Science.gov

Sample records for jackknifing

  1. Testing variance components by two jackknife methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. The Infinitesimal Jackknife with Exploratory Factor Analysis

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  3. Jackknife and bootstrap inferential procedures for censored survival data

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    ERIC Educational Resources Information Center

    Jennrich, Robert I.

    2008-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

    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%.

  6. Evaluation of Jackknife and Bootstrap for Defining Confidence Intervals for Pairwise Agreement Measures

    PubMed Central

    Severiano, Ana; Carriço, João A.; Robinson, D. Ashley; Ramirez, Mário; Pinto, Francisco R.

    2011-01-01

    Several research fields frequently deal with the analysis of diverse classification results of the same entities. This should imply an objective detection of overlaps and divergences between the formed clusters. The congruence between classifications can be quantified by clustering agreement measures, including pairwise agreement measures. Several measures have been proposed and the importance of obtaining confidence intervals for the point estimate in the comparison of these measures has been highlighted. A broad range of methods can be used for the estimation of confidence intervals. However, evidence is lacking about what are the appropriate methods for the calculation of confidence intervals for most clustering agreement measures. Here we evaluate the resampling techniques of bootstrap and jackknife for the calculation of the confidence intervals for clustering agreement measures. Contrary to what has been shown for some statistics, simulations showed that the jackknife performs better than the bootstrap at accurately estimating confidence intervals for pairwise agreement measures, especially when the agreement between partitions is low. The coverage of the jackknife confidence interval is robust to changes in cluster number and cluster size distribution. PMID:21611165

  7. Use of the Multinomial Jackknife and Bootstrap in Generalized Nonlinear Canonical Correlation Analysis. Research Report 87-4.

    ERIC Educational Resources Information Center

    van der Burg, Eeke; de Leeuw, Jan

    The estimation of mean and standard errors of the eigenvalues and category quantifications in generalized non-linear canonical correlation analysis (OVERALS) is discussed. Starting points are the delta method equations. The jackknife and bootstrap methods are compared for providing finite difference approximations to the derivatives. Examining the…

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

    PubMed

    Dexter, Troy A; Kowalewski, Michał

    2013-12-01

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

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

    PubMed

    Preziosi, Brian M; Bowden, Timothy J

    2016-05-01

    The Atlantic jackknife clam, Ensis directus, is currently being researched as a potential species for aquaculture operations in Maine. The goal of this study was to describe the hemocytes of this species for the first time and provide a morphological classification scheme. We viewed hemocytes under light microscopy (using Hemacolor, neutral red, and Pappenheim's stains) as well as transmission electron microscopy (TEM). The 2 main types of hemocytes found were granulocytes and hyalinocytes (agranular cells). The granulocytes were subdivided into large and small granulocytes while the hyalinocytes were subdivided into large and small hyalinocytes. The large hemocytes had both a larger diameter and smaller nucleus to cell diameter ratio than their smaller counterparts. A rare cell type, the vesicular cell, was also observed and it possessed many vesicles but few or no granules. Using TEM, granulocytes were found to contain both electron-lucent and electron-dense granules of various sizes. These numerous granules were the only structures that took up the neutral red stain. Hyalinocytes had few of these granules relative to granulocytes. Large hyalinocytes had both various organelles and large vesicles in their abundant cytoplasm while small hyalinocytes had little room for organelles in their scant cytoplasm. Total hemocyte counts averaged 1.96×10(6) cells mL(-1) while differential hemocyte counts averaged 11% for small hyalinocytes, 12% for large hyalinocytes, 59% for small granulocytes, and 18% for large granulocytes. The results of this study provide a starting point for future studies on E. directus immune function. PMID:27015289

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

    PubMed

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

    2015-02-01

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

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

    PubMed Central

    Park, Soo Young; Park, Jong Cook

    2010-01-01

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

  12. 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

    Shoemaker, David M.

    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)

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

    PubMed

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

    2014-02-01

    This video demonstrates a laparoscopic abdominal perineal resection for a fixed 4.8-cm mass involving the posterior and left rectal walls and left puborectalis, 2 cm from the anal verge (see Video, Supplemental Digital Content 1, http://links.lww.com/DCR/A127). We detail the steps of the procedure, all completed in lithotomy, including lateral-to-medial dissection; identification and protection of the left ureter and presacral nerves; division of the inferior mesenteric artery; medial-to-lateral dissection, with meeting the previous dissection plane; total mesorectal excision and pelvic dissection; perineal dissection and layered closure; and abdominal inspection and colostomy creation. Total operative time was 181 minutes. The specimen total mesorectal excision was complete with a negative circumferential radial margin (greater than 1 cm). Final pathology was T3N2M0. PMID:24401888

  14. The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region.

    PubMed

    Yuan, Yang; Li, Qi; Kong, Lingfeng; Yu, Hong

    2012-02-01

    Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. The complete mitochondrial genome of Solen grandis (Bivalvia: Solenidae) was determined using long-PCR and genome walking techniques. The entire mitochondrial genome sequence of S. grandis is 16,784 bp in length, and contains 36 genes including 12 protein-coding genes (atp8 is absent), 2 ribosomal RNAs, and 22 tRNAs. All genes are encoded on the same strand. Compared with other species, it bears a novel gene order. Besides these, we find a peculiar non-coding region of 435 bp with a microsatellite-like (TA)(12) element, poly-structures and many hairpin structures. In contrast to the available heterodont mitochondrial genomes from GenBank, the complete mtDNA of S. grandis has the shortest cox3 gene, and the longest atp6, nad4, nad5 genes. PMID:21598108

  15. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... manufacturer's type or size designation. (b) Instructions for can opener. With each jackknife the manufacturer shall supply instructions, complete with an illustration, indicating the proper method for using the...

  16. 46 CFR 169.527 - Required equipment for lifeboats.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ...—Jackknife 1 None n—Ladder, lifeboat, gunwale 1 None o—Lantern 1 1 p—Lifeline 1 1 q—Life preservers 2 2 r...—Painter 2 1 z—Plug 1 1 aa—Provisions (per person) 2 None bb—Rowlocks (units) 1 1 cc—Rudder and tiller...

  17. 46 CFR 169.527 - Required equipment for lifeboats.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...—Jackknife 1 None n—Ladder, lifeboat, gunwale 1 None o—Lantern 1 1 p—Lifeline 1 1 q—Life preservers 2 2 r...—Painter 2 1 z—Plug 1 1 aa—Provisions (per person) 2 None bb—Rowlocks (units) 1 1 cc—Rudder and tiller...

  18. 46 CFR 169.527 - Required equipment for lifeboats.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...—Jackknife 1 None n—Ladder, lifeboat, gunwale 1 None o—Lantern 1 1 p—Lifeline 1 1 q—Life preservers 2 2 r...—Painter 2 1 z—Plug 1 1 aa—Provisions (per person) 2 None bb—Rowlocks (units) 1 1 cc—Rudder and tiller...

  19. 46 CFR 169.527 - Required equipment for lifeboats.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ...—Jackknife 1 None n—Ladder, lifeboat, gunwale 1 None o—Lantern 1 1 p—Lifeline 1 1 q—Life preservers 2 2 r...—Painter 2 1 z—Plug 1 1 aa—Provisions (per person) 2 None bb—Rowlocks (units) 1 1 cc—Rudder and tiller...

  20. The use and misuse of statistics in space physics

    NASA Technical Reports Server (NTRS)

    Reiff, Patricia H.

    1990-01-01

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

  1. Variance Estimation for NAEP Data Using a Resampling-Based Approach: An Application of Cognitive Diagnostic Models. Research Report. ETS RR-10-26

    ERIC Educational Resources Information Center

    Hsieh, Chueh-an; Xu, Xueli; von Davier, Matthias

    2010-01-01

    This paper presents an application of a jackknifing approach to variance estimation of ability inferences for groups of students, using a multidimensional discrete model for item response data. The data utilized to demonstrate the approach come from the National Assessment of Educational Progress (NAEP). In contrast to the operational approach…

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

    ERIC Educational Resources Information Center

    White, David J.; Williver, S. Todd

    2014-01-01

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

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

    ERIC Educational Resources Information Center

    Stapleton, Laura M.

    2008-01-01

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

  4. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 6 2014-10-01 2014-10-01 false Marking and packing. 160.043-6 Section 160.043-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant Vessels § 160.043-6 Marking and packing. (a)...

  5. 46 CFR 160.043-6 - Marking and packing.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 6 2012-10-01 2012-10-01 false Marking and packing. 160.043-6 Section 160.043-6 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant Vessels § 160.043-6 Marking and packing. (a)...

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

    ERIC Educational Resources Information Center

    Kromrey, Jeffrey D.; Hines, Constance V.

    1995-01-01

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

  7. 46 CFR 160.043-4 - Construction and workmanship.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 6 2014-10-01 2014-10-01 false Construction and workmanship. 160.043-4 Section 160.043-4 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Jackknife (With Can Opener) for Merchant Vessels § 160.043-4 Construction and workmanship....

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

    ERIC Educational Resources Information Center

    Larwin, Karen; Harvey, Milton

    2012-01-01

    Establishing model parsimony is an important component of structural equation modeling (SEM). Unfortunately, little attention has been given to developing systematic procedures to accomplish this goal. To this end, the current study introduces an innovative application of the jackknife approach first presented in Rensvold and Cheung (1999). Unlike…

  9. 16 CFR 1632.1 - Definitions.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ...-back lounges, push-back sofas, sleep lounges, sofa beds (including jackknife sofa beds), sofa lounges... by any other method which produces a series of depressions on the surface. (i) Manufacturer means an... with § 1632.7. (l) Surface means one side of a mattress or mattress pad which is intended for...

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

    PubMed

    You, Jinhong; Zhou, Haibo

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Mobberley, M. P.

    2010-02-01

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

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

    PubMed Central

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

    2014-01-01

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

  13. Life table and consumption capacity of corn earworm, Helicoverpa armigera, fed asparagus, Asparagus officinalis.

    PubMed

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

    2014-01-01

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

  14. Estimators for the truncated beta-binomial distribution

    SciTech Connect

    Atwood, C.L.

    1980-01-01

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

  15. Validating Livanow: molecular data agree that leeches, Branchiobdellidans, and Acanthobdella peledina form a monophyletic group of oligochaetes.

    PubMed

    Siddall, M E; Apakupakul, K; Burreson, E M; Coates, K A; Erséus, C; Gelder, S R; Källersjö, M; Trapido-Rosenthal, H

    2001-12-01

    To investigate the phylogenetic relationships of leeches, branchiobdellidans, and acanthobdellidans, whole nuclear 18S rDNA and over 650 bp of mitochondrial cytochrome c oxidase subunit I were acquired from 101 annelids, including 36 leeches, 18 branchiobdellidans, Acanthobdella peledina, as well as 28 oligochaetes and combined with homologous data for 17 polychaete outgroup taxa. Parsimony analysis of the combined aligned dataset supported monophyly of leeches, branchiobdellidans, and acanthobdellidans in 100% of jackknife replicates. Monophyly of the oligochaete order Lumbriculida with Acanthobdellida, Branchiobdellida, and Hirudinea was supported in 84% of jackknife replicates. These results provide support for the hypotheses that leeches and branchiobdellidans are sister groups, that acanthobdellidans are sister to them, and that together with the family Lumbriculidae they all constitute a clade within Oligochaeta. Results support synonymy of the classes Clitellata and the more commonly used Oligochaeta. Leeches branchiobdellidans, and acanthobdellidans should be regarded as orders equal to their closest relatives, the order Lumbriculida. PMID:11741378

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

    USGS Publications Warehouse

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

    1978-01-01

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

  17. [Growth of Octopus maya (Mollusca: Cephalopoda) of the Yucatan coast, Mexico: a long-term analysis].

    PubMed

    Nepita Villanueva, M R; Defeo, O

    2001-03-01

    Growth of the octopus (Octopus maya) off Yucatan (Mexico) was estimated from a long-term study (seven years) by the length-based methods ELEFAN, PROJMAT and SLCA. Some 19,251 octopuses with a range of mantle length between 50 and 240 mm were sampled from commercial landings in 1983-1987, 1989 and 1992. The jackknife technique was applied to deal with uncertainty in growth estimates resulting from chance variations in sampling design. The growth index phi' was used for comparative purposes. Results differed markedly among methods: ELEFAN produced parameter estimates within the range reported in the literature, whereas PROJMAT and SLCA showed problems to converge in an optimum combination of parameters, and tended to underestimate them. Jackknife analysis revealed very low intraannual variability in phi' but high variability among years, especially when applying PROJMAT. No significant differences were found in precision parameters--percent error and coefficient of variation--among methods. Estimates of phi' derived by ELEFAN varied between 4.19 and 5.23 and agreed with those reported in the literature (between 4.25 and 4.91), whereas PROJMAT and SLCA estimates were significantly lower. We suggest the use of ELEFAN, together with jackknife, to estimate growth parameters of Octopus maya. PMID:11795175

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

    USGS Publications Warehouse

    McNew, Lance B.; Handel, Colleen M.

    2015-01-01

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

  19. On population size estimators in the Poisson mixture model.

    PubMed

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

    2013-09-01

    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

  20. Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm.

    PubMed

    Sadeghi, Mehdi; Parto, Sahar; Arab, Shahriar; Ranjbar, Bijan

    2005-06-20

    We have used a statistical approach for protein secondary structure prediction based on information theory and simultaneously taking into consideration pairwise residue types and conformational states. Since the prediction of residue secondary structure by one residue window sliding make ambiguity in state prediction, we used a dynamic programming algorithm to find the path with maximum score. A score system for residue pairs in particular conformations is derived for adjacent neighbors up to ten residue apart in sequence. The three state overall per-residue accuracy, Q3, of this method in a jackknife test with dataset created from PDBSELECT is more than 70%. PMID:15936021

  1. HEXT, a software supporting tree-based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test

    PubMed Central

    Schneider, Kevin; Koblmüller, Stephan; Sefc, Kristina M.

    2016-01-01

    Summary The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time. Excess increase in bootstrap support for certain nodes upon exclusion of a particular taxon indicates the hybrid (the excluded taxon) and its parents (the clades with increased support). We introduce a new software program, hext, which generates the taxon-jackknife data sets, runs the bootstrap tree calculations, and identifies excess bootstrap increases as outlier values in boxplot graphs. hext is written in r language and accepts binary data (0/1; e.g. AFLP) as well as co-dominant SNP and genotype data. We demonstrate the usefulness of hext in large SNP data sets containing putative hybrids and their parents. For instance, using published data of the genus Vitis (~6,000 SNP loci), hext output supports V. × champinii as a hybrid between V. rupestris and V. mustangensis. With simulated SNP and AFLP data sets, excess increases in bootstrap support were not always connected with the hybrid taxon (false positives), whereas the expected bootstrap signal failed to appear on several occasions (false negatives). Potential causes for both types of spurious results are discussed. With both empirical and simulated data sets, the taxon-jackknife output generated by hext provided additional signatures of hybrid taxa, including changes in tree topology across trees, consistent effects of exclusions of the hybrid and the parent taxa, and moderate (rather than excessive) increases in

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

    PubMed

    Winter, David J

    2012-11-01

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

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

    PubMed Central

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

    2013-01-01

    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. PMID:21500633

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

    PubMed Central

    Shahrudin, Shahriza

    2015-01-01

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

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

    SciTech Connect

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

    2015-12-31

    Data re-sampling methods such as the delete-one jackknife are a common tool for estimating the covariance of large scale structure probes. In this paper we investigate the concepts of internal covariance estimation in the context of cosmic shear two-point statistics. We demonstrate how to use log-normal simulations of the convergence field and the corresponding shear field to carry out realistic tests of internal covariance estimators and find that most estimators such as jackknife or sub-sample covariance can reach a satisfactory compromise between bias and variance of the estimated covariance. In a forecast for the complete, 5-year DES survey we show that internally estimated covariance matrices can provide a large fraction of the true uncertainties on cosmological parameters in a 2D cosmic shear analysis. The volume inside contours of constant likelihood in the $\\Omega_m$-$\\sigma_8$ plane as measured with internally estimated covariance matrices is on average $\\gtrsim 85\\%$ of the volume derived from the true covariance matrix. The uncertainty on the parameter combination $\\Sigma_8 \\sim \\sigma_8 \\Omega_m^{0.5}$ derived from internally estimated covariances is $\\sim 90\\%$ of the true uncertainty.

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

    DOE PAGESBeta

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

    2015-12-31

    Data re-sampling methods such as the delete-one jackknife are a common tool for estimating the covariance of large scale structure probes. In this paper we investigate the concepts of internal covariance estimation in the context of cosmic shear two-point statistics. We demonstrate how to use log-normal simulations of the convergence field and the corresponding shear field to carry out realistic tests of internal covariance estimators and find that most estimators such as jackknife or sub-sample covariance can reach a satisfactory compromise between bias and variance of the estimated covariance. In a forecast for the complete, 5-year DES survey we show that internally estimated covariance matrices can provide a large fraction of the true uncertainties on cosmological parameters in a 2D cosmic shear analysis. The volume inside contours of constant likelihood in themore » $$\\Omega_m$$-$$\\sigma_8$$ plane as measured with internally estimated covariance matrices is on average $$\\gtrsim 85\\%$$ of the volume derived from the true covariance matrix. The uncertainty on the parameter combination $$\\Sigma_8 \\sim \\sigma_8 \\Omega_m^{0.5}$$ derived from internally estimated covariances is $$\\sim 90\\%$$ of the true uncertainty.« less

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  8. Using increment of diversity to predict mitochondrial proteins of malaria parasite: integrating pseudo-amino acid composition and structural alphabet.

    PubMed

    Chen, Ying-Li; Li, Qian-Zhong; Zhang, Li-Qing

    2012-04-01

    Due to the complexity of Plasmodium falciparum (PF) genome, predicting mitochondrial proteins of PF is more difficult than other species. In this study, using the n-peptide composition of reduced amino acid alphabet (RAAA) obtained from structural alphabet named Protein Blocks as feature parameter, the increment of diversity (ID) is firstly developed to predict mitochondrial proteins. By choosing the 1-peptide compositions on the N-terminal regions with 20 residues as the only input vector, the prediction performance achieves 86.86% accuracy with 0.69 Mathew's correlation coefficient (MCC) by the jackknife test. Moreover, by combining with the hydropathy distribution along protein sequence and several reduced amino acid alphabets, we achieved maximum MCC 0.82 with accuracy 92% in the jackknife test by using the developed ID model. When evaluating on an independent dataset our method performs better than existing methods. The results indicate that the ID is a simple and efficient prediction method for mitochondrial proteins of malaria parasite. PMID:21191803

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

    PubMed

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

    2005-09-01

    PsN-Toolkit is a collection of statistical tools for pharmacometric data analysis using the non-linear mixed effect modeling software NONMEM. The toolkit is object oriented and written in the programming language Perl using the programming library Perl-speaks-NONMEM (PsN). Five methods: the Bootstrap, the Jackknife, Log-likelihood Profiling, Case-deletion Diagnostics and Stepwise Covariate Model building are included as separate classes and may be used in user-written Perl scripts or through stand-alone command line applications. The tools are designed with the ability to cooperate and with an emphasis on common structures for workflow and result handling. Parallel execution of independent tool sections is supported on shared memory multiprocessor (SMP) computers, Mosix/openMosix clusters and distributed computing environments following the NorduGrid standard. In conclusion, PsN-Toolkit makes it easier to use the Bootstrap, the Jackknife, Log-likelihood Profiling, Case-deletion Diagnostics and Stepwise Covariate Model building in pharmacometric data analysis. PMID:16023764

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

    SciTech Connect

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

    1980-05-29

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

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

    SciTech Connect

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

    1981-01-01

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

  12. CAUSAL MARKOV RANDOM FIELD FOR BRAIN MR IMAGE SEGMENTATION

    PubMed Central

    Razlighi, Qolamreza R.; Orekhov, Aleksey; Laine, Andrew; Stern, Yaakov

    2013-01-01

    We propose a new Bayesian classifier, based on the recently introduced causal Markov random field (MRF) model, Quadrilateral MRF (QMRF). We use a second order inhomogeneous anisotropic QMRF to model the prior and likelihood probabilities in the maximum a posteriori (MAP) classifier, named here as MAP-QMRF. The joint distribution of QMRF is given in terms of the product of two dimensional clique distributions existing in its neighboring structure. 20 manually labeled human brain MR images are used to train and assess the MAP-QMRF classifier using the jackknife validation method. Comparing the results of the proposed classifier and FreeSurfer on the Dice overlap measure shows an average gain of 1.8%. We have performed a power analysis to demonstrate that this increase in segmentation accuracy substantially reduces the number of samples required to detect a 5% change in volume of a brain region. PMID:23366607

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

    NASA Astrophysics Data System (ADS)

    Zhang, Jianxi; Yu, Huaizhi; Wang, Jiamin

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

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

    PubMed

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

    2014-09-01

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

  15. Avian community response to small-scale habitat disturbance in Maine

    USGS Publications Warehouse

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

    1989-01-01

    The effects of small clearcuts (1 - 8 ha) on avian communities in the forest of eastern Maine were studied using point counts during spring 1978 - 1981. Surveys were conducted in uncut (control) and clear-cut (treatment) plots in three stand types: conifer, hardwood, and mixed growth. We used a mark-recapture model and its associated jackknife species richness estimator (N), as an indicator of avian community structure. Increases in estimated richness (N) and Shannon - Weaver diversity (H') were noted in the treated hardwood and mixed growth, but not in the conifer stands. Seventeen avian species increased in relative abundance, whereas two species declined. Stand treatment was associated with important changes in bird species composition. Increased habitat patchiness and the creation of forest edge are hypothesized as causes for the greater estimates of richness and diversity.

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

    PubMed Central

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

    2015-01-01

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

  17. A novel predictor for protein structural class based on integrated information of the secondary structure sequence.

    PubMed

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang; Liu, Shuxia

    2014-08-01

    The structural class has become one of the most important features for characterizing the overall folding type of a protein and played important roles in many aspects of protein research. At present, it is still a challenging problem to accurately predict protein structural class for low-similarity sequences. In this study, an 18-dimensional integrated feature vector is proposed by fusing the information about content and position of the predicted secondary structure elements. The consistently high accuracies of jackknife and 10-fold cross-validation tests on different low-similarity benchmark datasets show that the proposed method is reliable and stable. Comparison of our results with other methods demonstrates that our method is an effective computational tool for protein structural class prediction, especially for low-similarity sequences. PMID:24859536

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

    PubMed

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

    2014-07-21

    Knowledge of protein structural classes plays an important role in understanding protein folding patterns. Prediction of protein structural class based solely on sequence data remains to be a challenging problem. In this study, we extract the long-range correlation information and linear correlation information from position-specific score matrix (PSSM). A total of 3600 features are extracted, then, 278 features are selected by a filter feature selection method based on 1189 dataset. To verify the performance of our method (named by LCC-PSSM), jackknife tests are performed on three widely used low similarity benchmark datasets. Comparison of our results with the existing methods shows that our method provides the favorable performance for protein structural class prediction. Stand-alone version of the proposed method (LCC-PSSM) is written in MATLAB language and it can be downloaded from http://bioinfo.zstu.edu.cn/LCC-PSSM/. PMID:24607742

  19. Improving the prediction accuracy of protein structural class: approached with alternating word frequency and normalized Lempel-Ziv complexity.

    PubMed

    Zhang, Shengli; Liang, Yunyun; Yuan, Xiguo

    2014-01-21

    Prediction of protein structural class for low-similarity sequences remains a challenging problem. In this study, the new computational method has been developed to predict protein structural class by incorporating alternating word frequency and normalized Lempel-Ziv complexity. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on three widely used benchmark datasets, 25PDB, 1189 and 640, respectively. We report 83.6%, 81.8% and 83.6% prediction accuracies for 25PDB, 1189 and 640 benchmarks, respectively. Comparison of our results with other methods shows that the proposed method is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity datasets and may at least play an important complementary role to existing methods. PMID:24140787

  20. A protein structural class prediction method based on novel features.

    PubMed

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang

    2013-09-01

    In this study, a 12-dimensional feature vector is constructed to reflect the general contents and spatial arrangements of the secondary structural elements of a given protein sequence. Among the 12 features, 6 novel features are specially designed to improve the prediction accuracies for α/β and α + β classes based on the distributions of α-helices and β-strands and the characteristics of parallel β-sheets and anti-parallel β-sheets. To evaluate our method, the jackknife cross-validating test is employed on two widely-used datasets, 25PDB and 1189 datasets with sequence similarity lower than 40% and 25%, respectively. The performance of our method outperforms the recently reported methods in most cases, and the 6 newly-designed features have significant positive effect to the prediction accuracies, especially for α/β and α + β classes. PMID:23770446

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

    PubMed

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

    2015-11-10

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

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

    PubMed

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

    2015-12-01

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

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

    USGS Publications Warehouse

    Cohn, T.A.

    2005-01-01

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

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

    PubMed

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

    2014-02-01

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

  5. Small-angle X-ray scattering- and nuclear magnetic resonance-derived conformational ensemble of the highly flexible antitoxin PaaA2.

    PubMed

    Sterckx, Yann G J; Volkov, Alexander N; Vranken, Wim F; Kragelj, Jaka; Jensen, Malene Ringkjøbing; Buts, Lieven; Garcia-Pino, Abel; Jové, Thomas; Van Melderen, Laurence; Blackledge, Martin; van Nuland, Nico A J; Loris, Remy

    2014-06-10

    Antitoxins from prokaryotic type II toxin-antitoxin modules are characterized by a high degree of intrinsic disorder. The description of such highly flexible proteins is challenging because they cannot be represented by a single structure. Here, we present a combination of SAXS and NMR data to describe the conformational ensemble of the PaaA2 antitoxin from the human pathogen E. coli O157. The method encompasses the use of SAXS data to filter ensembles out of a pool of conformers generated by a custom NMR structure calculation protocol and the subsequent refinement by a block jackknife procedure. The final ensemble obtained through the method is validated by an established residual dipolar coupling analysis. We show that the conformational ensemble of PaaA2 is highly compact and that the protein exists in solution as two preformed helices, connected by a flexible linker, that probably act as molecular recognition elements for toxin inhibition. PMID:24768114

  6. A Gram-Negative Bacterial Secreted Protein Types Prediction Method Based on PSI-BLAST Profile

    PubMed Central

    2016-01-01

    Prediction of secreted protein types based solely on sequence data remains to be a challenging problem. In this study, we extract the long-range correlation information and linear correlation information from position-specific score matrix (PSSM). A total of 6800 features are extracted at 17 different gaps; then, 309 features are selected by a filter feature selection method based on the training set. To verify the performance of our method, jackknife and independent dataset tests are performed on the test set and the reported overall accuracies are 93.60% and 100%, respectively. Comparison of our results with the existing method shows that our method provides the favorable performance for secreted protein type prediction. PMID:27563663

  7. Discrepancies in the Estimation of Gene Flow in Partula

    PubMed Central

    Johnson, M. S.; Clarke, B.; Murray, J.

    1988-01-01

    Methods for estimating gene flow (Nm) from genetic data should provide important insights into the dynamics of natural populations. If they are to be used with confidence, however, the methods must be shown to produce valid results. Estimates of Nm have been obtained for the snails Partula taeniata and Partula suturalis, based on F(ST) and on the frequencies of private alleles, p(1). Jackknifing was used to reduce the bias of estimates and to obtain confidence limits. The estimates derived from F(ST) are consistent with the low vagility of snails, and with direct field studies of gene flow in P. taeniata. In contrast, the estimates derived from p(1) were up to seven times as large, less precise and less consistent. Although the underlying causes of these discrepancies are not clear, the results suggest that F(ST) is the more reliable indirect estimator of gene flow, at least for Partula. PMID:17246477

  8. Linear regression in astronomy. II

    NASA Technical Reports Server (NTRS)

    Feigelson, Eric D.; Babu, Gutti J.

    1992-01-01

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

  9. Alignment-free microbial phylogenomics under scenarios of sequence divergence, genome rearrangement and lateral genetic transfer

    PubMed Central

    Bernard, Guillaume; Chan, Cheong Xin; Ragan, Mark A.

    2016-01-01

    Alignment-free (AF) approaches have recently been highlighted as alternatives to methods based on multiple sequence alignment in phylogenetic inference. However, the sensitivity of AF methods to genome-scale evolutionary scenarios is little known. Here, using simulated microbial genome data we systematically assess the sensitivity of nine AF methods to three important evolutionary scenarios: sequence divergence, lateral genetic transfer (LGT) and genome rearrangement. Among these, AF methods are most sensitive to the extent of sequence divergence, less sensitive to low and moderate frequencies of LGT, and most robust against genome rearrangement. We describe the application of AF methods to three well-studied empirical genome datasets, and introduce a new application of the jackknife to assess node support. Our results demonstrate that AF phylogenomics is computationally scalable to multi-genome data and can generate biologically meaningful phylogenies and insights into microbial evolution. PMID:27363362

  10. Using reduced amino acid composition to predict defensin family and subfamily: Integrating similarity measure and structural alphabet.

    PubMed

    Zuo, Yong-Chun; Li, Qian-Zhong

    2009-10-01

    Defensins are essentially ancient natural antibiotics with potent activity extending from lower organisms to humans. They can inhibit the growth or virulence of micro-organisms directly or indirectly enhance the host's immune system. The successful prediction of defensin peptides will provide very useful information and insights for the basic research of defensins. In this study, by selecting the N-peptide composition of reduced amino acid alphabet (RAAA) obtained from structural alphabet named Protein Blocks as the feature parameters, the increment of diversity (ID) is firstly developed to predict defensins family and subfamily. The jackknife test based on 2-peptide composition of reduced amino acid alphabet (RAAA) with 13 reduced amino acids shows that the overall accuracy of prediction are 91.36% for defensin family, and 94.21% for defensin subfamily. The results indicate that ID_RAAA is a simple and efficient prediction method for defensin peptides. PMID:19591890

  11. Prediction of Golgi-resident protein types using general form of Chou's pseudo-amino acid compositions: Approaches with minimal redundancy maximal relevance feature selection.

    PubMed

    Jiao, Ya-Sen; Du, Pu-Feng

    2016-08-01

    Recently, several efforts have been made in predicting Golgi-resident proteins. However, it is still a challenging task to identify the type of a Golgi-resident protein. Precise prediction of the type of a Golgi-resident protein plays a key role in understanding its molecular functions in various biological processes. In this paper, we proposed to use a mutual information based feature selection scheme with the general form Chou's pseudo-amino acid compositions to predict the Golgi-resident protein types. The positional specific physicochemical properties were applied in the Chou's pseudo-amino acid compositions. We achieved 91.24% prediction accuracy in a jackknife test with 49 selected features. It has the best performance among all the present predictors. This result indicates that our computational model can be useful in identifying Golgi-resident protein types. PMID:27155042

  12. Predicting Subcellular Localization of Apoptosis Proteins Combining GO Features of Homologous Proteins and Distance Weighted KNN Classifier

    PubMed Central

    Wang, Xiao; Li, Hui; Zhang, Qiuwen; Wang, Rong

    2016-01-01

    Apoptosis proteins play a key role in maintaining the stability of organism; the functions of apoptosis proteins are related to their subcellular locations which are used to understand the mechanism of programmed cell death. In this paper, we utilize GO annotation information of apoptosis proteins and their homologous proteins retrieved from GOA database to formulate feature vectors and then combine the distance weighted KNN classification algorithm with them to solve the data imbalance problem existing in CL317 data set to predict subcellular locations of apoptosis proteins. It is found that the number of homologous proteins can affect the overall prediction accuracy. Under the optimal number of homologous proteins, the overall prediction accuracy of our method on CL317 data set reaches 96.8% by Jackknife test. Compared with other existing methods, it shows that our proposed method is very effective and better than others for predicting subcellular localization of apoptosis proteins. PMID:27213149

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

    PubMed

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

    2016-08-15

    Population attributable risk measures the public health impact of the removal of a risk factor. To apply this concept to epidemiological data, the calculation of a confidence interval to quantify the uncertainty in the estimate is desirable. However, because perhaps of the confusion surrounding the attributable risk measures, there is no standard confidence interval or variance formula given in the literature. In this paper, we implement a fully Bayesian approach to confidence interval construction of the population attributable risk for cross-sectional studies. We show that, in comparison with a number of standard Frequentist methods for constructing confidence intervals (i.e. delta, jackknife and bootstrap methods), the Bayesian approach is superior in terms of percent coverage in all except a few cases. This paper also explores the effect of the chosen prior on the coverage and provides alternatives for particular situations. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26799685

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

    PubMed

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

    2013-09-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    USGS Publications Warehouse

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

    2016-01-01

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

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

    PubMed

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

    2015-01-01

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

  18. PACo: A Novel Procrustes Application to Cophylogenetic Analysis

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

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

    PubMed

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

    2010-02-01

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

  1. Pine Hollow Watershed Project : FY 2000 Projects.

    SciTech Connect

    Sherman County Soil and Water Conservation District

    2001-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-01-01

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

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

    USGS Publications Warehouse

    Kery, M.; Royle, J. Andrew

    2008-01-01

    1. Species richness is the most widely used biodiversity metric, but cannot be observed directly as, typically, some species are overlooked. Imperfect detectability must therefore be accounted for to obtain unbiased species-richness estimates. When richness is assessed at multiple sites, two approaches can be used to estimate species richness: either estimating for each site separately, or pooling all samples. The first approach produces imprecise estimates, while the second loses site-specific information. 2. In contrast, a hierarchical Bayes (HB) multispecies site-occupancy model benefits from the combination of information across sites without losing site-specific information and also yields occupancy estimates for each species. The heart of the model is an estimate of the incompletely observed presence-absence matrix, a centrepiece of biogeography and monitoring studies. We illustrate the model using Swiss breeding bird survey data, and compare its estimates with the widely used jackknife species-richness estimator and raw species counts. 3. Two independent observers each conducted three surveys in 26 1-km(2) quadrats, and detected 27-56 (total 103) species. The average estimated proportion of species detected after three surveys was 0.87 under the HB model. Jackknife estimates were less precise (less repeatable between observers) than raw counts, but HB estimates were as repeatable as raw counts. The combination of information in the HB model thus resulted in species-richness estimates presumably at least as unbiased as previous approaches that correct for detectability, but without costs in precision relative to uncorrected, biased species counts. 4. Total species richness in the entire region sampled was estimated at 113.1 (CI 106-123); species detectability ranged from 0.08 to 0.99, illustrating very heterogeneous species detectability; and species occupancy was 0.06-0.96. Even after six surveys, absolute bias in observed occupancy was estimated at up to 0

  4. From data to probability densities without histograms

    NASA Astrophysics Data System (ADS)

    Berg, Bernd A.; Harris, Robert C.

    2008-09-01

    When one deals with data drawn from continuous variables, a histogram is often inadequate to display their probability density. It deals inefficiently with statistical noise, and binsizes are free parameters. In contrast to that, the empirical cumulative distribution function (obtained after sorting the data) is parameter free. But it is a step function, so that its differentiation does not give a smooth probability density. Based on Fourier series expansion and Kolmogorov tests, we introduce a simple method, which overcomes this problem. Error bars on the estimated probability density are calculated using a jackknife method. We give several examples and provide computer code reproducing them. You may want to look at the corresponding figures 4 to 9 first. Program summaryProgram title: cdf_to_pd Catalogue identifier: AEBC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBC_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.: 2758 No. of bytes in distributed program, including test data, etc.: 18 594 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: 4.14, 9 Nature of problem: When one deals with data drawn from continuous variables, a histogram is often inadequate to display the probability density. It deals inefficiently with statistical noise, and binsizes are free parameters. In contrast to that, the empirical cumulative distribution function (obtained after sorting the data) is parameter free. But it is a step function, so that its differentiation does not give a smooth probability density. Solution method: Based on Fourier series expansion and Kolmogorov tests, we introduce a simple method, which

  5. RNA-MethylPred: A high-accuracy predictor to identify N6-methyladenosine in RNA.

    PubMed

    Jia, Cang-Zhi; Zhang, Jia-Jia; Gu, Wei-Zhen

    2016-10-01

    N6-methyladenosine (m(6)A) is present ubiquitously in the RNA of living organisms from Escherichia coli to humans. Nonetheless, the exact molecular mechanism of this modification remains unclear. The experimental identification of m(6)A modification is time-consuming and expensive; therefore, bioinformatics tools with high accuracy represent desirable alternatives for the large-scale, rapid identification of N6-methyladenosine sites. In this study, RNA-MethylPred, a new bioinformatics model, was developed by incorporating bi-profile Bayes, dinucleotide composition, and k nearest neighbor (KNN) scores for three feature extractions. RNA-MethylPred yielded a Matthew's correlation coefficient (MCC) of 0.53 in a jackknife test, which was 0.24 higher than that of iRNA-Methyl and 0.13 higher than that of pRNAm-PC. The obvious improvements demonstrated that RNA-MethylPred might be a powerful and complementary tool for further experimental investigation of N6-methyladenosine modification. PMID:27338301

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

    SciTech Connect

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

    1989-02-01

    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).

  7. Hypothesis tests for hydrologic alteration

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

  8. RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes.

    PubMed

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

    2016-01-01

    N(1)-methyladenosine (m(1)A) is a prominent RNA modification involved in many biological processes. Accurate identification of m(1)A site is invaluable for better understanding the biological functions of m(1)A. However, limitations in experimental methods preclude the progress towards the identification of m(1)A site. As an excellent complement of experimental methods, a support vector machine based-method called RAMPred is proposed to identify m(1)A sites in H. sapiens, M. musculus and S. cerevisiae genomes for the first time. In this method, RNA sequences are encoded by using nucleotide chemical property and nucleotide compositions. RAMPred achieves promising performances in jackknife tests, cross cell line tests and cross species tests, indicating that RAMPred holds very high potential to become a useful tool for identifying m(1)A sites. For the convenience of experimental scientists, a web-server based on the proposed model was constructed and could be freely accessible at http://lin.uestc.edu.cn/server/RAMPred. PMID:27511610

  9. Estimation of abbreviated mycophenolic acid area under the concentration-time curve during early posttransplant period by limited sampling strategy.

    PubMed

    Mohammadpour, A-H; Nazemian, F; Abtahi, B; Naghibi, M; Gholami, K; Rezaee, S; Nazari, M-R A; Rajabi, O

    2008-12-01

    Area under the concentration curve (AUC) of mycophenolic acid (MPA) could help to optimize therapeutic drug monitoring during the early post-renal transplant period. The aim of this study was to develop a limited sampling strategy to estimate an abbreviated MPA AUC within the first month after renal transplantation. In this study we selected 19 patients in the early posttransplant period with normal renal graft function (glomerular filtration rate > 70 mL/min). Plasma MPA concentrations were measured using reverse-phase high-performance liquid chromatography. MPA AUC(0-12h) was calculated using the linear trapezoidal rule. Multiple stepwise regression analysis was used to determine the minimal and convenient time points of MPA levels that could be used to derive model equations best fitted to MPA AUC(0-12h). The regression equation for AUC estimation that gave the best performance was AUC = 14.46 C(10) + 15.547 (r(2) = .882). The validation of the method was performed using the jackknife method. Mean prediction error of this model was not different from zero (P > .05) and had a high root mean square prediction error (8.06). In conclusion, this limited sampling strategy provided an effective approach for therapeutic drug monitoring during the early posttransplant period. PMID:19100462

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

    PubMed Central

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

    2015-01-01

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

  11. Identifying Antioxidant Proteins by Using Optimal Dipeptide Compositions.

    PubMed

    Feng, Pengmian; Chen, Wei; Lin, Hao

    2016-06-01

    Antioxidant proteins are a kind of molecules that can terminate cellular and DNA damages caused by free radical intermediates. The use of antioxidant proteins for prevention of diseases has been intensively studied in recent years. Thus, accurate identification of antioxidant proteins is essential for understanding their roles in pharmacology. In this study, a support vector machine-based predictor called AodPred was developed for identifying antioxidant proteins. In this predictor, the sequence was formulated by using the optimal 3-gap dipeptides obtained by using feature selection method. It was observed by jackknife cross-validation test that AodPred can achieve an overall accuracy of 74.79 % in identifying antioxidant proteins. As a user-friendly tool, AodPred is freely accessible at http://lin.uestc.edu.cn/server/AntioxiPred . To maximize the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web server to obtain the desired results. PMID:26345449

  12. Prediction of Cancer Drugs by Chemical-Chemical Interactions

    PubMed Central

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

    2014-01-01

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

  13. Modeling habitat suitability for complex species distributions by environmental-distance geometric mean.

    PubMed

    Hirzel, Alexandre H; Arlettaz, Raphaël

    2003-11-01

    This paper presents a new habitat suitability modeling method whose main properties are as follows: (1) It is based on the density of observation points in the environmental space, which enables it to fit complex distributions (e.g. nongaussian, bimodal, asymmetrical, etc.). (2) This density is modeled by computing the geometric mean to all observation points, which we show to be a good trade-off between goodness of fit and prediction power. (3) It does not need any absence information, which is generally difficult to collect and of dubious reliability. (4) The environmental space is represented either by an expert-selection of standardized variables or the axes of a factor analysis [in this paper we used the Ecological Niche Factor Analysis (ENFA)]. We first explain the details of the geometric mean algorithm and then we apply it to the bearded vulture (Gypaetus barbatus) habitat in the Swiss Alps. The results are compared to those obtained by the "median algorithm" and tested by jack-knife cross-validation. We also discuss other related algorithms (BIOCLIM, HABITAT, and DOMAIN). All these analyses were implemented into and performed with the ecology-oriented GIS software BIOMAPPER 2.0.The results show the geometric mean to perform better than the median algorithm, as it produces a tighter fit to the bimodal distribution of the bearded vulture in the environmental space. However, the "median algorithm" being quicker, it could be preferred when modeling more usual distribution. PMID:15015699

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

    PubMed

    Tattar, Prabhanjan N; Vaman, H J

    2014-07-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2015-06-01

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

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

    SciTech Connect

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

    2010-03-10

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

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

    PubMed Central

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

    2014-01-01

    The σ54 promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapidly and effectively identifying the σ54 promoters. Here, a predictor called ‘iPro54-PseKNC’ was developed. In the predictor, the samples of DNA sequences were formulated by a novel feature vector called ‘pseudo k-tuple nucleotide composition’, which was further optimized by the incremental feature selection procedure. The performance of iPro54-PseKNC was examined by the rigorous jackknife cross-validation tests on a stringent benchmark data set. As a user-friendly web-server, iPro54-PseKNC is freely accessible at http://lin.uestc.edu.cn/server/iPro54-PseKNC. For the convenience of the vast majority of experimental scientists, a step-by-step protocol guide was provided on how to use the web-server to get the desired results without the need to follow the complicated mathematics that were presented in this paper just for its integrity. Meanwhile, we also discovered through an in-depth statistical analysis that the distribution of distances between the transcription start sites and the translation initiation sites were governed by the gamma distribution, which may provide a fundamental physical principle for studying the σ54 promoters. PMID:25361964

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

    PubMed

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

    2016-08-15

    Motivated by an investigation of the effect of surface water temperature on the presence of Vibrio cholerae in water samples collected from different fixed surface water monitoring sites in Haiti in different months, we investigated methods to adjust for unmeasured confounding due to either of the two crossed factors site and month. In the process, we extended previous methods that adjust for unmeasured confounding due to one nesting factor (such as site, which nests the water samples from different months) to the case of two crossed factors. First, we developed a conditional pseudolikelihood estimator that eliminates fixed effects for the levels of each of the crossed factors from the estimating equation. Using the theory of U-Statistics for independent but non-identically distributed vectors, we show that our estimator is consistent and asymptotically normal, but that its variance depends on the nuisance parameters and thus cannot be easily estimated. Consequently, we apply our estimator in conjunction with a permutation test, and we investigate use of the pigeonhole bootstrap and the jackknife for constructing confidence intervals. We also incorporate our estimator into a diagnostic test for a logistic mixed model with crossed random effects and no unmeasured confounding. For comparison, we investigate between-within models extended to two crossed factors. These generalized linear mixed models include covariate means for each level of each factor in order to adjust for the unmeasured confounding. We conduct simulation studies, and we apply the methods to the Haitian data. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26892025

  20. Predicting protein structural class with AdaBoost Learner.

    PubMed

    Niu, Bing; Cai, Yu-Dong; Lu, Wen-Cong; Li, Guo-Zheng; Chou, Kuo-Chen

    2006-01-01

    The structural class is an important feature in characterizing the overall topological folding type of a protein or the domains therein. Prediction of protein structural classification has attracted the attention and efforts from many investigators. In this paper a novel predictor, the AdaBoost Learner, was introduced to deal with this problem. The essence of the AdaBoost Learner is that a combination of many 'weak' learning algorithms, each performing just slightly better than a random guessing algorithm, will generate a 'strong' learning algorithm. Demonstration thru jackknife cross-validation on two working datasets constructed by previous investigators indicated that AdaBoost outperformed other predictors such as SVM (support vector machine), a powerful algorithm widely used in biological literatures. It has not escaped our notice that AdaBoost may hold a high potential for improving the quality in predicting the other protein features as well, such as subcellular location and receptor type, among many others. Or at the very least, it will play a complementary role to many of the existing algorithms in this regard. PMID:16800803

  1. Prediction of Protein Submitochondrial Locations by Incorporating Dipeptide Composition into Chou's General Pseudo Amino Acid Composition.

    PubMed

    Ahmad, Khurshid; Waris, Muhammad; Hayat, Maqsood

    2016-06-01

    Mitochondrion is the key organelle of eukaryotic cell, which provides energy for cellular activities. Submitochondrial locations of proteins play crucial role in understanding different biological processes such as energy metabolism, program cell death, and ionic homeostasis. Prediction of submitochondrial locations through conventional methods are expensive and time consuming because of the large number of protein sequences generated in the last few decades. Therefore, it is intensively desired to establish an automated model for identification of submitochondrial locations of proteins. In this regard, the current study is initiated to develop a fast, reliable, and accurate computational model. Various feature extraction methods such as dipeptide composition (DPC), Split Amino Acid Composition, and Composition and Translation were utilized. In order to overcome the issue of biasness, oversampling technique SMOTE was applied to balance the datasets. Several classification learners including K-Nearest Neighbor, Probabilistic Neural Network, and support vector machine (SVM) are used. Jackknife test is applied to assess the performance of classification algorithms using two benchmark datasets. Among various classification algorithms, SVM achieved the highest success rates in conjunction with the condensed feature space of DPC, which are 95.20 % accuracy on dataset SML3-317 and 95.11 % on dataset SML3-983. The empirical results revealed that our proposed model obtained the highest results so far in the literatures. It is anticipated that our proposed model might be useful for future studies. PMID:26746980

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

    SciTech Connect

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

    2010-09-13

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

  3. Spinal hemianesthesia: Unilateral and posterior

    PubMed Central

    Imbelloni, Luiz Eduardo

    2014-01-01

    The injection of a non-isobaric local anesthetic should induce a unilateral spinal anesthesia in patients in a lateral decubitus position. The posterior spinal hemianesthesia only be obtained with hypobaric solutions injected in the jackknife position. The most important factors to be considered when performing a spinal hemianesthesia are: type and gauge of the needle, density of the local anesthetic relative to the CSF, position of the patient, speed of administration of the solution, time of stay in position, and dose/concentration/volume of the anesthetic solution. The distance between the spinal roots on the right-left sides and anterior-posterior is, approximately, 10-15 mm. This distance allows performing unilateral spinal anesthesia or posterior spinal anesthesia. The great advantage of obtaining spinal hemianesthesia is the reduction of cardiovascular changes. Likewise, both the dorsal and unilateral sensory block predominates in relation to the motor block. Because of the numerous advantages of producing spinal hemianesthesia, anesthesiologists should apply this technique more often. This review considers the factors which are relevant, plausible and proven to obtain spinal hemianesthesia. PMID:25886320

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

    PubMed

    Tang, Hua; Chen, Wei; Lin, Hao

    2016-04-01

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

  5. iNuc-STNC: a sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept of SAAC and Chou's PseAAC.

    PubMed

    Tahir, Muhammad; Hayat, Maqsood

    2016-07-19

    The nucleosome is the fundamental unit of eukaryotic chromatin, which participates in regulating different cellular processes. Owing to the huge exploration of new DNA primary sequences, it is indispensable to develop an automated model. However, identification of novel protein sequences using conventional methods is difficult or sometimes impossible because of vague motifs and the intricate structure of DNA. In this regard, an effective and high throughput automated model "iNuc-STNC" has been proposed in order to identify accurately and reliably nucleosome positioning in genomes. In this proposed model, DNA sequences are expressed into three distinct feature extraction strategies containing dinucleotide composition, trinucleotide composition and split trinucleotide composition (STNC). Various statistical models were utilized as learner hypotheses. Jackknife test was employed to evaluate the success rates of the proposed model. The experiential results expressed that SVM, in combination with STNC, has obtained an outstanding performance on all benchmark datasets. The predicted outcomes of the proposed model "iNuc-STNC" is higher than current state of the art methods in the literature so far. It is ascertained that the "iNuc-STNC" model will provide a rudimentary framework for the pharmaceutical industry in the development of drug design. PMID:27271822

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

    PubMed

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

    2016-10-15

    Because soil contaminated with Toxoplasma gondii oocysts is increasingly recognized as a major source of infection for humans, in this study, we investigated the spatial pattern of soil contamination with T. gondii oocysts in urban area of northeastern Mainland China. From April 2014 to May 2015, more than 9000 soil samples were collected. Detection of T. gondii oocysts was performed applying real-time quantitative PCR. Sensitivity was improved by analyzing four replicates for each sampling point. T. gondii was detected in 30.3% of all samples. Subsequently, a maximum entropy model was used to evaluate the effect of land use and intrinsic soil properties on the risk of contamination with oocysts. Jackknife analysis revealed that the likelihood for positive results is significantly enhanced in soil originating from foci of human habitation, wood land and grass land. Furthermore, soil temperature and humidity significantly influence the probability of contamination with T. gondii oocysts. Our findings indicate that land use may affect distribution of T. gondii oocysts in urban areas. PMID:27373378

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

    PubMed Central

    Morales, Jesús; Mandow, Anthony; Martínez, Jorge L.; Reina, Antonio J.; García-Cerezo, Alfonso

    2013-01-01

    Driving vehicles with one or more passive trailers has difficulties in both forward and backward motion due to inter-unit collisions, jackknife, and lack of visibility. Consequently, advanced driver assistance systems (ADAS) for multi-trailer combinations can be beneficial to accident avoidance as well as to driver comfort. The ADAS proposed in this paper aims to prevent unsafe steering commands by means of a haptic handwheel. Furthermore, when driving in reverse, the steering-wheel and pedals can be used as if the vehicle was driven from the back of the last trailer with visual aid from a rear-view camera. This solution, which can be implemented in drive-by-wire vehicles with hitch angle sensors, profits from two methods previously developed by the authors: safe steering by applying a curvature limitation to the leading unit, and a virtual tractor concept for backward motion that includes the complex case of set-point propagation through on-axle hitches. The paper addresses system requirements and provides implementation details to tele-operate two different off- and on-axle combinations of a tracked mobile robot pulling and pushing two dissimilar trailers. PMID:23552102

  8. Estimating biogas production of biologically treated municipal solid waste.

    PubMed

    Scaglia, Barbara; Confalonieri, Roberto; D'Imporzano, Giuliana; Adani, Fabrizio

    2010-02-01

    In this work, a respirometric approach, i.e., Dynamic Respiration Index (DRI), was used to predict the anaerobic biogas potential (ABP), studying 46 waste samples coming directly from MBT full-scale plants. A significant linear regression model was obtained by a jackknife approach: ABP=(34.4+/-2.5)+(0.109+/-0.003).DRI. The comparison of the model of this work with those of the previous works using a different respirometric approach (Sapromat-AT(4)), allowed obtaining similar results and carrying out direct comparison of different limits to accept treated waste in landfill, proposed in the literature. The results indicated that on an average, MBT treatment allowed 56% of ABP reduction after 4weeks of treatment, and 79% reduction after 12weeks of treatment. The obtainment of another regression model allowed transforming Sapromat-AT(4) limit in DRI units, and achieving a description of the kinetics of DRI and the corresponding ABP reductions vs. MBT treatment-time. PMID:19783431

  9. Fusing face-verification algorithms and humans.

    PubMed

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

    2007-10-01

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

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

    PubMed

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

    2008-01-01

    The generic richness and abundance of Bethylidae collected in four different hillside areas of Atlantic rain forest from Espírito Santo, Brazil were studied. The sites are Santa Maria de Jetibá (SMJ), Domingos Martins (DM), Pancas (P) and Atílio Vivacqua (AV). A total of 2,840 specimens of 12 genera were collected. Lepidosternopsis Ogloblin and Bakeriella Kieffer are first recorded from the State. Richness of taxa was calculated using first-order Jackknife richness with EstimateS program. Genera accumulation curves were ran to evaluate the samples. Abundance data were adjusted to the geometric distribution. Parameter k was used to compare areas. The generic profile was not equal for the sites we studied. The areas were considered disturbed. SMJ and DM presented genera richness bigger than in P and AV. The differences in the sites reflect the different preservation of each environment. Pseudisobrachium Kieffer and Dissomphalus Ashmead are most dominant genera in SMJ, DM and P, and Anisepyris Kieffer in AV. This study emphasizes the fact of Dissomphalus as the most abundant genus in rain forests. The generic profile found in AV is similar to that of some areas of Brazilian savannah. PMID:18506293

  11. Chloroplast Genetics of Chlamydomonas. III. Closing the Circle

    PubMed Central

    Singer, Burt; Sager, Ruth; Ramanis, Zenta

    1976-01-01

    A novel mapping procedure is presented for organelle genes or any other genetic system exhibiting a measurable frequency of exchanges occurring at a constant rate over a measurable time interval. For a set of markers in a multiply-marked cross, the exchange rates measure relative map distances from a centromere-like attachment point. With this method, we present mapping data and a linear map of genes in the chlcroplast genome of Chlamydomonas. The data are plotted as log (percent remaining heterozygotes) against time and map distances are taken as proportional to slope. A statistical method which is an adaptation of jackknife methodology to a regression problem was developed to estimate slope values. A single line is fitted to pooled data for each marker from several crosses, and then lines are re-fit to a series of pooled data sets in each of which the observations from a single cross have been omitted. From these data sets a final summary slope is computed as well as a statement of its variability. The relative positions of new markers present in single crosses can then be estimated utilizing data from many crosses. The method does not distinguish between one-armed and two-armed linear or circular maps. However, evaluation of this map in conjunction with cosegregation frequency data (Sager and Ramanis 1976b) provides unambiguous evidence of the genetic circularity of the Chlamydomonas chloroplast genome. PMID:17248718

  12. Computer-aided assessment of cardiac computed tomographic images

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

    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.

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

    PubMed Central

    Yang, Ya; Smith, Stephen A.

    2014-01-01

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

  14. Benthic macroinvertebrate community in the Sinos river drainage basin, Rio Grande do Sul, Brazil.

    PubMed

    Barros, M P; Gayeski, L M; Tundisi, J G

    2016-06-27

    Aquatic macroinvertebrate fauna is a relevant component of limnic continental aquatic ecosystems, playing an important role in several processes with relevant biocomplexity. The present study characterized the benthic macroinvertebrate fauna found in three hydric bodies in the Sinos river drainage basin regarding community structure. Sample was collected from January to December 2013 in three locations in the basin: the city of Caraá (29 °45'45.5"S/50°19'37.3"W), the city of Rolante (29°38'34.4"S/50°32'33.2"W) and the city of Igrejinha (29°36'10.84"S/50°48'49.3"W). Abiotic components (pH, dissolved oxygen and temperature) were registered and collected samples were identified up to family type. Average annual pH, dissolved oxygen and temperature were similar in all locations. A total of 26,170 samples were collected. Class Insecta (Arthropods) represented 85.5% of total sample. Platyhelmintes, Mollusca and Annelida samples were also registered. A total of 57 families were identified for the drainage basin and estimators (Chao-1, Chao-2 and jackknife 2) estimated richness varying from 60 to 72 families. PMID:27355982

  15. Predicting the subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition.

    PubMed

    Zhu, Pan-Pan; Li, Wen-Chao; Zhong, Zhe-Jin; Deng, En-Ze; Ding, Hui; Chen, Wei; Lin, Hao

    2015-02-01

    Mycobacterium tuberculosis is a bacterium that causes tuberculosis, one of the most prevalent infectious diseases. Predicting the subcellular localization of mycobacterial proteins in this bacterium may provide vital clues for the prediction of protein function as well as for drug discovery and design. Therefore, a computational method that can predict the subcellular localization of mycobacterial proteins with high precision is highly desirable. We propose a computational method to predict the subcellular localization of mycobacterial proteins. An objective and strict benchmark dataset was constructed after collecting 272 non-redundant proteins from the universal protein resource (the UniProt database). Subsequently, a novel feature selection strategy based on binomial distribution was used to optimize the feature vector. Finally, a subset containing 219 chosen tripeptide features was imported into a support vector machine-based method to estimate the performance of the dataset in accurately and sensitively identifying these proteins. We found that the proposed method gave a maximum overall accuracy of 89.71% with an average accuracy of 81.12% in the jackknife cross-validation. The results indicate that our prediction method gave an efficient and powerful performance when compared with other published methods. We made the proposed method available on a purpose built Web server called MycoSub that is freely accessible at . We anticipate that MycoSub will become a useful tool for studying the functions of mycobacterial proteins and for designing and developing anti-mycobacterium drugs. PMID:25437899

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

    PubMed

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

    2003-08-01

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

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

    PubMed Central

    Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

    2015-01-01

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

  18. Isotopic and Elemental Composition of Roasted Coffee as a Guide to Authenticity and Origin.

    PubMed

    Carter, James F; Yates, Hans S A; Tinggi, Ujang

    2015-06-24

    This study presents the stable isotopic and elemental compositions of single-origin, roasted coffees available to retail consumers. The δ(13)C, δ(15)N, and δ(18)O compositions were in agreement with those previously reported for green coffee beans. The δ(15)N composition was seen to be related to organic cultivation, reflected in both δ(2)H and δ(18)O compositions. The δ(13)C composition of extracted caffeine differed little from that of the bulk coffee. Stepwise discriminant analysis with jackknife tests, using isotopic and elemental data, provided up to 77% correct classification of regions of production. Samples from Africa and India were readily classified. The wide range in both isotopic and elemental compositions of samples from other regions, specifically Central/South America, resulted in poor discrimination between or within these regions. Simpler X-Y and geo-spatial plots of the isotopic data provided effective visual means to distinguish between coffees from different regions. PMID:26001050

  19. Analysis of bifurcation and stability for a tractor semi-trailer in planar motion

    NASA Astrophysics Data System (ADS)

    Ding, Nenggen; Shi, Xiaobo; Zhang, Yipeng; Chen, Wen

    2014-12-01

    This paper is intended for bifurcation analysis of a nonlinear tractor semi-trailer vehicle model in planar motion and for investigating its stability under constant running conditions. Bifurcation analysis shows that bifurcation diagrams of a tractor semi-trailer are quite different from those of a single-unit vehicle. Some instability phenomena of the vehicle system such as jackknifing, sideslip, and spinning are explained by correlating them with the behaviour in the neighbourhood of unstable fixed points based on analysis of eigenvectors, phase trajectories, and status of lateral tyre force saturation. It is also found that yaw planar instability of a tractor semi-trailer is caused by lateral tyre force saturation of the tractor's rear axles and/or the trailer's axles. Moreover, the stability region in the state space is demarcated, and a stability index for evaluating size of the stability region in a feasible domain is proposed. Yaw stability under constant driving conditions is analysed by using the proposed stability index.

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

    PubMed

    Morales, Jesús; Mandow, Anthony; Martínez, Jorge L; Reina, Antonio J; García-Cerezo, Alfonso

    2013-01-01

    Driving vehicles with one or more passive trailers has difficulties in both forward and backward motion due to inter-unit collisions, jackknife, and lack of visibility. Consequently, advanced driver assistance systems (ADAS) for multi-trailer combinations can be beneficial to accident avoidance as well as to driver comfort. The ADAS proposed in this paper aims to prevent unsafe steering commands by means of a haptic handwheel. Furthermore, when driving in reverse, the steering-wheel and pedals can be used as if the vehicle was driven from the back of the last trailer with visual aid from a rear-view camera. This solution, which can be implemented in drive-by-wire vehicles with hitch angle sensors, profits from two methods previously developed by the authors: safe steering by applying a curvature limitation to the leading unit, and a virtual tractor concept for backward motion that includes the complex case of set-point propagation through on-axle hitches. The paper addresses system requirements and provides implementation details to tele-operate two different off- and on-axle combinations of a tracked mobile robot pulling and pushing two dissimilar trailers. PMID:23552102

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

    NASA Astrophysics Data System (ADS)

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

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

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

    PubMed

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

    2012-10-01

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

  3. Classifying Multifunctional Enzymes by Incorporating Three Different Models into Chou's General Pseudo Amino Acid Composition.

    PubMed

    Zou, Hong-Liang; Xiao, Xuan

    2016-08-01

    With the avalanche of the newly found protein sequences in the post-genomic epoch, there is an increasing trend for annotating a number of newly discovered enzyme sequences. Among the various proteins, enzyme was considered as the one of the largest kind of proteins. It takes part in most of the biochemical reactions and plays a key role in metabolic pathways. Multifunctional enzyme is enzyme that plays multiple physiological roles. Given a multifunctional enzyme sequence, how can we identify its class? Especially, how can we deal with the multi-classes problem since an enzyme may simultaneously belong to two or more functional classes? To address these problems, which are obviously very important both to basic research and drug development, a multi-label classifier was developed via three different prediction models with multi-label K-nearest algorithm. Experimental results obtained on a stringent benchmark dataset of enzymes by jackknife cross-validation test show that the predicting results were exciting, indicating that the current method could be an effective and promising high throughput method in the enzyme research. We hope it could play an important complementary role to the existing predictors in identifying the classes of enzymes. PMID:27113936

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

    PubMed

    Liang, Yunyun; Liu, Sanyang; Zhang, Shengli

    2015-01-01

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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

    2015-12-01

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

  7. Structural class prediction of protein using novel feature extraction method from chaos game representation of predicted secondary structure.

    PubMed

    Zhang, Lichao; Kong, Liang; Han, Xiaodong; Lv, Jinfeng

    2016-07-01

    Protein structural class prediction plays an important role in protein structure and function analysis, drug design and many other biological applications. Extracting good representation from protein sequence is fundamental for this prediction task. In recent years, although several secondary structure based feature extraction strategies have been specially proposed for low-similarity protein sequences, the prediction accuracy still remains limited. To explore the potential of secondary structure information, this study proposed a novel feature extraction method from the chaos game representation of predicted secondary structure to mainly capture sequence order information and secondary structure segments distribution information in a given protein sequence. Several kinds of prediction accuracies obtained by the jackknife test are reported on three widely used low-similarity benchmark datasets (25PDB, 1189 and 640). Compared with the state-of-the-art prediction methods, the proposed method achieves the highest overall accuracies on all the three datasets. The experimental results confirm that the proposed feature extraction method is effective for accurate prediction of protein structural class. Moreover, it is anticipated that the proposed method could be extended to other graphical representations of protein sequence and be helpful in future research. PMID:27084358

  8. Mem-PHybrid: hybrid features-based prediction system for classifying membrane protein types.

    PubMed

    Hayat, Maqsood; Khan, Asifullah

    2012-05-01

    Membrane proteins are a major class of proteins and encoded by approximately 20% to 30% of genes in most organisms. In this work, a two-layer novel membrane protein prediction system, called Mem-PHybrid, is proposed. It is able to first identify the protein query as a membrane or nonmembrane protein. In the second level, it further identifies the type of membrane protein. The proposed Mem-PHybrid prediction system is based on hybrid features, whereby a fusion of both the physicochemical and split amino acid composition-based features is performed. This enables the proposed Mem-PHybrid to exploit the discrimination capabilities of both types of feature extraction strategy. In addition, minimum redundancy and maximum relevance has also been applied to reduce the dimensionality of a feature vector. We employ random forest, evidence-theoretic K-nearest neighbor, and support vector machine (SVM) as classifiers and analyze their performance on two datasets. SVM using hybrid features yields the highest accuracy of 89.6% and 97.3% on dataset1 and 91.5% and 95.5% on dataset2 for jackknife and independent dataset tests, respectively. The enhanced prediction performance of Mem-PHybrid is largely attributed to the exploitation of the discrimination power of the hybrid features and of the learning capability of SVM. Mem-PHybrid is accessible at http://www.111.68.99.218/Mem-PHybrid. PMID:22342883

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

    PubMed

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

    2015-12-01

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

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

    PubMed Central

    Wu, Yun

    2016-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    PubMed

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

    2005-03-01

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

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

    USGS Publications Warehouse

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

    1999-01-01

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

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

    PubMed Central

    Li, Guoqing; Du, Sheng; Wen, Zhongming

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    Wang, Xiaofeng; Yan, Renxiang; Song, Jiangning

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  18. Rapid discrimination of the phenotypic variants of von Willebrand disease.

    PubMed

    Roberts, Jonathan C; Morateck, Patti A; Christopherson, Pamela A; Yan, Ke; Hoffmann, Raymond G; Gill, Joan Cox; Montgomery, Robert R

    2016-05-19

    Approximately 20% to 25% of patients with von Willebrand disease (VWD) have a qualitative defect of the von Willebrand factor (VWF) protein activities. Variant VWD typically is classified as type 1C, 2A, 2B, 2M, or 2N depending on the VWF activity defect. Traditionally, diagnosis has relied on multiple clinical laboratory assays to assign VWD phenotype. We developed an enzyme-linked immunosorbent assay (ELISA) to measure the various activities of VWF on a single plate and evaluated 160 patient samples enrolled in the Zimmerman Program for the Molecular and Clinical Biology of von Willebrand Disease with type 2 VWD. Using linear discriminate analysis (LDA), this assay was able to identify type 1C, 2A, 2B, 2M, or 2N VWD with an overall accuracy of 92.5% in the patient study cohort. LDA jackknife analysis, a statistical resampling technique, identified variant VWD with an overall accuracy of 88.1%, which predicts the assay's performance in the general population. In addition, this assay demonstrated correlation with traditional clinical laboratory VWF assays. The VWF multiplex activity assay may be useful as a same-day screening assay when considering the diagnosis of variant VWD in an individual patient. PMID:26917779

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  20. RAMPred: identifying the N1-methyladenosine sites in eukaryotic transcriptomes

    PubMed Central

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

    2016-01-01

    N1-methyladenosine (m1A) is a prominent RNA modification involved in many biological processes. Accurate identification of m1A site is invaluable for better understanding the biological functions of m1A. However, limitations in experimental methods preclude the progress towards the identification of m1A site. As an excellent complement of experimental methods, a support vector machine based-method called RAMPred is proposed to identify m1A sites in H. sapiens, M. musculus and S. cerevisiae genomes for the first time. In this method, RNA sequences are encoded by using nucleotide chemical property and nucleotide compositions. RAMPred achieves promising performances in jackknife tests, cross cell line tests and cross species tests, indicating that RAMPred holds very high potential to become a useful tool for identifying m1A sites. For the convenience of experimental scientists, a web-server based on the proposed model was constructed and could be freely accessible at http://lin.uestc.edu.cn/server/RAMPred. PMID:27511610

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

    PubMed

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

    2013-06-01

    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

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

    PubMed

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

    2015-01-01

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

  3. Number of mammography cases read per year is a strong predictor of sensitivity

    PubMed Central

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

    2014-01-01

    Abstract. Early detection of breast cancers affects the 5-year recurrence rates and treatment options for diagnosed patients, and consequently, many countries have instituted nationwide screening programs. This study compared the performance of expert radiologists from Australia and the United States in detection of breast cancer. Forty-one radiologists, 21 from Australia and 20 from the United States, reviewed 30 mammographic cases containing two-view mammograms. Twenty cases had abnormal findings and 10 cases had normal findings. Radiologists were asked to locate malignancies and assign a level of confidence. A jackknife free-response receiver operating characteristic, figure of merit (JAFROC, FOM), inferred receiver operating characteristic, area under curve (ROC, AUC), specificity, sensitivity, and location sensitivity were calculated using Ziltron software and JAFROC v4.1. A Mann-Whitney U test was used to compare the performance of Australian and U.S. radiologists. The results showed that when experience and the number of mammograms read per year were taken into account, the Australian radiologists sampled showed significantly higher sensitivity and location sensitivity (p≤0.001). JAFROC (FOM) and inferred ROC (AUC) analysis showed no difference between the overall performance of the two countries. ROC (AUC) and location sensitivity were higher for the Australian radiologists who read the most cases per year. PMID:26158030

  4. Number of mammography cases read per year is a strong predictor of sensitivity.

    PubMed

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

    2014-04-01

    Early detection of breast cancers affects the 5-year recurrence rates and treatment options for diagnosed patients, and consequently, many countries have instituted nationwide screening programs. This study compared the performance of expert radiologists from Australia and the United States in detection of breast cancer. Forty-one radiologists, 21 from Australia and 20 from the United States, reviewed 30 mammographic cases containing two-view mammograms. Twenty cases had abnormal findings and 10 cases had normal findings. Radiologists were asked to locate malignancies and assign a level of confidence. A jackknife free-response receiver operating characteristic, figure of merit (JAFROC, FOM), inferred receiver operating characteristic, area under curve (ROC, AUC), specificity, sensitivity, and location sensitivity were calculated using Ziltron software and JAFROC v4.1. A Mann-Whitney U test was used to compare the performance of Australian and U.S. radiologists. The results showed that when experience and the number of mammograms read per year were taken into account, the Australian radiologists sampled showed significantly higher sensitivity and location sensitivity ([Formula: see text]). JAFROC (FOM) and inferred ROC (AUC) analysis showed no difference between the overall performance of the two countries. ROC (AUC) and location sensitivity were higher for the Australian radiologists who read the most cases per year. PMID:26158030

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

    PubMed

    Wang, Xiaofeng; Yan, Renxiang; Song, Jiangning

    2016-01-01

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

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

    PubMed

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

    2016-06-01

    2'-O-methylationation is an important post-transcriptional modification and plays important roles in many biological processes. Although experimental technologies have been proposed to detect 2'-O-methylationation sites, they are cost-ineffective. As complements to experimental techniques, computational methods will facilitate the identification of 2'-O-methylationation sites. In the present study, we proposed a support vector machine-based method to identify 2'-O-methylationation sites. In this method, RNA sequences were formulated by nucleotide chemical properties and nucleotide compositions. In the jackknife cross-validation test, the proposed method obtained an accuracy of 95.58% for identifying 2'-O-methylationation sites in the human genome. Moreover, the model was also validated by identifying 2'-O-methylation sites in the Mus musculus and Saccharomyces cerevisiae genomes, and the obtained accuracies are also satisfactory. These results indicate that the proposed method will become a useful tool for the research on 2'-O-methylation. PMID:27191866

  7. Body height estimation based on dimensions of sacral and coccygeal vertebrae.

    PubMed

    Pelin, Can; Duyar, Izzet; Kayahan, Esra M; Zağyapan, Ragiba; Ağildere, A Muhteşem; Erar, Aydin

    2005-03-01

    This study is to evaluate whether it is possible to predict living stature from sacral and coccygeal vertebral dimensions. Individual vertebral body heights, sacral height (SH), and sacrococcygeal height (SCH) were recorded from the magnetic resonance images of 42 adult males. Sum of the heights of five sacral vertebrae (sigmaS), the first four coccygeal vertebrae (sigmaC), and the total height of the sacral and the first four coccygeal vertebrae together (sigmaSC) were also recorded. Linear regression equations for stature estimation were produced using the above mentioned variables. The regression equations were constructed and tested by using jack-knife procedure. Statistical analyses indicated that the combined variables (SH, SCH, sigmaS, sigmaC, sigmaSC) were more accurate predictors of stature than the heights of individual vertebrae. The results of the study pointed out that the equations derived from sacrococcygeal dimensions perform somewhat better than ones based on foot and head variables, but worse than those based on long-bone length. As a conclusion, the dimensions of sacral and coccygeal vertebrae could be used for stature estimation when long bones are not available. PMID:15813539

  8. Using Chou's pseudo amino acid composition to predict protein quaternary structure: a sequence-segmented PseAAC approach.

    PubMed

    Zhang, Shao-Wu; Chen, Wei; Yang, Feng; Pan, Quan

    2008-10-01

    In the protein universe, many proteins are composed of two or more polypeptide chains, generally referred to as subunits, which associate through noncovalent interactions and, occasionally, disulfide bonds to form protein quaternary structures. It has long been known that the functions of proteins are closely related to their quaternary structures; some examples include enzymes, hemoglobin, DNA polymerase, and ion channels. However, it is extremely labor-expensive and even impossible to quickly determine the structures of hundreds of thousands of protein sequences solely from experiments. Since the number of protein sequences entering databanks is increasing rapidly, it is highly desirable to develop computational methods for classifying the quaternary structures of proteins from their primary sequences. Since the concept of Chou's pseudo amino acid composition (PseAAC) was introduced, a variety of approaches, such as residue conservation scores, von Neumann entropy, multiscale energy, autocorrelation function, moment descriptors, and cellular automata, have been utilized to formulate the PseAAC for predicting different attributes of proteins. Here, in a different approach, a sequence-segmented PseAAC is introduced to represent protein samples. Meanwhile, multiclass SVM classifier modules were adopted to classify protein quaternary structures. As a demonstration, the dataset constructed by Chou and Cai [(2003) Proteins 53:282-289] was adopted as a benchmark dataset. The overall jackknife success rates thus obtained were 88.2-89.1%, indicating that the new approach is quite promising for predicting protein quaternary structure. PMID:18427713

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

    Goovaerts, P.

    2008-01-01

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

  11. Predictability of Zimbabwe summer rainfall

    NASA Astrophysics Data System (ADS)

    Makarau, Amos; Jury, Mark R.

    1997-11-01

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

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

    PubMed Central

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

    2000-01-01

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

  13. A multi-label classifier for prediction membrane protein functional types in animal.

    PubMed

    Zou, Hong-Liang

    2014-11-01

    Membrane protein is an important composition of cell membrane. Given a membrane protein sequence, how can we identify its type(s) is very important because the type keeps a close correlation with its functions. According to previous studies, membrane protein can be divided into the following eight types: single-pass type I, single-pass type II, single-pass type III, single-pass type IV, multipass, lipid-anchor, GPI-anchor, peripheral membrane protein. With the avalanche of newly found protein sequences in the post-genomic age, it is urgent to develop an automatic and effective computational method to rapid and reliable prediction of the types of membrane proteins. At present, most of the existing methods were based on the assumption that one membrane protein only belongs to one type. Actually, a membrane protein may simultaneously exist at two or more different functional types. In this study, a new method by hybridizing the pseudo amino acid composition with multi-label algorithm called LIFT (multi-label learning with label-specific features) was proposed to predict the functional types both singleplex and multiplex animal membrane proteins. Experimental result on a stringent benchmark dataset of membrane proteins by jackknife test show that the absolute-true obtained was 0.6342, indicating that our approach is quite promising. It may become a useful high-through tool, or at least play a complementary role to the existing predictors in identifying functional types of membrane proteins. PMID:25107302

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

    NASA Astrophysics Data System (ADS)

    Noori, Navideh; Kalin, Latif

    2016-02-01

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

  15. Analysis of Secondary Outcomes in Nested Case-Control Study Designs

    PubMed Central

    Kim, Ryung S.; Kaplan, Robert C.

    2014-01-01

    One of the main perceived advantages of using a case-cohort design compared to a nested case-control design in an epidemiologic study is the ability to evaluate with the same subcohort outcomes other than the primary outcome of interest. In this paper, we show that valid inferences about secondary outcomes can also be achieved in nested case-control studies by using the inclusion probability weighting method originally proposed by Samuelsen (1997) in combination with an approximate jackknife standard error that can be computed using existing software. Simulation studies demonstrate that when the sample size is sufficient, this approach yields valid type 1 error and coverage rates for the analysis of secondary outcomes in nested case-control designs. Interestingly, the statistical power of the nested case-control design was comparable to that of the case-cohort design when the primary and secondary outcomes were positively correlated. The proposed method is illustrated with data from a cohort in Cardiovascular Health Study to study the association of C-reactive protein levels and the incidence of congestive heart failure. PMID:24919979

  16. Improving N(6)-methyladenosine site prediction with heuristic selection of nucleotide physical-chemical properties.

    PubMed

    Zhang, Ming; Sun, Jia-Wei; Liu, Zi; Ren, Ming-Wu; Shen, Hong-Bin; Yu, Dong-Jun

    2016-09-01

    N(6)-methyladenosine (m(6)A) is one of the most common and abundant post-transcriptional RNA modifications found in viruses and most eukaryotes. m(6)A plays an essential role in many vital biological processes to regulate gene expression. Because of its widespread distribution across the genomes, the identification of m(6)A sites from RNA sequences is of significant importance for better understanding the regulatory mechanism of m(6)A. Although progress has been achieved in m(6)A site prediction, challenges remain. This article aims to further improve the performance of m(6)A site prediction by introducing a new heuristic nucleotide physical-chemical property selection (HPCS) algorithm. The proposed HPCS algorithm can effectively extract an optimized subset of nucleotide physical-chemical properties under the prescribed feature representation for encoding an RNA sequence into a feature vector. We demonstrate the efficacy of the proposed HPCS algorithm under different feature representations, including pseudo dinucleotide composition (PseDNC), auto-covariance (AC), and cross-covariance (CC). Based on the proposed HPCS algorithm, we implemented an m(6)A site predictor, called M6A-HPCS, which is freely available at http://csbio.njust.edu.cn/bioinf/M6A-HPCS. Experimental results over rigorous jackknife tests on benchmark datasets demonstrated that the proposed M6A-HPCS achieves higher success rates and outperforms existing state-of-the-art sequence-based m(6)A site predictors. PMID:27293216

  17. Predicting cancerlectins by the optimal g-gap dipeptides

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  18. Effect of varying the gas headspace to meat ratio on the quality and shelf-life of beef steaks packaged in high oxygen modified atmosphere packs.

    PubMed

    Murphy, K M; O'Grady, M N; Kerry, J P

    2013-08-01

    Beef steaks (M. longissimus dorsi) were stored in modified atmosphere packs (MAP) (80% O₂:20% CO₂) with gas headspace to meat ratios of 2:1, 1:1 and 0.5:1 for 14 days at 4 °C. The pH, surface colour, texture and microbiology of beef steaks were unaffected (P>0.05) by varying the gas headspace to meat ratio. APLSR (ANOVA-partial least squares regression) and jack-knife uncertainty testing indicated that lipid oxidation (TBARS) was significantly positively correlated with days 10 (P<0.05) and 14 (P<0.001) of storage. Chemical and sensory detection of lipid oxidation in beef steaks were in agreement on day 14 of storage. The sensory quality and acceptability of beef steaks were similar in gas headspace to meat ratios of 2:1 or 1:1 and unacceptable in 0.5:1. Results indicate that pack size and gas volume can be reduced without negatively affecting fresh beef quality and shelf-life. PMID:23618740

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

    USGS Publications Warehouse

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

    1985-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

    We present measurements of weak gravitational lensing cosmic shear two-point statistics using Dark Energy Survey Science Verification data. We demonstrate that our results are robust to the choice of shear measurement pipeline, either ngmix or im3shape, and robust to the choice of two-point statistic, including both real and Fourier-space statistics. Our results pass a suite of null tests including tests for B-mode contamination and direct tests for any dependence of the two-point functions on a set of 16 observing conditions and galaxy properties, such as seeing, airmass, galaxy color, galaxy magnitude, etc. We furthermore use a large suite of simulations to compute the covariance matrix of the cosmic shear measurements and assign statistical significance to our null tests. We find that our covariance matrix is consistent with the halo model prediction, indicating that it has the appropriate level of halo sample variance. We compare the same jackknife procedure applied to the data and the simulations in order to search for additional sources of noise not captured by the simulations. We find no statistically significant extra sources of noise in the data. The overall detection significance with tomography for our highest source density catalog is 9.7 σ . Cosmological constraints from the measurements in this work are presented in a companion paper [DES et al., Phys. Rev. D 94, 022001 (2016).].

  1. A Computational Model for Predicting RNase H Domain of Retrovirus.

    PubMed

    Wu, Sijia; Zhang, Xinman; Han, Jiuqiang

    2016-01-01

    RNase H (RNH) is a pivotal domain in retrovirus to cleave the DNA-RNA hybrid for continuing retroviral replication. The crucial role indicates that RNH is a promising drug target for therapeutic intervention. However, annotated RNHs in UniProtKB database have still been insufficient for a good understanding of their statistical characteristics so far. In this work, a computational RNH model was proposed to annotate new putative RNHs (np-RNHs) in the retroviruses. It basically predicts RNH domains through recognizing their start and end sites separately with SVM method. The classification accuracy rates are 100%, 99.01% and 97.52% respectively corresponding to jack-knife, 10-fold cross-validation and 5-fold cross-validation test. Subsequently, this model discovered 14,033 np-RNHs after scanning sequences without RNH annotations. All these predicted np-RNHs and annotated RNHs were employed to analyze the length, hydrophobicity and evolutionary relationship of RNH domains. They are all related to retroviral genera, which validates the classification of retroviruses to a certain degree. In the end, a software tool was designed for the application of our prediction model. The software together with datasets involved in this paper can be available for free download at https://sourceforge.net/projects/rhtool/files/?source=navbar. PMID:27574780

  2. Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences.

    PubMed

    Duff, R J; Nickrent, D L

    1999-03-01

    Phylogenetic relationships among embryophytes (tracheophytes, mosses, liverworts, and hornworts) were examined using 21 newly generated mitochondrial small-subunit (19S) rDNA sequences. The "core" 19S rDNA contained more phylogenetically informative sites and lower homoplasy than either nuclear 18S or plastid 16S rDNA. Results of phylogenetic analyses using parsimony (MP) and likelihood (ML) were generally congruent. Using MP, two trees were obtained that resolved either liverworts or hornworts as the basal land plant clade. The optimal ML tree showed hornworts as basal. That topology was not statistically different from the two MP trees, thus both appear to be equally viable evolutionary hypotheses. High bootstrap support was obtained for the majority of higher level embryophyte clades named in a recent morphologically based classification, e.g., Tracheophyta, Euphyllophytina, Lycophytina, and Spermatophytata. Strong support was also obtained for the following monophyletic groups: hornworts, liverworts, mosses, lycopsids, leptosporangiate and eusporangiate ferns, gymnosperms and angiosperms. This molecular analysis supported a sister relationship between Equisetum and leptosporangiate ferns and a monophyletic gymnosperms sister to angiosperms. The topologies of deeper clades were affected by taxon inclusion (particularly hornworts) as demonstrated by jackknife analyses. This study represents the first use of mitochondrial 19S rDNA for phylogenetic purposes and it appears well-suited for examining intermediate to deep evolutionary relationships among embryophytes. PMID:10077500

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

    PubMed

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

    2009-01-01

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

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

    PubMed

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

    2013-01-01

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

  5. Heritable changes in regional cortical thickness with age.

    PubMed

    Chouinard-Decorte, Francois; McKay, D Reese; Reid, Andrew; Khundrakpam, Budhachandra; Zhao, Lu; Karama, Sherif; Rioux, Pierre; Sprooten, Emma; Knowles, Emma; Kent, Jack W; Curran, Joanne E; Göring, Harald H H; Dyer, Thomas D; Olvera, Rene L; Kochunov, Peter; Duggirala, Ravi; Fox, Peter T; Almasy, Laura; Blangero, John; Bellec, Pierre; Evans, Alan C; Glahn, David C

    2014-06-01

    It is now well established that regional indices of brain structure such as cortical thickness, surface area or grey matter volume exhibit spatially variable patterns of heritability. However, a recent study found these patterns to change with age during development, a result supported by gene expression studies. Changes in heritability have not been investigated in adulthood so far and could have important implications in the study of heritability and genetic correlations in the brain as well as in the discovery of specific genes explaining them. Herein, we tested for genotype by age (G ×A) interactions, an extension of genotype by environment interactions, through adulthood and healthy aging in 902 subjects from the Genetics of Brain Structure (GOBS) study. A "jackknife" based method for the analysis of stable cortical thickness clusters (JASC) and scale selection is also introduced. Although additive genetic variance remained constant throughout adulthood, we found evidence for incomplete pleiotropy across age in the cortical thickness of paralimbic and parieto-temporal areas. This suggests that different genetic factors account for cortical thickness heritability at different ages in these regions. PMID:24752552

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Bonaccorso, Brunella; Aronica, Giuseppe

    2016-04-01

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

  8. Hinged plakin domains provide specialized degrees of articulation in envoplakin, periplakin and desmoplakin.

    PubMed

    Al-Jassar, Caezar; Bernadό, Pau; Chidgey, Martyn; Overduin, Michael

    2013-01-01

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

  9. Molecular phylogeny of the Haplosporidia based on two independent gene sequences.

    PubMed

    Reece, Kimberly S; Siddall, Mark E; Stokes, Nancy A; Burreson, Eugene M

    2004-10-01

    The phylogenetic position of the Haplosporidia has confounded taxonomists for more than a century because of the unique morphology of these parasites. We collected DNA sequence data for small subunit (SSU) ribosomal RNA and actin genes from haplosporidians and other protists for conducting molecular phylogenetic analyses to help elucidate relationships of taxa within the group, as well as placement of this group among Eukaryota. Analyses were conducted using DNA sequence data from more than 100 eukaryotic taxa with various combinations of data sets including nucleotide sequence data for each gene separately and combined, as well as SSU ribosomal DNA data combined with translated actin amino acids. In almost all analyses, the Haplosporidia was sister to the Cercozoa with moderate bootstrap and jackknife support. Analysis with actin amino acid sequences alone grouped haplosporidians with the foraminiferans and cercozoans. The haplosporidians Minchinia and Urosporidium were found to be monophyletic, whereas Haplosporidium was paraphyletic. "Microcell" parasites, Bonamia spp. and Mikrocytos roughleyi, were sister to Minchinia, the most derived genus, with Haplosporidium falling between the "microcells" and the more basal Urosporidium. Two recently discovered parasites, one from abalone in New Zealand and another from spot prawns in British Columbia, fell at the base of the Haplosporidia with very strong support, indicating a taxonomic affinity to this group. PMID:15562612

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

    USGS Publications Warehouse

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

    2006-01-01

    Little information currently exists on habitat use by subyearling fall Chinook salmon Oncorhynchus tshawytscha rearing in large, main-stem habitats. We collected habitat use information on subyearlings in the Hanford Reach of the Columbia River during May 1994 and April-May 1995 using point abundance electrofishing. We analyzed measures of physical habitat using logistic regression to predict fish presence and absence in shoreline habitats. The difference between water temperature at the point of sampling and in the main river channel was the most important variable for predicting the presence and absence of subyearlings. Mean water velocities of 45 cm/s or less and habitats with low lateral bank slopes were also associated with a greater likelihood of subyearling presence. Intermediate-sized gravel and cobble substrates were significant predictors of fish presence, but small (<32-mm) and boulder-sized (>256-mm) substrates were not. Our rearing model was accurate at predicting fish presence and absence using jackknifing (80% correct) and classification of observations from an independent data set (76% correct). The habitat requirements of fall Chinook salmon in the Hanford Reach are similar to those reported for juvenile Chinook salmon in smaller systems but are met in functionally different ways in a large river.

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

    NASA Astrophysics Data System (ADS)

    Li, Guoqing; Du, Sheng; Wen, Zhongming

    2016-07-01

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

  12. Distinguishing centrarchid genera by use of lateral line scales

    USGS Publications Warehouse

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

    2007-01-01

    Predator-prey relations involving fishes are often evaluated using scales remaining in gut contents or feces. While several reliable keys help identify North American freshwater fish scales to the family level, none attempt to separate the family Centrarchidae to the genus level. Centrarchidae is of particular concern in the midwestern United States because it contains several popular sport fishes, such as smallmouth bass Micropterus dolomieu, largemouth bass M. salmoides, and rock bass Ambloplites rupestris, as well as less-sought-after species of sunfishes Lepomis spp. and crappies Pomoxis spp. Differentiating sport fish from non-sport fish has important management implications. Morphological characteristics of lateral line scales (n = 1,581) from known centrarchid fishes were analyzed. The variability of measurements within and between genera was examined to select variables that were the most useful in further classifying unknown centrarchid scales. A linear discriminant analysis model was developed using 10 variables. Based on this model, 84.4% of Ambloplites scales, 81.2% of Lepomis scales, and 86.6% of Micropterus scales were classified correctly using a jackknife procedure. ?? Copyright by the American Fisheries Society 2007.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  14. Patterns of connectivity among populations of a coral reef fish

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    PubMed Central

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

    2015-01-01

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

  16. Application of species richness estimators for the assessment of fungal diversity.

    PubMed

    Unterseher, Martin; Schnittler, Martin; Dormann, Carsten; Sickert, Andreas

    2008-05-01

    Species richness and distribution patterns of wood-inhabiting fungi and mycetozoans (slime moulds) were investigated in the canopy of a Central European temperate mixed deciduous forest. Species richness was described with diversity indices and species-accumulation curves. Nonmetrical multidimensional scaling was used to assess fungal species composition on different tree species. Different species richness estimators were used to extrapolate species richness beyond our own data. The reliability of the abundance-based coverage estimator, Chao, Jackknife and other estimators of species richness was evaluated for mycological surveys. While the species-accumulation curve of mycetozoans came close to saturation, that of wood-inhabiting fungi was continuously rising. The Chao 2 richness estimator was considered most appropriate to predict the number of species at the investigation site if sampling were continued. Gray's predictor of species richness should be used if statements of the number of species in larger areas are required. Multivariate analysis revealed the importance of different tree species for the conservation and maintenance of fungal diversity within forests, because each tree species possessed a characteristic fungal community. The described mathematical approaches of estimating species richness possess great potential to address fungal diversity on a regional, national, and global scale. PMID:18355274

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  18. Partial Least Squares local calibration of a UV-visible spectrometer used for in situ measurements of COD and TSS concentrations in urban drainage systems.

    PubMed

    Torres, A; Bertrand-Krajewski, J-L

    2008-01-01

    Recent UV-visible spectrometers deliver on line and in situ absorbance spectra in wastewater or stormwater transported in urban drainage systems. After calibration with local data sets, spectra can be used to estimate pollutant concentrations. Calibration methods are usually based on PLS (Partial Least Squares) regression. Their most important difficulty lies in the identification of the number of both i) the latent vectors and ii) the independent variables. A method is proposed to identify these variables, based on an exhaustive tests procedure (Jackknife cross validation and matrix of prediction indicator). It was applied to estimate TSS (total suspended solids) or COD (chemical oxygen demand) concentrations at the inlet of a storage-settling tank in a stormwater separate sewer system, and compared to three other calibration methods used either for turbidity meters or UV-visible spectrometers. With the available calibration data set: i) the spectrometer gives results with better prediction quality than the turbidity meter, ii) for the spectrometer, local calibration gives better results than global calibration, iii) the proposed PLS method gives results with a similar order of magnitude in uncertainties as the manufacturer local calibration method, but is more open and transparent for the user. Similar results were obtained for a second data set. PMID:18359999

  19. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.

    PubMed

    Yang, Ya; Smith, Stephen A

    2014-11-01

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

  20. Multivariate Analysis of the Ecoregion Delineation for Aquatic Systems

    NASA Astrophysics Data System (ADS)

    Jenerette, G. Darrel; Lee, Jay; Waller, David W.; Carlson, Robert E.

    2002-01-01

    The ecoregion concept is a popular method of understanding the spatial distribution of the environment', however, it has yet to be adequately demonstrated that the environment is distributed in accordance with these bounded units. In this paper, we generated a testable hypothesis based on the current usage of ecoregions: the ecoregion classification will allow for discrimination between lakes of different water quality. The ecoregion classification should also be more effective better than a comparably scaled classification based on political boundaries, land-use class, or random grouping. To test this hypothesis we used the Environmental Monitoring and Assessment Program (EMAP) lake water chemistry data from the northeast United States. The water chemistry data were reduced to four components using principal component analysis. For comparison to an optimal grouping of these data we used K-means cluster analysis to define the extent at which these lakes could be segregated into distinct classes. Jackknifed discriminant analysis was used to determine the classification rate of ecoregions, the three alternative spatial classification methods, and the clustering algorithm. The classification based on ecoregions was successful for 35% of the lakes included in this study, in comparison to the clustered groups accuracy of 98%. These results suggest that the large scale spatial distribution of ecosystem types is more complicated than that suggested by the present ecoregion boundaries. Further tests of ecoregion delineations are needed and alternative large-scale management strategies should be investigated.

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

    SciTech Connect

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

    2015-09-29

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

  2. Predicting discovery rates of genomic features.

    PubMed

    Gravel, Simon

    2014-06-01

    Successful sequencing experiments require judicious sample selection. However, this selection must often be performed on the basis of limited preliminary data. Predicting the statistical properties of the final sample based on preliminary data can be challenging, because numerous uncertain model assumptions may be involved. Here, we ask whether we can predict "omics" variation across many samples by sequencing only a fraction of them. In the infinite-genome limit, we find that a pilot study sequencing 5% of a population is sufficient to predict the number of genetic variants in the entire population within 6% of the correct value, using an estimator agnostic to demography, selection, or population structure. To reach similar accuracy in a finite genome with millions of polymorphisms, the pilot study would require ∼15% of the population. We present computationally efficient jackknife and linear programming methods that exhibit substantially less bias than the state of the art when applied to simulated data and subsampled 1000 Genomes Project data. Extrapolating based on the National Heart, Lung, and Blood Institute Exome Sequencing Project data, we predict that 7.2% of sites in the capture region would be variable in a sample of 50,000 African Americans and 8.8% in a European sample of equal size. Finally, we show how the linear programming method can also predict discovery rates of various genomic features, such as the number of transcription factor binding sites across different cell types. PMID:24637199

  3. Seasonal variations in socially and legally unacceptable sexual behaviour.

    PubMed

    Bicakova-Rocher, A; Smolensky, M; Reinberg, A; De Prins, J

    1985-01-01

    The calendar dates, over the 15-year span 1966-1980, of committed rapes by eight male recidivists and offences of sexually indecent or immoral behaviour by eight other male recidivists were gathered from the files of the Préfecture de Police, Paris, France. Each offender of the first group had committed from two to six rapes, while each offender of the second had committed from two to 16 incidences of indecent behaviour. Although the reported rapes took place during several calendar years, almost all, 18 out of 22 offences, were committed by the eight rape-recidivists during the 4-month span of July-October. Single cosinor analysis of these data revealed a circannual rhythmicity (P less than 0.03) with luminal diameter being 10 August +/- 34 days (the 95% CL). The peak time of indecent sexual behaviour, exclusive of rape, against females occurred during September with secondary peaks in February and June; such offences directed against males peaked in October. 'Bootstrap' and 'Jackknife' methods confirmed seasonality within all data sets, except for the offences of indecent behaviour. PMID:3870851

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

    PubMed

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

    2010-07-27

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a "jackknife model" in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers. PMID:20518483

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    Cameron, Kenneth M.

    2009-01-01

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

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

    PubMed

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

    2007-01-01

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

  8. Fish diversity of floodplain lakes on the lower stretch of the Solimões river.

    PubMed

    Siqueira-Souza, F K; Freitas, C E C

    2004-08-01

    The fish community of the Solimões floodplain lakes was studied by bimonthly samples taken from May 2001 to April 2002. These were carried out at lakes Maracá (03 degrees 51'33"S, 62 degrees 35'08,6"W), Samaúma (03 degrees 50'42,1"S, 61 degrees 39'49,3"W), and Sumaúma and Sacambú (03 degrees 17'11,6"S and 60 degrees 04'31,4"W), located between the town of Coari and the confluence of the Solimões and Negro rivers. Collections were done with 15 gillnets of standardized dimensions with several mesh sizes. We collected 1,313 animals distributed in 77 species, belonging to 55 genera of 20 families and 5 orders. Characiformes was the most abundant Order, with a larger number of representatives in the Serrasalmidae and Curimatidae. The most abundant species in the samplings were Psectrogaster rutiloides (132 individuals), Pigocentrus nattereri (115 individuals), and Serrasalmus elongatus (109 individuals). Lakes Samaúma, Sacambú, and Sumaúma were adjusted to logarithmic and lognormal series. The diversity exhibited an inverse gradient to the river flow, showing the highest diversity at Lake Sumaúma, followed by Samaúma, Sacambú, and Maracá. Species richness estimated through the jackknife technique ranged from 78 to 107 species. PMID:15622847

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

    PubMed Central

    Feng, Pengmian; Zuo, Yongchun

    2014-01-01

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

  10. Microfluidic co-culture platform to quantify chemotaxis of primary stem cells.

    PubMed

    Tatárová, Z; Abbuehl, J P; Maerkl, S; Huelsken, J

    2016-05-21

    Functional analysis of primary tissue-specific stem cells is hampered by their rarity. Here we describe a greatly miniaturized microfluidic device for the multiplexed, quantitative analysis of the chemotactic properties of primary, bone marrow-derived mesenchymal stem cells (MSC). The device was integrated within a fully customized platform that both increased the viability of stem cells ex vivo and simplified manipulation during multidimensional acquisition. Since primary stem cells can be isolated only in limited number, we optimized the design for efficient cell trapping from low volume and low concentration cell suspensions. Using nanoliter volumes and automated microfluidic controls for pulsed medium supply, our platform is able to create stable gradients of chemoattractant secreted from mammalian producer cells within the device, as was visualized by a secreted NeonGreen fluorescent reporter. The design was functionally validated by a CXCL/CXCR ligand/receptor combination resulting in preferential migration of primary, non-passaged MSC. Stable gradient formation prolonged assay duration and resulted in enhanced response rates for slowly migrating stem cells. Time-lapse video microscopy facilitated determining a number of migratory properties based on single cell analysis. Jackknife-resampling revealed that our assay requires only 120 cells to obtain statistically significant results, enabling new approaches in the research on rare primary stem cells. Compartmentalization of the device not only facilitated such quantitative measurements but will also permit future, high-throughput functional screens. PMID:27137768

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

    DOE PAGESBeta

    Becker, M. R.

    2016-07-06

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

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

    PubMed

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

    2014-01-01

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

  13. A computational approach to identify genes for functional RNAs in genomic sequences

    PubMed Central

    Carter, Richard J.; Dubchak, Inna; Holbrook, Stephen R.

    2001-01-01

    Currently there is no successful computational approach for identification of genes encoding novel functional RNAs (fRNAs) in genomic sequences. We have developed a machine learning approach using neural networks and support vector machines to extract common features among known RNAs for prediction of new RNA genes in the unannotated regions of prokaryotic and archaeal genomes. The Escherichia coli genome was used for development, but we have applied this method to several other bacterial and archaeal genomes. Networks based on nucleotide composition were 80–90% accurate in jackknife testing experiments for bacteria and 90–99% for hyperthermophilic archaea. We also achieved a significant improvement in accuracy by combining these predictions with those obtained using a second set of parameters consisting of known RNA sequence motifs and the calculated free energy of folding. Several known fRNAs not included in the training datasets were identified as well as several hundred predicted novel RNAs. These studies indicate that there are many unidentified RNAs in simple genomes that can be predicted computationally as a precursor to experimental study. Public access to our RNA gene predictions and an interface for user predictions is available via the web. PMID:11574674

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

    PubMed

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

    2015-02-01

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

  15. Computerized screening of children congenital heart diseases.

    PubMed

    Sepehri, Amir A; Hancq, Joel; Dutoit, Thierry; Gharehbaghi, Arash; Kocharian, Armen; Kiani, A

    2008-11-01

    In this paper, we propose a method for automated screening of congenital heart diseases in children through heart sound analysis techniques. Our method relies on categorizing the pathological murmurs based on the heart sections initiating them. We show that these pathelogical murmur categories can be identified by examining the heart sound energy over specific frequency bands, which we call, Arash-Bands. To specify the Arash-Band for a category, we evaluate the energy of the heart sound over all possible frequency bands. The Arash-Band is the frequency band that provides the lowest error in clustering the instances of that category against the normal ones. The energy content of the Arash-Bands for different categories constitue a feature vector that is suitable for classification using a neural network. In order to train, and to evaluate the performance of the proposed method, we use a training data-bank, as well as a test data-bank, collectively consisting of ninety samples (normal and abnormal). Our results show that in more than 94% of cases, our method correctly identifies children with congenital heart diseases. This percentage improves to 100%, when we use the Jack-Knife validation method over all the 90 samples. PMID:18718691

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

    PubMed Central

    Liu, Junbao; Li, Li-Peng; He, Yi-Chun; Gao, Ru-Jian; Cai, Yu-Dong; Jiang, Yang

    2015-01-01

    Cancer is a serious disease responsible for many deaths every year in both developed and developing countries. One reason is that the mechanisms underlying most types of cancer are still mysterious, creating a great block for the design of effective treatments. In this study, we attempted to clarify the mechanism underlying esophageal cancer by searching for novel genes and chemicals. To this end, we constructed a hybrid network containing both proteins and chemicals, and generalized an existing computational method previously used to identify disease genes to identify new candidate genes and chemicals simultaneously. Based on jackknife test, our generalized method outperforms or at least performs at the same level as those obtained by a widely used method - the Random Walk with Restart (RWR). The analysis results of the final obtained genes and chemicals demonstrated that they highly shared gene ontology (GO) terms and KEGG pathways with direct and indirect associations with esophageal cancer. In addition, we also discussed the likelihood of selected candidate genes and chemicals being novel genes and chemicals related to esophageal cancer. PMID:26058041

  17. Investigating different similarity measures for a case-based reasoning classifier to predict breast cancer

    NASA Astrophysics Data System (ADS)

    Bilska-Wolak, Anna O.; Floyd, Carey E., Jr.

    2001-07-01

    This paper investigates the effects of using different similarity measures for a case-based reasoning (CBR) classifier to predict breast cancer. The CBR classifier used a mammographer's BI-RADSTM description of a lesion to predict breast biopsy outcome. The classifier compared the case to be examined to a reference collection of cases and identified those that were similar. The decision variable was formed as the ratio of similar cases that were malignant to all similar cases. A reference collection of 1027 biopsy-proven cases from Duke University Medical Center was used as input. Both Euclidean and Hamming distance measures were compared using all possible combinations of nine BI-RADSTM features and age. Performance was evaluated using jackknife sampling and ROC analysis. For all combinations of features, it was found that Euclidean distance measure produced greater ROC areas and partial ROC areas than Hamming. The differences were significant at an alpha level of 0.05. The greatest ROC area of 0.82 +/- 0.01 was generated using six of the features and Euclidean distance measure. The results of both distance measures yielded greater ROC areas than previously reported values and were similar to results generated with an Artificial Neural Network using 10 features.

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

    USGS Publications Warehouse

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

    1999-01-01

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

  19. Nonparametric methods for drought severity estimation at ungauged sites

    NASA Astrophysics Data System (ADS)

    Sadri, S.; Burn, D. H.

    2012-12-01

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

  20. Regional low-flow frequency analysis using single and ensemble artificial neural networks

    NASA Astrophysics Data System (ADS)

    Ouarda, T. B. M. J.; Shu, C.

    2009-11-01

    In this paper, artificial neural networks (ANNs) are introduced to obtain improved regional low-flow estimates at ungauged sites. A multilayer perceptron (MLP) network is used to identify the functional relationship between low-flow quantiles and the physiographic variables. Each ANN is trained using the Levenberg-Marquardt algorithm. To improve the generalization ability of a single ANN, several ANNs trained for the same task are used as an ensemble. The bootstrap aggregation (or bagging) approach is used to generate individual networks in the ensemble. The stacked generalization (or stacking) technique is adopted to combine the member networks of an ANN ensemble. The proposed approaches are applied to selected catchments in the province of Quebec, Canada, to obtain estimates for several representative low-flow quantiles of summer and winter seasons. The jackknife validation procedure is used to evaluate the performance of the proposed models. The ANN-based approaches are compared with the traditional parametric regression models. The results indicate that both the single and ensemble ANN models provide superior estimates than the traditional regression models. The ANN ensemble approaches provide better generalization ability than the single ANN models.

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

    Wang, Xiaofeng; Zhou, Yuan; Yan, Renxiang

    2015-07-01

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

  4. The influence of protein coding sequences on protein folding rates of all-β proteins.

    PubMed

    Li, Rui Fang; Li, Hong

    2011-06-01

    It is currently believed that the protein folding rate is related to the protein structures and its amino acid sequence. However, few studies have been done on the problem that whether the protein folding rate is influenced by its corresponding mRNA sequence. In this paper, we analyzed the possible relationship between the protein folding rates and the corresponding mRNA sequences. The content of guanine and cytosine (GC content) of palindromes in protein coding sequence was introduced as a new parameter and added in the Gromiha's model of predicting protein folding rates to inspect its effect in protein folding process. The multiple linear regression analysis and jack-knife test show that the new parameter is significant. The linear correlation coefficient between the experimental and the predicted values of the protein folding rates increased significantly from 0.96 to 0.99, and the population variance decreased from 0.50 to 0.24 compared with Gromiha's results. The results show that the GC content of palindromes in the corresponding protein coding sequence really influences the protein folding rate. Further analysis indicates that this kind of effect mostly comes from the synonymous codon usage and from the information of palindrome structure itself, but not from the translation information from codons to amino acids. PMID:21613670

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

    DOE PAGESBeta

    Ade, P. A. R.; Ahmed, Z.; Aikin, R. W.; Alexander, K. D.; Barkats, D.; Benton, S. J.; Bischoff, C. A.; Bock, J. J.; Brevik, J. A.; Buder, I.; et al

    2015-09-29

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

  6. Cosmic Shear Measurements with DES Science Verification Data

    SciTech Connect

    Becker, M. R.

    2015-07-20

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2003-01-01

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

  10. Auditory morphology and hearing sensitivity in fossil New World monkeys.

    PubMed

    Coleman, Mark N; Kay, Richard F; Colbert, Matthew W

    2010-10-01

    In recent years it has become possible to investigate the hearing capabilities in fossils by analogy with studies in living taxa that correlate the bony morphology of the auditory system with hearing sensitivity. In this analysis, we used a jack-knife procedure to test the accuracy of one such study that examined the functional morphology of the primate auditory system and we found that low-frequency hearing (sound pressure level at 250 Hz) can be predicted with relatively high confidence (±3-8 dB depending on the structure). Based on these functional relationships, we then used high-resolution computed tomography to examine the auditory region of three fossil New World monkeys (Homunculus, Dolicocebus, and Tremacebus) and compared their morphology and predicted low-frequency sensitivity with a phylogenetically diverse sample of extant primates. These comparisons reveal that these extinct taxa shared many auditory characteristics with living platyrrhines. However, the fossil with the best preserved auditory region (Homunculus) also displayed a few unique features such as the relative size of the tympanic membrane and stapedial footplate and the degree of trabeculation of the anterior accessory cavity. Still, the majority of evidence suggests that these fossil species likely had similar low-frequency sensitivity to extant South American monkeys. This research adds to the small but growing body of evidence on the evolution of hearing abilities in extinct taxa and lays the groundwork for predicting hearing sensitivity in additional fossil primate specimens. PMID:20730868

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

    NASA Astrophysics Data System (ADS)

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

    1993-09-01

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

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

    PubMed Central

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

    2011-01-01

    Purpose To develop a bootstrap method to assess the quality of High Angular Resolution Diffusion Imaging (HARDI) data using Q-Ball imaging (QBI) reconstruction. Materials and Methods HARDI data were re-shuffled using regular bootstrap with jackknife sampling. For each bootstrap dataset, the diffusion orientation distribution function (ODF) was estimated voxel-wise using QBI reconstruction based on spherical harmonics functions. The reproducibility of the ODF was assessed using the Jensen-Shannon divergence (JSD) and the angular confidence interval was derived for the first and the second ODF maxima. The sensitivity of the bootstrap method was evaluated on a human subject by adding synthetic noise to the data, by acquiring a map of image signal-to-noise ratio (SNR) and by varying the echo time and the b-value. Results The JSD was directly linked to the image SNR. The impact of echo times and b-values was reflected by both the JSD and the angular confidence interval, proving the usefulness of the bootstrap method to evaluate specific features of HARDI data. Conclusion The bootstrap method can effectively assess the quality of HARDI data and can be used to evaluate new hardware and pulse sequences, perform multi-fiber probabilistic tractography, and provide reliability metrics to support clinical studies. PMID:21509879

  13. Predicting DNA binding proteins using support vector machine with hybrid fractal features.

    PubMed

    Niu, Xiao-Hui; Hu, Xue-Hai; Shi, Feng; Xia, Jing-Bo

    2014-02-21

    DNA-binding proteins play a vitally important role in many biological processes. Prediction of DNA-binding proteins from amino acid sequence is a significant but not fairly resolved scientific problem. Chaos game representation (CGR) investigates the patterns hidden in protein sequences, and visually reveals previously unknown structure. Fractal dimensions (FD) are good tools to measure sizes of complex, highly irregular geometric objects. In order to extract the intrinsic correlation with DNA-binding property from protein sequences, CGR algorithm, fractal dimension and amino acid composition are applied to formulate the numerical features of protein samples in this paper. Seven groups of features are extracted, which can be computed directly from the primary sequence, and each group is evaluated by the 10-fold cross-validation test and Jackknife test. Comparing the results of numerical experiments, the group of amino acid composition and fractal dimension (21-dimension vector) gets the best result, the average accuracy is 81.82% and average Matthew's correlation coefficient (MCC) is 0.6017. This resulting predictor is also compared with existing method DNA-Prot and shows better performances. PMID:24189096

  14. Prediction and Analysis of Protein Hydroxyproline and Hydroxylysine

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

    Cherian, Betsy Sheena; Nair, Achuthsankar S.

    2010-01-22

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

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

    SciTech Connect

    Lees, J.M.; Crosson, R.S. )

    1990-04-10

    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.

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

    NASA Astrophysics Data System (ADS)

    Aoi, Shinya; Egi, Yoshimasa; Tsuchiya, Kazuo

    2013-01-01

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

  18. Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach

    PubMed Central

    Honavar, Vasant; Dobbs, Drena

    2010-01-01

    In this paper, we describe a machine learning approach for sequence-based prediction of protein-protein interaction sites. A support vector machine (SVM) classifier was trained to predict whether or not a surface residue is an interface residue (i.e., is located in the protein-protein interaction surface), based on the identity of the target residue and its ten sequence neighbors. Separate classifiers were trained on proteins from two categories of complexes, antibody-antigen and protease-inhibitor. The effectiveness of each classifier was evaluated using leave-one-out (jack-knife) cross-validation. Interface and non-interface residues were classified with relatively high sensitivity (82.3% and 78.5%) and specificity (81.0% and 77.6%) for proteins in the antigen-antibody and protease-inhibitor complexes, respectively. The correlation between predicted and actual labels was 0.430 and 0.462, indicating that the method performs substantially better than chance (zero correlation). Combined with recently developed methods for identification of surface residues from sequence information, this offers a promising approach to predict residues involved in protein-protein interactions from sequence information alone. PMID:20526429

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

    NASA Technical Reports Server (NTRS)

    Hall, Timothy; Yonekura, Emmi

    2013-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2014-01-01

    If the nature of groundwater sources and sinks can be determined or predicted, the data can be used to forecast natural aquifer discharge. We present a procedure to forecast the relative contribution of individual aquifer sources and sinks to natural aquifer discharge. Using these individual aquifer recharge components, along with observed aquifer heads for each January, we generate a 1-year, monthly spring discharge forecast for the upcoming year with an existing numerical model and convolution. The results indicate that a forecast of natural aquifer discharge can be developed using only the dominant aquifer recharge sources combined with the effects of aquifer heads (initial conditions) at the time the forecast is generated. We also estimate how our forecast will perform in the future using a jackknife procedure, which indicates that the future performance of the forecast is good (Nash-Sutcliffe efficiency of 0.81). We develop a forecast and demonstrate important features of the procedure by presenting an application to the Eastern Snake Plain Aquifer in southern Idaho. PMID:23914881

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

    NASA Astrophysics Data System (ADS)

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

    2008-04-01

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

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

    PubMed

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

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  6. Comparison of mapping approaches of design annual maximum daily precipitation

    NASA Astrophysics Data System (ADS)

    Szolgay, J.; Parajka, J.; Kohnová, S.; Hlavčová, K.

    2009-05-01

    In this study 2-year and 100-year annual maximum daily precipitation for rainfall-runoff studies and estimating flood hazard were mapped. The daily precipitation measurements at 23 climate stations from 1961-2000 were used in the upper Hron basin in central Slovakia. The choice of data preprocessing and interpolation methods was guided by their practical applicability and acceptance in the engineering hydrologic community. The main objective was to discuss the quality and properties of maps of design precipitation with a given return period with respect to the expectations of the end user. Four approaches to the preprocessing of annual maximum 24-hour precipitation data were used, and three interpolation methods employed. The first approach is the direct mapping of at-site estimates of distribution function quantiles; the second is the direct mapping of local estimates of the three parameters of the GEV distribution. In the third, the daily precipitation totals were interpolated into a regular grid network, and then the time series of the maximum daily precipitation totals in each grid point of the selected region were statistically analysed. In the fourth, the spatial distribution of the design precipitation was modeled by quantiles predicted by regional precipitation frequency analysis using the Hosking and Wallis procedure. The three interpolation methods used were the inverse distance weighting, nearest neighbor and the kriging method. Visual inspection and jackknife cross-validation were used to compare the combination of approaches.

  7. Consistency of methods for analysing location-specific data

    PubMed Central

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

    2010-01-01

    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

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

    PubMed Central

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

    2015-01-01

    Abstract. The aim of this study was to investigate the diagnostic performance of radiological technologists (RTs) in the detection of malignant microcalcifications and to evaluate how much computer-aided detection (CADe) improved their performances compared with those by expert breast radiologists (BRs). Six board-certified breast RTs and four board-certified BRs participated in a free-response receiver operating characteristic observer study. The dataset consisted of 75 cases (25 malignant, 25 benign, and 25 normal cases) of digital mammograms, selected from the digital database for screening mammography provided by the University of South Florida. Average figure of merit (FOM) of the RTs’ performances was statistically analyzed using jack-knife free-response receiver operating characteristic and compared with that of expert BRs. The detection performance of RTs was significantly improved by using CADe; average sensitivity was increased from 46.7% to 56.7%, with a decrease in the average number of false positives per case from 0.19 to 0.13. Detection accuracy of an average FOM was improved from 0.680 to 0.816 (p=0.001) and the difference in FOMs between RTs and radiologists failed to reach statistical significance. RTs’ performances for the identification of malignant microcalcifications on digital mammography were sufficiently high and comparable to those of radiologists by using CADe. PMID:26158109

  9. Prediction of change in protein unfolding rates upon point mutations in two state proteins.

    PubMed

    Chaudhary, Priyashree; Naganathan, Athi N; Gromiha, M Michael

    2016-09-01

    Studies on protein unfolding rates are limited and challenging due to the complexity of unfolding mechanism and the larger dynamic range of the experimental data. Though attempts have been made to predict unfolding rates using protein sequence-structure information there is no available method for predicting the unfolding rates of proteins upon specific point mutations. In this work, we have systematically analyzed a set of 790 single mutants and developed a robust method for predicting protein unfolding rates upon mutations (Δlnku) in two-state proteins by combining amino acid properties and knowledge-based classification of mutants with multiple linear regression technique. We obtain a mean absolute error (MAE) of 0.79/s and a Pearson correlation coefficient (PCC) of 0.71 between predicted unfolding rates and experimental observations using jack-knife test. We have developed a web server for predicting protein unfolding rates upon mutation and it is freely available at https://www.iitm.ac.in/bioinfo/proteinunfolding/unfoldingrace.html. Prominent features that determine unfolding kinetics as well as plausible reasons for the observed outliers are also discussed. PMID:27264959

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

    Luebben, Jens; Gruene, Tim

    2015-01-01

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

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

    PubMed Central

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

    2008-01-01

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

  13. Recent Developments in the Dorfman-Berbaum-Metz Procedure for Multireader ROC Study Analysis

    PubMed Central

    Hillis, Stephen L.; Berbaum, Kevin S.; Metz, Charles E.

    2009-01-01

    Rationale and Objectives The Dorfman-Berbaum-Metz (DBM) method has been one of the most popular methods for analyzing multireader receiver operating characteristic (ROC) studies since it was proposed in 1992. Despite its popularity, the original procedure has several drawbacks: it is limited to jackknife accuracy estimates, it is substantially conservative, and it is not based on a satisfactory conceptual or theoretical model. Recently, solutions to these problems have been presented in three papers. Our purpose is to summarize and provide an overview of these recent developments. Materials and Methods We present and discuss the recently proposed solutions for the various drawbacks of the original DBM method. Results We compare the solutions in a simulation study and find that they result in improved performance for the DBM procedure. We also compare the solutions using two real data studies and find that the modified DBM procedure that incorporates these solutions yields more significant results and clearer interpretations of the variance component parameters than the original DBM procedure. Conclusions We recommend using the modified DBM procedure that incorporates the recent developments. PMID:18423323

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

    PubMed

    Li, Guoqing; Du, Sheng; Wen, Zhongming

    2016-01-01

    Oriental arborvitae (Platycladus orientalis) is an important afforestation and ornamental tree species, which is native in eastern Asian. Therefore, a global suitable habitat map for oriental arborvitae is urgently needed for global promotion and cultivation. Here, the potential habitat and climatic requirements of oriental arborvitae at global scale were simulated using herbariums data and 13 thermal-moisture variables as input data for maximum entropy model (MaxEnt). The simulation performance of MaxEnt is evaluated by ten-fold cross-validation and a jackknife procedure. Results show that the potential habitat and climate envelop of oriental arborvitae can be successfully simulated by MaxEnt at global scale, with a mean test AUC value of 0.93 and mean training AUC value of 0.95. Thermal factors play more important roles than moisture factors in controlling the distribution boundary of oriental arborvitae's potential ranges. There are about 50 countries suitable for introduction and cultivation of oriental arborvitae with an area of 2.0 × 10(7) km(2), which occupied 13.8% of land area on the earth. This unique study will provide valuable information and insights needed to identify new regions with climatically suitable habitats for cultivation and introduction of oriental arborvitae around the world. PMID:27443221

  15. Predicting cancerlectins by the optimal g-gap dipeptides

    PubMed Central

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

    2015-01-01

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

  16. Demographic history and rare allele sharing among human populations.

    PubMed

    Gravel, Simon; Henn, Brenna M; Gutenkunst, Ryan N; Indap, Amit R; Marth, Gabor T; Clark, Andrew G; Yu, Fuli; Gibbs, Richard A; Bustamante, Carlos D

    2011-07-19

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

  17. Metric optimisation for analogue forecasting by simulated annealing

    NASA Astrophysics Data System (ADS)

    Bliefernicht, J.; Bárdossy, A.

    2009-04-01

    It is well known that weather patterns tend to recur from time to time. This property of the atmosphere is used by analogue forecasting techniques. They have a long history in weather forecasting and there are many applications predicting hydrological variables at the local scale for different lead times. The basic idea of the technique is to identify past weather situations which are similar (analogue) to the predicted one and to take the local conditions of the analogues as forecast. But the forecast performance of the analogue method depends on user-defined criteria like the choice of the distance function and the size of the predictor domain. In this study we propose a new methodology of optimising both criteria by minimising the forecast error with simulated annealing. The performance of the methodology is demonstrated for the probability forecast of daily areal precipitation. It is compared with a traditional analogue forecasting algorithm, which is used operational as an element of a hydrological forecasting system. The study is performed for several meso-scale catchments located in the Rhine basin in Germany. The methodology is validated by a jack-knife method in a perfect prognosis framework for a period of 48 years (1958-2005). The predictor variables are derived from the NCEP/NCAR reanalysis data set. The Brier skill score and the economic value are determined to evaluate the forecast skill and value of the technique. In this presentation we will present the concept of the optimisation algorithm and the outcome of the comparison. It will be also demonstrated how a decision maker should apply a probability forecast to maximise the economic benefit from it.

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

    USGS Publications Warehouse

    Thieler, E. Robert; Danforth, William W.

    1994-01-01

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

  19. A phantom-based JAFROC observer study of two CT reconstruction methods: the search for optimisation of lesion detection and effective dose

    NASA Astrophysics Data System (ADS)

    Thompson, John D.; Chakraborty, Dev P.; Szczepura, Katy; Vamvakas, Ioannis; Tootell, Andrew; Manning, David J.; Hogg, Peter

    2015-03-01

    Purpose: To investigate the dose saving potential of iterative reconstruction (IR) in a computed tomography (CT) examination of the thorax. Materials and Methods: An anthropomorphic chest phantom containing various configurations of simulated lesions (5, 8, 10 and 12mm; +100, -630 and -800 Hounsfield Units, HU) was imaged on a modern CT system over a tube current range (20, 40, 60 and 80mA). Images were reconstructed with (IR) and filtered back projection (FBP). An ATOM 701D (CIRS, Norfolk, VA) dosimetry phantom was used to measure organ dose. Effective dose was calculated. Eleven observers (15.11+/-8.75 years of experience) completed a free response study, localizing lesions in 544 single CT image slices. A modified jackknife alternative free-response receiver operating characteristic (JAFROC) analysis was completed to look for a significant effect of two factors: reconstruction method and tube current. Alpha was set at 0.05 to control the Type I error in this study. Results: For modified JAFROC analysis of reconstruction method there was no statistically significant difference in lesion detection performance between FBP and IR when figures-of-merit were averaged over tube current (F(1,10)=0.08, p = 0.789). For tube current analysis, significant differences were revealed between multiple pairs of tube current settings (F(3,10) = 16.96, p<0.001) when averaged over image reconstruction method. Conclusion: The free-response study suggests that lesion detection can be optimized at 40mA in this phantom model, a measured effective dose of 0.97mSv. In high-contrast regions the diagnostic value of IR, compared to FBP, is less clear.

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

    PubMed

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

    2015-07-15

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

  1. Classification of Birds and Bats Using Flight Tracks

    SciTech Connect

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

    2015-05-01

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

  2. Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers.

    PubMed

    Myer, Phillip R; Kim, MinSeok; Freetly, Harvey C; Smith, Timothy P L

    2016-08-01

    Next generation sequencing technologies have vastly changed the approach of sequencing of the 16S rRNA gene for studies in microbial ecology. Three distinct technologies are available for large-scale 16S sequencing. All three are subject to biases introduced by sequencing error rates, amplification primer selection, and read length, which can affect the apparent microbial community. In this study, we compared short read 16S rRNA variable regions, V1-V3, with that of near-full length 16S regions, V1-V8, using highly diverse steer rumen microbial communities, in order to examine the impact of technology selection on phylogenetic profiles. Short paired-end reads from the Illumina MiSeq platform were used to generate V1-V3 sequence, while long "circular consensus" reads from the Pacific Biosciences RSII instrument were used to generate V1-V8 data. The two platforms revealed similar microbial operational taxonomic units (OTUs), as well as similar species richness, Good's coverage, and Shannon diversity metrics. However, the V1-V8 amplified ruminal community resulted in significant increases in several orders of taxa, such as phyla Proteobacteria and Verrucomicrobia (P < 0.05). Taxonomic classification accuracy was also greater in the near full-length read. UniFrac distance matrices using jackknifed UPGMA clustering also noted differences between the communities. These data support the consensus that longer reads result in a finer phylogenetic resolution that may not be achieved by shorter 16S rRNA gene fragments. Our work on the cattle rumen bacterial community demonstrates that utilizing near full-length 16S reads may be useful in conducting a more thorough study, or for developing a niche-specific database to use in analyzing data from shorter read technologies when budgetary constraints preclude use of near-full length 16S sequencing. PMID:27282101

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

    NASA Astrophysics Data System (ADS)

    Ferraro, Steven P.; Cole, Faith A.

    2007-02-01

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

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

    PubMed Central

    2009-01-01

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

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

    PubMed Central

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

    2008-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-03-15

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

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

    PubMed

    Princé, Karine; Zuckerberg, Benjamin

    2015-02-01

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

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

    PubMed Central

    2015-01-01

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

  11. Quantifying variability in earthquake rupture models using multidimensional scaling: application to the 2011 Tohoku earthquake

    NASA Astrophysics Data System (ADS)

    Razafindrakoto, Hoby N. T.; Mai, P. Martin; Genton, Marc G.; Zhang, Ling; Thingbaijam, Kiran K. S.

    2015-07-01

    Finite-fault earthquake source inversion is an ill-posed inverse problem leading to non-unique solutions. In addition, various fault parametrizations and input data may have been used by different researchers for the same earthquake. Such variability leads to large intra-event variability in the inferred rupture models. One way to understand this problem is to develop robust metrics to quantify model variability. We propose a Multi Dimensional Scaling (MDS) approach to compare rupture models quantitatively. We consider normalized squared and grey-scale metrics that reflect the variability in the location, intensity and geometry of the source parameters. We test the approach on two-dimensional random fields generated using a von Kármán autocorrelation function and varying its spectral parameters. The spread of points in the MDS solution indicates different levels of model variability. We observe that the normalized squared metric is insensitive to variability of spectral parameters, whereas the grey-scale metric is sensitive to small-scale changes in geometry. From this benchmark, we formulate a similarity scale to rank the rupture models. As case studies, we examine inverted models from the Source Inversion Validation (SIV) exercise and published models of the 2011 Mw 9.0 Tohoku earthquake, allowing us to test our approach for a case with a known reference model and one with an unknown true solution. The normalized squared and grey-scale metrics are respectively sensitive to the overall intensity and the extension of the three classes of slip (very large, large, and low). Additionally, we observe that a three-dimensional MDS configuration is preferable for models with large variability. We also find that the models for the Tohoku earthquake derived from tsunami data and their corresponding predictions cluster with a systematic deviation from other models. We demonstrate the stability of the MDS point-cloud using a number of realizations and jackknife tests, for

  12. Predicting membrane protein types by incorporating protein topology, domains, signal peptides, and physicochemical properties into the general form of Chou's pseudo amino acid composition.

    PubMed

    Chen, Yen-Kuang; Li, Kuo-Bin

    2013-02-01

    The type information of un-annotated membrane proteins provides an important hint for their biological functions. The experimental determination of membrane protein types, despite being more accurate and reliable, is not always feasible due to the costly laboratory procedures, thereby creating a need for the development of bioinformatics methods. This article describes a novel computational classifier for the prediction of membrane protein types using proteins' sequences. The classifier, comprising a collection of one-versus-one support vector machines, makes use of the following sequence attributes: (1) the cationic patch sizes, the orientation, and the topology of transmembrane segments; (2) the amino acid physicochemical properties; (3) the presence of signal peptides or anchors; and (4) the specific protein motifs. A new voting scheme was implemented to cope with the multi-class prediction. Both the training and the testing sequences were collected from SwissProt. Homologous proteins were removed such that there is no pair of sequences left in the datasets with a sequence identity higher than 40%. The performance of the classifier was evaluated by a Jackknife cross-validation and an independent testing experiments. Results show that the proposed classifier outperforms earlier predictors in prediction accuracy in seven of the eight membrane protein types. The overall accuracy was increased from 78.3% to 88.2%. Unlike earlier approaches which largely depend on position-specific substitution matrices and amino acid compositions, most of the sequence attributes implemented in the proposed classifier have supported literature evidences. The classifier has been deployed as a web server and can be accessed at http://bsaltools.ym.edu.tw/predmpt. PMID:23137835

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

    PubMed

    Li, Guoqing; Du, Sheng; Guo, Ke

    2015-01-01

    Chinese sea buckthorn (Hippophae rhamnoides subsp. sinensis) has considerable economic potential and plays an important role in reclamation and soil and water conservation. For scientific cultivation of this species across China, we identified the key climatic factors and explored climatically suitable habitat in order to maximize survival of Chinese sea buckthorn using MaxEnt and GIS tools, based on 98 occurrence records from herbarium and publications and 13 climatic factors from Bioclim, Holdridge life zone and Kria' index variables. Our simulation showed that the MaxEnt model performance was significantly better than random, with an average test AUC value of 0.93 with 10-fold cross validation. A jackknife test and the regularized gain change, which were applied to the training algorithm, showed that precipitation of the driest month (PDM), annual precipitation (AP), coldness index (CI) and annual range of temperature (ART) were the most influential climatic factors in limiting the distribution of Chinese sea buckthorn, which explained 70.1% of the variation. The predicted map showed that the core of climatically suitable habitat was distributed from the southwest to northwest of Gansu, Ningxia, Shaanxi and Shanxi provinces, where the most influential climate variables were PDM of 1.0-7.0 mm, AP of 344.0-1089.0 mm, CI of -47.7-0.0°C, and ART of 26.1-45.0°C. We conclude that the distribution patterns of Chinese sea buckthorn are related to the northwest winter monsoon, the southwest summer monsoon and the southeast summer monsoon systems in China. PMID:26177033

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    We present measurements of the luminosity and color-dependence of galaxy clustering at 0.2 < z < 1.0 in the Prism Multi-object Survey. We quantify the clustering with the redshift-space and projected two-point correlation functions, ξ(rp , π) and wp (rp ), using volume-limited samples constructed from a parent sample of over ~130, 000 galaxies with robust redshifts in seven independent fields covering 9 deg2 of sky. We quantify how the scale-dependent clustering amplitude increases with increasing luminosity and redder color, with relatively small errors over large volumes. We find that red galaxies have stronger small-scale (0.1 Mpc h -1 < rp < 1 Mpc h -1) clustering and steeper correlation functions compared to blue galaxies, as well as a strong color dependent clustering within the red sequence alone. We interpret our measured clustering trends in terms of galaxy bias and obtain values of b gal ≈ 0.9-2.5, quantifying how galaxies are biased tracers of dark matter depending on their luminosity and color. We also interpret the color dependence with mock catalogs, and find that the clustering of blue galaxies is nearly constant with color, while redder galaxies have stronger clustering in the one-halo term due to a higher satellite galaxy fraction. In addition, we measure the evolution of the clustering strength and bias, and we do not detect statistically significant departures from passive evolution. We argue that the luminosity- and color-environment (or halo mass) relations of galaxies have not significantly evolved since z ~ 1. Finally, using jackknife subsampling methods, we find that sampling fluctuations are important and that the COSMOS field is generally an outlier, due to having more overdense structures than other fields; we find that "cosmic variance" can be a significant source of uncertainty for high-redshift clustering measurements.

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

    NASA Astrophysics Data System (ADS)

    Takara, K. T.

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  17. Experience in reading digital images may decrease observer accuracy in mammography

    NASA Astrophysics Data System (ADS)

    Rawashdeh, Mohammad A.; Lewis, Sarah J.; Lee, Warwick; Mello-Thoms, Claudia; Reed, Warren M.; McEntee, Mark; Tapia, Kriscia; Brennan, Patrick C.

    2015-03-01

    Rationale and Objectives: To identify parameters linked to higher levels of performance in screening mammography. In particular we explored whether experience in reading digital cases enhances radiologists' performance. Methods: A total of 60 cases were presented to the readers, of which 20 contained cancers and 40 showed no abnormality. Each case comprised of four images and 129 breast readers participated in the study. Each reader was asked to identify and locate any malignancies using a 1-5 confidence scale. All images were displayed using 5MP monitors, supported by radiology workstations with full image manipulation capabilities. A jack-knife free-response receiver operating characteristic, figure of merit (JAFROC, FOM) methodology was employed to assess reader performance. Details were obtained from each reader regarding their experience, qualifications and breast reading activities. Spearman and Mann Whitney U techniques were used for statistical analysis. Results: Higher performance was positively related to numbers of years professionally qualified (r= 0.18; P<0.05), number of years reading breast images (r= 0.24; P<0.01), number of mammography images read per year (r= 0.28; P<0.001) and number of hours reading mammographic images per week (r= 0.19; P<0.04). Unexpectedly, higher performance was inversely linked to previous experience with digital images (r= - 0.17; p<0.05) and further analysis, demonstrated that this finding was due to changes in specificity. Conclusion: This study suggests suggestion that readers with experience in digital images reporting may exhibit a reduced ability to correctly identify normal appearances requires further investigation. Higher performance is linked to number of cases read per year.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2014-04-01

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

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

    PubMed

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

    2015-04-15

    Variations in interannual rainfall totals can lead to large uncertainties in annual N2O emission budget estimates from short term field studies. The interannual variation in nitrous oxide (N2O) emissions from a subtropical pasture in Queensland, Australia, was examined using continuous measurements of automated chambers over 2 consecutive years. Nitrous oxide emissions were highest during the summer months and were highly episodic, related more to the size and distribution of rain events than soil water content. Over 48% of the total N2O emitted was lost in just 16% of measurement days. Interannual variation in annual N2O estimates was high, with cumulative emissions increasing with decreasing rainfall. Cumulative emissions averaged 1826.7±199.9 g N2O-N ha(-1) yr(-1) over the two year period, though emissions from 2008 (2148±273 g N2O-N ha(-1) yr(-1)) were 42% higher than 2007 (1504±126 g N2O-N ha(-1) yr(-1)). This increase in annual emissions coincided with almost half of the summer precipitation from 2007 to 2008. Emissions dynamics were chiefly driven by the distribution and size of rain events which varied on a seasonal and annual basis. Sampling frequency effects on cumulative N2O flux estimation were assessed using a jackknife technique to inform future manual sampling campaigns. Test subsets of the daily measured data were generated for the pasture and two adjacent land-uses (rainforest and lychee orchard) by selecting measured flux values at regular time intervals ranging from 1 to 30 days. Errors associated with weekly sampling were up to 34% of the sub-daily mean and were highly biased towards overestimation if strategically sampled following rain events. Sampling time of day also played a critical role. Morning sampling best represented the 24 hour mean in the pasture, whereas sampling at noon proved the most accurate in the shaded rainforest and lychee orchard. PMID:25613765

  1. iDNA-Prot: identification of DNA binding proteins using random forest with grey model.

    PubMed

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

    2011-01-01

    DNA-binding proteins play crucial roles in various cellular processes. Developing high throughput tools for rapidly and effectively identifying DNA-binding proteins is one of the major challenges in the field of genome annotation. Although many efforts have been made in this regard, further effort is needed to enhance the prediction power. By incorporating the features into the general form of pseudo amino acid composition that were extracted from protein sequences via the "grey model" and by adopting the random forest operation engine, we proposed a new predictor, called iDNA-Prot, for identifying uncharacterized proteins as DNA-binding proteins or non-DNA binding proteins based on their amino acid sequences information alone. The overall success rate by iDNA-Prot was 83.96% that was obtained via jackknife tests on a newly constructed stringent benchmark dataset in which none of the proteins included has ≥25% pairwise sequence identity to any other in a same subset. In addition to achieving high success rate, the computational time for iDNA-Prot is remarkably shorter in comparison with the relevant existing predictors. Hence it is anticipated that iDNA-Prot may become a useful high throughput tool for large-scale analysis of DNA-binding proteins. As a user-friendly web-server, iDNA-Prot is freely accessible to the public at the web-site on http://icpr.jci.edu.cn/bioinfo/iDNA-Prot or http://www.jci-bioinfo.cn/iDNA-Prot. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results. PMID:21935457

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

    PubMed Central

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

    2012-01-01

    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

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

    PubMed

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

    1997-03-01

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

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

    PubMed

    Saravanan, Vijayakumar; Lakshmi, P T V

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

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

    PubMed

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

    2011-05-01

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

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

    PubMed

    Khan, Asifullah; Majid, Abdul; Hayat, Maqsood

    2011-08-10

    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

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

    PubMed

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

    2014-04-01

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

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed

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

    2006-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2004-01-01

    We present a determination of the bispectrum of the flux in the Lyman α 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 cent. For wavenumbers in the range 0.03 < k < 0.1 s km-1 the observed bispectrum agrees within the errors with that of the synthetic absorption spectra obtained from numerical hydro-simulations of a ΛCDM model with and without feedback from star formation. Including galactic feedback changes the bispectrum by less than 10 per cent. At smaller wavenumbers, the associated metal absorption lines contribute about 50 per cent to the bispectrum and the observed bispectrum exceeds that of the simulations. At wavenumbers k < 0.03 s km-1, second-order perturbation theory applied to the flux spectrum gives a reasonable (errors smaller than 30 per cent) approximation to the bispectra of observed and simulated absorption spectra. The bispectrum of the observed absorption spectra also agrees, within the errors, with that of a randomized set of absorption spectra where a random shift in wavelength has been added to absorption lines identified with VPFIT. This suggests that for a sample of the size presented here, the errors on the bispectrum are too large to discriminate between models with very different 3D distribution of Lyman α absorption. If it were possible to substantially reduce these errors for larger samples of absorption spectra, the bispectrum might become an important statistical tool for probing the growth of gravitational structure in the Universe at redshift z>~ 2.

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

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

    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.

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

    PubMed Central

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

    2008-01-01

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

  14. Familial associations of lipid profiles: a generalized estimating equations approach.

    PubMed

    Ziegler, A; Kastner, C; Brunner, D; Blettner, M

    2000-12-30

    Elevated plasma levels of apolipoproteins A1 (apoA1) and B (apoB) are important protective factors and risk factors, respectively, for atherosclerosis and coronary heart disease. It is well known that both apoA1 and apoB reveal strong familial aggregation. Our goal was to investigate whether exogenous variables influence these associations. We used marginal regression models for the mean and association structure (generalized estimating equations 2; GEE2) to analyse data from 1435 family members within 469 families of different sizes included in the Donolo-Tel Aviv Three-Generation Offspring Study. The usual robust variance matrix was approximated by extensions of jack-knife estimators of variance to GEE2 models. Estimation of standard errors in models with quite complex correlation structures was possible using this approach. All analyses were easily carried out using a menu-driven stand-alone software tool for marginal regression modelling. We demonstrate that a variety of hypotheses can be tested using Wald statistics by modelling regression matrices for the association structure. We show that correlation for apoB between parent-offspring pairs increased with decreasing age difference and that pairs with individuals of the same gender had more similar apoA1 levels than individuals of different gender. Associations between different relative pairs did not all agree with those expected from differences in kinship coefficients. The analysis using GEE2 models revealed structures that would not have been detected by other models and should therefore be used in addition to traditional approaches of analysing family data. GEE2 should be considered a standard method for the investigation of familial aggregation. PMID:11122500

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

    PubMed Central

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

    2013-01-01

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

  16. Absolute and relative locations of earthquakes at Mount St. Helens, Washington, using continuous data: implications for magmatic processes: Chapter 4 in A volcano rekindled: the renewed eruption of Mount St. Helens, 2004-2006

    USGS Publications Warehouse

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

    2008-01-01

    This study uses a combination of absolute and relative locations from earthquake multiplets to investigate the seismicity associated with the eruptive sequence at Mount St. Helens between September 23, 2004, and November 20, 2004. Multiplets, a prominent feature of seismicity during this time period, occurred as volcano-tectonic, hybrid, and low-frequency earthquakes spanning a large range of magnitudes and lifespans. Absolute locations were improved through the use of a new one-dimensional velocity model with excellent shallow constraints on P-wave velocities. We used jackknife tests to minimize possible biases in absolute and relative locations resulting from station outages and changing station configurations. In this paper, we show that earthquake hypocenters shallowed before the October 1 explosion along a north-dipping structure under the 1980-86 dome. Relative relocations of multiplets during the initial seismic unrest and ensuing eruption showed rather small source volumes before the October 1 explosion and larger tabular source volumes after October 5. All multiplets possess absolute locations very close to each other. However, the highly dissimilar waveforms displayed by each of the multiplets analyzed suggest that different sources and mechanisms were present within a very small source volume. We suggest that multiplets were related to pressurization of the conduit system that produced a stationary source that was highly stable over long time periods. On the basis of their response to explosions occurring in October 2004, earthquakes not associated with multiplets also appeared to be pressure dependent. The pressure source for these earthquakes appeared, however, to be different from the pressure source of the multiplets.

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

    NASA Astrophysics Data System (ADS)

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

    2008-09-01

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

  18. Predicting protein subnuclear location with optimized evidence-theoretic K-nearest classifier and pseudo amino acid composition

    SciTech Connect

    Shen Hongbin; Chou Kuochen . E-mail: kchou@san.rr.com

    2005-11-25

    The nucleus is the brain of eukaryotic cells that guides the life processes of the cell by issuing key instructions. For in-depth understanding of the biochemical process of the nucleus, the knowledge of localization of nuclear proteins is very important. With the avalanche of protein sequences generated in the post-genomic era, it is highly desired to develop an automated method for fast annotating the subnuclear locations for numerous newly found nuclear protein sequences so as to be able to timely utilize them for basic research and drug discovery. In view of this, a novel approach is developed for predicting the protein subnuclear location. It is featured by introducing a powerful classifier, the optimized evidence-theoretic K-nearest classifier, and using the pseudo amino acid composition [K.C. Chou, PROTEINS: Structure, Function, and Genetics, 43 (2001) 246], which can incorporate a considerable amount of sequence-order effects, to represent protein samples. As a demonstration, identifications were performed for 370 nuclear proteins among the following 9 subnuclear locations: (1) Cajal body, (2) chromatin, (3) heterochromatin, (4) nuclear diffuse, (5) nuclear pore, (6) nuclear speckle, (7) nucleolus, (8) PcG body, and (9) PML body. The overall success rates thus obtained by both the re-substitution test and jackknife cross-validation test are significantly higher than those by existing classifiers on the same working dataset. It is anticipated that the powerful approach may also become a useful high throughput vehicle to bridge the huge gap occurring in the post-genomic era between the number of gene sequences in databases and the number of gene products that have been functionally characterized. The OET-KNN classifier will be available at www.pami.sjtu.edu.cn/people/hbshen.

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

    PubMed Central

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

    2016-01-01

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

  20. Prediction of apoptosis protein locations with genetic algorithms and support vector machines through a new mode of pseudo amino acid composition.

    PubMed

    Kandaswamy, Krishna Kumar; Pugalenthi, Ganesan; Möller, Steffen; Hartmann, Enno; Kalies, Kai-Uwe; Suganthan, P N; Martinetz, Thomas

    2010-12-01

    Apoptosis is an essential process for controlling tissue homeostasis by regulating a physiological balance between cell proliferation and cell death. The subcellular locations of proteins performing the cell death are determined by mostly independent cellular mechanisms. The regular bioinformatics tools to predict the subcellular locations of such apoptotic proteins do often fail. This work proposes a model for the sorting of proteins that are involved in apoptosis, allowing us to both the prediction of their subcellular locations as well as the molecular properties that contributed to it. We report a novel hybrid Genetic Algorithm (GA)/Support Vector Machine (SVM) approach to predict apoptotic protein sequences using 119 sequence derived properties like frequency of amino acid groups, secondary structure, and physicochemical properties. GA is used for selecting a near-optimal subset of informative features that is most relevant for the classification. Jackknife cross-validation is applied to test the predictive capability of the proposed method on 317 apoptosis proteins. Our method achieved 85.80% accuracy using all 119 features and 89.91% accuracy for 25 features selected by GA. Our models were examined by a test dataset of 98 apoptosis proteins and obtained an overall accuracy of 90.34%. The results show that the proposed approach is promising; it is able to select small subsets of features and still improves the classification accuracy. Our model can contribute to the understanding of programmed cell death and drug discovery. The software and dataset are available at http://www.inb.uni-luebeck.de/tools-demos/apoptosis/GASVM. PMID:20666727

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

    NASA Astrophysics Data System (ADS)

    Chevrot, S.; Zhao, L.

    2007-04-01

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

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

    USGS Publications Warehouse

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

    2000-01-01

    A hybrid (physical-statistical) scheme is developed to resolve the finescale distribution of daily precipitation over complex terrain. The scheme generates precipitation by combining information from the upper-air conditions and from sparsely distributed station measurements; thus, it proceeds in two steps. First, an initial estimate of the precipitation is made using a simplified orographic precipitation model. It is a steady-state, multilayer, and two-dimensional model following the concepts of Rhea. The model is driven by the 2.5?? ?? 2.5?? gridded National Oceanic and Atmospheric Administration-National Centers for Environmental Prediction upper-air profiles, and its parameters are tuned using the observed precipitation structure of the region. Precipitation is generated assuming a forced lifting of the air parcels as they cross the mountain barrier following a straight trajectory. Second, the precipitation is adjusted using errors between derived precipitation and observations from nearby sites. The study area covers the northern half of California, including coastal mountains, central valley, and the Sierra Nevada. The model is run for a 5-km rendition of terrain for days of January-March over the period of 1988-95. A jackknife analysis demonstrates the validity of the approach. The spatial and temporal distributions of the simulated precipitation field agree well with the observed precipitation. Further, a mapping of model performance indices (correlation coefficients, model bias, root-mean-square error, and threat scores) from an array of stations from the region indicates that the model performs satisfactorily in resolving daily precipitation at 5-km resolution.

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

    PubMed

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

    2016-01-01

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

  4. Noise-reducing algorithms do not necessarily provide superior dose optimisation for hepatic lesion detection with multidetector CT

    PubMed Central

    Dobeli, K L; Lewis, S J; Meikle, S R; Thiele, D L; Brennan, P C

    2013-01-01

    Objective: To compare the dose-optimisation potential of a smoothing filtered backprojection (FBP) and a hybrid FBP/iterative algorithm to that of a standard FBP algorithm at three slice thicknesses for hepatic lesion detection with multidetector CT. Methods: A liver phantom containing a 9.5-mm opacity with a density of 10 HU below background was scanned at 125, 100, 75, 50 and 25 mAs. Data were reconstructed with standard FBP (B), smoothing FBP (A) and hybrid FBP/iterative (iDose4) algorithms at 5-, 3- and 1-mm collimation. 10 observers marked opacities using a four-point confidence scale. Jackknife alternative free-response receiver operating characteristic figure of merit (FOM), sensitivity and noise were calculated. Results: Compared with the 125-mAs/5-mm setting for each algorithm, significant reductions in FOM (p<0.05) and sensitivity (p<0.05) were found for all three algorithms for all exposures at 1-mm thickness and for all slice thicknesses at 25 mAs, with the exception of the 25-mAs/5-mm setting for the B algorithm. Sensitivity was also significantly reduced for all exposures at 3-mm thickness for the A algorithm (p<0.05). Noise for the A and iDose4 algorithms was approximately 13% and 21% lower, respectively, than for the B algorithm. Conclusion: Superior performance for hepatic lesion detection was not shown with either a smoothing FBP algorithm or a hybrid FBP/iterative algorithm compared with a standard FBP technique, even though noise reduction with thinner slices was demonstrated with the alternative approaches. Advances in knowledge: Reductions in image noise with non-standard CT algorithms do not necessarily translate to an improvement in low-contrast object detection. PMID:23392194

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

    PubMed Central

    Rowlett, Veronica Wells

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  8. Analysis and prediction of affinity of TAP binding peptides using cascade SVM.

    PubMed

    Bhasin, Manoj; Raghava, G P S

    2004-03-01

    The generation of cytotoxic T lymphocyte (CTL) epitopes from an antigenic sequence involves number of intracellular processes, including production of peptide fragments by proteasome and transport of peptides to endoplasmic reticulum through transporter associated with antigen processing (TAP). In this study, 409 peptides that bind to human TAP transporter with varying affinity were analyzed to explore the selectivity and specificity of TAP transporter. The abundance of each amino acid from P1 to P9 positions in high-, intermediate-, and low-affinity TAP binders were examined. The rules for predicting TAP binding regions in an antigenic sequence were derived from the above analysis. The quantitative matrix was generated on the basis of contribution of each position and residue in binding affinity. The correlation of r = 0.65 was obtained between experimentally determined and predicted binding affinity by using a quantitative matrix. Further a support vector machine (SVM)-based method has been developed to model the TAP binding affinity of peptides. The correlation (r = 0.80) was obtained between the predicted and experimental measured values by using sequence-based SVM. The reliability of prediction was further improved by cascade SVM that uses features of amino acids along with sequence. An extremely good correlation (r = 0.88) was obtained between measured and predicted values, when the cascade SVM-based method was evaluated through jackknife testing. A Web service, TAPPred (http://www.imtech.res.in/raghava/tappred/ or http://bioinformatics.uams.edu/mirror/tappred/), has been developed based on this approach. PMID:14978300

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

    SciTech Connect

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

    2007-02-15

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

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

    PubMed Central

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

    2014-01-01

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

  11. Efficacy of digital breast tomosynthesis for breast cancer diagnosis

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    USGS Publications Warehouse

    Letcher, B.H.

    2003-01-01

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

  13. Testate Amoebae as Paleohydrological Proxies in the Florida Everglades

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

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

    PubMed

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

    2009-09-01

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

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

    SciTech Connect

    Robert J. Englar

    2000-06-19

    Under contract to the DOE Office of Heavy Vehicle Technologies, the Georgia Tech Research Institute (GTRI) is developing and evaluating pneumatic (blown) aerodynamic devices to improve the performance, economics, stability and safety of operation of Heavy Vehicles. The objective of this program is to apply the pneumatic aerodynamic aircraft technology previously developed and flight-tested by GTRI personnel to the design of an efficient blown tractor-trailer configuration. Recent experimental results obtained by GTRI using blowing have shown drag reductions of 35% on a streamlined automobile wind-tunnel model. Also measured were lift or down-load increases of 100-150% and the ability to control aerodynamic moments about all 3 axes without any moving control surfaces. Similar drag reductions yielded by blowing on bluff afterbody trailers in current US trucking fleet operations are anticipated to reduce yearly fuel consumption by more than 1.2 billion gallons, while even further reduction is possible using pneumatic lift to reduce tire rolling resistance. Conversely, increased drag and down force generated instantaneously by blowing can greatly increase braking characteristics and control in wet/icy weather due to effective ''weight'' increases on the tires. Safety is also enhanced by controlling side loads and moments caused on these Heavy Vehicles by winds, gusts and other vehicles passing. This may also help to eliminate the jack-knifing problem if caused by extreme wind side loads on the trailer. Lastly, reduction of the turbulent wake behind the trailer can reduce splash and spray patterns and rough air being experienced by following vehicles. To be presented by GTRI in this paper will be results developed during the early portion of this effort, including a preliminary systems study, CFD prediction of the blown flowfields, and design of the baseline conventional tractor-trailer model and the pneumatic wind-tunnel model.

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

    SciTech Connect

    Sandvol, E.; Seber, D.; Calvert, A.; Barazangi, M.

    1998-11-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

    Li, Guoqing; Du, Sheng; Guo, Ke

    2015-01-01

    Chinese sea buckthorn (Hippophae rhamnoides subsp. sinensis) has considerable economic potential and plays an important role in reclamation and soil and water conservation. For scientific cultivation of this species across China, we identified the key climatic factors and explored climatically suitable habitat in order to maximize survival of Chinese sea buckthorn using MaxEnt and GIS tools, based on 98 occurrence records from herbarium and publications and 13 climatic factors from Bioclim, Holdridge life zone and Kria' index variables. Our simulation showed that the MaxEnt model performance was significantly better than random, with an average test AUC value of 0.93 with 10-fold cross validation. A jackknife test and the regularized gain change, which were applied to the training algorithm, showed that precipitation of the driest month (PDM), annual precipitation (AP), coldness index (CI) and annual range of temperature (ART) were the most influential climatic factors in limiting the distribution of Chinese sea buckthorn, which explained 70.1% of the variation. The predicted map showed that the core of climatically suitable habitat was distributed from the southwest to northwest of Gansu, Ningxia, Shaanxi and Shanxi provinces, where the most influential climate variables were PDM of 1.0–7.0 mm, AP of 344.0–1089.0 mm, CI of -47.7–0.0°C, and ART of 26.1–45.0°C. We conclude that the distribution patterns of Chinese sea buckthorn are related to the northwest winter monsoon, the southwest summer monsoon and the southeast summer monsoon systems in China. PMID:26177033

  20. Demographic history and rare allele sharing among human populations

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2014-12-01

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

  2. A software system for the simulation of chest lesions

    NASA Astrophysics Data System (ADS)

    Ryan, John T.; McEntee, Mark; Barrett, Saoirse; Evanoff, Michael; Manning, David; Brennan, Patrick

    2007-03-01

    We report on the development of a novel software tool for the simulation of chest lesions. This software tool was developed for use in our study to attain optimal ambient lighting conditions for chest radiology. This study involved 61 consultant radiologists from the American Board of Radiology. Because of its success, we intend to use the same tool for future studies. The software has two main functions: the simulation of lesions and retrieval of information for ROC (Receiver Operating Characteristic) and JAFROC (Jack-Knife Free Response ROC) analysis. The simulation layer operates by randomly selecting an image from a bank of reportedly normal chest x-rays. A random location is then generated for each lesion, which is checked against a reference lung-map. If the location is within the lung fields, as derived from the lung-map, a lesion is superimposed. Lesions are also randomly selected from a bank of manually created chest lesion images. A blending algorithm determines which are the best intensity levels for the lesion to sit naturally within the chest x-ray. The same software was used to run a study for all 61 radiologists. A sequence of images is displayed in random order. Half of these images had simulated lesions, ranging from subtle to obvious, and half of the images were normal. The operator then selects locations where he/she thinks lesions exist and grades the lesion accordingly. We have found that this software was very effective in this study and intend to use the same principles for future studies.

  3. Combining pseudo dinucleotide composition with the Z curve method to improve the accuracy of predicting DNA elements: a case study in recombination spots.

    PubMed

    Dong, Chuan; Yuan, Ya-Zhou; Zhang, Fa-Zhan; Hua, Hong-Li; Ye, Yuan-Nong; Labena, Abraham Alemayehu; Lin, Hao; Chen, Wei; Guo, Feng-Biao

    2016-08-16

    Pseudo dinucleotide composition (PseDNC) and Z curve showed excellent performance in the classification issues of nucleotide sequences in bioinformatics. Inspired by the principle of Z curve theory, we improved PseDNC to give the phase-specific PseDNC (psPseDNC). In this study, we used the prediction of recombination spots as a case to illustrate the capability of psPseDNC and also PseDNC fused with Z curve theory based on a novel machine learning method named large margin distribution machine (LDM). We verified that combining the two widely used approaches could generate better performance compared to only using PseDNC with a support vector machine based (SVM-based) model. The best Mathew's correlation coefficient (MCC) achieved by our LDM-based model was 0.7037 through the rigorous jackknife test and improved by ∼6.6%, ∼3.2%, and ∼2.4% compared with three previous studies. Similarly, the accuracy was improved by 3.2% compared with our previous iRSpot-PseDNC web server through an independent data test. These results demonstrate that the joint use of PseDNC and Z curve enhances performance and can extract more information from a biological sequence. To facilitate research in this area, we constructed a user-friendly web server for predicting hot/cold spots, HcsPredictor, which can be freely accessed from . In summary, we provided a united algorithm by integrating Z curve with PseDNC. We hope this united algorithm could be extended to other classification issues in DNA elements. PMID:27410247

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

    PubMed

    Domene, Pablo A; Easton, Chris

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

    2013-01-01

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

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

    PubMed

    Xia, Xuhua

    2016-09-01

    While pairwise sequence alignment (PSA) by dynamic programming is guaranteed to generate one of the optimal alignments, multiple sequence alignment (MSA) of highly divergent sequences often results in poorly aligned sequences, plaguing all subsequent phylogenetic analysis. One way to avoid this problem is to use only PSA to reconstruct phylogenetic trees, which can only be done with distance-based methods. I compared the accuracy of this new computational approach (named PhyPA for phylogenetics by pairwise alignment) against the maximum likelihood method using MSA (the ML+MSA approach), based on nucleotide, amino acid and codon sequences simulated with different topologies and tree lengths. I present a surprising discovery that the fast PhyPA method consistently outperforms the slow ML+MSA approach for highly diverged sequences even when all optimization options were turned on for the ML+MSA approach. Only when sequences are not highly diverged (i.e., when a reliable MSA can be obtained) does the ML+MSA approach outperforms PhyPA. The true topologies are always recovered by ML with the true alignment from the simulation. However, with MSA derived from alignment programs such as MAFFT or MUSCLE, the recovered topology consistently has higher likelihood than that for the true topology. Thus, the failure to recover the true topology by the ML+MSA is not because of insufficient search of tree space, but by the distortion of phylogenetic signal by MSA methods. I have implemented in DAMBE PhyPA and two approaches making use of multi-gene data sets to derive phylogenetic support for subtrees equivalent to resampling techniques such as bootstrapping and jackknifing. PMID:27377322

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2014-11-28

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

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

    PubMed Central

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

    2015-01-01

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

  15. Comparing halo bias from abundance and clustering

    NASA Astrophysics Data System (ADS)

    Hoffmann, K.; Bel, J.; Gaztañaga, E.

    2015-06-01

    We model the abundance of haloes in the ˜(3 Gpc h-1)3 volume of the MICE Grand Challenge simulation by fitting the universal mass function with an improved Jackknife error covariance estimator that matches theory predictions. We present unifying relations between different fitting models and new predictions for linear (b1) and non-linear (c2 and c3) halo clustering bias. Different mass function fits show strong variations in their performance when including the low mass range (Mh ≲ 3 × 1012 M⊙ h-1) in the analysis. Together with fits from the literature, we find an overall variation in the amplitudes of around 10 per cent in the low mass and up to 50 per cent in the high mass (galaxy cluster) range (Mh > 1014 M⊙ h-1). These variations propagate into a 10 per cent change in b1 predictions and a 50 per cent change in c2 or c3. Despite these strong variations, we find universal relations between b1 and c2 or c3 for which we provide simple fits. Excluding low-mass haloes, different models fitted with reasonable goodness in this analysis, show per cent level agreement in their b1 predictions, but are systematically 5-10 per cent lower than the bias directly measured with two-point halo-mass clustering. This result confirms previous findings derived from smaller volumes (and smaller masses). Inaccuracies in the bias predictions lead to 5-10 per cent errors in growth measurements. They also affect any halo occupation distribution fitting or (cluster) mass calibration from clustering measurements.

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

    PubMed

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

    2015-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Simaiakis, Stylianos Michail; Martínez-Morales, Miguel Angel

    2010-05-01

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

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

    PubMed

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

    2015-09-01

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

  19. Structure and dynamics of the taxocenoses of Pimplinae, Poemeniinae, Rhyssinae, Anomaloninae and Metopiinae in an urban secondary semideciduous montane forest.

    PubMed

    Tanque, R L; Kumagai, A F; Souza, B; Korasaki, V

    2015-06-01

    Ichneumonidae (Hymenoptera) is one of the largest families of Insecta, but information on family diversity and distribution in Brazil is limited. The aim of the study was to assess the abundance, richness and seasonal distribution of Ichneumonidae in an urban secondary semideciduous montane forest. Insect specimens were captured in a Malaise trap placed within a restored sub-evergreen forest and sampling was performed every week during three non-consecutive 12-month periods. Of the 507 specimens collected, 338 were captured between May 1991 and May 1992, 95 between May 2000 and May 2001, and 74 between May 2007 and May 2008. Specimens were distributed among the subfamilies Pimplinae (n = 444), Anomaloninae (n = 42), Metopiinae (n = 16), Poemeniinae (n = 3) and Rhyssinae (n = 2). Species richness was highest in 1991-1992 with 33 rare and eight common species captured, followed by 2000-2001 with 31 rare and one common species captured, and 2007-2008 with 24 rare and one common species captured. The Shannon-Wiener diversity index (H') and Jackknife 1 species richness (S) values for the respective periods were 2.75/59.6, 3.15/35.8 and 2.83/35.8. In the 1991-1992 and 2000-2001 periods, parasitoid abundance was higher during the rainy season, while in 2007-2008 abundance was higher during the dry season. Colpotrochia mexicana (Cresson), Colpotrochia neblina Gauld & Sithole and Exochus izbus Gauld & Sithole were recorded for the first time in Brazil. PMID:26013266

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2012-12-01

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

  2. Detection of calcification clusters in digital breast tomosynthesis slices at different dose levels utilizing a SRSAR reconstruction and JAFROC

    NASA Astrophysics Data System (ADS)

    Timberg, P.; Dustler, M.; Petersson, H.; Tingberg, A.; Zackrisson, S.

    2015-03-01

    Purpose: To investigate detection performance for calcification clusters in reconstructed digital breast tomosynthesis (DBT) slices at different dose levels using a Super Resolution and Statistical Artifact Reduction (SRSAR) reconstruction method. Method: Simulated calcifications with irregular profile (0.2 mm diameter) where combined to form clusters that were added to projection images (1-3 per abnormal image) acquired on a DBT system (Mammomat Inspiration, Siemens). The projection images were dose reduced by software to form 35 abnormal cases and 25 normal cases as if acquired at 100%, 75% and 50% dose level (AGD of approximately 1.6 mGy for a 53 mm standard breast, measured according to EUREF v0.15). A standard FBP and a SRSAR reconstruction method (utilizing IRIS (iterative reconstruction filters), and outlier detection using Maximum-Intensity Projections and Average-Intensity Projections) were used to reconstruct single central slices to be used in a Free-response task (60 images per observer and dose level). Six observers participated and their task was to detect the clusters and assign confidence rating in randomly presented images from the whole image set (balanced by dose level). Each trial was separated by one weeks to reduce possible memory bias. The outcome was analyzed for statistical differences using Jackknifed Alternative Free-response Receiver Operating Characteristics. Results: The results indicate that it is possible reduce the dose by 50% with SRSAR without jeopardizing cluster detection. Conclusions: The detection performance for clusters can be maintained at a lower dose level by using SRSAR reconstruction.

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

    PubMed Central

    Braun, Edward L.

    2014-01-01

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

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

    USGS Publications Warehouse

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

    2005-01-01

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

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

    PubMed

    Ahmed, Altayeb Abdalla; Omer, Nosyba

    2015-09-01

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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

    2014-04-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    Fletcher, Joel G.; Yu, Lifeng; Li, Zhoubo; Manduca, Armando; Blezek, Daniel J.; Hough, David M.; Venkatesh, Sudhakar K.; Brickner, Gregory C.; Cernigliaro, Joseph C.; Hara, Amy K.; Fidler, Jeff L.; Lake, David S.; Shiung, Maria; Lewis, David; Leng, Shuai; Augustine, Kurt E.; Carter, Rickey E.; Holmes, David R.; McCollough, Cynthia H.

    2015-01-01

    Purpose To determine if lower-dose computed tomographic (CT) scans obtained with adaptive image-based noise reduction (adaptive nonlocal means [ANLM]) or iterative reconstruction (sinogram-affirmed iterative reconstruction [SAFIRE]) result in reduced observer performance in the detection of malignant hepatic nodules and masses compared with routine-dose scans obtained with filtered back projection (FBP). Materials and Methods This study was approved by the institutional review board and was compliant with HIPAA. Informed consent was obtained from patients for the retrospective use of medical records for research purposes. CT projection data from 33 abdominal and 27 liver or pancreas CT examinations were collected (median volume CT dose index, 13.8 and 24.0 mGy, respectively). Hepatic malignancy was defined by progression or regression or with histopathologic findings. Lower-dose data were created by using a validated noise insertion method (10.4 mGy for abdominal CT and 14.6 mGy for liver or pancreas CT) and images reconstructed with FBP, ANLM, and SAFIRE. Four readers evaluated routine-dose FBP images and all lower-dose images, circumscribing liver lesions and selecting diagnosis. The jack-knife free-response receiver operating characteristic figure of merit (FOM) was calculated on a per-malignant nodule or per-mass basis. Noninferiority was defined by the lower limit of the 95% confidence interval (CI) of the difference between lower-dose and routine-dose FOMs being less than −0.10. Results Twenty-nine patients had 62 malignant hepatic nodules and masses. Estimated FOM differences between lower-dose FBP and lower-dose ANLM versus routine-dose FBP were noninferior (difference: −0.041 [95% CI: −0.090, 0.009] and −0.003 [95% CI: −0.052, 0.047], respectively). In patients with dedicated liver scans, lower-dose ANLM images were noninferior (difference: +0.015 [95% CI: −0.077, 0.106]), whereas lower-dose FBP images were not (difference −0.049 [95% CI:

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2003-09-01

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

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

    PubMed

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

    2016-09-01

    Healthcare professionals with limited access to ergospirometry remain in need of valid and simple submaximal exercise tests to predict maximal oxygen uptake (VO2max ). Despite previous validation studies concerning fixed-rate step tests, accurate equations for the estimation of VO2max remain to be formulated from a large sample of healthy adults between age 18-75 years (n > 100). The aim of this study was to develop a valid equation to estimate VO2max from a fixed-rate step test in a larger sample of healthy adults. A maximal ergospirometry test, with assessment of cardiopulmonary parameters and VO2max , and a 5-min fixed-rate single-stage step test were executed in 112 healthy adults (age 18-75 years). During the step test and subsequent recovery, heart rate was monitored continuously. By linear regression analysis, an equation to predict VO2max from the step test was formulated. This equation was assessed for level of agreement by displaying Bland-Altman plots and calculation of intraclass correlations with measured VO2max . Validity further was assessed by employing a Jackknife procedure. The linear regression analysis generated the following equation to predict VO2max (l min(-1) ) from the step test: 0·054(BMI)+0·612(gender)+3·359(body height in m)+0·019(fitness index)-0·012(HRmax)-0·011(age)-3·475. This equation explained 78% of the variance in measured VO2max (F = 66·15, P<0·001). The level of agreement and intraclass correlation was high (ICC = 0·94, P<0·001) between measured and predicted VO2max . From this study, a valid fixed-rate single-stage step test equation has been developed to estimate VO2max in healthy adults. This tool could be employed by healthcare professionals with limited access to ergospirometry. PMID:26046474

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

    PubMed

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

    2015-01-01

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

  16. IMPROVED MEASUREMENTS OF THE TEMPERATURE AND POLARIZATION OF THE COSMIC MICROWAVE BACKGROUND FROM QUaD

    SciTech Connect

    Brown, M. L.; Ade, P.; Bowden, M.; Gear, W. K.; Gupta, S.; Orlando, A.; Bock, J.; Leitch, E.; Cahill, G.; Murphy, J. A.; Castro, P. G.; Memari, Y.; Church, S.; Hinderks, J.; Culverhouse, T.; Friedman, R. B.; Ganga, K.; Melhuish, S. J.

    2009-11-01

    We present an improved analysis of the final data set from the QUaD experiment. Using an improved technique to remove ground contamination, we double the effective sky area and hence increase the precision of our cosmic microwave background (CMB) power spectrum measurements by approx30% versus that previously reported. In addition, we have improved our modeling of the instrument beams and have reduced our absolute calibration uncertainty from 5% to 3.5% in temperature. The robustness of our results is confirmed through extensive jackknife tests, and by way of the agreement that we find between our two fully independent analysis pipelines. For the standard six-parameter LAMBDACDM model, the addition of QUaD data marginally improves the constraints on a number of cosmological parameters over those obtained from the WMAP experiment alone. The impact of QUaD data is significantly greater for a model extended to include either a running in the scalar spectral index, or a possible tensor component, or both. Adding both the QUaD data and the results from the Arcminute Cosmology Bolometer Array Receiver experiment, the uncertainty in the spectral index running is reduced by approx25% compared to WMAP alone, while the upper limit on the tensor-to-scalar ratio is reduced from r < 0.48 to r < 0.33 (95% c.l.). This is the strongest limit on tensors to date from the CMB alone. We also use our polarization measurements to place constraints on parity-violating interactions to the surface of last scattering, constraining the energy scale of Lorentz violating interactions to <1.5 x 10{sup -43} GeV (68% c.l.). Finally, we place a robust upper limit on the strength of the lensing B-mode signal. Assuming a single flat band power between l = 200 and l = 2000, we constrain the amplitude of B-modes to be <0.57 muK{sup 2} (95% c.l.).

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

    PubMed

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

    2014-06-20

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

  18. Where's that Slab?: Simultaneous Inversion and Resolution of the Cascadia Slab Reflector Geometry, Wavespeeds and Hypocenters

    NASA Astrophysics Data System (ADS)

    Preston, L.; Creager, K.; Crosson, R.; Symons, N.

    2002-12-01

    The 1998 Wet SHIPS experiment, an onshore-offshore active source experiment within NW Washington State and SW British Columbia, provided travel times for over 1200 secondary arrivals that we interpret as wide-angle reflections from the subducting Juan de Fuca slab. The reflection points are distributed over a broad area under the Olympic Peninsula, WA. Using a nonlinear, iterative inverse procedure incorporating full 3-D ray tracing, we combine these reflected arrivals with 100,000 first arrivals obtained from SHIPS and other active source experiments and from local earthquakes to simultaneously determine smooth 3-D velocity structure, smooth slab geometry and hypocentral positions. The inversion converges stably after many iterations to the same solution over the range of starting models we have tested. The reflector is generally parallel to and within the upper half of the intraslab events, which form a 6-km thick dipping zone. The vast majority of these earthquakes occur where seismic velocities exceed 7.5 km/s. We are especially interested in testing the hypothesis that dehydration embrittlement, associated with the basalt to eclogite phase transformation, is responsible for the intraslab earthquakes. This hypothesis predicts that the majority of the intraslab events should occur within the subducted oceanic crust above a Moho reflector. An unambiguous interpretation requires knowledge of the reflector depth, relative to the earthquakes, with relative errors less than a few km. We present results from a variety of empirical and numerical error and resolution tests including jack-knife and checkerboard analyses. We analyze the interrelationships and trade-offs among the reflector position, intraslab earthquakes, and the fine-scale deep velocity structure to determine error and resolution bounds in this crucial area of our model. In general, the active source experiments provide dense crossing rays with known source locations to give excellent resolution and

  19. iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition.

    PubMed

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

    2013-04-01

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

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

    PubMed

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

    2009-03-01

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

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

    PubMed Central

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

    2014-01-01

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

  2. Prices, infrastructure, household characteristics and child height.

    PubMed

    Thomas, D; Strauss, J

    1992-10-01

    A Brazilian household survey, ENDEF, in 1974-75 and the 1974 Informacoes Basicas Municipais (IBM) provided data for the analysis of the impact of community services and infrastructure and household characteristics on the logarithm of child height, standardized for age and gender. The sample was comprised of 36,974 children stratified by residential location, the child's age, and the educational level of the mother. Variance and covariance matrices were estimated with the jackknife developed by Efron (1982). Household characteristics included the logarithm of per capita expenditure as a measure of household resource availability, income, and parental education. Community characteristics were local market price indices for 6 food groups (dairy products, beans, cereals, meat, fish, and sugar), level of urbanization, buildings with sewage, water, and electricity connections per capita, per capita number of buildings, and population density. Health services were measured as per capita number of hospitals and clinics and doctors and nurses, and the number of beds are hospital. Educational services include a measure of student teacher ratios, elementary school class size, and per capita number of teachers living in the community. the results show that expenditure had a positive, significant effect on the height of children 2 years and older. Expenditure was a significant determinant for literate and illiterate mothers, and not well educated mothers. The impact of maternal education was largest on the length of babies and declined with the age of the child. Father's education had not impact of length of babies. The effect of parents' education was complementary. The effect of father's education was largest when mothers had some education. Better educated parents had healthier children. Maternal rather than paternal height had an impact of the length of a baby. In the community models, prices had a significant effect on child height, in both urban and rural areas, in all

  3. Automated determination of P-phase arrival times at regional and local distances using higher order statistics

    NASA Astrophysics Data System (ADS)

    Küperkoch, L.; Meier, T.; Lee, J.; Friederich, W.; Working Group, EGELADOS

    2010-05-01

    We present an algorithm for automatic P-phase arrival time determination for local and regional seismic events based on higher order statistics (HOS). Using skewness or kurtosis a characteristic function is determined to which a new iterative picking algorithm is applied. For P-phase identification we apply the Akaike Information Criterion to the characteristic function, while for a precise determination of the P-phase arrival time a pragmatic picking algorithm is applied to a recalculated characteristic function. In addition, an automatic quality estimate is obtained, based on the slope and the signal-to-noise ratio, both calculated from the characteristic function. To get rid of erroneous picks, a Jackknife procedure and an envelope function analysis is used. The algorithm is applied to a large data set with very heterogeneous qualities of P-onsets acquired by a temporary, regional seismic network of the EGELADOS-project in the southern Aegean. The reliability and robustness of the proposed algorithm is tested by comparing more than 3000 manually derived P readings, serving as reference picks, with the corresponding automatically estimated P-wave arrival times. We find an average deviation from the reference picks of 0.26 +/- 0.64s when using kurtosis and 0.38 +/- 0.75s when using skewness. If automatically as excellent classified picks are considered only, the average difference from the reference picks is 0.07 +/- 0.31s and 0.07 +/- 0.41s, respectively. However, substantially more P-arrival times are determined when using kurtosis, indicating that the characteristic function derived from kurtosis estimation is to be preferred. Since the characteristic function is calculated recursively, the algorithm is very fast and hence suited for earthquake early warning purposes. Furthermore, a comparative study with automatically derived P-readings using Allen's and Baer & Kradolfer's picking algorithms applied to the same data set demonstrates better quantitative and

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

    identifying bad array elements through a jackknifing process to isolate the anomalous channels, so that an automated analysis system might discard them prior to FK analysis and beamforming on events of interest.

  5. Modelling and mapping the local distribution of representative species on the Le Danois Bank, El Cachucho Marine Protected Area (Cantabrian Sea)

    NASA Astrophysics Data System (ADS)

    García-Alegre, Ana; Sánchez, Francisco; Gómez-Ballesteros, María; Hinz, Hilmar; Serrano, Alberto; Parra, Santiago

    2014-08-01

    The management and protection of potentially vulnerable species and habitats require the availability of detailed spatial data. However, such data are often not readily available in particular areas that are challenging for sampling by traditional sampling techniques, for example seamounts. Within this study habitat modelling techniques were used to create predictive maps of six species of conservation concern for the Le Danois Bank (El Cachucho Marine Protected Area in the South of the Bay of Biscay). The study used data from ECOMARG multidisciplinary surveys that aimed to create a representative picture of the physical and biological composition of the area. Classical fishing gear (otter trawl and beam trawl) was used to sample benthic communities that inhabit sedimentary areas, and non-destructive visual sampling techniques (ROV and photogrammetric sled) were used to determine the presence of epibenthic macrofauna in complex and vulnerable habitats. Multibeam echosounder data, high-resolution seismic profiles (TOPAS system) and geological data from box-corer were used to characterize the benthic terrain. ArcGIS software was used to produce high-resolution maps (75×75 m2) of such variables in the entire area. The Maximum Entropy (MAXENT) technique was used to process these data and create Habitat Suitability maps for six species of special conservation interest. The model used seven environmental variables (depth, rugosity, aspect, slope, Bathymetric Position Index (BPI) in fine and broad scale and morphosedimentary characteristics) to identify the most suitable habitats for such species and indicates which environmental factors determine their distribution. The six species models performed highly significantly better than random (p<0.0001; Mann-Whitney test) when Area Under the Curve (AUC) values were tested. This indicates that the environmental variables chosen are relevant to distinguish the distribution of these species. The Jackknife test estimated depth

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

    SciTech Connect

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

    2013-08-10

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

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

    PubMed Central

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

    2016-01-01

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

  8. Colorectal Cancer Liver Metastases: Diagnostic Performance and Prognostic Value of PET/MR Imaging.

    PubMed

    Lee, Dong Ho; Lee, Jeong Min; Hur, Bo Yun; Joo, Ijin; Yi, Nam-Joon; Suh, Kyung-Suk; Kang, Keon Wook; Han, Joon Koo

    2016-09-01

    Purpose To evaluate the diagnostic performance of combined positron emission tomography (PET) and magnetic resonace (MR) imaging (hereafter, PET/MR imaging) in the detection of liver metastases and to assess its prognostic value in patients with colorectal cancer liver metastases (CRLMs). Materials and Methods Institutional review board approval was obtained for this retrospective study, with waiver of informed consent. A total of 55 patients with 98 CRLMs who underwent PET/MR imaging and multidetector computed tomography (CT) between January 2013 and June 2014 comprised the study population. Of these patients, 34 underwent hepatic resection, 18 of whom also underwent neoadjuvant chemotherapy (NAC). Two board-certificated radiologists independently assessed the four image sets (ie, multidetector CT, whole-body PET, MR imaging with a liver-specific contrast agent [hereafter, EOB MR imaging], and PET/MR imaging). To compare the diagnostic performance of each imaging modality, jackknife alternative free-response receiver operating characteristic and generalized estimating equations were used. To assess prognostic value, recurrence-free survival of the 18 patients who underwent NAC followed by hepatic resection was analyzed by using the Kaplan-Meier method and log-rank test. Results The reader-averaged figure of merit of PET/MR imaging was significantly higher than that of either multidetector CT (P = .003) or PET (P = .020) in the detection of CRLMs. However, no significant difference was observed between figure of merit for PET/MR imaging and that for EOB MR imaging (P = .231). After NAC, six of the 18 patients had isometabolic CRLMs on PET images, and 12 patients had hypermetabolic CRLMs. The 1-year recurrence-free survival rate was 80% in patients with isometabolic CRLMs and 14% in patients with hypermetabolic CRLMs, showing a significant difference (P = .026). Conclusion PET/MR imaging can yield significantly higher diagnostic performance in the detection of CRLMs

  9. Developing Pedotransfer Functions for Saline and Saline-Alkali Soils

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

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

    SciTech Connect

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

    2011-04-15

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

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

    SciTech Connect

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

    2014-04-01

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

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

    SciTech Connect

    Masotti, Matteo; Lanconelli, Nico; Campanini, Renato

    2009-02-15

    when compared to the previous one. Specifically, at 60%, 65%, and 70% per-mammogram sensitivity, the new CAD system achieves 0.50, 0.68, and 0.92 FP marks per mammogram, whereas at 70%, 75%, and 80% per-case sensitivity it achieves 0.37, 0.48, and 0.71 FP marks per mammogram, respectively. Conversely, at the same sensitivities, the previous CAD system reached 0.71, 0.87, and 1.15 FP marks per mammogram, and 0.57, 0.73, and 0.92 FPs per mammogram. Also, statistical significance of the difference between the two per-mammogram and per-case FROC curves is demonstrated by the p-value<0.001 returned by jackknife FROC analysis performed on the two CAD systems.

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Spencer, Roy W.; Braswell, William D.

    2001-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  17. A regional high-resolution carbon flux inversion of North America for 2004

    NASA Astrophysics Data System (ADS)

    Schuh, A. E.; Denning, A. S.; Corbin, K. D.; Baker, I. T.; Uliasz, M.; Parazoo, N.; Andrews, A. E.; Worthy, D. E. J.

    2010-05-01

    . We perform the inversion with two independently derived boundary inflow conditions and calculate jackknife-based statistics to test the robustness of the model results. We then compare final results to estimates obtained from the CarbonTracker inversion system and at the Southern Great Plains flux site. Results are promising, showing the ability to correct carbon fluxes from the biosphere models over annual and seasonal time scales, as well as over the different GPP and ER components. Additionally, the correlation of an estimated sink of carbon in the South Central United States with regional anomalously high precipitation in an area of managed agricultural and forest lands provides interesting hypotheses for future work.

  18. A regional high-resolution carbon flux inversion of North America for 2004

    NASA Astrophysics Data System (ADS)

    Schuh, A. E.; Denning, A. S.; Corbin, K. D.; Baker, I. T.; Uliasz, M.; Parazoo, N.; Andrews, A. E.; Worthy, D. E. J.

    2009-11-01

    Resolving the discrepancies between NEE estimates based upon (1) ground studies and (2) atmospheric inversion results, demands increasingly sophisticated techniques. In this paper we present a high-resolution inversion based upon a regional meteorology model (RAMS) and an underlying biosphere (SiB3) model, both running on an identical 40 km grid over most of North America. Previous papers have utilized inversion regions formed by collapsing biome-similar grid cells into large aggregated regions. The effect of this is that the NEE correction imposed on forested regions on the east coast of the United States might be the same as that imposed on forests on the west coast of the United States while, in reality, there likely exist subtle differences in the two areas, both natural and anthropogenic. Our current inversion framework utilizes a combination of previously employed inversion techniques while allowing carbon flux corrections to be biome independent. Temporally and spatially high-resolution results utilizing biome-independent corrections provide insight into carbon dynamics in North America. In particular, we analyze hourly CO2 mixing ratio data from a sparse network of eight towers in North America for 2004. A prior estimate of carbon fluxes due to gross primary productivity (GPP) and ecosystem respiration (ER) is constructed from the SiB3 biosphere model on a 40 km grid. A combination of transport from the RAMS and the parameterized chemical transport model (PCTM) models is used to forge a connection between upwind biosphere fluxes and downwind observed CO2 mixing ratio data. A Kalman filter procedure is used to estimate weekly corrections to biosphere fluxes based upon observed CO2. RMSE-weighted annual NEE estimates, over an ensemble of potential inversion parameter sets, show a mean estimate 0.57 Pg/yr sink in North America. We perform the inversion with two independently derived boundary inflow conditions and calculate jackknife-based statistics to test

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2013-02-01

    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

  2. Extreme Precipitation Mapping for Flood Risk Assessment in Ungauged Basins

    NASA Astrophysics Data System (ADS)

    Kohnova, S.; Parajka, J.; Szolgay, J.; Hlavcova, K.

    2009-04-01

    The poster present a study of mapping 2-year and 100-year annual maximum daily precipitation for rainfall-runoff studies and estimating flood hazard. The main objective was to discuss the quality and properties of maps of design precipitation with a given return period with respect to the expectations of the end user community. Four approaches to the preprocessing of annual maximum 24-hour precipitation data were used, and three interpolation methods employed. The first method is the direct mapping of at-site estimates of distribution function quantiles; the second is the direct mapping of local estimates of the three parameters of the GEV distribution. In the third method, the daily measurements of the precipitation totals were interpolated into a regular grid network, and then the time series of the maximum daily precipitation totals in each grid point of the selected region were statistically analysed. In the fourth method, the spatial distribution of the design precipitation was modeled by quantiles predicted by regional precipitation frequency analysis using the Hosking and Wallis procedure. Homogeneity of the region of interest was tested, and the index value (the mean annual maximum daily precipitation) was mapped using spatial interpolation (instead of the more usual regional regression). Quantiles were derived through the dimensionless regional frequency distribution estimated by using L-moments. The three interpolation methods used were the inverse distance weighting, nearest neighbor and the kriging method. The daily precipitation measurements at 23 climate stations from 1961-2000 were used in the upper Hron basin in central Slovakia. Visual inspection and jackknife cross-validation was used to compare the combination of approaches. Under the specific regime dominated by thermal and frontal convective events, the potential advantage of using mapping of daily precipitation series as a basis for quantile estimation was not shown and under the given

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    We present deep radio observations of four nearby dwarf spheroidal (dSph) galaxies, designed to detect extended synchrotron emission resulting from weakly interacting massive particle (WIMP) dark matter annihilations in their halos. Models by Colafrancesco et al. (CPU07) predict the existence of angularly large, smoothly distributed radio halos in such systems, which stem from electron and positron annihilation products spiraling in a turbulent magnetic field. We map a total of 40.5 deg2 around the Draco, Ursa Major II, Coma Berenices, and Willman 1 dSphs with the Green Bank Telescope (GBT) at 1.4 GHz to detect this annihilation signature, greatly reducing discrete-source confusion using the NVSS catalog. We achieve a sensitivity of σsub <~ 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 <= σast <= 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 χ = 100 GeV annihilating into b\\bar{b} final states and B = 1 μG, upper limits on the annihilation cross-section for Ursa Major II and Willman I are log (langσvrangχ, cm3 s-1) <~ -25 for the preferred set of charged particle propagation parameters adopted by CPU07; this is comparable to

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed Central

    2012-01-01

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

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

    PubMed Central

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

    2015-01-01

    a greater reduction in MAEs. A jack-knife procedure was also performed to determine a suitable number of additional soil samples that would need to be collected for RK of SOC for the whole of Northern Ireland depending on the availability of ancillary data. We recommend i) if only legacy soil polygon map data are available, they should be disaggregated using AtoP kriging, ii) if ancillary data are also available legacy data should be disaggregated using AtoP RK and iii) if new soil measurements are available in addition to ancillary and legacy soil map data, the legacy soil map data should be first disaggregated using AtoP kriging and these data used along with ancillary data as the fixed effects for RK of the new soil measurements. PMID:25729090

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  9. Improved Measurements of the Temperature and Polarization of the Cosmic Microwave Background from QUaD

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

    We present an improved analysis of the final data set from the QUaD experiment. Using an improved technique to remove ground contamination, we double the effective sky area and hence increase the precision of our cosmic microwave background (CMB) power spectrum measurements by ~30% versus that previously reported. In addition, we have improved our modeling of the instrument beams and have reduced our absolute calibration uncertainty from 5% to 3.5% in temperature. The robustness of our results is confirmed through extensive jackknife tests, and by way of the agreement that we find between our two fully independent analysis pipelines. For the standard six-parameter ΛCDM model, the addition of QUaD data marginally improves the constraints on a number of cosmological parameters over those obtained from the WMAP experiment alone. The impact of QUaD data is significantly greater for a model extended to include either a running in the scalar spectral index, or a possible tensor component, or both. Adding both the QUaD data and the results from the Arcminute Cosmology Bolometer Array Receiver experiment, the uncertainty in the spectral index running is reduced by ~25% compared to WMAP alone, while the upper limit on the tensor-to-scalar ratio is reduced from r < 0.48 to r < 0.33 (95% c.l.). This is the strongest limit on tensors to date from the CMB alone. We also use our polarization measurements to place constraints on parity-violating interactions to the surface of last scattering, constraining the energy scale of Lorentz violating interactions to <1.5 × 10-43 GeV (68% c.l.). Finally, we place a robust upper limit on the strength of the lensing B-mode signal. Assuming a single flat band power between ell = 200 and ell = 2000, we constrain the amplitude of B-modes to be <0.57 μK2 (95% c.l.).

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  11. 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

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

    2013-01-01

    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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  15. Casimir interactions between magnetic flux tubes in a dense lattice

    NASA Astrophysics Data System (ADS)

    Mazur, Dan; Heyl, Jeremy S.

    2015-03-01

    form of jackknife analysis which deals with both of these problems.

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

    PubMed Central

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

    2015-01-01

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

  17. Reproducibility and optimization of in vivo human diffusion-weighted MRS of the corpus callosum at 3 T and 7 T.

    PubMed

    Wood, Emily T; Ercan, Ayse Ece; Branzoli, Francesca; Webb, Andrew; Sati, Pascal; Reich, Daniel S; Ronen, Itamar

    2015-08-01

    Diffusion-weighted MRS (DWS) of brain metabolites enables the study of cell-specific alterations in tissue microstructure by probing the diffusion of intracellular metabolites. In particular, the diffusion properties of neuronal N-acetylaspartate (NAA), typically co-measured with N-acetylaspartyl glutamate (NAAG) (NAA + NAAG = tNAA), have been shown to be sensitive to intraneuronal/axonal damage in pathologies such as stroke and multiple sclerosis. Lacking, so far, are empirical assessments of the reproducibility of DWS measures across time and subjects, as well as a systematic investigation of the optimal acquisition parameters for DWS experiments, both of which are sorely needed for clinical applications of the method. In this study, we acquired comprehensive single-volume DWS datasets of the human corpus callosum at 3 T and 7 T. We investigated the inter- and intra-subject variability of empirical and modeled diffusion properties of tNAA [D(avg) (tNAA) and D(model) (tNAA), respectively]. Subsequently, we used a jackknife-like resampling approach to explore the variance of these properties in partial data subsets reflecting different total scan durations. The coefficients of variation (C(V)) and repeatability coefficients (C(R)) for D(avg) (tNAA) and D(model) (tNAA) were calculated for both 3 T and 7 T, with overall lower variability in the 7 T results. Although this work is limited to the estimation of the diffusion properties in the corpus callosum, we show that a careful choice of diffusion-weighting conditions at both field strengths allows the accurate measurement of tNAA diffusion properties in clinically relevant experimental time. Based on the resampling results, we suggest optimized acquisition schemes of 13-min duration at 3T and 10-min duration at 7 T, whilst retaining low variability (C(V) ≈ 8%) for the tNAA diffusion measures. Power calculations for the estimation of D(model )(tNAA) and D(avg) (tNAA) based on the suggested schemes show that

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

    PubMed Central

    2014-01-01

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

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

    PubMed Central

    2013-01-01

    Background The experience in the newborn intensive care nursery results in premature infants’ neurobehavioral and neurophysiological dysfunction and poorer brain structure. Preterms with severe intrauterine growth restriction are doubly jeopardized given their compromised brains. The Newborn Individualized Developmental Care and Assessment Program improved outcome at early school-age for preterms with appropriate intrauterine growth. It also showed effectiveness to nine months for preterms with intrauterine growth restriction. The current study tested effectiveness into school-age for preterms with intrauterine growth restriction regarding executive function (EF), electrophysiology (EEG) and neurostructure (MRI). Methods Twenty-three 9-year-old former growth-restricted preterms, randomized at birth to standard care (14 controls) or to the Newborn Individualized Developmental Care and Assessment Program (9 experimentals) were assessed with standardized measures of cognition, achievement, executive function, electroencephalography, and magnetic resonance imaging. The participating children were comparable to those lost to follow-up, and the controls to the experimentals, in terms of newborn background health and demographics. All outcome measures were corrected for mother’s intelligence. Analysis techniques included two-group analysis of variance and stepwise discriminate analysis for the outcome measures, Wilks’ lambda and jackknifed classification to ascertain two-group classification success per and across domains; canonical correlation analysis to explore relationships among neuropsychological, electrophysiological and neurostructural domains at school-age, and from the newborn period to school-age. Results Controls and experimentals were comparable in age at testing, anthropometric and health parameters, and in cognitive and achievement scores. Experimentals scored better in executive function, spectral coherence, and cerebellar volumes. Furthermore

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

    Tesfaye, Gashaw; Wolff, Matthias

    2015-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    SciTech Connect

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

    2014-02-15

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

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

    PubMed

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

    2014-07-01

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

  5. Evaluation of Projection Methods to Predict Wetlands Area Sizes: the Wetlands Inventory of the United States (sample Date Correction, Land Classification)

    NASA Astrophysics Data System (ADS)

    Terrazas-Gonzalez, Gerardo H.

    This research concerns different methods that can be applied for projection of wetlands areas at selected times. A method described by Frayer (1987) for a stratified random sampling design. The method was developed by W. E. Frayer in collaboration with D. C. Bowden and can be used in surveys where the sampling units have been measured at two different times, tsb1 and tsb2. A change matrix giving the amount of each wetland type at time tsb1 that is in each of the wetland types at time tsb2 is obtained for each sampling unit. Projections are based on a mean annual stratum matrix of changes. Methods of evaluating the reliability of FBSB projections have not been given previously. One objective of this project is to provide variance estimators for the FBSB projection method using jackknife and bootstrap techniques. Direct analytic techniques appear to require an unrealistic amount of time to develop given the complexity of the estimator. Interest in projections at an arbitrary time led to a more general description of the stratum basis estimator to include t < tsb1 and t between tsb1 and tsb2. Variations in the measurement times tsb1 and tsb2 among sampling units within stratum and other considerations including the complexity of the stratum basis estimator, motivated the use of simpler estimators. Two classes of methods for making projections are given. The first class of estimators are functions of summed estimated change matrices while the second class of estimators are functions of products of normalized estimated change matrices. Estimators within each of the classes are further differentiated by whether the changes matrices are on annual or observed time period (tsb2-tsb1) basis. The projections procedures address two different objectives. One objective is the estimation of the total of wetlands areas at a given time. The other objective is to estimate the amount of change among wetland types between 2 given times. All the methods can be used for both objectives

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

    PubMed

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

    2015-04-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    USGS Publications Warehouse

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

    2004-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Horálek, Josef; Šílený, Jan

    2013-08-01

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

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

    PubMed Central

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

    2015-01-01

    the websites of the National Inventory of Natural Heritage (http://www.inpn.fr) and the Global Biodiversity Information Facility (http://www.gbif.fr). SIFlore is regularly updated with additional data records. It is also planned to expand the scope of the dataset to include information about taxon biology, phenology, ecology, chorology, frequency, conservation status and seed banks. A map showing an estimation of the dataset completeness (based on Jackknife 1 estimator) is presented and included as a numerical appendix. Purpose: SIFlore aims to make the data of the flora of France available at the national level for conservation, policy management and scientific research. Such a dataset will provide enough information to allow for macro-ecological reviews of species distribution patterns and, coupled with climatic or topographic datasets, the identification of determinants of these patterns. This dataset can be considered as the primary indicator of the current state of knowledge of flora distribution across France. At a policy level, and in the context of global warming, this should promote the adoption of new measures aiming to improve and intensify flora conservation and surveys. PMID:26491386

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

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

  13. Azimuthal anisotropy beneath southern Africa from very broad-band surface-wave dispersion measurements

    NASA Astrophysics Data System (ADS)

    Adam, Joanne M.-C.; Lebedev, Sergei

    2012-10-01

    Seismic anisotropy within the lithosphere of cratons preserves an important record of their ancient assembly. In southern Africa, anisotropy across the Archean Kaapvaal Craton and Limpopo Belt has been detected previously by observations of SKS-wave splitting. Because SKS-splitting measurements lack vertical resolution, however, the depth distribution of anisotropy has remained uncertain. End-member interpretations invoked the dominance of either anisotropy in the lithosphere (due to the fabric formed by deformation in Archean or Palaeoproterozoic orogenies) or that in the asthenosphere (due to the fabric formed by the recent plate motion), each with significant geodynamic implications. To determine the distribution of anisotropy with depth, we measured phase velocities of seismic surface waves between stations of the Southern African Seismic Experiment. We applied two complementary measurement approaches, very broad-band cross-correlation and multimode waveform inversion. Robust, Rayleigh- and Love-wave dispersion curves were derived for four different subregions of the Archean southern Africa in a period range from 5 s to 250-400 s (Rayleigh) and 5 s to 100-250 s (Love), depending on the region. Rayleigh-wave anisotropy was determined in each region at periods from 5 s to 150-200 s, sampling from the upper crust down to the asthenosphere. The jackknife method was used to estimate uncertainties, and the F-test to verify the statistical significance of anisotropy. We detected strong anisotropy with a N-S fast-propagation azimuth in the upper crust of the Limpopo Belt. We attribute it to aligned cracks, formed by the regional, E-W extensional stress associated with the southward propagation of the East African Rift. Our results show that it is possible to estimate regional stress from short-period, surface wave anisotropy, measured in this study using broad-band array recordings of teleseismic surface waves. Rayleigh-wave anisotropy at 70-120 s periods shows that

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

    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.

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

    NASA Astrophysics Data System (ADS)

    Bazavov, Alexei; Berg, Bernd A.

    2013-03-01

    A new version STMCMUCA_V1_1 of our program package is available. It eliminates compatibility problems of our Fortran 77 code, originally developed for the g77 compiler, with Fortran 90 and 95 compilers. New version program summaryProgram title: STMC_U1MUCA_v1_1 Catalogue identifier: AEET_v1_1 Licensing provisions: Standard CPC license, http://cpc.cs.qub.ac.uk/licence/licence.html Programming language: Fortran 77 compatible with Fortran 90 and 95 Computers: Any capable of compiling and executing Fortran code Operating systems: Any capable of compiling and executing Fortran code RAM: 10 MB and up depending on lattice size used No. of lines in distributed program, including test data, etc.: 15059 No. of bytes in distributed program, including test data, etc.: 215733 Keywords: Markov chain Monte Carlo, multicanonical, Wang-Landau recursion, Fortran, lattice gauge theory, U(1) gauge group, phase transitions of continuous systems Classification: 11.5 Catalogue identifier of previous version: AEET_v1_0 Journal Reference of previous version: Computer Physics Communications 180 (2009) 2339-2347 Does the new version supersede the previous version?: Yes Nature of problem: Efficient Markov chain Monte Carlo simulation of U(1) lattice gauge theory (or other continuous systems) close to its phase transition. Measurements and analysis of the action per plaquette, the specific heat, Polyakov loops and their structure factors. Solution method: Multicanonical simulations with an initial Wang-Landau recursion to determine suitable weight factors. Reweighting to physical values using logarithmic coding and calculating jackknife error bars. Reasons for the new version: The previous version was developed for the g77 compiler Fortran 77 version. Compiler errors were encountered with Fortran 90 and Fortran 95 compilers (specified below). Summary of revisions: epsilon=one/10**10 is replaced by epsilon/10.0D10 in the parameter statements of the subroutines u1_bmha.f, u1_mucabmha.f, u1wl

  16. Implementing the national AIGA flash flood warning system in France

    NASA Astrophysics Data System (ADS)

    Organde, Didier; Javelle, Pierre; Demargne, Julie; Arnaud, Patrick; Caseri, Angelica; Fine, Jean-Alain; de Saint Aubin, Céline

    2015-04-01

    The French national hydro-meteorological and flood forecasting centre (SCHAPI) aims to implement a national flash flood warning system to improve flood alerts for small-to-medium (up to 1000 km2) ungauged basins. This system is based on the AIGA method, co-developed by IRSTEA these last 10 years. The method, initially set up for the Mediterranean area, is based on a simple event-based hourly hydrologic distributed model run every 15 minutes (Javelle et al. 2014). The hydrologic model ingests operational radar-gauge rainfall grids from Météo-France at a 1-km² resolution to produce discharges for successive outlets along the river network. Discharges are then compared to regionalized flood quantiles of given return periods and warnings (expressed as the range of the return period estimated in real-time) are provided on a river network map. The main interest of the method is to provide forecasters and emergency services with a synthetic view in real time of the ongoing flood situation, information that is especially critical in ungauged flood prone areas. In its enhanced national version, the hourly event-based distributed model is coupled to a continuous daily rainfall-runoff model which provides baseflow and a soil moisture index (for each 1-km² pixel) at the beginning of the hourly simulation. The rainfall-runoff models were calibrated on a selection of 700 French hydrometric stations with Météo-France radar-gauge reanalysis dataset for the 2002-2006 period. To estimate model parameters for ungauged basins, the 2 hydrologic models were regionalised by testing both regressions (using different catchment attributes, such as catchment area, soil type, and climate characteristic) and spatial proximity techniques (transposing parameters from neighbouring donor catchments), as well as different homogeneous hydrological areas. The most valuable regionalisation method was determined for each model through jack-knife cross-validation. The system performance was then

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

    NASA Astrophysics Data System (ADS)

    Eggermont, Hilde; Heiri, Oliver; Verschuren, Dirk

    2006-08-01

    We surveyed sub-fossil chironomid assemblages in surface sediments of 73 low- to mid-elevation lakes in tropical East Africa (Uganda, Kenya, Tanzania, Ethiopia) to develop inference models for quantitative paleosalinity reconstruction. Using a calibration data set of 67 lakes with surface-water conductivity between 34 and 68,800 μS/cm, trial models based on partial least squares (PLS), weighted-averaging (WA), weighted-averaging partial least squares (WA-PLS), maximum likelihood (ML), and the weighted modern analogue technique (WMAT) produced jack-knifed coefficients of determination ( r2) between 0.83 and 0.87, and root-mean-squared errors of prediction (RMSEP) between 0.27 and 0.31 log 10 conductivity units, values indicating that fossil assemblages of African Chironomidae can be valuable indicators of past salinity change. The new inference models improve on previous models, which were calibrated with presence-absence data from live collections, by the much greater information content of the calibration data set, and greater probability of finding good modern analogues for fossil assemblages. However, inferences still suffered to a greater (WA, WMAT) or lesser (WA-PLS, PLS and ML) extent from weak correlation between chironomid species distribution and salinity in a broad range of fresh waters, and apparent threshold response of African chironomid communities to salinity change near 3000 μS/cm. To improve model sensitivity in freshwater lakes we expanded the calibration data set with 11 dilute (6-61 μS/cm) high-elevation lakes on Mt. Kenya (Kenya) and the Ruwenzori Mts. (Uganda). This did not appreciably improve models' error statistics, in part because it introduced a secondary environmental gradient to the faunal data, probably temperature. To evaluate whether a chironomid-based salinity inference model calibrated in East African lakes could be meaningfully used for environmental reconstruction elsewhere on the continent, we expanded the calibration data

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

    SciTech Connect

    A. Hassan; J. Chapman

    2008-11-01

    -state assumption of the groundwater model is in error. To test the robustness of the model despite the transient nature of the heads, the newly acquired MV hydraulic head values were trended back to their likely values in 1999, the date of the calibration measurements. Additional statistical tests are performed using both the backward-projected MV heads and the observed heads to identify acceptable model realizations. A jackknife approach identified two possible threshold values to consider. For the analysis using the backward-trended heads, either 458 or 818 realizations (out of 1,000) are found acceptable, depending on the threshold chosen. The analysis using the observed heads found either 284 or 709 realizations acceptable. The impact of the refined set of realizations on the contaminant boundary was explored using an assumed starting mass of a single radionuclide and the acceptable realizations from the backward-trended analysis.