalian genomes, verifying that the support values match current thinking about the respective branches. Conclusions Our method is the first to provide a standard of assessment to match that of the classic phylogenetic bootstrap for aligned sequences. Its support values follow a similar scale and its receiver-operating characteristics are nearly identical, indicating that it provides similar levels of sensitivity and specificity. Thus our assessment method makes it possible to conduct phylogenetic analyses on whole genomes with the same degree of confidence as for analyses on aligned sequences. Extensions to search-based inference methods such as maximum parsimony and maximum likelihood are possible, but remain to be thoroughly tested.

2012-01-01

90

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

PubMed

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

Szijjárto, Gábor P; Tompos, András; Héberger, Károly; Margitfalvi, József L

2012-02-01

91

G-protein-coupled receptor prediction using pseudo-amino-acid composition and multiscale energy representation of different physiochemical properties.  

PubMed

G-protein-coupled receptors (GPCRs) are the largest family of cell surface receptors that, via trimetric guanine nucleotide-binding proteins (G-proteins), initiate some signaling pathways in the eukaryotic cell. Many diseases involve malfunction of GPCRs making their role evident in drug discovery. Thus, the automatic prediction of GPCRs can be very helpful in the pharmaceutical industry. However, prediction of GPCRs, their families, and their subfamilies is a challenging task. In this article, GPCRs are classified into families, subfamilies, and sub-subfamilies using pseudo-amino-acid composition and multiscale energy representation of different physiochemical properties of amino acids. The aim of the current research is to assess different feature extraction strategies and to develop a hybrid feature extraction strategy that can exploit the discrimination capability in both the spatial and transform domains for GPCR classification. Support vector machine, nearest neighbor, and probabilistic neural network are used for classification purposes. The overall performance of each classifier is computed individually for each feature extraction strategy. It is observed that using the jackknife test the proposed GPCR-hybrid method provides the best results reported so far. The GPCR-hybrid web predictor to help researchers working on GPCRs in the field of biochemistry and bioinformatics is available at http://111.68.99.218/GPCR. PMID:21295004

Ur-Rehman, Zia; Khan, Asifullah

2011-02-02

92

Application of universal kriging for estimation of earthquake ground motion: Statistical significance of results  

SciTech Connect

Universal kriging is compared with ordinary kriging for estimation of earthquake ground motion. Ordinary kriging is based on a stationary random function model; universal kriging is based on a nonstationary random function model representing first-order drift. Accuracy of universal kriging is compared with that for ordinary kriging; cross-validation is used as the basis for comparison. Hypothesis testing on these results shows that accuracy obtained using universal kriging is not significantly different from accuracy obtained using ordinary kriging. Test based on normal distribution assumptions are applied to errors measured in the cross-validation procedure; t and F tests reveal no evidence to suggest universal and ordinary kriging are different for estimation of earthquake ground motion. Nonparametric hypothesis tests applied to these errors and jackknife statistics yield the same conclusion: universal and ordinary kriging are not significantly different for this application as determined by a cross-validation procedure. These results are based on application to four independent data sets (four different seismic events).

Carr, J.R.; Roberts, K.P.

1989-02-01

93

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

2010-02-16

94

DNA-DNA hybridization phylogeny of sand dollars and highly reproducible extent of hybridization values.  

PubMed

A DNA hybridization phylogeny of four sand dollars using a sea biscuit as an outgroup is presented. The study is unusual in that the normalized percent hybridization (NPH) values were all less than 50%, yet the same topology was obtained regardless of which distance metric was used, i.e., whether reciprocal distances were averaged or not, or whether or not a molecular clock was assumed. The tree also appears robust under jackknifing and bootstrapping. The extent of hybridization between homologous hybrids was measured with a five- to sevenfold higher precision than is typical, and by implication NPH was also measured with a higher than normal precision. The ability to measure highly reproducible NPH values offers the possibility of examining the phylogeny of more widely divergent species than typically studied using DNA hybridization techniques, using 1/NPH as a distance metric. The hypothesis of a molecular clock within the sand dollars was rejected, adding sand dollars to the growing list of groups where significant rate variation is known. A small fraction of the sand dollar genomes hybridized with the distantly related regular sea urchin Lytechinus. These slowly evolving sequences probably represent conserved exonic components of the genome. PMID:1556742

Marshall, C R; Swift, H

1992-01-01

95

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

PubMed

In conservation and management of species it is important to make inferences about gene flow, dispersal and population structure. In this study, we used 613 georeferenced tissue samples from hazel grouse (Bonasa bonasia) where each individual was genotyped at 12 microsatellite loci to make inference on population genetic structure, gene flow and dispersal in northern Sweden. Observed levels of genetic diversity suggest that Swedish hazel grouse do not suffer loss of genetic diversity compared with other grouse species. We found significant F(IS) (deviation from Hardy-Weinberg expectations) over the entire sample using jack-knifed estimators over loci, which is most likely explained by a Wahlund effect. With the use of spatial autocorrelation methods, we detected significant isolation by distance among individuals. Neighbourhood size was estimated in the order of 62-158 individuals corresponding to a dispersal distance of 950-1500 m. Using a spatial statistical model for landscape genetics to infer the number of populations and the spatial location of genetic discontinuities between these populations we found indications that Swedish hazel grouse are divided into a northern and a southern population. We could not find a sharp border between these two populations and none of the observed borders appeared to coincide with any potential geographical barriers.These results imply that gene flow appears somewhat unrestricted in the boreal taiga forests of northern Sweden and that the two populations of hazel grouse in Sweden may be explained by the post-glacial reinvasion history of the Scandinavian Peninsula. PMID:18827838

Sahlsten, J; Thörngren, H; Höglund, J

2008-10-01

96

Temporal autocorrelations simulated by the ALARO-Climate RCM  

NASA Astrophysics Data System (ADS)

The first outputs of the ALARO-Climate/CZ regional climate model (ALARO RCM) are analyzed. The ALARO RCM is being developed in the Czech Hydrometeorological Institute in Prague from the numerical weather prediction model ALARO, which is operationally run by several meteorological services in Europe. The goal is to run the ALARO RCM in a high resolution of about 5 km. Here we perform a validation of its coarser-resolution version with a gridstep of 25 km, driven by ERA-40 reanalyses for period 1961-2000. The validation is conducted against the E-OBS database. We concentrate on temporal autocorrelations, the correct simulation of which is important for prolonged extreme events, such as heat waves, cold spells, droughts, and floods to be well reproduced. The examined variables are daily extreme temperatures and precipitation. The autocorrelation coefficients with a lag from 1 to 5 days are estimated for each calendar month to eliminate biases associated with annual cycles. The differences of autororrelation in model and observed data are computed using jackknife technique and are shown for individual seasons.

Pokorná, Lucie; Huth, Radan; Farda, Aleš; Metelka, Ladislav

2013-04-01

97

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

PubMed

Prior to the introduction of reflectance spectrophotometry into anthropological field research during the 1950s, human skin color was most commonly classified by visual skin color matching using the von Luschan tiles, a set of 36 standardized, opaque glass tiles arranged in a chromatic scale. Our goal was to establish a conversion formula between the tile-based color matching method and modern reflectance spectrophotometry to make historical and contemporary data comparable. Skin pigmentation measurements were taken on the forehead, inner upper arms, and backs of the hands using both the tiles and a spectrophotometer on 246 participants showing a broad range of skin pigmentation. From these data, a second-order polynomial conversion formula was derived by jackknife analysis to estimate melanin index (M-index) based on tile values. This conversion formula provides a means for comparing modern data to von Luschan tile measurements recorded in historical reports. This is particularly important for populations now extinct, extirpated, or admixed for which tile-based measures of skin pigmentation are the only data available. PMID:23633083

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

2013-04-30

98

Statistical evaluation of bacterial source tracking data obtained by rep-PCR DNA fingerprinting of Escherichia coli.  

PubMed

Pattern recognition has been applied to environmental systems for identification of numerous pollution sources including aerosolized lead and petroleum hydrocarbons. In recent years, DNA fingerprinting has gained widespread application as a means to characterize genetic variations for such purposes as microbial source tracking. This approach, however, is strongly dependent on the statistical and image analyses applied. Several statistical analyses of rep-PCR DNA fingerprints were assessed as a means to differentiate between potential sources of fecal contamination. GelCompar II and methods based on penalized discriminant analysis (PDA) and k-nearest neighbors (KNN) classification procedures were used to differentiate between 10 source groups within a library containing DNA fingerprints of 548 Escherichia coli isolates from known human and nonhuman sources. KNN performed significantly better than PDA in a jackknife analysis, though the library was not large enough to detect significant differences between GelCompar II and the other two methods. GelCompar II and KNN both attained > or = 90% correct classification in a holdout procedure. In addition, interpoint distance analyses indicate coherency within source groups, while library randomization demonstrated that KNN does not create artificial groupings. This investigation stresses the need to understand limitations of statistical analyses used in pattern recognition of DNA fingerprints. PMID:14594360

Albert, John M; Munakata-Marr, Junko; Tenorio, Luis; Siegrist, Robert L

2003-10-15

99

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

NASA Astrophysics Data System (ADS)

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

Häge, Martin; Blascheck, Patrick; Joswig, Manfred

2013-01-01

100

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

101

Geostatistical methods for hydrological extremes assessment in ungauged river basins  

NASA Astrophysics Data System (ADS)

Low flows and peak discharges knowledge is fundamental to characterize the associated droughts and floods and to determine all the processes related to the flow discharges and to the river ecosystems. Low flow characteristics and peak discharges are usually estimated from stream gauging stations. However hydrological data are not always available at the site of interest. Regional frequency analysis is commonly used for the estimation of flow characteristics at sites where little or no data exists. Once that homogeneous regions are determined, specific investigations tools are needed to estimate low and high flows. Spatial interpolation is used to regionalize the desired streamflow index (e.g., low-flow index, flood quantile, peak discharges, etc.), by applying Top-kriging over a geographical space. Top-kriging is chosen because it is intimately connected to the stream network structure and geometric layout. The analysis is carried out on the discharge data of 65 consistent hydrometric stations in Tuscany region, in Central Italy with data from 1949 to 2008. The results are validated using the jack-knife method. Different interpolation techniques geostatistic as well as deterministic (Inverse Distance, Ordinary kriging, Physiographical Spaced Based Interpolation PSBI) and multivariate regression methods are carried out. Different error measurement (mean square error, mean relative error, etc.) are also assessed to compare the results, to quantify the accuracy of the different techniques and to define the most suitable procedure for extremes flow regionalization.

Rossi, G.; Chiarello, V.; Caporali, E.

2012-04-01

102

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

103

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

2013-01-05

104

Predicting Drugs Side Effects Based on Chemical-Chemical Interactions and Protein-Chemical Interactions  

PubMed Central

A drug side effect is an undesirable effect which occurs in addition to the intended therapeutic effect of the drug. The unexpected side effects that many patients suffer from are the major causes of large-scale drug withdrawal. To address the problem, it is highly demanded by pharmaceutical industries to develop computational methods for predicting the side effects of drugs. In this study, a novel computational method was developed to predict the side effects of drug compounds by hybridizing the chemical-chemical and protein-chemical interactions. Compared to most of the previous works, our method can rank the potential side effects for any query drug according to their predicted level of risk. A training dataset and test datasets were constructed from the benchmark dataset that contains 835 drug compounds to evaluate the method. By a jackknife test on the training dataset, the 1st order prediction accuracy was 86.30%, while it was 89.16% on the test dataset. It is expected that the new method may become a useful tool for drug design, and that the findings obtained by hybridizing various interactions in a network system may provide useful insights for conducting in-depth pharmacological research as well, particularly at the level of systems biomedicine.

Chen, Lei; Huang, Tao; Zhang, Jian; Zheng, Ming-Yue; Feng, Kai-Yan; Cai, Yu-Dong; Chou, Kuo-Chen

2013-01-01

105

[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

106

A Swiss Watch Running on Chilean Time: A Progress Report on Two New Automated CORALIE RV Pipelines  

NASA Astrophysics Data System (ADS)

We present the current status of two new fully automated reduction and analysis pipelines, built for the Euler telescope and the CORALIE spectrograph. Both pipelines have been designed and built independently at the Universidad de Chile and Universidad Catolica by the two authors. Each pipeline has also been written on two different platforms, IDL and Python, and both can run fully automatically through full reduction and analysis of CORALIE datasets. The reduction goes through all standard steps from bias subtraction, flat-fielding, scattered light removal, optimal extraction and full wavelength calibration of the data using well exposed ThAr arc lamps. The reduced data are then cross-correlated with a binary template matched to the spectral type of each star and the cross-correlation functions are fit with a Gaussian to extract precision radial-velocities. For error analysis we are currently testing bootstrap, jackknifing and cross validation methods to properly determine uncertainties directly from the data. Our pipelines currently show long term stability at the 12-15m/s level, measured by observations of two known radial-velocity standard stars. In the near future we plan to get the stability down to the 5-6m/s level and also transfer these pipelines to other instruments like HARPS.

Jenkins, J. S.; Jordán, A.

2011-12-01

107

Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach  

PubMed Central

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

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

2011-01-01

108

A revision of chiggers of the minuta species-group (Acari: Trombiculidae: Neotrombicula Hirst, 1925) using multivariate morphometrics.  

PubMed

We revise chiggers belonging to the minuta-species group (genus Neotrombicula Hirst, 1925) from the Palaearctic using size-free multivariate morphometrics. This approach allowed us to resolve several diagnostic problems. We show that the widely distributed Neotrombicula scrupulosa Kudryashova, 1993 forms three spatially and ecologically isolated groups different from each other in size or shape (morphometric property) only: specimens from the Caucasus are distinct from those from Asia in shape, whereas the Asian specimens from plains and mountains are different from each other in size. We developed a multivariate classification model to separate three closely related species: N. scrupulosa, N. lubrica Kudryashova, 1993 and N. minuta Schluger, 1966. This model is based on five shape variables selected from an initial 17 variables by a best subset analysis using a custom size-correction subroutine. The variable selection procedure slightly improved the predictive power of the model, suggesting that it not only removed redundancy but also reduced 'noise' in the dataset. The overall classification accuracy of this model is 96.2, 96.2 and 95.5%, as estimated by internal validation, external validation and jackknife statistics, respectively. Our analyses resulted in one new synonymy: N. dimidiata Stekolnikov, 1995 is considered to be a synonym of N. lubrica. Both N. scrupulosa and N. lubrica are recorded from new localities. A key to species of the minuta-group incorporating results from our multivariate analyses is presented. PMID:20700698

Stekolnikov, Alexandr A; Klimov, Pavel B

2010-08-11

109

Instability-based mechanism for body undulations in centipede locomotion.  

PubMed

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

Aoi, Shinya; Egi, Yoshimasa; Tsuchiya, Kazuo

2013-01-22

110

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

PubMed

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

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

2012-04-01

111

Position-Specific Analysis and Prediction of Protein Pupylation Sites Based on Multiple Features  

PubMed Central

Pupylation is one of the most important posttranslational modifications of proteins; accurate identification of pupylation sites will facilitate the understanding of the molecular mechanism of pupylation. Besides the conventional experimental approaches, computational prediction of pupylation sites is much desirable for their convenience and fast speed. In this study, we developed a novel predictor to predict the pupylation sites. First, the maximum relevance minimum redundancy (mRMR) and incremental feature selection methods were made on five kinds of features to select the optimal feature set. Then the prediction model was built based on the optimal feature set with the assistant of the support vector machine algorithm. As a result, the overall jackknife success rate by the new predictor on a newly constructed benchmark dataset was 0.764, and the Mathews correlation coefficient was 0.522, indicating a good prediction. Feature analysis showed that all features types contributed to the prediction of protein pupylation sites. Further site-specific features analysis revealed that the features of sites surrounding the central lysine contributed more to the determination of pupylation sites than the other sites.

Zhao, Xiaowei; Dai, Jiangyan; Ning, Qiao; Ma, Zhiqiang; Yin, Minghao; Sun, Pingping

2013-01-01

112

Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou's PseAAC via discrete wavelet transform.  

PubMed

In vivo, some proteins exist as monomers and others as oligomers. Oligomers can be further classified into homo-oligomers (formed by identical subunits) and hetero-oligomers (formed by different subunits), and they form the structural components of various biological functions, including cooperative effects, allosteric mechanism and ion-channel gating. Therefore, with the avalanche of protein sequences generated in the post-genomic era, it is very important for both basic research and the pharmaceutical industry to acquire the possible knowledge about quaternary structural attributes of their proteins of interest. In view of this, a high throughput method (DWT_DT), a 2-layer approach by fusing discrete wavelet transform (DWT) and decision-tree algorithm (DT) with physicochemical features, has been developed to predict protein quaternary structures. The 1st layer is to assign a query protein to one of the 10 main quaternary structural attributes. The 2nd layer is to evaluate whether the protein in question is composed of homo- or hetero-oligomers. The overall accuracy by jackknife test for the 1st layer identification was 89.60%. The overall accuracy of the 2nd layer varies from 88.23 to 100%. The results suggest that this newly developed protocol (DWT_DT) is very promising in predicting quaternary structures with complicated composition. PMID:22990717

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

2012-10-30

113

Predicting homo-oligomers and hetero-oligomers by pseudo-amino acid composition: an approach from discrete wavelet transformation.  

PubMed

Many proteins exist in vivo as oligomers with different quaternary structural attributes rather than as individual chains. These proteins are the structural components of various biological functions, including cooperative effects, allosteric mechanisms and ion-channel gating. With the dramatic increase in the number of protein sequences submitted to the public databank, it is important for both basic research and drug discovery research to acquire the knowledge about possible quaternary structural attributes of their interested proteins in a timely manner. A high-throughput method (DWT_SVM), fusing discrete wavelet transform (DWT) and support vector machine (SVM) classifier algorithm with various physicochemical features, has been developed to predict protein quaternary structure. The accuracy in distinguishing candidate proteins as homo-oligomer or hetero-oligomer using the dataset R(2720) was 85.95% and 85.49% respectively by jackknife, showing that DWT_SVM is guide promising in predicting protein quaternary structures. The online service is available at http://bioinfo.ncu.edu.cn/Services.aspx . Protein sequences in FASTA format can be directly fed to the system OligoPred. The processed results will be presented in a diagram that includes the information of feature extraction and the classification error rate. PMID:21466835

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

2011-04-03

114

Regional estimation of extreme rainfall using generalised DDF equations  

NASA Astrophysics Data System (ADS)

Producing a reliable estimate of the design storm for the site of interest is often an essential task for assessing the flood risk of urban and rural areas and for analysing the reliability and safety of hydraulic structures. Design storms, defined herein as rainfall depths expected for given storm duration and return periods, are usually estimated by analysing observed rainfall extremes. When data record lengths are short as compared to the return period of interest, the design storm may be evaluated using regional approaches. This study presents a regional approach for the identification of generalised Depth-Duration-Frequency (DDF) equations, and for the assessment of the reliability and robustness of such equations. This is shown through an application of the proposed approach to a wide region of northern-central Italy. Firstly, the study derives generalised DDF equations for estimating design storms with duration from one to 24 hours and recurrence intervals up to 100 years in any location of the study region. Secondly, the reliability of the proposed DDF equations is assessed by means of a jack-knife resampling procedure. Finally, the performance of the proposed generalised DDF equations is compared with the performance of a regional approach that was recently presented for the study region. The results indicate that the identified DDF equations represent a practical and effective computational tool for estimating the design storm at gauged and ungauged sites. Future analyses will address the applicability of the approach to different geographical areas and climatic conditions.

Castellarin, A.

2003-04-01

115

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

NASA Astrophysics Data System (ADS)

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

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

1999-05-01

116

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

117

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

118

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

PubMed

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

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

2009-12-30

119

Predicting membrane protein types with bragging learner.  

PubMed

The membrane protein type is an important feature in characterizing the overall topological folding type of a protein or its domains therein. Many investigators have put their efforts to the prediction of membrane protein type. Here, we propose a new approach, the bootstrap aggregating method or bragging learner, to address this problem based on the protein amino acid composition. As a demonstration, the benchmark dataset constructed by K.C. Chou and D.W. Elrod was used to test the new method. The overall success rate thus obtained by jackknife cross-validation was over 84%, indicating that the bragging learner as presented in this paper holds a quite high potential in predicting the attributes of proteins, or at least can play a complementary role to many existing algorithms in this area. It is anticipated that the prediction quality can be further enhanced if the pseudo amino acid composition can be effectively incorporated into the current predictor. An online membrane protein type prediction web server developed in our lab is available at http://chemdata.shu.edu.cn/protein/protein.jsp. PMID:18680454

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

2008-01-01

120

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

PubMed

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

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

2012-09-26

121

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

122

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

PubMed

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

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

2013-10-01

123

Improved Statistical Processing for Common Conversion Point Stacked Receiver Functions  

NASA Astrophysics Data System (ADS)

The interpretation of teleseismic receiver functions is typically limited by poor constraints on the uncertainty of amplitudes of converted phases. In continental regions these problems are overcome by stacking large amounts of data. In oceanic regions, however, data quality is notoriously noisy and the number of events are limited by significantly shorter station deployment times. In order to obtain maximum value from a data set, it is necessary to have estimates of uncertainty. Here we combine a common-conversion point stacking technique with multiple-taper correlation RF estimates that allow frequency domain weighting. We then compute jackknife uncertainties to estimate local uncertainties in RF amplitude. We apply this technique to a continental station in Arabia (RAYN) as a benchmark, and also to the ocean island station at Raratonga, Cook Islands (RAR). The structure we recover matches previous crustal studies at both stations, and provides new interpretations of conversions in the upper mantle. At single stations, this technique works well to resolve crust and mantle structure up to a depth of 100 km. Geographical dispersion of raypaths at larger depths decreases the number of events per bin, and therefore increases the uncertainty in converted amplitude. We therefore propose that this method will be well suited to the analysis of data from seismic arrays.

Leahy, G. M.; Collins, J. A.

2008-12-01

124

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

PubMed Central

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

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

2010-01-01

125

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

PubMed Central

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

Goovaerts, P.

2008-01-01

126

Roselliniella revealed as an overlooked genus of Hypocreales, with the description of a second species on parmelioid lichens.  

PubMed

Based on newly obtained 28S rDNA sequences from Roselliniella atlantica and R. euparmeliicola sp. nov., the genus Roselliniella has to be placed in Hypocreales and not in Sordariales; however, the family placement could not be resolved from the sequences obtained. The mature ascospores are single-celled and brown, but young ascospores are hyaline and sometimes have a median septum. The new species occurs on a Parmelia s.str. species in China, and differs in 24 nucleotide substitution positions in the nu-LSU rDNA region and ascospore size from R. atlantica. In this case, small variations in ascospore sizes and shape prove to be phylogenetically and taxonomically informative. The two species occur in the same clade with 95 % jack-knife support. Roselliniella atlantica occurs on Xanthoparmelia and Melanohalea species in Europe, whereas R. euparmeliicola was found on the species of Parmelia s.str. DNA was successfully recovered from a dried specimen of R. atlantica collected in 1992. Two unidentified fungi were also recovered from the Chinese specimen, and these belong to Sordariomycetidae and Dothideomycetes; whether these two are additional fungi living endolichenically in the lichen host, saprobes, or contaminants could not be ascertained. PMID:20664756

Hawksworth, D L; Millanes, A M; Wedin, M

2010-01-21

127

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

PubMed Central

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

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

2000-01-01

128

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

PubMed

We explore how the reconstruction efficiency of fast spike population codes varies with population size, population composition and code complexity. Our study is based on experiments with moving light patterns which are projected onto the isolated retina of a turtle Pseudemys scripta elegans. The stimulus features to reconstruct are sequences of velocities kept constant throughout segments of 500 ms. The reconstruction is based on the spikes of a retinal ganglion cell (RGC) population recorded extracellularly via a multielectrode array. Subsequent spike sorting yields the parallel spike trains of 107 RGCs as input to the reconstruction method, here a discriminant analysis trained and tested in jack-knife fashion. Motivated by behavioral response times, we concentrate on fast reconstruction, i.e., within 150 ms following a trigger event defined via significant changes of the population spike rate. Therefore, valid codes involve only few (?3) spikes per cell. Using only the latency t(1) of each cell (with reference to the trigger event) corresponds to the most parsimonious population code considered. We evaluate the gain in reconstruction efficiency when supplementing t(1) by spike times t(2) and t(3). Furthermore, we investigate whether sub-populations of smaller size benefit significantly from a selection process or whether random compilations are equally efficient. As selection criteria we try different concepts (directionality, reliability, and discriminability). Finally, we discuss the implications of a selection process and its inter-relation with code complexity for optimized reconstruction. PMID:21287355

Cerquera, Alexander; Freund, Jan

2011-02-02

129

Combination of statistical approaches for analysis of 2-DE data gives complementary results.  

PubMed

Five methods for finding significant changes in proteome data have been used to analyze a two-dimensional gel electrophoresis data set. We used both univariate (ANOVA) and multivariate (Partial Least Squares with jackknife, Cross Model Validation, Power-PLS and CovProc) methods. The gels were taken from a time-series experiment exploring the changes in metabolic enzymes in bovine muscle at five time-points after slaughter. The data set consisted of 1377 protein spots, and for each analysis, the data set were preprocessed to fit the requirements of the chosen method. The generated results were one list from each analysis method of proteins found to be significantly changed according to the experimental design. Although the number of selected variables varied between the methods, we found that this was dependent on the specific aim of each method. CovProc and P-PLS focused more on getting the minimum necessary subset of proteins to explain properties of the samples. These methods ended up with less selected proteins. There was also a correlation between level of significance and frequency of selection for the selected proteins. PMID:19367717

Grove, Harald; Jørgensen, Bo M; Jessen, Flemming; Søndergaard, Ib; Jacobsen, Susanne; Hollung, Kristin; Indahl, Ulf; Faergestad, Ellen M

2008-12-01

130

Resampling methods for model fitting and model selection.  

PubMed

Resampling procedures for fitting models and model selection are considered in this article. Nonparametric goodness-of-fit statistics are generally based on the empirical distribution function. The distribution-free property of these statistics does not hold in the multivariate case or when some of the parameters are estimated. Bootstrap methods to estimate the underlying distributions are discussed in such cases. The results hold not only in the case of one-dimensional parameter space, but also for the vector parameters. Bootstrap methods for inference, when the data is from an unknown distribution that may or may not belong to a specified family of distributions, are also considered. Most of the information criteria-based model selection procedures such as the Akaike information criterion, Bayesian information criterion, and minimum description length use estimation of bias. The bias, which is inevitable in model selection problems, arises mainly from estimating the distance between the "true" model and an estimated model. A jackknife type procedure for model selection is discussed, which instead of bias estimation is based on bias reduction. PMID:22023685

Babu, G Jogesh

2011-11-01

131

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

132

Prediction of ketoacyl synthase family using reduced amino acid alphabets.  

PubMed

Ketoacyl synthases are enzymes involved in fatty acid synthesis and can be classified into five families based on primary sequence similarity. Different families have different catalytic mechanisms. Developing cost-effective computational models to identify the family of ketoacyl synthases will be helpful for enzyme engineering and in knowing individual enzymes' catalytic mechanisms. In this work, a support vector machine-based method was developed to predict ketoacyl synthase family using the n-peptide composition of reduced amino acid alphabets. In jackknife cross-validation, the model based on the 2-peptide composition of a reduced amino acid alphabet of size 13 yielded the best overall accuracy of 96.44% with average accuracy of 93.36%, which is superior to other state-of-the-art methods. This result suggests that the information provided by n-peptide compositions of reduced amino acid alphabets provides efficient means for enzyme family classification and that the proposed model can be efficiently used for ketoacyl synthase family annotation. PMID:22042516

Chen, Wei; Feng, Pengmian; Lin, Hao

2011-10-26

133

A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxus.  

PubMed

The WNT: gene family is large, and new members are still being discovered. We constructed a parsimony tree for the WNT: family based on all 82 of the full-length sequences currently available. The inclusion of sequences from the cephalochordate amphioxus is especially useful in comprehensive gene trees, because the amphioxus genes in each subfamily often mark the base of the vertebrate diversification. We thus isolated full-length cDNAs of five amphioxus WNT: genes (AmphiWnt1, AmphiWnt4, AmphiWnt7, AmphiWnt8, and AmphiWnt11) for addition to the overall WNT: family tree. The analysis combined amino acid and nucleotide sequences (excluding third codon positions), taking into account 97% of the available data for each sequence. This combinatorial method had the advantage of generating a single most-parsimonious tree that was trichotomy-free. The reliability of the nodes was assessed by both jackknifing and Bremer support (decay index). A regression analysis revealed that branch length was strongly correlated with branch support, and possible reasons for this pattern are discussed. The tree topology suggested that in amphioxus, at least an AmphiWnt5 and an AmphiWnt10 have yet to be discovered. PMID:11110906

Schubert, M; Holland, L Z; Holland, N D; Jacobs, D K

2000-12-01

134

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

NASA Astrophysics Data System (ADS)

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

Goovaerts, P.

2009-06-01

135

Predicting Chemical Toxicity Effects Based on Chemical-Chemical Interactions  

PubMed Central

Toxicity is a major contributor to high attrition rates of new chemical entities in drug discoveries. In this study, an order-classifier was built to predict a series of toxic effects based on data concerning chemical-chemical interactions under the assumption that interactive compounds are more likely to share similar toxicity profiles. According to their interaction confidence scores, the order from the most likely toxicity to the least was obtained for each compound. Ten test groups, each of them containing one training dataset and one test dataset, were constructed from a benchmark dataset consisting of 17,233 compounds. By a Jackknife test on each of these test groups, the 1st order prediction accuracies of the training dataset and the test dataset were all approximately 79.50%, substantially higher than the rate of 25.43% achieved by random guesses. Encouraged by the promising results, we expect that our method will become a useful tool in screening out drugs with high toxicity.

Zhang, Jian; Feng, Kai-Rui; Zheng, Ming-Yue; Cai, Yu-Dong

2013-01-01

136

Computing camera heading: A study  

NASA Astrophysics Data System (ADS)

An accurate estimate of the motion of a camera is a crucial first step for the 3D reconstruction of sites, objects, and buildings from video. Solutions to the camera heading problem can be readily applied to many areas, such as robotic navigation, surgical operation, video special effects, multimedia, and lately even in internet commerce. From image sequences of a real world scene, the problem is to calculate the directions of the camera translations. The presence of rotations makes this problem very hard. This is because rotations and translations can have similar effects on the images, and are thus hard to tell apart. However, the visual angles between the projection rays of point pairs are unaffected by rotations, and their changes over time contain sufficient information to determine the direction of camera translation. We developed a new formulation of the visual angle disparity approach, first introduced by Tomasi, to the camera heading problem. Our new derivation makes theoretical analysis possible. Most notably, a theorem is obtained that locates all possible singularities of the residual function for the underlying optimization problem. This allows identifying all computation trouble spots beforehand, and to design reliable and accurate computational optimization methods. A bootstrap-jackknife resampling method simultaneously reduces complexity and tolerates outliers well. Experiments with image sequences show accurate results when compared with the true camera motion as measured with mechanical devices.

Zhang, John Jiaxiang

2000-08-01

137

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

PubMed Central

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

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

2011-01-01

138

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

PubMed

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

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

2009-10-01

139

THE LARGE-SCALE THREE-POINT CORRELATION FUNCTION OF SLOAN DIGITAL SKY SURVEY LUMINOUS RED GALAXIES  

SciTech Connect

We present new measurements of the redshift-space three-point correlation function (3PCF) of Luminous Red Galaxies (LRGs) from the Sloan Digital Sky Survey (SDSS). Using the largest data set to date, the Data Release 7 LRGs, and an improved binning scheme compared to previous measurements, we measure the LRG 3PCF on large scales up to {approx}90 h{sup -1} Mpc, from the mildly nonlinear to quasi-linear regimes. Comparing the LRG correlations to the dark matter two- and three-point correlation functions, obtained from N-body simulations we infer linear and nonlinear bias parameters. As expected, LRGs are highly biased tracers of large-scale structure, with a linear bias b{sub 1} {approx} 2; the LRGs also have a large positive nonlinear bias parameter, in agreement with predictions of galaxy population models. The use of the 3PCF to estimate biasing helps to also make estimates of the cosmological parameter {sigma}{sub 8}, as well as to infer best-fit parameters of the halo occupation distribution parameters for LRGs. We also use a large suite of public mock catalogs to characterize the error covariance matrix for the 3PCF and compare the variance among simulation results with jackknife error estimates.

Marin, Felipe, E-mail: fmarin@astro.swin.edu.au [Department of Astronomy and Astrophysics and Kavli Institute for Cosmological Physics, University of Chicago, Chicago, IL 60637 (United States); Centre for Astrophysics and Supercomputing, Swinburne University of Technology, P.O. Box 218, Hawthorn, VIC 3122 (Australia)

2011-08-20

140

Gray matter atrophy in progressive supranuclear palsy: meta-analysis of voxel-based morphometry studies.  

PubMed

Voxel-based morphometry (VBM) studies have provided cumulative evidence of gray matter (GM) atrophy in patients with progressive supranuclear palsy (PSP) relative to healthy controls (HC). However, not all findings have been entirely concordant. Herein, we performed a quantitative meta-analysis study in order to consistently quantify GM anomalies in PSP. We conducted a systematic search for VBM studies of PSP patients and HC using PubMed and Embase databases from January 2000 to May 2012. Meta-analysis of these VBM studies was performed using a newly improved voxel-based meta-analytic technique, effect-size signed differential mapping. A total of 9 cross-sectional VBM studies that involved 143 PSP patients and 216 HC subjects met the inclusion criteria. Considerable regional GM volume decrease was detected in the thalamus, basal ganglia, midbrain, insular cortex, and frontal cortex. These findings remained largely unchanged following jackknife sensitivity analyses. The present meta-analysis provided evidence of PSP-specific GM atrophy. This finding might help contribute to our understanding of the neurobiological basis underlying PSP. PMID:23543378

Shi, Hai Cun; Zhong, Jian Guo; Pan, Ping Lei; Xiao, Pei Rong; Shen, Yuan; Wu, Li Juan; Li, Hua Liang; Song, Yuan Ying; He, Gui Xiang; Li, Hong Ye

2013-03-30

141

Limited sampling strategy models for estimating the AUC of gliclazide in Chinese healthy volunteers.  

PubMed

The aim of this work is to reduce the cost of required sampling for the estimation of the area under the gliclazide plasma concentration versus time curve within 60 h (AUC0-60t ). The limited sampling strategy (LSS) models were established and validated by the multiple regression model within 4 or fewer gliclazide concentration values. Absolute prediction error (APE), root of mean square error (RMSE) and visual prediction check were used as criterion. The results of Jack-Knife validation showed that 10 (25.0 %) of the 40 LSS based on the regression analysis were not within an APE of 15 % using one concentration-time point. 90.2, 91.5 and 92.4 % of the 40 LSS models were capable of prediction using 2, 3 and 4 points, respectively. Limited sampling strategies were developed and validated for estimating AUC0-60t of gliclazide. This study indicates that the implementation of an 80 mg dosage regimen enabled accurate predictions of AUC0-60t by the LSS model. This study shows that 12, 6, 4, 2 h after administration are the key sampling times. The combination of (12, 2 h), (12, 8, 2 h) or (12, 8, 4, 2 h) can be chosen as sampling hours for predicting AUC0-60t in practical application according to requirement. PMID:22638844

Huang, Ji-Han; Wang, Kun; Huang, Xiao-Hui; He, Ying-Chun; Li, Lu-Jin; Sheng, Yu-Cheng; Yang, Juan; Zheng, Qing-Shan

2012-05-26

142

Extended analysis of the effect of learning with feedback on the detectability of pulmonary nodules in chest tomosynthesis  

NASA Astrophysics Data System (ADS)

In chest tomosynthesis, low-dose projections collected over a limited angular range are used for reconstruction of section images of the chest, resulting in a reduction of disturbing anatomy at a moderate increase in radiation dose compared to chest radiography. In a previous study, we investigated the effects of learning with feedback on the detection of pulmonary nodules in chest tomosynthesis. Six observers with varying degrees of experience of chest tomosynthesis analyzed tomosynthesis cases for presence of pulmonary nodules. The cases were analyzed before and after learning with feedback. Multidetector computed tomography (MDCT) was used as reference. The differences in performance between the two readings were calculated using the jackknife alternative free-response receiver operating characteristics (JAFROC-2) as primary measure of detectability. Significant differences between the readings were found only for observers inexperienced in chest tomosynthesis. The purpose of the present study was to extend the statistical analysis of the results of the previous study, including JAFROC-1 analysis and FROC curves in the analysis. The results are consistent with the results of the previous study and, furthermore, JAFROC-1 gave lower p-values than JAFROC-2 for the observers who improved their performance after learning with feedback.

Asplund, Sara; Johnsson, Åse A.; Vikgren, Jenny; Svalkvist, Angelica; Boijsen, Marianne; Fisichella, Valeria; Flinck, Agneta; Wiksell, Åsa; Ivarsson, Jonas; Rystedt, Hans; Månsson, Lars Gunnar; Kheddache, Susanne; Båth, Magnus

2011-03-01

143

Nonparametric methods for drought severity estimation at ungauged sites  

NASA Astrophysics Data System (ADS)

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

Sadri, S.; Burn, D. H.

2012-12-01

144

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.

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

2012-01-01

145

Estimation of Distribution Overlap of Urn Models  

PubMed Central

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

Hampton, Jerrad; Lladser, Manuel E.

2012-01-01

146

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

147

AcalPred: A Sequence-Based Tool for Discriminating between Acidic and Alkaline Enzymes  

PubMed Central

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

Lin, Hao; Chen, Wei; Ding, Hui

2013-01-01

148

The early history of modern birds inferred from DNA sequences of nuclear and mitochondrial ribosomal genes.  

PubMed

The traditional view of avian evolution places ratites and tinamous at the base of the phylogenetic tree of modern birds (Neornithes). In contrast, most recent molecular studies suggest that neognathous perching birds (Passeriformes) compose the oldest lineage of modern birds. Here, we report significant molecular support for the traditional view of neognath monophyly based on sequence analyses of nuclear and mitochondrial DNA (4.4 kb) from every modern avian order. Phylogenetic analyses further show that the ducks and gallinaceous birds are each other's closest relatives and together form the basal lineage of neognathous birds. To investigate why other molecular studies sampling fewer orders have reached different conclusions regarding neognath monophyly, we performed jackknife analyses on our mitochondrial data. Those analyses indicated taxon-sampling effects when basal galloanserine birds were included in combination with sparse taxon sampling. Our phylogenetic results suggest that the earliest neornithines were heavy-bodied, ground-dwelling, nonmarine birds. This inference, coupled with a fossil bias toward marine environments, provides a possible explanation for the large gap in the early fossil record of birds. PMID:10723745

van Tuinen, M; Sibley, C G; Hedges, S B

2000-03-01

149

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

150

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

PubMed

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

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

2012-09-29

151

AcalPred: A Sequence-Based Tool for Discriminating between Acidic and Alkaline Enzymes.  

PubMed

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

Lin, Hao; Chen, Wei; Ding, Hui

2013-10-09

152

[Suitable distribution area of Eriosoma lanigerum (Hausmann) in China and related affecting factors].  

PubMed

Eriosoma lanigerum (Hausmann) is an important quarantine insect of apple tree, and usually causes serious economic losses in apple production area every year. To predict the suitable distribution area of E. lanigerum and the environmental factors affecting the insect' s colonization and dispersal could provide references for the forecast of the insect's distribution area, the constitution of effective quarantine measures, and the control decisions. In this study, niche model MaxEnt and ArcGIS were applied to analyze and predict the suitable distribution area of E. lanigerum, ROC was used to evaluate the prediction model and the prediction results, and Jackknife analysis was made to analyze the most important environmental factors affecting the occurrence of E. lanigerum. The results showed that E. lanigerum had a wide distribution area in China, its suitable distribution index was the highest in Liaoning, Shandong, Henan, Hebei, Anhui, Jiangsu, and Shaanxi provinces, and the most important environmental factors affecting the occurrence of E. lanigerum were temperature-dependent factors. PMID:22803484

Hong, Bo; Wang, Ying-Lun; Zhao, Hui-Yan

2012-04-01

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.

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

2003-01-01

154

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

PubMed

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

Kovacs, Amir; Yacoby, Keren; Gophna, Uri

2010-02-04

155

Improved methods for daily streamflow estimates at ungauged sites  

NASA Astrophysics Data System (ADS)

In this paper, improved flow duration curve (FDC) and area ratio (AR) based methods are developed to obtain better daily streamflow estimation at ungauged sites. A regression based logarithmic interpolation method which makes no assumption on the distribution or shape of a FDC is introduced in this paper to estimate regional FDCs. The estimated FDC is combined with a spatial interpolation algorithm to obtain daily streamflow estimates. Multiple source sites based AR methods, especially the geographical distance weighted AR (GWAR) method, are introduced in an effort to maximize the use of regional information and improve the standard AR method (SAR). Performances of the proposed approaches are evaluated using a jackknife procedure. The application to 109 stations in the province of Quebec, Canada indicates that the FDC based methods outperform AR based methods in all the summary statistics including Nash, root mean squared error (RMSE), and Bias. The number of sites that show better performances using the FDC based approaches is also significantly larger than the number of sites showing better performances using AR based methods. Using geographical distance weighted multiple sources sites based approaches can improve the performance at the majority of the catchments comparing with using the single source site based approaches.

Shu, Chang; Ouarda, Taha B. M. J.

2012-02-01

156

Tomographic imaging of local earthquake delay times for three-dimensional velocity variation in western Washington  

SciTech Connect

Tomographic inversion is applied to delay times from local earthquakes to image three dimensional velocity variations in the Puget Sound region of western Washington. The 37,500 square km region is represented by nearly cubic blocks of 5 km per side. P-wave arrival time observations from 4,387 crustal earthquakes, with depths of 0 to 40 km, were used as sources producing 36,865 rays covering the target region. A conjugate gradient method (LSQR) is used to invert the large, sparse system of equations. To diminish the effects of noisy data, the Laplacian is constrained to be zero within horizontal layers, providing smoothing of the model. The resolution is estimated by calculating impulse responses at blocks of interest and estimates of standard errors are calculated by the jackknife statistical procedure. Results of the inversion are correlated with some known geologic features and independent geophysical measurements. High P-wave velocities along the eastern flank of the Olympic Peninsula are interpreted to reflect the subsurface extension of Crescent terrane. Low velocities beneath the Puget Sound further to the east are inferred to reflect thick sediment accumulations. The Crescent terrane appears to extend beneath Puget Sound, consistent with its interpretation as a major accretionary unit. In the southern Puget Sound basin, high velocity anomalies at depths of 10-20 km are interpreted as Crescent terrane and are correlated with a region of low seismicity. Near Mt. Ranier, high velocity anomalies may reflect buried plutons.

Lees, J.M.; Crosson, R.S. (Univ. of Washington, Seattle (United States))

1990-04-10

157

A limited sampling strategy for tacrolimus in renal transplant patients  

PubMed Central

AIMS To develop and validate limited sampling strategy (LSS) equations to estimate area under the curve (AUC0–12) in renal transplant patients. METHODS Twenty-nine renal transplant patients (3–6 months post transplant) who were at steady state with respect to tacrolimus kinetics were included in this study. The blood samples starting with the predose (trough) and collected at fixed time points for 12 h were analysed by microparticle enzyme immunoassay. Linear regression analysis estimated the correlations of tacrolimus concentrations at different sampling time points with the total measured AUC0–12. By applying multiple stepwise linear regression analysis, LSS equations with acceptable correlation coefficients (R2), bias and precision were identified. The predictive performance of these models was validated by the jackknife technique. RESULTS Three models were identified, all with R2 ? 0.907. Two point models included one with trough (C0) and 1.5 h postdose (C1.5), another with trough and 4 h postdose. Increasing the number of sampling time points to more than two increased R2 marginally (0.951 to 0.990). After jackknife validation, the two sampling time point (trough and 1.5 h postdose) model accurately predicted AUC0–12. Regression coefficient R2 = 0.951, intraclass correlation = 0.976, bias [95% confidence interval (CI)] 0.53% (?2.63, 3.69) and precision (95% CI) 6.35% (4.36, 8.35). CONCLUSION The two-point LSS equation [AUC0–12 = 19.16 + (6.75.C0) + (3.33.C1.5)] can be used as a predictable and accurate measure of AUC0–12 in stable renal transplant patients prescribed prednisolone and mycophenolate. WHAT IS ALREADY KNOWN ABOUT THE SUBJECTTacrolimus trough concentration is being currently used for dose individualization.Limited sampling strategies (LSS) have been developed and validated for renal transplant patients.Earlier literature has suggested that measurement of tacrolimus AUC is more reliable than trough with respect to both rejection and nephrotoxicity. WHAT THIS STUDY ADDS Four thousand renal transplants take place annually in India, with many patients prescribed tacrolimus in combination with mycophenolate and steroid.In this study a LSS with two points, i.e. trough and 1.5 h postdose was developed and validated to estimate AUC0–12.The added benefit of only a single additional sample with completion of blood collection in 1.5 h and minimum additional cost makes this a viable LSS algorithm in renal transplant patients.In patients having tacrolimus trough concentrations outside the recommended range (<3 and >10 ng ml?1 in the treatment protocol in our institution) or having side-effects in spite of trough concentrations in the desired range, we can estimate AUC using this LSS for a better prediction of exposure.

Mathew, Binu S; Fleming, Denise H; Jeyaseelan, Visalakshi; Chandy, Sujith J; Annapandian, V M; Subbanna, P K; John, George T

2008-01-01

158

Life history dependent morphometric variation in stream-dwelling Atlantic salmon  

USGS Publications Warehouse

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

Letcher, B. H.

2003-01-01

159

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

2013-01-07

160

A perceptually relevant channelized joint observer (PCJO) for the detection-localization of parametric signals.  

PubMed

Many numerical observers have been proposed in the framework of task-based approach for medical image quality assessment. However, the existing numerical observers are still limited in diagnostic tasks: the detection task has been largely studied, while the localization task concerning one signal has been little studied and the localization of multiple signals has not been studied yet. In addition, most existing numerical observers need a priori knowledge about all the parameters of the underdetection signals, while only a few of them need at least two signal parameters. In this paper, we propose a novel numerical observer called the perceptually relevant channelized joint observer (PCJO), which cannot only detect but also localize multiple signals with unknown amplitude, orientation, size and location. We validated the PCJO for predicting human observer task performance by conducting a clinically relevant free-response subjective experiment in which six radiologists (including two experts) had to detect and localize multiple sclerosis (MS) lesions on magnetic resonance (MR) images. By using the jackknife alternative free-response operating characteristic (JAFROC) as the figure of merit (FOM), the detection-localization task performance of the PCJO was evaluated and then compared to that of the radiologists and two other numerical observers--channelized hotelling observer (CHO) and Goossenss CHO for detecting asymmetrical signals with random orientations. Overall, the results show that the PCJO performance was closer to that of the experts than to that of the other radiologists. The JAFROC1 FOMs of the PCJO (around 0.75) are not significantly different from those of the two experts (0.7672 and 0.7110), while the JAFROC1 FOMs of the numerical observers mentioned above (always over 0.84) outperform those of the experts. This indicates that the PCJO is a promising method for predicting radiologists' performance in the joint detection-localization task. PMID:22736639

Zhang, Lu; Cavaro-Ménard, Christine; Le Callet, Patrick; Tanguy, Jean-Yves

2012-06-19

161

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

PubMed

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

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

2001-08-01

162

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

163

CE-PLoc: an ensemble classifier for predicting protein subcellular locations by fusing different modes of pseudo amino acid composition.  

PubMed

Precise information about protein locations in a cell facilitates in the understanding of the function of a protein and its interaction in the cellular environment. This information further helps in the study of the specific metabolic pathways and other biological processes. We propose an ensemble approach called "CE-PLoc" for predicting subcellular locations based on fusion of individual classifiers. The proposed approach utilizes features obtained from both dipeptide composition (DC) and amphiphilic pseudo amino acid composition (PseAAC) based feature extraction strategies. Different feature spaces are obtained by varying the dimensionality using PseAAC for a selected base learner. The performance of the individual learning mechanisms such as support vector machine, nearest neighbor, probabilistic neural network, covariant discriminant, which are trained using PseAAC based features is first analyzed. Classifiers are developed using same learning mechanism but trained on PseAAC based feature spaces of varying dimensions. These classifiers are combined through voting strategy and an improvement in prediction performance is achieved. Prediction performance is further enhanced by developing CE-PLoc through the combination of different learning mechanisms trained on both DC based feature space and PseAAC based feature spaces of varying dimensions. The predictive performance of proposed CE-PLoc is evaluated for two benchmark datasets of protein subcellular locations using accuracy, MCC, and Q-statistics. Using the jackknife test, prediction accuracies of 81.47 and 83.99% are obtained for 12 and 14 subcellular locations datasets, respectively. In case of independent dataset test, prediction accuracies are 87.04 and 87.33% for 12 and 14 class datasets, respectively. PMID:21864791

Khan, Asifullah; Majid, Abdul; Hayat, Maqsood

2011-05-27

164

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

PubMed

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

Hayat, Maqsood; Khan, Asifullah

2010-11-24

165

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

2011-08-18

166

Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.  

PubMed

The EC (Enzyme Commission) numbers represent a hierarchical classification of enzymatic reactions, but they are also commonly utilized as identifiers of enzymes or enzyme genes in the analysis of complete genomes. This duality of the EC numbers makes it possible to link the genomic repertoire of enzyme genes to the chemical repertoire of metabolic pathways, the process called metabolic reconstruction. Unfortunately, there are numerous reactions known to be present in various pathways, but they will never get EC numbers because the EC number assignment requires published articles on full characterization of enzymes. Here we report a computerized method to automatically assign the EC numbers up to the sub-subclasses, i.e., without the fourth serial number for substrate specificity, given pairs of substrates and products. The method is based on a new classification scheme of enzymatic reactions, named the RC (reaction classification) number. Each reaction in the current dataset of the EC numbers is first decomposed into reactant pairs. Each pair is then structurally aligned to identify the reaction center, the matched region, and the difference region. The RC number represents the conversion patterns of atom types in these three regions. We examined the correspondence between computationally assigned RC numbers and manually assigned EC numbers by the jackknife cross-validation test and found that the EC sub-subclasses could be assigned with the accuracy of about 90%. Furthermore, we examined the correlation with genomic information as represented by the KEGG ortholog clusters (OC) and confirmed that the RC numbers are correlated not only with elementary reaction mechanisms but also with protein families. PMID:15600352

Kotera, Masaaki; Okuno, Yasushi; Hattori, Masahiro; Goto, Susumu; Kanehisa, Minoru

2004-12-22

167

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

PubMed

Recently, single nucleotide polymorphisms (SNPs) located in specific loci or genes have been identified associated with susceptibility to colorectal cancer (CRC) in Genome-Wide Association Studies (GWAS). However, in different ethnicities and regions, the genetic variations and the environmental factors can widely vary. Therefore, here we propose a post-GWAS analysis method to investigate the CRC susceptibility SNPs in Taiwan by conducting a replication analysis and bioinformatics analysis. One hundred and forty-four significant SNPs from published GWAS results were collected by a literature survey, and two hundred and eighteen CRC samples and 385 normal samples were collected for post-GWAS analysis. Finally, twenty-six significant SNPs were identified and reported as associated with susceptibility to colorectal cancer, other cancers, obesity, and celiac disease in a previous GWAS study. Functional analysis results of 26 SNPs indicate that most biological processes identified are involved in regulating immune responses and apoptosis. In addition, an efficient prediction model was constructed by applying Jackknife feature selection and ANOVA testing. As compared to another risk prediction model of CRC for European Caucasians population, which performs 0.616 of AUC by using 54 SNPs, the proposed model shows good performance in predicting CRC risk within the Taiwanese population, i.e., 0.724 AUC by using 16 SNPs. We believe that the proposed risk prediction model is highly promising for predicting CRC risk within the Taiwanese population. In addition, the functional analysis results could be helpful to explore the potential associated regulatory mechanisms that may be involved in CRC development. PMID:23262349

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

2012-12-20

168

Program package for multicanonical simulations of U(1) lattice gauge theory  

NASA Astrophysics Data System (ADS)

We document our Fortran 77 code for multicanonical simulations of 4D U(1) lattice gauge theory in the neighborhood of its phase transition. This includes programs and routines for canonical simulations using biased Metropolis heatbath updating and overrelaxation, determination of multicanonical weights via a Wang-Landau recursion, and multicanonical simulations with fixed weights supplemented by overrelaxation sweeps. Measurements are performed for the action, Polyakov loops and some of their structure factors. Many features of the code transcend the particular application and are expected to be useful for other lattice gauge theory models as well as for systems in statistical physics. Catalogue identifier: AEET_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEET_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.: 18?376 No. of bytes in distributed program, including test data, etc.: 205?183 Distribution format: tar.gz Programming language: Fortran 77 Computer: Any capable of compiling and executing Fortran code Operating system: Any capable of compiling and executing Fortran code Classification: 11.5 Nature of problem: Efficient Markov chain Monte Carlo simulation of U(1) lattice gauge theory close to its phase transition. Measurements and analysis of the action per plaquette, the specific heat, Polyakov loops and their structure factors. Solution method: Multicanonical simulations with an initial Wang-Landau recursion to determine suitable weight factors. Reweighting to physical values using logarithmic coding and calculating jackknife error bars. Running time: The prepared tests runs took up to 74 minutes to execute on a 2 GHz PC.

Bazavov, Alexei; Berg, Bernd A.

2009-11-01

169

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.

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

2010-01-01

170

Predicting Secretory Proteins of Malaria Parasite by Incorporating Sequence Evolution Information into Pseudo Amino Acid Composition via Grey System Model  

PubMed Central

The malaria disease has become a cause of poverty and a major hindrance to economic development. The culprit of the disease is the parasite, which secretes an array of proteins within the host erythrocyte to facilitate its own survival. Accordingly, the secretory proteins of malaria parasite have become a logical target for drug design against malaria. Unfortunately, with the increasing resistance to the drugs thus developed, the situation has become more complicated. To cope with the drug resistance problem, one strategy is to timely identify the secreted proteins by malaria parasite, which can serve as potential drug targets. However, it is both expensive and time-consuming to identify the secretory proteins of malaria parasite by experiments alone. To expedite the process for developing effective drugs against malaria, a computational predictor called “iSMP-Grey” was developed that can be used to identify the secretory proteins of malaria parasite based on the protein sequence information alone. During the prediction process a protein sample was formulated with a 60D (dimensional) feature vector formed by incorporating the sequence evolution information into the general form of PseAAC (pseudo amino acid composition) via a grey system model, which is particularly useful for solving complicated problems that are lack of sufficient information or need to process uncertain information. It was observed by the jackknife test that iSMP-Grey achieved an overall success rate of 94.8%, remarkably higher than those by the existing predictors in this area. As a user-friendly web-server, iSMP-Grey is freely accessible to the public at http://www.jci-bioinfo.cn/iSMP-Grey. Moreover, for the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematical equations involved in this paper.

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

2012-01-01

171

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

PubMed

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

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

2012-11-12

172

Spring flood reconstruction from continuous and discrete tree ring series  

NASA Astrophysics Data System (ADS)

This study proposes a method to reconstruct past spring flood discharge from continuous and discrete tree ring chronologies, since both have their respective strengths and weaknesses in northern environments. Ring width or density series provide uninterrupted records that are indirectly linked to regional discharge through a concomitant effect of climate on tree growth and streamflow. Conversely, discrete event chronologies constitute conspicuous records of past high water levels since they are constructed from trees that are directly damaged by the flood. However, the uncertainty of discrete series increases toward the past, and their relationships with spring discharge are often nonlinear. To take advantage of these two sources of information, we introduce a new transfer model technique on the basis of generalized additive model (GAM) theory. The incorporation of discrete predictors and the evaluation of the robustness of the nonlinear relationships are assessed using a jackknife procedure. We exemplify our approach in a reconstruction of May water supplies to the Caniapiscau hydroelectric reservoir in northern Quebec, Canada. We used earlywood density measurements as continuous variables and ice-scar dates around Lake Montausier in the James Bay area as a discrete variable. Strong calibration (0.57 < 0.61 < 0.75) and validation (0.27 < 0.44 < 0.58) R2 statistics were obtained, thus highlighting the usefulness of the model. Our reconstruction suggests that, since ˜1965, spring floods have become more intense and variable in comparison with the last 150 years. We argue that a similar procedure can be used in each case where discrete and continuous tree ring proxies are used together to reconstruct past spring floods.

Boucher, ÉTienne; Ouarda, Taha B. M. J.; BéGin, Yves; Nicault, Antoine

2011-07-01

173

Improved classification of lung cancer tumors based on structural and physicochemical properties of proteins using data mining models.  

PubMed

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

2013-03-07

174

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

PubMed Central

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

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

2008-01-01

175

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

176

Comparison between chest digital tomosynthesis and CT as a screening method to detect artificial pulmonary nodules: a phantom study  

PubMed Central

Objectives The objective of this study was to evaluate the imaging capabilities of chest digital tomosynthesis (DT) as a screening method for the detection of artificial pulmonary nodules, and to compare its efficiency with that of CT. Methods DT and CT were used to detect artificial pulmonary nodules (5 mm and 8 mm in diameter, ground-glass opacities) placed in a chest phantom. Using a three-dimensional filtered back-projection algorithm at acquisition angles of 8°, 20°, 30° and 40°, DT images of the desired layer thicknesses were reconstructed from the image data acquired during a single tomographic scan. Both standard and sharp CT reconstruction kernels were used, and the detectability index (DI) valves computed for both the DT scan acquisition angles and CT reconstruction kernel types were considered. For the observer study, we examined 50 samples of artificial pulmonary nodules using both DT and CT imaging. On the basis of evaluations made by five thoracic radiologists, a jackknife free-response receiver operating characteristic (JAFROC) study was performed to compare and assess the differences in detection accuracy between CT and DT imaging. Results For each increased acquisition angle, DI obtained by DT imaging was similar to that obtained by CT imaging. The difference in the observer-averaged JAFROC figure of merit for the five readings was 0.0363 (95% confidence interval: ?0.18, 0.26; F=0.101; p=0.75). Conclusion With the advantages of a decreased radiation dose and the practical accessibility of examination, DT may be a useful alternative to CT for the detection of artificial pulmonary nodules.

Gomi, T; Nakajima, M; Fujiwara, H; Takeda, T; Saito, K; Umeda, T; Sakaguchi, K

2012-01-01

177

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

178

Microbial Diversity of Biofilms in Dental Unit Water Systems  

PubMed Central

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

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

2003-01-01

179

Generating Distributed Forcing Fields for Spatial Hydrologic Modeling  

NASA Astrophysics Data System (ADS)

Spatial hydrologic modeling requires the development of distributed forcing fields of weather and precipitation. This is particularly difficult in mountainous regions of the western US, where measurement sites are limited and the landscape is dominated by complex terrain and variations in vegetation cover. The Reynolds Creek Experimental Watershed (RCEW), in southwestern Idaho offers a unique opportunity to evaluate the sensitivity of interpolation techniques to the number and location of measurement sites. The RCEW, a 239 km2 hydro-climatic observatory operated by the USDA Agricultural Research Service since the early 1960's, contains 36 hydro-climatic measurement sites for monitoring the range of weather, snow and precipitation conditions across this complex mountain watershed. The MicroMet weather distribution utility, a process and topographically based weather interpolation tool (Liston and Elder, 2006), is used to generate surfaces of temperature, humidity, wind and precipitation over the snow-dominated 55 km2 (elevation range1398-2244m) Tollgate sub-catchment of RCEW. Nineteen meteorological stations were used to simulate the distribution of weather and precipitation for a series of storms during the 2004 water year. Measured and simulated values were compared to evaluate the accuracy of the model, and a jackknife approach was used to evaluate its sensitivity to data from particular stations. To evaluate the effect of elevation and storm track, different combinations of stations were selected, and to evaluate topographic exposure and vegetation shelter stations were divided into groups based on wind exposure. Results show that, even using a sophisticated weather distribution utility like MicroMet, the interpolation is very sensitive to station location and wind exposure. A certain amount of smoothing occurs even when using all 19 stations, but significant differences occur if only protected sites (similar to NRCS Snotel sites), or only wind-exposed sites are used. This research shows that citing hydro-meteorological monitoring stations is critical to improved hydrologic modeling in mountainous regions.

Nayak, A.; Marks, D.; Chandler, D.; Winstral, A.

2006-12-01

180

Designing coarse grained-and atom based-potentials for protein-protein docking  

PubMed Central

Background Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s) upon binding. The major challenge is to define a scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations. Results Using a linear programming (LP) technique, we developed two types of potentials: (i) Side chain-based and (ii) Heavy atom-based. To achieve this we considered a set of 161 transient complexes and generated a large set of putative docked structures (decoys), based on a shape complementarity criterion, for each complex. The demand on the potentials was to yield, for the native (correctly docked) structure, a potential energy lower than those of any of the non-native (misdocked) structures. We show that the heavy atom-based potentials were able to comply with this requirement but not the side chain-based one. Thus, despite the smaller number of parameters, the capability of heavy atom-based potentials to discriminate between native and "misdocked" conformations is improved relative to those of the side chain-based potentials. The performance of the atom-based potentials was evaluated by a jackknife test on a set of 50 complexes taken from the Zdock2.3 decoys set. Conclusions Our results show that, using the LP approach, we were able to train our potentials using a dataset of transient complexes only the newly developed potentials outperform three other known potentials in this test.

2010-01-01

181

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

182

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.; Zotti, G. De; 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.; Werf, P. van der; Vieira, J. D.

2013-11-01

183

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.; Zotti, G. De; 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.; Werf, P. van der; Vieira, J. D.

2013-09-01

184

Measuring modality ordering consistency of observer performance paradigms  

NASA Astrophysics Data System (ADS)

Two observer performance paradigms applied to the same modalities, readers and cases are said to order the modalities consistently if both confirm the same sign (positive or negative) of the figure of merit difference. The aim of this work was to develop a modality ordering consistency measure. The paradigms considered were receiver operating characteristic (ROC) and jackknife alternative free-response ROC (JAFROC). Clinical FROC data from a previous study was used. Using the highest rating method ROC ratings were inferred from FROC ratings. JAFROC analyses of the FROC data and Dorfman-Berbaum-Metz multiple-reader multiple-case (DBM-MRMC) analysis of the inferred ROC data showed significant and consistent differences in the two figures of merit. Additionally 2000 bootstrap data sets were sampled and analyzed by JAFROC and DBM-MRMC. It was found that a positive JAFROC figure of merit difference was 101 times more likely when the ROC difference was positive than when the ROC difference was negative (odds ratio = 101). Valid modality ordering consistency (or inconsistency) claims are possible only when both figures of merit differences are statistically significant. For those bootstraps where both JAFROC and ROC yielded significant differences there were no inconsistent orderings. The effect of artificially degrading JAFROC performance was investigated. It was found that the odds ratio was more sensitive to the degradation. The results in this work are likely to be optimistic. A more realistic test of modality ordering consistency would require two separate studies (FROC and ROC) using the same readers and cases.

Chakraborty, D. P.; Zanca, Federica

2010-03-01

185

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

186

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.

2012-01-01

187

Computer-Aided Detection of Malignant Lung Nodules on Chest Radiographs: Effect on Observers' Performance  

PubMed Central

Objective To evaluate the effect of computer-aided detection (CAD) system on observer performance in the detection of malignant lung nodules on chest radiograph. Materials and Methods Two hundred chest radiographs (100 normal and 100 abnormal with malignant solitary lung nodules) were evaluated. With CT and histological confirmation serving as a reference, the mean nodule size was 15.4 mm (range, 7-20 mm). Five chest radiologists and five radiology residents independently interpreted both the original radiographs and CAD output images using the sequential testing method. The performances of the observers for the detection of malignant nodules with and without CAD were compared using the jackknife free-response receiver operating characteristic analysis. Results Fifty-nine nodules were detected by the CAD system with a false positive rate of 1.9 nodules per case. The detection of malignant lung nodules significantly increased from 0.90 to 0.92 for a group of observers, excluding one first-year resident (p = 0.04). When lowering the confidence score was not allowed, the average figure of merit also increased from 0.90 to 0.91 (p = 0.04) for all observers after a CAD review. On average, the sensitivities with and without CAD were 87% and 84%, respectively; the false positive rates per case with and without CAD were 0.19 and 0.17, respectively. The number of additional malignancies detected following true positive CAD marks ranged from zero to seven for the various observers. Conclusion The CAD system may help improve observer performance in detecting malignant lung nodules on chest radiographs and contribute to a decrease in missed lung cancer.

Lee, Kyung Hee; Park, Chang Min; Lee, Hyun Ju; Jin, Kwang Nam

2012-01-01

188

Grid search modeling of receiver functions: Implications for crustal structure in the Middle East and North Africa  

SciTech Connect

A grid search is used to estimate average crustal thickness and shear wave velocity structure beneath 12 three-component broadband seismic stations in the Middle East, North Africa, and nearby regions. The crustal thickness in these regions is found to vary from a minimum of 8.0{plus_minus}1.5&hthinsp;km in East Africa (Afar) region to possibly a maximum of 64{plus_minus}4.8&hthinsp;km in the lesser Caucasus. Stations located within the stable African platform indicate a crustal thickness of about 40 km. Teleseismic three-component waveform data produced by 165 earthquakes are used to create receiver function stacks for each station. Using a grid search, we have solved for the optimal and most simple shear velocity models beneath all 12 stations. Unlike other techniques (linearized least squares or forward modeling), the grid search methodology guarantees that we solve for the global minimum within our defined model parameter space. Using the grid search, we also qualitatively estimate the least number of layers required to model the observed receiver functions{close_quote} major seismic phases (e.g., PS{sub Moho}). A jackknife error estimation method is used to test the stability of our receiver function inversions for all 12 stations in the region that had recorded a sufficient number of high-quality broadband teleseismic waveforms. Five of the 12 estimates of crustal thicknesses are consistent with what is known of crustal structure from prior geophysical work. Furthermore, the remaining seven estimates of crustal structure are in regions for which previously there were few or no data about crustal thickness. {copyright} 1998 American Geophysical Union

Sandvol, E.; Seber, D.; Calvert, A.; Barazangi, M. [Institute for the Study of the Continents, Cornell University, Ithaca, New York (United States)

1998-11-01

189

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.

Chakraborty, Dev P.

2009-01-01

190

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

NASA Astrophysics Data System (ADS)

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

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

2010-03-01

191

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

192

Normal modes splitting estimations from recent large earthquakes  

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

193

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

PubMed

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

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

2013-03-01

194

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

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

2009-01-01

195

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

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.

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

2010-01-01

197

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

NASA Astrophysics Data System (ADS)

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

Simaiakis, Stylianos Michail; Martínez-Morales, Miguel Angel

198

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

PubMed Central

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

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

2013-01-01

199

Prediction and Analysis of Antibody Amyloidogenesis from Sequences  

PubMed Central

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.

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

2013-01-01

200

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

201

Markers of good performance in mammography depend on number of annual readings.  

PubMed

Purpose: To explore relationships between reader performance and reader characteristics in mammography for specific radiologist groupings on the basis of annual number of readings. Materials and Methods: The institutional review board approved the study and waived the need for patient consent to use all images. Readers gave informed consent. One hundred sixteen radiologists independently reviewed 60 mammographic cases: 20 cases with cancer and 40 cases with normal findings. Readers located any visualized cancer, and levels of confidence were scored from 1 to 5. A jackknifing free response operating characteristic (JAFROC) method was used, and figures of merit along with sensitivity and specificity were correlated with reader characteristics by using Spearman techniques and standard multiple regressions. Results: Reader performance was positively correlated with number of years since qualification as a radiologist (P ? .01), number of years reading mammograms (P ? .03), and number of readings per year (P ? .0001). The number of years since qualification as a radiologist (P ? .004) and number of years of reading mammograms (P ? .002) were negatively related to JAFROC values for radiologists with annual volumes of less than 1000 mammographic readings. For individuals with more than 5000 mammographic readings per year, JAFROC values were positively related to the number of years that the reader was qualified as a radiologist (P ? .01), number of years of reading mammograms (P ? .002), and number of hours per week of reading mammograms (P ? .003). Number of mammographic readings per year was positively related with JAFROC scores for readers with an annual volume between 1000 and 5000 readings (P ? .03). Differences in JAFROC scores appear to be more related to specificity than location sensitivity, with the former demonstrating significant relationships with four of the five characteristics analyzed, whereas no relationships were shown for the latter. Conclusion: Radiologists' determinants of performance are associated with annual reading volumes. Ability to recognize normal images is a discriminating factor in individuals with a high volume of mammographic readings. © RSNA, 2013. PMID:23737538

Rawashdeh, Mohammad A; Lee, Warwick B; Bourne, Roger M; Ryan, Elaine A; Pietrzyk, Mariusz W; Reed, Warren M; Heard, Robert C; Black, Deborah A; Brennan, Patrick C

2013-06-04

202

Benthic macrofauna habitat associations in Willapa Bay, Washington, USA  

NASA Astrophysics Data System (ADS)

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

Ferraro, Steven P.; Cole, Faith A.

2007-02-01

203

Estimation of sex from cranial measurements in a Western Australian population.  

PubMed

It is widely accepted that the most accurate statistical estimations of biological attributes in the human skeleton (e.g., sex, age and stature) are produced using population-specific standards. As we previously demonstrated that the application of foreign standards to Western Australian individuals results in an unacceptably large sex bias (females frequently misclassified), the need for population-specific standards is duly required and greatly overdue. We report here on the first morphometric cranial sexing standards formulated specifically for application in, and based on the statistical analysis of, contemporary Western Australian individuals. The primary aim is to investigate the nature of cranial sexual dimorphism in this population and outline a series of statistically robust standards suitable for estimating sex in the complete bone and/or associated diagnostic fragments. The sample analysed comprised multi-detector computed tomography cranial scans of 400 individuals equally distributed by sex. Following 3D volume rendering, 31 landmarks were acquired using OsiriX, from which a total of 18 linear inter-landmark measurements were calculated. Measurements were analysed using basic descriptive statistics and discriminant function analyses employing jackknife validations of classification results. All measurements (except frontal breadth and orbital height - Bonferroni corrected) are sexually dimorphic with sex differences explaining 3.5-48.9% of sample variance. Bizygomatic breadth and maximum length of the cranium and the cranial base contribute most significantly to sex discrimination; the maximum classification accuracy was 90%, with a -2.1% sex-bias. We conclude that the cranium is both highly dimorphic and a reliable bone for estimating sex in Western Australian individuals. PMID:23537716

Franklin, Daniel; Cardini, Andrea; Flavel, Ambika; Kuliukas, Algis

2013-03-26

204

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.

2013-01-01

205

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

206

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.

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

2010-01-01

207

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

PubMed

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

Shen, Hong-Bin; Chou, Kuo-Chen

2007-02-15

208

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

PubMed

Predicting the fertility outcome of ejaculates is very important in the field of porcine reproduction. The aims of this study were to determine the effects of different osmotic treatments on boar spermatozoa and to correlate them with fertility and prolificacy, assessed as non-return rates within 60 days (NRR(60d)) of the first inseminations, and litter size (LS), respectively. Sperm samples (n=100) from one hundred healthy Piétrain boars were used to assess 48 treatments combining different osmolalities (ranged between 100 and 4000 mOsm kg(-1)), different compounds used to prepare anisotonic solutions, and two different modalities: return and non-return to isotonic conditions. Sperm quality was evaluated before and after applying the treatments on the basis of analyses of sperm viability, motility, morphology and percentages of acrosome-intact spermatozoa. Statistical analyses were performed using a one-way ANOVA and post hoc Tukey's test, linear regression analyses (Pearson correlation and multiple regression) and Jackknife cross-validation. Although three conventional parameters: sperm viability, sperm morphology and the percentages of acrosome-intact spermatozoa were significantly correlated with NRR(60d) and with LS, their respective osmotic tolerance parameters (defined for each parameter and treatment regarding with negative control) presented a higher Pearson coefficient with both fertility and prolificacy in three treatments (150 mOsm kg(-1) with non-return to isotonic conditions, 200 mOsm kg(-1) with return and 500 mOsm kg(-1) using sodium citrate and non-return to isotonic conditions). We conclude that osmotic resistance in sperm viability, sperm morphology and acrosome-intactness in the treatments mentioned above could be assessed along with classical parameters to better predict the fertilising ability of a given ejaculate. PMID:20227204

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

2010-02-19

209

Predicting secretory proteins of malaria parasite by incorporating sequence evolution information into pseudo amino acid composition via grey system model.  

PubMed

The malaria disease has become a cause of poverty and a major hindrance to economic development. The culprit of the disease is the parasite, which secretes an array of proteins within the host erythrocyte to facilitate its own survival. Accordingly, the secretory proteins of malaria parasite have become a logical target for drug design against malaria. Unfortunately, with the increasing resistance to the drugs thus developed, the situation has become more complicated. To cope with the drug resistance problem, one strategy is to timely identify the secreted proteins by malaria parasite, which can serve as potential drug targets. However, it is both expensive and time-consuming to identify the secretory proteins of malaria parasite by experiments alone. To expedite the process for developing effective drugs against malaria, a computational predictor called "iSMP-Grey" was developed that can be used to identify the secretory proteins of malaria parasite based on the protein sequence information alone. During the prediction process a protein sample was formulated with a 60D (dimensional) feature vector formed by incorporating the sequence evolution information into the general form of PseAAC (pseudo amino acid composition) via a grey system model, which is particularly useful for solving complicated problems that are lack of sufficient information or need to process uncertain information. It was observed by the jackknife test that iSMP-Grey achieved an overall success rate of 94.8%, remarkably higher than those by the existing predictors in this area. As a user-friendly web-server, iSMP-Grey is freely accessible to the public at http://www.jci-bioinfo.cn/iSMP-Grey. Moreover, for the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematical equations involved in this paper. PMID:23189138

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

2012-11-26

210

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.

Ramani, R. Geetha; Jacob, Shomona Gracia

2013-01-01

211

Multivariate discrimination among cryptic species of the mite genus Chaetodactylus (Acari: Chaetodactylidae) associated with bees of the genus Lithurgus (Hymenoptera: Megachilidae) in North America.  

PubMed

Twenty-seven morphological characters from 111 heteromorphic deutonymphs of the mite genus Chaetodactylus Rondani (Acari: Chaetodactylidae) were analyzed. The mites were collected from four species of bees of the genus Lithurgus Berthold (Hymenoptera: Megachilidae) in continental North America. Principal component and canonical variates analyses on Darroch and Mosimann shape and size-and-shape variables revealed the presence of three cryptic species. Chaetodactylus gibbosi sp. n. (Florida) is geographically isolated from C. lithurgi sp. n. distributed in Texas, New Mexico, Arizona, Colorado, and Idaho. Sympatric C. lithurgi and C. abditus sp. n. (USA: Arizona, Mexico: Socorro Is.) are seasonally isolated in Arizona. Chaetodactylus gibbosi is associated with a single bee species, Lithurgus gibbosus Smith in Florida. The host range of C. lithurgi includes bees flying predominantly in the spring: L. apicalis Cresson, L. littoralis Cockerell, and western L. gibbosus. Chaetodactylus abditus sp. n. is associated with L. planifrons Friese and L. echinocacti Cockerell, flying predominantly in the fall in Arizona. No distinct groups separated by geographic locality or size were detected in any species. A six-variable model developed by the canonical variates analysis and estimated using jackknife resampling and external validation (n = 100) is capable of classifying the three species with 100% accuracy. Factors that influenced speciation of cryptic species of Chaetodactylus associated with Lithurgus are discussed. Based on morphological and geographical data and data on mite associates, the western and eastern populations of the bee L. gibbosus are distinct. Therefore, the taxonomic status of L. gibbosus s. lat. should be reevaluated. PMID:15347022

Klimov, Pavel B; OConnor, Barry M

2004-01-01

212

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

PubMed

Involved in many diseases such as cancer, diabetes, neurodegenerative, inflammatory and respiratory disorders, G-protein-coupled receptors (GPCRs) are among the most frequent targets of therapeutic drugs. It is time-consuming and expensive to determine whether a drug and a GPCR are to interact with each other in a cellular network purely by means of experimental techniques. Although some computational methods were developed in this regard based on the knowledge of the 3D (dimensional) structure of protein, unfortunately their usage is quite limited because the 3D structures for most GPCRs are still unknown. To overcome the situation, a sequence-based classifier, called "iGPCR-drug", was developed to predict the interactions between GPCRs and drugs in cellular networking. In the predictor, the drug compound is formulated by a 2D (dimensional) fingerprint via a 256D vector, GPCR by the PseAAC (pseudo amino acid composition) generated with the grey model theory, and the prediction engine is operated by the fuzzy K-nearest neighbour algorithm. Moreover, a user-friendly web-server for iGPCR-drug was established at http://www.jci-bioinfo.cn/iGPCR-Drug/. For the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated math equations presented in this paper just for its integrity. The overall success rate achieved by iGPCR-drug via the jackknife test was 85.5%, which is remarkably higher than the rate by the existing peer method developed in 2010 although no web server was ever established for it. It is anticipated that iGPCR-Drug may become a useful high throughput tool for both basic research and drug development, and that the approach presented here can also be extended to study other drug - target interaction networks. PMID:24015221

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

2013-08-27

213

Potential for lower absorbed dose in digital mammography: a JAFROC experiment using clinical hybrid images with simulated dose reduction  

NASA Astrophysics Data System (ADS)

Purpose: To determine how image quality linked to tumor detection is affected by reducing the absorbed dose to 50% and 30% of the clinical levels represented by an average glandular dose (AGD) level of 1.3 mGy for a standard breast according to European guidelines. Materials and methods: 90 normal, unprocessed images were acquired from the screening department using a full-field digital mammography (FFDM) unit Mammomat Novation (Siemens). Into 40 of these, one to three simulated tumors were inserted per image at various positions. These tumors represented irregular-shaped malignant masses. Dose reduction was simulated in all 90 images by adding simulated quantum noise to represent images acquired at 50% and 30% of the original dose, resulting in 270 images, which were subsequently processed for final display. Four radiologists participated in a free-response receiver operating characteristics (FROC) study in which they searched for and marked suspicious positions of the masses as well as rated their degree of suspicion of occurrence on a one to four scale. Using the jackknife FROC (JAFROC) method, a score between 0 and 1 (where 1 represents best performance), referred to as a figure-of-merit (FOM), was calculated for each dose level. Results: The FOM was 0.73, 0.70, and 0.68 for the 100%, 50% and 30% dose levels, respectively. Using Analysis of the Variance (ANOVA) to test for statistically significant differences between any two of the three FOMs revealed that they were not statistically distinguishable (p-value of 0.26). Conclusion: For the masses used in this experiment, there was no significant change in detection by increasing quantum noise, thus indicating a potential for dose reduction.

Timberg, Pontus; Ruschin, Mark; Båth, Magnus; Hemdal, Bengt; Andersson, Ingvar; Mattsson, Sören; Chakraborty, Dev; Saunders, Rob; Samei, Ehsan; Tingberg, Anders

2006-03-01

214

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

PubMed Central

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

Chakraborty, Dev P.

2012-01-01

215

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

216

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

PubMed

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. PMID:19291970

Masotti, Matteo; Lanconelli, Nico; Campanini, Renato

2009-02-01

217

Preliminary clinical evaluation of a noninvasive device for the measurement of coagulability in the elderly.  

PubMed

The feasibility of the noninvasive assessment of blood 'coagulability' (the tendency to coagulate) has been tested by using a novel device, the Thrombo-Monitor. It monitors, by using the principles of near infra-red (NIR) dynamic light scattering, the tendency of blood to create clots. The Thrombo-Monitor observes the very initial changes of blood viscosity, which occurs due to the temporarily induced stasis of capillary blood of the finger. One hundred and fifteen patients aged >65 years (matched by age and sex) participated in the study. Patients were initially divided into four groups based on the patient's medical therapy. The study groups were: warfarin, enoxaparin, aspirin and/or clopidogrel, and a control group. The medications were given according to the patient's comorbidities (eg, atrial fibrillation [AF], status post pulmonary embolism [S/p PE], status post cerebrovascular accident [S/p CVA]). The Thrombo-Monitor Index (TMI) is a noninvasive index, derived on the basis of laboratory test results of international normalized ratio (INR) and prothrombin time (PT) values. For the group of patients who were treated only with warfarin, TMI was adjusted by using the jackknife statistical approach to create maximum correlation and linearity with INR and PT values that ranged from 1.1 to 5.0. For all warfarin patients (N = 35) the TMI was found to have a good correlation with INR and PT values (R(2) = 0.64, P < 0.00001); mean TMI = 1.86 (SD = 0.91); mean INR and PT = 2.3 (SD = 0.91). The calibration curve thus generated was used to calculate the TMI for all other groups: aspirin group, mean TMI = 1.3 (SD = 0.14, N = 23), corresponding approximately to INR and PT values of 1.036; enoxaparin group (N = 24), mean TMI = 1.34 (SD = 0.304), corresponding to mean INR and PT values of 1.07 (SD = 0.3); control group, INR and PT ? 1 (N = 32), mean TMI = 1.24 (SD = 0.32). R(2) of all control and warfarin patients (N = 67) was 0.55 (P < 0.00001). In summary, the newly introduced TMI index is significantly correlated with INR and PT values. PMID:22287870

Lerman, Yaffa; Werber, Moshe M; Fine, Ilya; Kemelman, Polina

2011-08-18

218

Fine-scale Genetic Structure among Genetic Individuals of the Clone-Forming Monotypic Genus Echinosophora koreensis (Fabaceae)  

PubMed Central

• Background and Aims For rare endemics or endangered plant species that reproduce both sexually and vegetatively it is critical to understand the extent of clonality because assessment of clonal extent and distribution has important ecological and evolutionary consequences with conservation implications. A survey was undertaken to understand clonal effects on fine-scale genetic structure (FSGS) in two populations (one from a disturbed and the other from an undisturbed locality) of Echinosophora koreensis, an endangered small shrub belonging to a monotypic genus in central Korea that reproduces both sexually and vegetatively via rhizomes. • Methods Using inter-simple sequence repeats (ISSRs) as genetic markers, the spatial distribution of individuals was evaluated using Ripley's L(d)-statistics and quantified the spatial scale of clonal spread and spatial distribution of ISSR genotypes using spatial autocorrelation analysis techniques (join-count statistics and kinship coefficient, Fij) for total samples and samples excluding clones. • Key Results A high degree of differentiation between populations was observed (?ST(g) = 0·184, P < 0·001). Ripley's L(d)-statistics revealed a near random distribution of individuals in a disturbed population, whereas significant aggregation of individuals was found in an undisturbed site. The join-count statistics revealed that most clones significantly aggregate at ?6-m interplant distance. The Sp statistic reflecting patterns of correlograms revealed a strong pattern of FSGS for all four data sets (Sp = 0·072–0·154), but these patterns were not significantly different from each other. At small interplant distances (?2?m), however, jackknifed 95?% CIs revealed that the total samples exhibited significantly higher Fij values than the same samples excluding clones. • Conclusion The strong FSGS from genets is consistent with two biological and ecological traits of E. koreensis: bee-pollination and limited seed dispersal. Furthermore, potential clone mates over repeated generations would contribute to the observed high Fij values among genets at short distance. To ensure long-term ex situ genetic variability of the endangered E. koreensis, individuals located at distances of 10?12?m should be collected across entire populations of E. koreensis.

CHUNG, JAE MIN; LEE, BYEUNG CHEUN; KIM, JIN SEOK; PARK, CHONG-WOOK; YOON CHUNG, MI; GI CHUNG, MYONG

2006-01-01

219

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

220

iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition.  

PubMed

Heat shock proteins (HSPs) are a type of functionally related proteins present in all living organisms, both prokaryotes and eukaryotes. They play essential roles in protein-protein interactions such as folding and assisting in the establishment of proper protein conformation and prevention of unwanted protein aggregation. Their dysfunction may cause various life-threatening disorders, such as Parkinson's, Alzheimer's, and cardiovascular diseases. Based on their functions, HSPs are usually classified into six families: (i) HSP20 or sHSP, (ii) HSP40 or J-class proteins, (iii) HSP60 or GroEL/ES, (iv) HSP70, (v) HSP90, and (vi) HSP100. Although considerable progress has been achieved in discriminating HSPs from other proteins, it is still a big challenge to identify HSPs among their six different functional types according to their sequence information alone. With the avalanche of protein sequences generated in the post-genomic age, it is highly desirable to develop a high-throughput computational tool in this regard. To take up such a challenge, a predictor called iHSP-PseRAAAC has been developed by incorporating the reduced amino acid alphabet information into the general form of pseudo amino acid composition. One of the remarkable advantages of introducing the reduced amino acid alphabet is being able to avoid the notorious dimension disaster or overfitting problem in statistical prediction. It was observed that the overall success rate achieved by iHSP-PseRAAAC in identifying the functional types of HSPs among the aforementioned six types was more than 87%, which was derived by the jackknife test on a stringent benchmark dataset in which none of HSPs included has ?40% pairwise sequence identity to any other in the same subset. It has not escaped our notice that the reduced amino acid alphabet approach can also be used to investigate other protein classification problems. As a user-friendly web server, iHSP-PseRAAAC is accessible to the public at http://lin.uestc.edu.cn/server/iHSP-PseRAAAC. PMID:23756733

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

2013-06-10

221

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

PubMed Central

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

2012-01-01

222

EEG spectral coherence data distinguish chronic fatigue syndrome patients from healthy controls and depressed patients-A case control study  

PubMed Central

Background Previous studies suggest central nervous system involvement in chronic fatigue syndrome (CFS), yet there are no established diagnostic criteria. CFS may be difficult to differentiate from clinical depression. The study's objective was to determine if spectral coherence, a computational derivative of spectral analysis of the electroencephalogram (EEG), could distinguish patients with CFS from healthy control subjects and not erroneously classify depressed patients as having CFS. Methods This is a study, conducted in an academic medical center electroencephalography laboratory, of 632 subjects: 390 healthy normal controls, 70 patients with carefully defined CFS, 24 with major depression, and 148 with general fatigue. Aside from fatigue, all patients were medically healthy by history and examination. EEGs were obtained and spectral coherences calculated after extensive artifact removal. Principal Components Analysis identified coherence factors and corresponding factor loading patterns. Discriminant analysis determined whether spectral coherence factors could reliably discriminate CFS patients from healthy control subjects without misclassifying depression as CFS. Results Analysis of EEG coherence data from a large sample (n = 632) of patients and healthy controls identified 40 factors explaining 55.6% total variance. Factors showed highly significant group differentiation (p < .0004) identifying 89.5% of unmedicated female CFS patients and 92.4% of healthy female controls. Recursive jackknifing showed predictions were stable. A conservative 10-factor discriminant function model was subsequently applied, and also showed highly significant group discrimination (p < .001), accurately classifying 88.9% unmedicated males with CFS, and 82.4% unmedicated male healthy controls. No patient with depression was classified as having CFS. The model was less accurate (73.9%) in identifying CFS patients taking psychoactive medications. Factors involving the temporal lobes were of primary importance. Conclusions EEG spectral coherence analysis identified unmedicated patients with CFS and healthy control subjects without misclassifying depressed patients as CFS, providing evidence that CFS patients demonstrate brain physiology that is not observed in healthy normals or patients with major depression. Studies of new CFS patients and comparison groups are required to determine the possible clinical utility of this test. The results concur with other studies finding neurological abnormalities in CFS, and implicate temporal lobe involvement in CFS pathophysiology.

2011-01-01

223

Detection of Recurrent Hepatocellular Carcinoma in Cirrhotic Liver after Transcatheter Arterial Chemoembolization: Value of Quantitative Color Mapping of the Arterial Enhancement Fraction of the Liver  

PubMed Central

Objective To investigate the additional diagnostic value of color mapping of the hepatic arterial enhancement fraction (AEF) for detecting recurrent or residual hepatocellular carcinoma (HCC) in patients treated with transcatheter arterial chemoembolization (TACE). Materials and Methods Seventy-six patients with 126 HCCs, all of whom had undergone previous TACE, and subsequently, underwent follow-up multiphasic liver CT scans, were included in this study. Quantitative color maps of the AEF of the whole liver were created, by using prototype software with non-rigid registration. The AEF was defined as the ratio of the attenuation increment during the arterial phase to the attenuation increment during the portal phase. Two radiologists independently analyzed the two image sets at a two-week interval, i.e., the multiphasic CT image set and the second image set of the AEF color maps and the CT images. The additional diagnostic value of the AEF color mapping was determined, by the use of the jackknife-alternative free-response receiver-operating-characteristic analysis. The sensitivity and positive predictive values for detecting HCCs of each image set were also evaluated and compared. Results The reader-averaged figures of merit were 0.699 on the initial interpretation of the MDCT image set, and 0.831 on the second interpretation of the combined image set; the difference between the two interpretations was significant (p value < 0.001). The mean sensitivity for residual or recurrent HCC detection increased from 62.7% on the initial analysis to 82.1% on the second analysis using the AEF color maps (p value < 0.001). The mean positive predictive value for HCC detection was 74.5% on the initial analysis using MDCT, and 71.6% on the second analysis using AEF color mapping. Conclusion Quantitative color mapping of the hepatic AEF may have the possibility to increase the diagnostic performance of MDCT for the detection of recurrent or residual HCC without the potential risk of radiation-related hazards.

Lee, Dong Ho; Klotz, Ernst; Kim, Soo Jin; Kim, Kyung Won; Han, Joon Koo; Choi, Byung Ihn

2013-01-01

224

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

PubMed

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

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

2012-09-08

225

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

226

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

NASA Astrophysics Data System (ADS)

Actual evapotranspiration (ET) of agricultural land and forestland surfaces play an important role in the redistribution of water on the Earth's surface. Any change in evapotranspiration, either through change in vegetation or climate change, directly effects the available water resources. For quantifying these effects physical models need to be constructed. Most hydrological models have to deal with a lack of good spatial resolution, despite their good temporal information. Remote sensing techniques on the contrary determine the spatial pattern of landscape features and hence are very useful on large scales. The main objective of this research is the combination of the spatial pattern of remote sensing (using visible and thermal infrared spectrum) with the temporal pattern of the water balance model WAVE (Vanclooster et al., 1994 and 1996). To realise this, the following objectives are formulated: (i) relate soil and vegetation surface temperatures to actual evapotranspiration of forest and crops simulated with the water balance model WAVE using remote sensing derived parameters. Three methods will be used and mutually compared. Both airborne and satellite imagery will be implemented; (1) compare the spatial pattern of evapotranspiration, as a result of the three methods, with the energy balance model SEBAL (Bastiaanssen et al., 1998) and finally; (2) subject the up-scaled WAVE and SEBAL models to an uncertainty analysis using the GLUE-approach (Generalised Likelihood Uncertainty Estimate) (Beven en Binley, 1992). To study the behaviour of the model beyond the field-scale (micro-scale), a meso-scale study was conducted at the test-site of DURAS (50°50'38"N, 5°08'50"W, Sint-Truiden). Airborne imagery from the DAIS/ROSIS sensor are available. For the determination of the spatial pattern of actual evapotranspiration the next two methods are considered: (1) relations between surface temperature, surface albedo and vegetation indices are linked with field-simulations of the water balance model WAVE on some specific locations (derived from Price, 1990 and Bastiaanssen et al., 1998) and; (2) determining the spatial input parameters of WAVE in order to simulate the spatial patterns of evapotranspiration (based on D'Urso); the Split-Data, Split-Window, Jack-knife, and cross-correlation techniques will take care of the temporal and spatial validation of the results.

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

2003-04-01

227

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

PubMed Central

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

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

2013-01-01

228

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

PubMed

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

Chakraborty, Dev P

2012-04-20

229

Tests for intact and collapsed magnetofossil chains  

NASA Astrophysics Data System (ADS)

In recent years, new techniques for the detection of magnetofossils have been proposed, based on their unique first-order reversal curves (FORC) and ferromagnetic resonance (FMR) signatures. These signatures are related to the non-interacting (FORC) and strongly uniaxial anisotropy (FMR) of isolated chains of magnetic particles. However, little is known about the fate of these signatures in sediments where magnetosome chains collapsed during early diagenetic processes. Due to the impossibility of observing the particle arrangement in-situ, the structure of collapsed chains can only be inferred from TEM images of magnetic extracts and from first-principles consideration on the mechanical stability of magnetosome chains once the biological material around them is dissolved. The magnetic properties of double chains, produced by some strains of cocci, are also not known. According to these considerations, four main magnetofossil structures were taken into consideration: (1) isolated, linear chains, (2) double, half-staggered chains, where the gaps of one chain face the magnetosomes in the other chain, (3) double chains with side-to-side magnetosomes, which might result from a "jackknife" type of collapse of a single, long chain, and (4) zig-zag collapsed chains of elongated crystals, where the magnetosome long axes are perpendicular to the chain axis. The collapsed structures might be relevant in sediments where magnetofossils carry a significant part of the remanent magnetization, because chain collapse tends to cancel the original natural remanent magnetization. Detailed models for the hysteretic and anhysteretic properties of structures (1-4) have been calculated by taking realistic distributions of magnetosome size, elongation, and spacing into account, as inferred from a number of published TEM observations. Model calculations took a total of >2 years continuous running time on two computers in an effort to obtain realistic results, which are shown here for the first time. These results match measurements obtained previously on magnetosome-rich sediments in smallest details, showing that the identification of distinct intact and collapsed chain structures is possible. On the other hand, these results show that caution should be used when interpreting sediment hysteresis properties as mixtures of single domain (SD), multidomain (MD), and superparamagnetic (SP) particles; because some collapsed chain structures closely mimic SD-MD-SP mixing trends in a Day plot, although being made only of SD particles.

Egli, R.

2012-04-01

230

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

NASA Astrophysics Data System (ADS)

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

Chakraborty, Dev P.

2012-05-01

231

Complex Faulting within the New Madrid Seismic Zone  

NASA Astrophysics Data System (ADS)

Relative relocations derived using double-difference tomography techniques reveal a complex sequence of faulting within the New Madrid Seismic Zone (NMSZ) and upper Mississippi Embayment. The majority of NMSZ seismicity recorded over the last 30 years occurs along four limbs: 1) a NE-SW trending dextral strike-slip fault, termed the Axial fault, coincident with the central valley of the Cambrian Reelfoot Rift system; 2) the SE-NW trending Reelfoot thrust fault; 3) a E-W trending left lateral strike-slip fault extending off of the northern terminus of the Reelfoot fault, here termed New Madrid west; and 4) a NE-SW dextral strike-slip fault also extending off of the northern terminus of the Reelfoot fault, here termed New Madrid north. Each of these segments is thought to have ruptured during the 1811-1812 large earthquake sequence. A fifth segment, the Bootheel lineament, is marked by 1811-1812 related liquefaction features but appears largely aseismic, though we suggest there are at least five events in the catalog associated with this feature. Geological and geophysical evidence across the embayment suggests that the region is crossed by additional faults at shallow depths (<1-2 km), while seismicity is generally confined to the 3-20 km depth range. Here we present relative relocations derived using catalog and waveform cross-correlation differential times of the 1989-1992 local PANDA network and the 1995-2010 Cooperative New Madrid Seismic Network. We show that the four known seismic lineations exhibit internal complexity. For example, New Madrid north is composed of two parallel faults rather then a single fault, and seismicity associated with the Axial lineation exhibits temporal changes along strike and becomes spatially more diffuse south of the Axial fault/Bootheel lineament intersection. Seismicity along the southern Reelfoot fault does not define a dipping plane consistent with thrust faulting, unlike the northern Reelfoot fault, and is associated with anomalously low P wave velocities. Swarm activity along the southern portion of the Reelfoot fault and near the northern portion of the Reelfoot fault terminus may be related to fault intersections within this complicated transpressional system. Recent reflection data of the upper 1 km imaged along the Mississippi River indicate that both the north termini of the Reelfoot and Axial faults are characterized by splay faulting, while at depth microseismicity is planar. Absolute and relative error will be assessed by computing locations within two 3D P and S wave velocity models of the study area, using finite difference and pseudo-bending ray tracing approaches, and jack-knife approaches to test dependence on network geometry.

Deshon, H. R.; Powell, C. A.; Magnani, M.; Bisrat, S. T.

2010-12-01

232

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

PubMed

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

Gómez-Díaz, Elena; González-Solis, Jacob

2007-07-01

233

CT neuroradiological evaluation of intra-axial and extra-axial lesions: an ROC study of film and 1K workstation  

NASA Astrophysics Data System (ADS)

Digital display workstations are now commonly used for cross-sectional image viewing; however, few receiver operating characteristic (ROC) studies have been performed to evaluate the diagnostic efficiency of hard copy versus a workstation display for neuroradiology applications. We have performed an ROC study of film and 1K workstation based on the diagnostic performance of neuroradiology fellows to detect subtle intra- axial (high density (HD) and low density (LD)) and extra-axial (fluid, blood) lesions presented on computed tomographic (CT) images. An ROC analysis of the interpretation of approximately 200 CT images (1/2 normals and 1/2 abnormals) was performed by five experienced observers. The total number of abnormal images were equally divided among the three represented types of lesions (HD, LD, and extra-axial lesions). The images comprising the extra-axial lesion group were further subdivided into the following three distinct types: subdural hemorrhage, subarachnoid hemorrhage, and epidural hemorrhage. A fraction of the abnormal images were represented by more than one type of lesion, e.g., one abnormal image could contain both a HD and LD lesion. The digitized CT images were separated into four groups and read on the standard light box and a 1K workstation monitor equipped with simple image processing functions. Confidence ratings were scaled on a range from 0 (least confident) to 4 (most confident). Reader order sequences were randomized for each reader and for each modality. Each observer read from a total of eight different groups with a four-week intermission following the fourth group. The randomly assigned image number, lesion type and approximate location, incidental findings and comments, and confidence ratings were reported in individual worksheets for each image. ROC curves that were generated and analyzed for the various subgroups are presented in addition to the overall generalized jackknifed estimates of the grouped data. Also, 95% confidence intervals are presented for the differences in the area under the ROC curves. Although there were no statistically significant differences in the diagnostic accuracy between the original CT slice with HD and LD lesions viewed on the light box and on the 1K display workstation, the observers tended to record extra- axial lesions more frequently and with more confidence on the 1K display in comparison to the light box primarily due to the added advantage of adjusting the display window levels.

El-Saden, Suzie; Hademenos, George J.; Zhu, Wei; Sayre, James W.; Glenn, Brad; Steidler, Jim; Kode, L.; King, Brian; Quinones, Diana; Valentino, Daniel J.; Bentsen, John R.

1995-04-01

234

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

235

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

236

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

NASA Astrophysics Data System (ADS)

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

Lisowski, M.; Battaglia, M.

2011-12-01

237

Estimating river low flows statistics in ungauged sites  

NASA Astrophysics Data System (ADS)

Knowledge of low flow events frequency is required for water resources planning and management and their definition is necessary for several purposes, including water supply planning and irrigation systems running and moreover to maintain amount and quality of water. Low flow regime is tightly dependent on the catchment hydrogeological feature and a detailed surface and groundwater catchment analysis is necessary for an accurate characterization. However on a practical perspective, although scientifically proven, statistical analysis is widely apply to derive indices to characterize low flow regimes and as a measure for environmental minimum flow. With these indices it is possible to identify the occurrence, the extent and magnitude of the hydrological droughts, the ones that affect mainly water supply systems. Low flow indices are commonly evaluated at gauged sites from observed streamflow time series. Their reliability can be affected by the lack of observed streamflow data, a diffuse problem in the real world. In order to overcome these problems and to estimate low flow statistics in ungauged sites it is possible to refer to a regional frequency analysis, widely used since long time and in different disciplines. It consists in inferring data in ungauged stations using hydrological and statistical methods applied over a more or less wide area, a region. The methods employ catchment and climatic characteristics, supposed to be measured over the investigated area, as independent variables, and data from other catchments where stream flow data are recorded. The analysis of low flow indices is carried out on the flow data of 65 consistent hydrometric stations located in Tuscany region, in Central Italy, recorded from 1949 to 2008. The area is subdivided into different regions using the L-moments method applied to indices derived from the flow duration curve (Q70 annual series), to the 7-day annual minimum (Q7,T) series and to the annual SQI, Standardized Discharge Index. The division into subregions is validated using discordancy and heterogeneity tests. Several subdivisions are tested, starting from previous studies on different hydrological extreme values and introducing some hydrological features. For every river section of interest the catchment area is identified and an appropriate set of catchment physiographic and climatic characteristics is defined. A physiographical space-based method is used to relate the duration and annual minimum indices of low flow to the rivers basins characteristics. The new space is built as a power correlation of the catchment geomorphologic and climatic characteristics. In this space several interpolation techniques, either deterministic or geostatistical, such as Inverse Distance, Thiessen polygon methods and Kriging, are applied. The results are valuated using the jack-knife method. Different error measurement (mean square error, mean relative error…) are also assessed to compare the results, to quantify the accuracy of the different techniques and to define the most suitable procedure for low flow regionalization.

Rossi, G.; Caporali, E.

2010-12-01