Science.gov

Sample records for abundance estimates based

  1. Estimation of lunar FeO abundance based on imaging by LRO Diviner

    NASA Astrophysics Data System (ADS)

    Tang, Xiao; Luo, Xiao-Xing; Jiang, Yun; Xu, Ao-Ao; Wang, Zhen-Chao; Zhang, Xue-Wei; Chen, Yuan; Zhang, Xiao-Meng; Cai, Wei; Wu, Yun-Zhao

    2016-02-01

    Understanding the abundance and distribution characteristics of FeO on the surface of the Moon is important for investigating its evolution. The current high resolution maps of the global FeO abundance are mostly produced with visible and near infrared reflectance spectra. The Christiansen Feature (CF) in mid-infrared has strong sensitivity to lunar minerals and correlates to major elements composing minerals. This paper investigates the possibility of mapping global FeO abundance using the CF values from the Diviner Lunar Radiometer Experiment aboard the Lunar Reconnaissance Orbiter (LRO) mission. A high correlation between the CF values and FeO abundances from the Apollo samples was found. Based on this high correlation, a new global map (±60°) of FeO was produced using the CF map. The results show that the global FeO average is 8.2 wt.%, the highland average is 4.7 wt.%, the global modal abundance is 5.4 wt.% and the lunar mare mode is 15.7 wt.%. These results are close to those derived from data provided by Clementine, the Lunar Prospector Gamma Ray Spectrometer (LP-GRS) and the Chang'e-1 Interference Imaging Spectrometer (IIM), demonstrating the feasibility of estimating FeO abundance based on the Diviner CF data. The near global FeO abundance map shows an enrichment of lunar major elements.

  2. Abundance estimation and conservation biology

    USGS Publications Warehouse

    Nichols, J.D.; MacKenzie, D.I.

    2004-01-01

    should be focused on relationships between demographic processes such as survival and recruitment, the two quantities responsible for changes in abundance, rather than simply on the magnitudes of these quantities. They describe a type of Jolly–Seber capture–recapture model that permits inference about the underlying relationship between per capita recruitment rates and survival rates (Link & Barker, this volume). Implementation used Bayesian Markov Chain Monte Carlo methods and appeared to work well, yielding inferences about the relationship between recruitment and survival that were robust to selection of prior distribution. We believe that readers will find their arguments compelling, and we expect to see increased use of hierarchical modeling approaches in capture–recapture and related fields. Otto (presentation without paper) also recommended use of hierarchical models in analysis of multiple data sources dealing with population dynamics of North American mallards. He integrated survival inferences from ringing data, abundance information from aerial survey data, and recruitment information based on age ratios from a harvest survey. He used a Leslie matrix population projection model as an integrating framework and obtained estimates of breeding population size using all data.Otto’s approach also permitted inference about biases in estimated quantities. As with the work of Link & Barker (2004), we find Otto’s recommendation to use hierarchical models to integrate data from multiple sources to be very compelling. Alisauskas et al. (2004) report results of an analysis of capture–recapture data for a askatchewan population of white–winged scoters. They used the approach of Pradel (1996) to estimate population growth rate (See the PDF) directly. Estimates for 1975–1985 were quite low, but estimates for the recent period, 2000–2003,increased to values > 1. Parameter estimates for seniority, survival and per capita recruitment (Pradel, 1996) led to the

  3. Evaluating abundance estimate precision and the assumptions of a count-based index for small mammals

    USGS Publications Warehouse

    Wiewel, A.S.; Adams, A.A.Y.; Rodda, G.H.

    2009-01-01

    Conservation and management of small mammals requires reliable knowledge of population size. We investigated precision of markrecapture and removal abundance estimates generated from live-trapping and snap-trapping data collected at sites on Guam (n 7), Rota (n 4), Saipan (n 5), and Tinian (n 3), in the Mariana Islands. We also evaluated a common index, captures per unit effort (CPUE), as a predictor of abundance. In addition, we evaluated cost and time associated with implementing live-trapping and snap-trapping and compared species-specific capture rates of selected live- and snap-traps. For all species, markrecapture estimates were consistently more precise than removal estimates based on coefficients of variation and 95 confidence intervals. The predictive utility of CPUE was poor but improved with increasing sampling duration. Nonetheless, modeling of sampling data revealed that underlying assumptions critical to application of an index of abundance, such as constant capture probability across space, time, and individuals, were not met. Although snap-trapping was cheaper and faster than live-trapping, the time difference was negligible when site preparation time was considered. Rattus diardii spp. captures were greatest in Haguruma live-traps (Standard Trading Co., Honolulu, HI) and Victor snap-traps (Woodstream Corporation, Lititz, PA), whereas Suncus murinus and Mus musculus captures were greatest in Sherman live-traps (H. B. Sherman Traps, Inc., Tallahassee, FL) and Museum Special snap-traps (Woodstream Corporation). Although snap-trapping and CPUE may have utility after validation against more rigorous methods, validation should occur across the full range of study conditions. Resources required for this level of validation would likely be better allocated towards implementing rigorous and robust methods.

  4. Improving removal-based estimates of abundance by sampling a population of spatially distinct subpopulations

    USGS Publications Warehouse

    Dorazio, R.M.; Jelks, H.L.; Jordan, F.

    2005-01-01

     A statistical modeling framework is described for estimating the abundances of spatially distinct subpopulations of animals surveyed using removal sampling. To illustrate this framework, hierarchical models are developed using the Poisson and negative-binomial distributions to model variation in abundance among subpopulations and using the beta distribution to model variation in capture probabilities. These models are fitted to the removal counts observed in a survey of a federally endangered fish species. The resulting estimates of abundance have similar or better precision than those computed using the conventional approach of analyzing the removal counts of each subpopulation separately. Extension of the hierarchical models to include spatial covariates of abundance is straightforward and may be used to identify important features of an animal's habitat or to predict the abundance of animals at unsampled locations.

  5. Effects of sampling conditions on DNA-based estimates of American black bear abundance

    USGS Publications Warehouse

    Laufenberg, Jared S.; Van Manen, Frank T.; Clark, Joseph D.

    2013-01-01

    DNA-based capture-mark-recapture techniques are commonly used to estimate American black bear (Ursus americanus) population abundance (N). Although the technique is well established, many questions remain regarding study design. In particular, relationships among N, capture probability of heterogeneity mixtures A and B (pA and pB, respectively, or p, collectively), the proportion of each mixture (π), number of capture occasions (k), and probability of obtaining reliable estimates of N are not fully understood. We investigated these relationships using 1) an empirical dataset of DNA samples for which true N was unknown and 2) simulated datasets with known properties that represented a broader array of sampling conditions. For the empirical data analysis, we used the full closed population with heterogeneity data type in Program MARK to estimate N for a black bear population in Great Smoky Mountains National Park, Tennessee. We systematically reduced the number of those samples used in the analysis to evaluate the effect that changes in capture probabilities may have on parameter estimates. Model-averaged N for females and males were 161 (95% CI = 114–272) and 100 (95% CI = 74–167), respectively (pooled N = 261, 95% CI = 192–419), and the average weekly p was 0.09 for females and 0.12 for males. When we reduced the number of samples of the empirical data, support for heterogeneity models decreased. For the simulation analysis, we generated capture data with individual heterogeneity covering a range of sampling conditions commonly encountered in DNA-based capture-mark-recapture studies and examined the relationships between those conditions and accuracy (i.e., probability of obtaining an estimated N that is within 20% of true N), coverage (i.e., probability that 95% confidence interval includes true N), and precision (i.e., probability of obtaining a coefficient of variation ≤20%) of estimates using logistic regression. The capture probability

  6. Estimating stellar atmospheric parameters, absolute magnitudes and elemental abundances from the LAMOST spectra with Kernel-based Principal Component Analysis

    NASA Astrophysics Data System (ADS)

    Xiang, M.-S.; Liu, X.-W.; Shi, J.-R.; Yuan, H.-B.; Huang, Y.; Luo, A.-L.; Zhang, H.-W.; Zhao, Y.-H.; Zhang, J.-N.; Ren, J.-J.; Chen, B.-Q.; Wang, C.; Li, J.; Huo, Z.-Y.; Zhang, W.; Wang, J.-L.; Zhang, Y.; Hou, Y.-H.; Wang, Y.-F.

    2016-10-01

    Accurate determination of stellar atmospheric parameters and elemental abundances is crucial for Galactic archeology via large-scale spectroscopic surveys. In this paper, we estimate stellar atmospheric parameters - effective temperature Teff, surface gravity log g and metallicity [Fe/H], absolute magnitudes MV and MKs, α-element to metal (and iron) abundance ratio [α/M] (and [α/Fe]), as well as carbon and nitrogen abundances [C/H] and [N/H] from the LAMOST spectra with a multivariate regression method based on kernel-based principal component analysis, using stars in common with other surveys (Hipparcos, Kepler, APOGEE) as training data sets. Both internal and external examinations indicate that given a spectral signal-to-noise ratio (SNR) better than 50, our method is capable of delivering stellar parameters with a precision of ˜100 K for Teff, ˜0.1 dex for log g, 0.3 - 0.4 mag for MV and MKs, 0.1 dex for [Fe/H], [C/H] and [N/H], and better than 0.05 dex for [α/M] ([α/Fe]). The results are satisfactory even for a spectral SNR of 20. The work presents first determinations of [C/H] and [N/H] abundances from a vast data set of LAMOST, and, to our knowledge, the first reported implementation of absolute magnitude estimation directly based on the observed spectra. The derived stellar parameters for millions of stars from the LAMOST surveys will be publicly available in the form of value-added catalogues.

  7. Landscape ecology of eastern coyotes based on large-scale estimates of abundance.

    PubMed

    Kays, Roland W; Gompper, Matthew E; Ray, Justina C

    2008-06-01

    Since their range expansion into eastern North America in the mid-1900s, coyotes (Canis latrans) have become the region's top predator. Although widespread across the region, coyote adaptation to eastern forests and use of the broader landscape are not well understood. We studied the distribution and abundance of coyotes by collecting coyote feces from 54 sites across a diversity of landscapes in and around the Adirondacks of northern New York. We then genotyped feces with microsatellites and found a close correlation between the number of detected individuals and the total number of scats at a site. We created habitat models predicting coyote abundance using multi-scale vegetation and landscape data and ranked them with an information-theoretic model selection approach. These models allow us to reject the hypothesis that eastern forests are unsuitable habitat for coyotes as their abundance was positively correlated with forest cover and negatively correlated with measures of rural non-forest landscapes. However, measures of vegetation structure turned out to be better predictors of coyote abundance than generalized "forest vs. open" classification. The best supported models included those measures indicative of disturbed forest, especially more open canopies found in logged forests, and included natural edge habitats along water courses. These forest types are more productive than mature forests and presumably host more prey for coyotes. A second model with only variables that could be mapped across the region highlighted the lower density of coyotes in areas with high human settlement, as well as positive relationships with variables such as snowfall and lakes that may relate to increased numbers and vulnerability of deer. The resulting map predicts coyote density to be highest along the southwestern edge of the Adirondack State Park, including Tug Hill, and lowest in the mature forests and more rural areas of the central and eastern Adirondacks. Together, these

  8. Aerial survey estimates of fallow deer abundance

    USGS Publications Warehouse

    Gogan, Peter J.; Gates, Natalie B.; Lubow, Bruce C.; Pettit, Suzanne

    2012-01-01

    Reliable estimates of the distribution and abundance of an ungulate species is essential prior to establishing and implementing a management program. We used ground surveys to determine distribution and ground and aerial surveys and individually marked deer to estimate the abundance of fallow deer (Dama dama) in north-coastal California. Fallow deer had limited distribution and heterogeneous densities. Estimated post-rut densities across 4 annual surveys ranged from a low of 1.4 (SE=0.2) deer/km2 to a high of 3.3 (se=0.5) deer/km2 in a low density stratum and from 49.0 (SE=8.3) deer/km2 to 111.6 deer/km2 in a high density stratum. Sightability was positively influenced by the presence of white color-phase deer in a group and group size, and varied between airial and ground-based observers and by density strata. Our findings underscore the utility of double-observer surveys and aerial surveys with individually marked deer, both incorporating covariates to model sightability, to estimate deer abundance.

  9. Hydroacoustic estimates of fish abundance

    SciTech Connect

    Wilson, W.K.

    1991-03-01

    Hydroacoustics, as defined in the context of this report, is the use of a scientific sonar system to determine fish densities with respect to numbers and biomass. These two parameters provide a method of monitoring reservoir fish populations and detecting gross changes in the ecosystem. With respect to southeastern reservoirs, hydroacoustic surveys represent a new method of sampling open water areas and the best technology available. The advantages of this technology are large amounts of data can be collected in a relatively short period of time allowing improved statistical interpretation and data comparison, the pelagic (open water) zone can be sampled efficiently regardless of depth, and sampling is nondestructive and noninvasive with neither injury to the fish nor alteration of the environment. Hydroacoustics cannot provide species identification and related information on species composition or length/weight relationships. Also, sampling is limited to a minimum depth of ten feet which precludes the use of this equipment for sampling shallow shoreline areas. The objective of this study is to use hydroacoustic techniques to estimate fish standing stocks (i.e., numbers and biomass) in several areas of selected Tennessee Valley Reservoirs as part of a base level monitoring program to assess long-term changes in reservoir water quality.

  10. Occupancy as a surrogate for abundance estimation

    USGS Publications Warehouse

    MacKenzie, D.I.; Nichols, J.D.

    2004-01-01

    In many monitoring programmes it may be prohibitively expensive to estimate the actual abundance of a bird species in a defined area, particularly at large spatial scales, or where birds occur at very low densities. Often it may be appropriate to consider the proportion of area occupied by the species as an alternative state variable. However, as with abundance estimation, issues of detectability must be taken into account in order to make accurate inferences: the non?detection of the species does not imply the species is genuinely absent. Here we review some recent modelling developments that permit unbiased estimation of the proportion of area occupied, colonization and local extinction probabilities. These methods allow for unequal sampling effort and enable covariate information on sampling locations to be incorporated. We also describe how these models could be extended to incorporate information from marked individuals, which would enable finer questions of population dynamics (such as turnover rate of nest sites by specific breeding pairs) to be addressed. We believe these models may be applicable to a wide range of bird species and may be useful for investigating various questions of ecological interest. For example, with respect to habitat quality, we might predict that a species is more likely to have higher local extinction probabilities, or higher turnover rates of specific breeding pairs, in poor quality habitats.

  11. Robust Abundance Estimation in Animal Abundance Surveys with Imperfect Detection

    EPA Science Inventory

    Surveys of animal abundance are central to the conservation and management of living natural resources. However, detection uncertainty complicates the sampling process of many species. One sampling method employed to deal with this problem is depletion (or removal) surveys in whi...

  12. Lincoln estimates of mallard (Anas platyrhynchos) abundance in North America

    PubMed Central

    Alisauskas, Ray T; Arnold, Todd W; Leafloor, James O; Otis, David L; Sedinger, James S

    2014-01-01

    Estimates of range-wide abundance, harvest, and harvest rate are fundamental for sound inferences about the role of exploitation in the dynamics of free-ranging wildlife populations, but reliability of existing survey methods for abundance estimation is rarely assessed using alternative approaches. North American mallard populations have been surveyed each spring since 1955 using internationally coordinated aerial surveys, but population size can also be estimated with Lincoln's method using banding and harvest data. We estimated late summer population size of adult and juvenile male and female mallards in western, midcontinent, and eastern North America using Lincoln's method of dividing (i) total estimated harvest, , by estimated harvest rate, , calculated as (ii) direct band recovery rate, , divided by the (iii) band reporting rate, . Our goal was to compare estimates based on Lincoln's method with traditional estimates based on aerial surveys. Lincoln estimates of adult males and females alive in the period June–September were 4.0 (range: 2.5–5.9), 1.8 (range: 0.6–3.0), and 1.8 (range: 1.3–2.7) times larger than respective aerial survey estimates for the western, midcontinent, and eastern mallard populations, and the two population estimates were only modestly correlated with each other (western: r = 0.70, 1993–2011; midcontinent: r = 0.54, 1961–2011; eastern: r = 0.50, 1993–2011). Higher Lincoln estimates are predictable given that the geographic scope of inference from Lincoln estimates is the entire population range, whereas sampling frames for aerial surveys are incomplete. Although each estimation method has a number of important potential biases, our review suggests that underestimation of total population size by aerial surveys is the most likely explanation. In addition to providing measures of total abundance, Lincoln's method provides estimates of fecundity and population sex ratio and could be used in integrated population

  13. Estimates of brown bear abundance on Kodiak Island, Alaska

    USGS Publications Warehouse

    Barnes, V.G.; Smith, R.B.

    1998-01-01

    During 1987-94 we used capture-mark-resight (CMR) methodology and rates of observation (bears/hour and bears/100 km2) of unmarked brown bears (Ursus arctos middendorffi) during intensive aerial surveys (IAS) to estimate abundance of brown bears on Kodiak Island and to establish a baseline for monitoring population trends. CMR estimates were obtained on 3 study areas; density ranged from 216-234 bears/1,000 km2 for independent animals and 292-342 bears/1,000 km2 including dependent offspring. Rates of observation during IAS ranged from 1.4-5.4 independent bears/hour and 2.9-18.0 independent bears/100 km2. Density estimates for independent bears on each IAS area were obtained by dividing mean number of bears observed during replicate surveys by estimated sightability (based on CMR-derived sightability in areas with similar habitat. Brown bear abundance on 21 geographic units of Kodiak Island and 3 nearby islands was estimated by extrapolation from CMR and IAS data using comparisons of habitat characteristics and sport harvest information. Population estimates for independent and total bears were 1,800 and 2,600. The CMR and IAS procedures offer alternative means, depending on management objective and available resources, of measuring population trend of brown bears on Kodiak Island.

  14. Generalized estimators of avian abundance from count survey data

    USGS Publications Warehouse

    Royle, J. Andrew

    2004-01-01

    I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture?recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations) constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed.

  15. Toward Reliable Estimates of Abundance: Comparing Index Methods to Assess the Abundance of a Mammalian Predator

    PubMed Central

    Güthlin, Denise; Storch, Ilse; Küchenhoff, Helmut

    2014-01-01

    Due to time and financial constraints indices are often used to obtain landscape-scale estimates of relative species abundance. Using two different field methods and comparing the results can help to detect possible bias or a non monotonic relationship between the index and the true abundance, providing more reliable results. We used data obtained from camera traps and feces counts to independently estimate relative abundance of red foxes in the Black Forest, a forested landscape in southern Germany. Applying negative binomial regression models, we identified landscape parameters that influence red fox abundance, which we then used to predict relative red fox abundance. We compared the estimated regression coefficients of the landscape parameters and the predicted abundance of the two methods. Further, we compared the costs and the precision of the two field methods. The predicted relative abundances were similar between the two methods, suggesting that the two indices were closely related to the true abundance of red foxes. For both methods, landscape diversity and edge density best described differences in the indices and had positive estimated effects on the relative fox abundance. In our study the costs of each method were of similar magnitude, but the sample size obtained from the feces counts (262 transects) was larger than the camera trap sample size (88 camera locations). The precision of the camera traps was lower than the precision of the feces counts. The approach we applied can be used as a framework to compare and combine the results of two or more different field methods to estimate abundance and by this enhance the reliability of the result. PMID:24743565

  16. Toward reliable estimates of abundance: comparing index methods to assess the abundance of a Mammalian predator.

    PubMed

    Güthlin, Denise; Storch, Ilse; Küchenhoff, Helmut

    2014-01-01

    Due to time and financial constraints indices are often used to obtain landscape-scale estimates of relative species abundance. Using two different field methods and comparing the results can help to detect possible bias or a non monotonic relationship between the index and the true abundance, providing more reliable results. We used data obtained from camera traps and feces counts to independently estimate relative abundance of red foxes in the Black Forest, a forested landscape in southern Germany. Applying negative binomial regression models, we identified landscape parameters that influence red fox abundance, which we then used to predict relative red fox abundance. We compared the estimated regression coefficients of the landscape parameters and the predicted abundance of the two methods. Further, we compared the costs and the precision of the two field methods. The predicted relative abundances were similar between the two methods, suggesting that the two indices were closely related to the true abundance of red foxes. For both methods, landscape diversity and edge density best described differences in the indices and had positive estimated effects on the relative fox abundance. In our study the costs of each method were of similar magnitude, but the sample size obtained from the feces counts (262 transects) was larger than the camera trap sample size (88 camera locations). The precision of the camera traps was lower than the precision of the feces counts. The approach we applied can be used as a framework to compare and combine the results of two or more different field methods to estimate abundance and by this enhance the reliability of the result. PMID:24743565

  17. Spectral abundance fraction estimation of materials using Kalman filters

    NASA Astrophysics Data System (ADS)

    Wang, Su; Chang, Chein; Jensen, Janet L.; Jensen, James O.

    2004-12-01

    Kalman filter has been widely used in statistical signal processing for parameter estimation. Although a Kalman filter approach has been recently developed for spectral unmixing, referred to as Kalman filter-based linear unmixing (KFLU), its applicability to spectral characterization within a single pixel vector has not been explored. This paper presents a new application of Kalman filtering in spectral estimation and quantification. It develops a Kalman filter-based spectral signature esimator (KFSSE) which is different from the KFLU in the sense that the former performs a Kalman filter wavelength by wavelength across a spectral signature as opposed to the latter which implements a Kalman filter pixel vector by pixel vector in an image cube. The idea of the KFSSE is to implement the state equation to characterize the true spectral signature, while the measurement equation is being used to describe the spectral signature to be processed. Additionally, since a Kalman filter can accurately estimate spectral abundance fraction of a signature, our proposed KFSSE can further used for spectral quantification for subpixel targets and mixed pixel vectors, called Kalman filter-based spectral quantifier (KFSQ). Such spectral quantification is particularly important for chemical/biological defense which requires quantification of detected agents for damage control assessment. Several different types of hyperspectral data are used for experiments to demonstrate the ability of the KFSSE in estimation of spectral signature and the utility of the KFSQ in spectral quantification.

  18. CIDANE: comprehensive isoform discovery and abundance estimation.

    PubMed

    Canzar, Stefan; Andreotti, Sandro; Weese, David; Reinert, Knut; Klau, Gunnar W

    2016-01-01

    We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts efficiently with significantly higher sensitivity and precision than existing tools. Its algorithmic core not only reconstructs transcripts ab initio, but also allows the use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms. CIDANE supports the integrated analysis of RNA-seq and additional gene-boundary data and recovers splice junctions that are invisible to other methods. CIDANE is available at http://ccb.jhu.edu/software/cidane/.

  19. An easy field method for estimating the abundance of culicid larval instars.

    PubMed

    Carron, Alexandre; Duchet, Claire; Gaven, Bruno; Lagneau, Christophe

    2003-12-01

    A new method is proposed that avoids manual counting of mosquito larvae in order to estimate larval abundance in the field. This method is based on the visual comparison between abundance, in a standardized sampling tray (called an abacus), with 5 (abacus 5) or 10 (abacus 10) diagrammatically prepared abundance classes. Accuracy under laboratory and field conditions and individual bias have been evaluated and both abaci provide a reliable estimation of abundance in both conditions. There is no individual bias, whether people are familiar or not with its use. They could also be used for a quick estimation of larval treatment effectiveness, for the study of population dynamics and spatial distribution.

  20. Metagenomic abundance estimation and diagnostic testing on species level

    PubMed Central

    Lindner, Martin S.; Renard, Bernhard Y.

    2013-01-01

    One goal of sequencing-based metagenomic community analysis is the quantitative taxonomic assessment of microbial community compositions. In particular, relative quantification of taxons is of high relevance for metagenomic diagnostics or microbial community comparison. However, the majority of existing approaches quantify at low resolution (e.g. at phylum level), rely on the existence of special genes (e.g. 16S), or have severe problems discerning species with highly similar genome sequences. Yet, problems as metagenomic diagnostics require accurate quantification on species level. We developed Genome Abundance Similarity Correction (GASiC), a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach. We demonstrate GASiC’s superior performance over existing methods on simulated benchmark data as well as on real data. In addition, we present applications to datasets of both bacterial DNA and viral RNA source. We further discuss our approach as an alternative to PCR-based DNA quantification. PMID:22941661

  1. Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance.

    PubMed

    Mumma, Matthew A; Zieminski, Chris; Fuller, Todd K; Mahoney, Shane P; Waits, Lisette P

    2015-09-01

    Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23-39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances.

  2. Estimating site occupancy and abundance using indirect detection indices

    USGS Publications Warehouse

    Stanley, T.R.; Royle, J. Andrew

    2005-01-01

    Knowledge of factors influencing animal distribution and abundance is essential in many areas of ecological research, management, and policy-making. Because common methods for modeling and estimating abundance (e.g., capture-recapture, distance sampling) are sometimes not practical for large areas or elusive species, indices are sometimes used as surrogate measures of abundance. We present an extension of the Royle and Nichols (2003) generalization of the MacKenzie et al. (2002) site-occupancy model that incorporates length of the sampling interval into the, model for detection probability. As a result, we obtain a modeling framework that shows how useful information can be extracted from a class of index methods we call indirect detection indices (IDIs). Examples of IDIs include scent station, tracking tube, snow track, tracking plate, and hair snare surveys. Our model is maximum likelihood, and it can be used to estimate site occupancy and model factors influencing patterns of occupancy and abundance in space. Under certain circumstances, it can also be used to estimate abundance. We evaluated model properties using Monte Carlo simulations and illustrate the method with tracking tube and scent station data. We believe this model will be a useful tool for determining factors that influence animal distribution and abundance.

  3. Incorporating availability for detection in estimates of bird abundance

    USGS Publications Warehouse

    Diefenbach, D.R.; Marshall, M.R.; Mattice, J.A.; Brauning, D.W.

    2007-01-01

    Several bird-survey methods have been proposed that provide an estimated detection probability so that bird-count statistics can be used to estimate bird abundance. However, some of these estimators adjust counts of birds observed by the probability that a bird is detected and assume that all birds are available to be detected at the time of the survey. We marked male Henslow's Sparrows (Ammodramus henslowii) and Grasshopper Sparrows (A. savannarum) and monitored their behavior during May-July 2002 and 2003 to estimate the proportion of time they were available for detection. We found that the availability of Henslow's Sparrows declined in late June to <10% for 5- or 10-min point counts when a male had to sing and be visible to the observer; but during 20 May-19 June, males were available for detection 39.1% (SD = 27.3) of the time for 5-min point counts and 43.9% (SD = 28.9) of the time for 10-min point counts (n = 54). We detected no temporal changes in availability for Grasshopper Sparrows, but estimated availability to be much lower for 5-min point counts (10.3%, SD = 12.2) than for 10-min point counts (19.2%, SD = 22.3) when males had to be visible and sing during the sampling period (n = 80). For distance sampling, we estimated the availability of Henslow's Sparrows to be 44.2% (SD = 29.0) and the availability of Grasshopper Sparrows to be 20.6% (SD = 23.5). We show how our estimates of availability can be incorporated in the abundance and variance estimators for distance sampling and modify the abundance and variance estimators for the double-observer method. Methods that directly estimate availability from bird counts but also incorporate detection probabilities need further development and will be important for obtaining unbiased estimates of abundance for these species. ?? The American Ornithologists' Union, 2007.

  4. Estimating abundance in the presence of species uncertainty

    USGS Publications Warehouse

    Chambert, Thierry A; Hossack, Blake R.; Fishback, LeeAnn; Davenport, Jon M.

    2016-01-01

    1.N-mixture models have become a popular method for estimating abundance of free-ranging animals that are not marked or identified individually. These models have been used on count data for single species that can be identified with certainty. However, co-occurring species often look similar during one or more life stages, making it difficult to assign species for all recorded captures. This uncertainty creates problems for estimating species-specific abundance and it can often limit life stages to which we can make inference. 2.We present a new extension of N-mixture models that accounts for species uncertainty. In addition to estimating site-specific abundances and detection probabilities, this model allows estimating probability of correct assignment of species identity. We implement this hierarchical model in a Bayesian framework and provide all code for running the model in BUGS-language programs. 3.We present an application of the model on count data from two sympatric freshwater fishes, the brook stickleback (Culaea inconstans) and the ninespine stickleback (Pungitius pungitius), ad illustrate implementation of covariate effects (habitat characteristics). In addition, we used a simulation study to validate the model and illustrate potential sample size issues. We also compared, for both real and simulated data, estimates provided by our model to those obtained by a simple N-mixture model when captures of unknown species identification were discarded. In the latter case, abundance estimates appeared highly biased and very imprecise, while our new model provided unbiased estimates with higher precision. 4.This extension of the N-mixture model should be useful for a wide variety of studies and taxa, as species uncertainty is a common issue. It should notably help improve investigation of abundance and vital rate characteristics of organisms’ early life stages, which are sometimes more difficult to identify than adults.

  5. A collaborative approach for estimating terrestrial wildlife abundance

    USGS Publications Warehouse

    Ransom, Jason I.; Kaczensky, Petra; Lubow, Bruce C.; Ganbaatar, Oyunsaikhan; Altansukh, Nanjid

    2012-01-01

    Accurately estimating abundance of wildlife is critical for establishing effective conservation and management strategies. Aerial methodologies for estimating abundance are common in developed countries, but they are often impractical for remote areas of developing countries where many of the world's endangered and threatened fauna exist. The alternative terrestrial methodologies can be constrained by limitations on access, technology, and human resources, and have rarely been comprehensively conducted for large terrestrial mammals at landscape scales. We attempted to overcome these problems by incorporating local peoples into a simultaneous point count of Asiatic wild ass (Equus hemionus) and goitered gazelle (Gazella subgutturosa) across the Great Gobi B Strictly Protected Area, Mongolia. Paired observers collected abundance and covariate metrics at 50 observation points and we estimated population sizes using distance sampling theory, but also assessed individual observer error to examine potential bias introduced by the large number of minimally trained observers. We estimated 5671 (95% CI = 3611–8907) wild asses and 5909 (95% CI = 3762–9279) gazelle inhabited the 11,027 km2 study area at the time of our survey and found that the methodology developed was robust at absorbing the logistical challenges and wide range of observer abilities. This initiative serves as a functional model for estimating terrestrial wildlife abundance while integrating local people into scientific and conservation projects. This, in turn, creates vested interest in conservation by the people who are most influential in, and most affected by, the outcomes.

  6. Estimating the number of species in a stochastic abundance model.

    PubMed

    Chao, Anne; Bunge, John

    2002-09-01

    Consider a stochastic abundance model in which the species arrive in the sample according to independent Poisson processes, where the abundance parameters of the processes follow a gamma distribution. We propose a new estimator of the number of species for this model. The estimator takes the form of the number of duplicated species (i.e., species represented by two or more individuals) divided by an estimated duplication fraction. The duplication fraction is estimated from all frequencies including singleton information. The new estimator is closely related to the sample coverage estimator presented by Chao and Lee (1992, Journal of the American Statistical Association 87, 210-217). We illustrate the procedure using the Malayan butterfly data discussed by Fisher, Corbet, and Williams (1943, Journal of Animal Ecology 12, 42-58) and a 1989 Christmas Bird Count dataset collected in Florida, U.S.A. Simulation studies show that this estimator compares well with maximum likelihood estimators (i.e., empirical Bayes estimators from the Bayesian viewpoint) for which an iterative numerical procedure is needed and may be infeasible.

  7. The effects of acoustic misclassification on cetacean species abundance estimation.

    PubMed

    Caillat, Marjolaine; Thomas, Len; Gillespie, Douglas

    2013-09-01

    To estimate the density or abundance of a cetacean species using acoustic detection data, it is necessary to correctly identify the species that are detected. Developing an automated species classifier with 100% correct classification rate for any species is likely to stay out of reach. It is therefore necessary to consider the effect of misidentified detections on the number of observed data and consequently on abundance or density estimation, and develop methods to cope with these misidentifications. If misclassification rates are known, it is possible to estimate the true numbers of detected calls without bias. However, misclassification and uncertainties in the level of misclassification increase the variance of the estimates. If the true numbers of calls from different species are similar, then a small amount of misclassification between species and a small amount of uncertainty around the classification probabilities does not have an overly detrimental effect on the overall variance. However, if there is a difference in the encounter rate between species calls and/or a large amount of uncertainty in misclassification rates, then the variance of the estimates becomes very large and this dramatically increases the variance of the final abundance estimate.

  8. Evaluating noninvasive genetic sampling techniques to estimate large carnivore abundance.

    PubMed

    Mumma, Matthew A; Zieminski, Chris; Fuller, Todd K; Mahoney, Shane P; Waits, Lisette P

    2015-09-01

    Monitoring large carnivores is difficult because of intrinsically low densities and can be dangerous if physical capture is required. Noninvasive genetic sampling (NGS) is a safe and cost-effective alternative to physical capture. We evaluated the utility of two NGS methods (scat detection dogs and hair sampling) to obtain genetic samples for abundance estimation of coyotes, black bears and Canada lynx in three areas of Newfoundland, Canada. We calculated abundance estimates using program capwire, compared sampling costs, and the cost/sample for each method relative to species and study site, and performed simulations to determine the sampling intensity necessary to achieve abundance estimates with coefficients of variation (CV) of <10%. Scat sampling was effective for both coyotes and bears and hair snags effectively sampled bears in two of three study sites. Rub pads were ineffective in sampling coyotes and lynx. The precision of abundance estimates was dependent upon the number of captures/individual. Our simulations suggested that ~3.4 captures/individual will result in a < 10% CV for abundance estimates when populations are small (23-39), but fewer captures/individual may be sufficient for larger populations. We found scat sampling was more cost-effective for sampling multiple species, but suggest that hair sampling may be less expensive at study sites with limited road access for bears. Given the dependence of sampling scheme on species and study site, the optimal sampling scheme is likely to be study-specific warranting pilot studies in most circumstances. PMID:25693632

  9. New aerial survey and hierarchical model to estimate manatee abundance

    USGS Publications Warehouse

    Langimm, Cahterine A.; Dorazio, Robert M.; Stith, Bradley M.; Doyle, Terry J.

    2011-01-01

    Monitoring the response of endangered and protected species to hydrological restoration is a major component of the adaptive management framework of the Comprehensive Everglades Restoration Plan. The endangered Florida manatee (Trichechus manatus latirostris) lives at the marine-freshwater interface in southwest Florida and is likely to be affected by hydrologic restoration. To provide managers with prerestoration information on distribution and abundance for postrestoration comparison, we developed and implemented a new aerial survey design and hierarchical statistical model to estimate and map abundance of manatees as a function of patch-specific habitat characteristics, indicative of manatee requirements for offshore forage (seagrass), inland fresh drinking water, and warm-water winter refuge. We estimated the number of groups of manatees from dual-observer counts and estimated the number of individuals within groups by removal sampling. Our model is unique in that we jointly analyzed group and individual counts using assumptions that allow probabilities of group detection to depend on group size. Ours is the first analysis of manatee aerial surveys to model spatial and temporal abundance of manatees in association with habitat type while accounting for imperfect detection. We conducted the study in the Ten Thousand Islands area of southwestern Florida, USA, which was expected to be affected by the Picayune Strand Restoration Project to restore hydrology altered for a failed real-estate development. We conducted 11 surveys in 2006, spanning the cold, dry season and warm, wet season. To examine short-term and seasonal changes in distribution we flew paired surveys 1–2 days apart within a given month during the year. Manatees were sparsely distributed across the landscape in small groups. Probability of detection of a group increased with group size; the magnitude of the relationship between group size and detection probability varied among surveys. Probability

  10. A comparative study of iron abundance estimation methods: Application to the western nearside of the Moon

    NASA Astrophysics Data System (ADS)

    Bhatt, Megha; Mall, Urs; Wöhler, Christian; Grumpe, Arne; Bugiolacchi, Roberto

    2015-03-01

    The FeO weight percentage (wt.%) abundance of the Moon's western nearside (55°S-55°N and 5°E-40°W) is estimated using data from the InfraRed Spectrometer-2 (SIR-2) and the Moon Mineralogy Mapper (M3). In this study, we modified an FeO abundance estimation algorithm (Bhatt, M., Mall, U., Bugiolacchi, R., McKenna-Lawlor, S., Banaszkiewicz, M., Nathues, A., Ullaland, K. [2012]. Icarus 220, 51-64) which relies exclusively on the 2-μm absorption band parameters. The modified FeO abundance estimation algorithm and the regression-based elemental abundance estimation algorithm (Wöhler, C., Grumpe, A., Berezhnoy, A., Bhatt, M.U., Mall, U. [2014]. Icarus 235, 86-122) which is based on the 1-μm and 2-μm absorption band parameters is applied to the M3 data. We have compared results obtained from these two modified algorithms with a previously published Clementine's FeO wt.% map (Lucey, P.G., Blewett, D.T., Jolliff, B.L. [2000]. J. Geophys. Res. 105, 20297-20306). The effects of topography and space weathering on FeO wt.% estimates have been successfully minimized using the modified algorithm based on the 2-μm absorption band parameters. Thus, this algorithm can be successfully applied at middle to high latitudes. Furthermore, a correction for TiO2 is applied to the FeO abundance estimation algorithm based on the 2-μm absorption band parameters using the M3 data. Our comparative study shows a good correspondence between the three algorithms discussed. There are two locations: the crater Tycho and the region around Rima Bode which show major discrepancies. Our modified algorithm based on the 2-μm absorption parameters predicts 3-4 wt.% less FeO for the ray system of Tycho than for the surrounding region. The average iron abundance for the lunar highlands is about 6 wt.% and for the mare regions is about 16 wt.% using the regression-based elemental abundance estimation algorithm and the algorithm based on the 2-μm absorption parameters. This result is consistent with

  11. Estimating abundance of mountain lions from unstructured spatial sampling

    USGS Publications Warehouse

    Russell, Robin E.; Royle, J. Andrew; Desimone, Richard; Schwartz, Michael K.; Edwards, Victoria L.; Pilgrim, Kristy P.; Mckelvey, Kevin S.

    2012-01-01

    Mountain lions (Puma concolor) are often difficult to monitor because of their low capture probabilities, extensive movements, and large territories. Methods for estimating the abundance of this species are needed to assess population status, determine harvest levels, evaluate the impacts of management actions on populations, and derive conservation and management strategies. Traditional mark–recapture methods do not explicitly account for differences in individual capture probabilities due to the spatial distribution of individuals in relation to survey effort (or trap locations). However, recent advances in the analysis of capture–recapture data have produced methods estimating abundance and density of animals from spatially explicit capture–recapture data that account for heterogeneity in capture probabilities due to the spatial organization of individuals and traps. We adapt recently developed spatial capture–recapture models to estimate density and abundance of mountain lions in western Montana. Volunteers and state agency personnel collected mountain lion DNA samples in portions of the Blackfoot drainage (7,908 km2) in west-central Montana using 2 methods: snow back-tracking mountain lion tracks to collect hair samples and biopsy darting treed mountain lions to obtain tissue samples. Overall, we recorded 72 individual capture events, including captures both with and without tissue sample collection and hair samples resulting in the identification of 50 individual mountain lions (30 females, 19 males, and 1 unknown sex individual). We estimated lion densities from 8 models containing effects of distance, sex, and survey effort on detection probability. Our population density estimates ranged from a minimum of 3.7 mountain lions/100 km2 (95% Cl 2.3–5.7) under the distance only model (including only an effect of distance on detection probability) to 6.7 (95% Cl 3.1–11.0) under the full model (including effects of distance, sex, survey effort, and

  12. 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.

  13. Estimation of lunar major elemental abundances in Chang'E-3 landing site based on Active Particle-induced X-ray Spectrometer (APXS)

    NASA Astrophysics Data System (ADS)

    Wang, Jian; Wang, Xianmin

    2015-09-01

    Elemental abundance provides an effective vehicle to understand lunar petrologic characteristics and evolutional history. The APXS mounted on the Yutu rover provides a valuable opportunity to determine the major elemental abundances in lunar soil within a short distance. In this study, we processed the APXS spectra including energy calibration, dead time correction and nonlinear least-squares fitting, and determined the abundances of the lunar major elements using the fundamental parameter method. In the calculation of X-ray fluorescence yield, a finite element method (FEM) was employed to improve the accuracy. The major elemental abundances derived from Chang'E-3 (CE-3) APXS possess a good consistency with the result of LP-GRS (Lunar Prospector gamma-ray spectrometer) data in the landing region. Compared with the chemical composition of the returned lunar rock samples, we draw the conclusion that the lunar soils in CE-3 landing site are fragments of mare basalts. Our conclusion is supported by the geological map of Mare Imbrium.

  14. Estimating Culicoides sonorensis biting midge abundance using digital image analysis.

    PubMed

    Osborne, C J; Mayo, C E; Mullens, B A; Maclachlan, N J

    2014-12-01

    ImageJ is an open-source software tool used for a variety of scientific objectives including cell counting, shape analysis and image correction. This technology has previously been used to estimate mosquito abundance in surveillance efforts. However, the utility of this application for estimating abundance or parity in the surveillance of Culicoides spp. (Diptera: Ceratopogonidae) has not yet been tested. Culicoides sonorensis (Wirth and Jones), a biting midge often measuring 2.0-2.5 mm in length, is an economically important vector of ruminant arboviruses in California. Current surveillance methods use visual sorting for the characteristics of midges and are very time-intensive for large studies. This project tested the utility of ImageJ as a tool to assist in gross trap enumeration as well as in parity analysis of C. sonorensis in comparison with traditional visual methods of enumeration using a dissecting microscope. Results confirmed that automated counting of midges is a reliable means of approximating midge numbers under certain conditions. Further evaluation confirmed accurate and time-efficient parity analysis in comparison with hand sorting. The ImageJ software shows promise as a tool that can assist and expedite C. sonorensis surveillance. Further, these methods may be useful in other insect surveillance activities.

  15. Negative binomial models for abundance estimation of multiple closed populations

    USGS Publications Warehouse

    Boyce, Mark S.; MacKenzie, Darry I.; Manly, Bryan F.J.; Haroldson, Mark A.; Moody, David W.

    2001-01-01

    Counts of uniquely identified individuals in a population offer opportunities to estimate abundance. However, for various reasons such counts may be burdened by heterogeneity in the probability of being detected. Theoretical arguments and empirical evidence demonstrate that the negative binomial distribution (NBD) is a useful characterization for counts from biological populations with heterogeneity. We propose a method that focuses on estimating multiple populations by simultaneously using a suite of models derived from the NBD. We used this approach to estimate the number of female grizzly bears (Ursus arctos) with cubs-of-the-year in the Yellowstone ecosystem, for each year, 1986-1998. Akaike's Information Criteria (AIC) indicated that a negative binomial model with a constant level of heterogeneity across all years was best for characterizing the sighting frequencies of female grizzly bears. A lack-of-fit test indicated the model adequately described the collected data. Bootstrap techniques were used to estimate standard errors and 95% confidence intervals. We provide a Monte Carlo technique, which confirms that the Yellowstone ecosystem grizzly bear population increased during the period 1986-1998.

  16. Estimating the abundance of clustered animal population by using adaptive cluster sampling and negative binomial distribution

    NASA Astrophysics Data System (ADS)

    Bo, Yizhou; Shifa, Naima

    2013-09-01

    An estimator for finding the abundance of a rare, clustered and mobile population has been introduced. This model is based on adaptive cluster sampling (ACS) to identify the location of the population and negative binomial distribution to estimate the total in each site. To identify the location of the population we consider both sampling with replacement (WR) and sampling without replacement (WOR). Some mathematical properties of the model are also developed.

  17. Evaluation of PCR-based quantification techniques to estimate the abundance of atrazine chlorohydrolase gene atzA in rhizosphere soils.

    PubMed

    Thompson, Brian M; Lin, Chung-Ho; Hsieh, Hsin-Yeh; Kremer, Robert J; Lerch, Robert N; Garrett, Harold E

    2010-01-01

    There are many challenges in the accurate quantification of bacterial genes, such as the atrazine-degrading enzyme antA from Pseudomonas sp. strain ADP, from soil samples. We compared four quantitative methods for enumeration of atrazine-degrading bacteria in rhizosphere environments and utilized the optimal probe-based real-time polymerase chain reaction (PCR)-based method in an ongoing bioremediation experiment to monitor atzA copy number over time. We compared three quantitative PCR (qPCR) based methods--quantitative competitive PCR and two real-time qPCR methods--to traditional dilution-plate counting techniques. The optimal real-time qPCR assay was then used to monitor atzA copy number over time in the robust atrazine-degrading Pseudomonas sp. strain ADP-spiked rhizosphere environment. The use of sensitive and reliable probe-based real-time qPCRs for the enumeration of bacterial catabolic genes allows for their detection from soil samples and monitoring of potential degradative populations over time. The addition of arrazine-biodegrading bacteria into arrazine-contaminated sites to remove entrapped atrazine is a promising approach for mitigating atrazine pollution and its metabolites. The methodology contained herein will allow for optimal monitoring of atzA in rhizosphere soil with or without the addition of biodegradative Pseudomonas sp. strain ADP of bacteria.

  18. Helium abundances on the moon: Assumptions and estimates

    NASA Astrophysics Data System (ADS)

    Taylor, Lawrence A.

    Nuclear energy is a highly desirable source of energy, and He-3 is the most prized of the fusion reactants. As the Wisconsin Group has emphasized, He-3 may be the only true economic ore on the Moon. The lack of a shielding atmosphere on the Moon permits solar-wind alpha particles to impinge upon the lunar regolith and become implanted into the various solid components. In particular, large quantities of helium (5 to 50 ppm) are presented. The measured parameter of Is/FeO, a direct indicator of maturity and exposure age, can be used as a first approximation to predict the abundances of many solar-wind components in the soils. However, because ilmenite has a much higher retentivity for helium than the other phases, the TiO2 contents of the soils are better indicators of helium contents (Taylor, Space 90). High-Ti mare bassalt regions, such as at the Apollo 17 locale, appear to be the best areas for He mining (15 to 50 ppm HeT), versus 3 to 9 ppm in the Highlands. However, the relationships between Is/FeO, TiO2 and He-3 contents are complicated - e.g., many of the most He-rich soils are immature to submature. The amount of He-3 in the regolith of the moon is estimated at 220,000 tons in the outer 2 m of the Maria.

  19. Evaluation of an aerial survey to estimate abundance of wintering ducks in Mississippi

    USGS Publications Warehouse

    Pearse, A.T.; Dinsmore, S.J.; Kaminski, R.M.; Reinecke, K.J.

    2008-01-01

    Researchers have successfully designed aerial surveys that provided precise estimates of wintering populations of ducks over large physiographic regions, yet few conservation agencies have adopted these probability-based sampling designs for their surveys. We designed and evaluated an aerial survey to estimate abundance of wintering mallards {Anas platyrhynchos), dabbling ducks (tribe Anatini) other than mallards, diving ducks (tribes Aythini, Mergini, and Oxyurini), and total ducks in western Mississippi, USA. We used design-based sampling of fixed width transects to estimate population indices (I?), and we used model-based methods to correct population indices for visibility bias and estimate population abundance (N?) for 14 surveys during winters 2002-2004. Correcting for bias increased estimates of mallards, other dabbling ducks, and diving ducks by an average of 40-48% among all surveys and contributed 48-61% of the estimated variance of N?. However, mean-squared errors were consistently less for N? than I?. Estimates of N? met our goals for precision (CV < 15%) in 7 of 14 surveys for mallards, 5 surveys for other dabbling ducks, no surveys for diving ducks, and 10 surveys for total ducks. Generally, we estimated more mallards and other dabbling ducks in mid- and late winter (Jan-Feb) than early winter (Nov-Dec) and determined that population indices from the late 1980s were nearly 3 times greater than those from our study. We developed a method to display relative densities of ducks spatially as an additional application of survey data. Our study advanced methods of estimating abundance of wintering waterfowl, and we recommend this design for continued monitoring of wintering ducks in western Mississippi and similar physiographic regions.

  20. Evaluation of an aerial survey to estimate abundance of wintering ducks in Mississippi

    USGS Publications Warehouse

    Pearse, A.T.; Dinsmore, S.J.; Kaminski, R.M.; Reinecke, K.J.

    2008-01-01

    Researchers have successfully designed aerial surveys that provided precise estimates of wintering populations of ducks over large physiographic regions, yet few conservation agencies have adopted these probability-based sampling designs for their surveys. We designed and evaluated an aerial survey to estimate abundance of wintering mallards {Anas platyrhynchos), dabbling ducks (tribe Anatini) other than mallards, diving ducks (tribes Aythini, Mergini, and Oxyurini), and total ducks in western Mississippi, USA. We used design-based sampling of fixed width transects to estimate population indices (I??), and we used model-based methods to correct population indices for visibility bias and estimate population abundance (N??) for 14 surveys during winters 2002-2004. Correcting for bias increased estimates of mallards, other dabbling ducks, and diving ducks by an average of 40-48% among all surveys and contributed 48-61% of the estimated variance of N??. However, mean-squared errors were consistently less for N?? than I??. Estimates of N?? met our goals for precision (CV ??? 15%) in 7 of 14 surveys for mallards, 5 surveys for other dabbling ducks, no surveys for diving ducks, and 10 surveys for total ducks. Generally, we estimated more mallards and other dabbling ducks in mid- and late winter (Jan-Feb) than early winter (Nov-Dec) and determined that population indices from the late 1980s were nearly 3 times greater than those from our study. We developed a method to display relative densities of ducks spatially as an additional application of survey data. Our study advanced methods of estimating abundance of wintering waterfowl, and we recommend this design for continued monitoring of wintering ducks in western Mississippi and similar physiographic regions.

  1. Optimal sampling design for estimating spatial distribution and abundance of a freshwater mussel population

    USGS Publications Warehouse

    Pooler, P.S.; Smith, D.R.

    2005-01-01

    We compared the ability of simple random sampling (SRS) and a variety of systematic sampling (SYS) designs to estimate abundance, quantify spatial clustering, and predict spatial distribution of freshwater mussels. Sampling simulations were conducted using data obtained from a census of freshwater mussels in a 40 X 33 m section of the Cacapon River near Capon Bridge, West Virginia, and from a simulated spatially random population generated to have the same abundance as the real population. Sampling units that were 0.25 m 2 gave more accurate and precise abundance estimates and generally better spatial predictions than 1-m2 sampling units. Systematic sampling with ???2 random starts was more efficient than SRS. Estimates of abundance based on SYS were more accurate when the distance between sampling units across the stream was less than or equal to the distance between sampling units along the stream. Three measures for quantifying spatial clustering were examined: Hopkins Statistic, the Clumping Index, and Morisita's Index. Morisita's Index was the most reliable, and the Hopkins Statistic was prone to false rejection of complete spatial randomness. SYS designs with units spaced equally across and up stream provided the most accurate predictions when estimating the spatial distribution by kriging. Our research indicates that SYS designs with sampling units equally spaced both across and along the stream would be appropriate for sampling freshwater mussels even if no information about the true underlying spatial distribution of the population were available to guide the design choice. ?? 2005 by The North American Benthological Society.

  2. A Bayesian Hierarchical Model for Estimation of Abundance and Spatial Density of Aedes aegypti

    PubMed Central

    Villela, Daniel A. M.; Codeço, Claudia T.; Figueiredo, Felipe; Garcia, Gabriela A.; Maciel-de-Freitas, Rafael; Struchiner, Claudio J.

    2015-01-01

    Strategies to minimize dengue transmission commonly rely on vector control, which aims to maintain Ae. aegypti density below a theoretical threshold. Mosquito abundance is traditionally estimated from mark-release-recapture (MRR) experiments, which lack proper analysis regarding accurate vector spatial distribution and population density. Recently proposed strategies to control vector-borne diseases involve replacing the susceptible wild population by genetically modified individuals’ refractory to the infection by the pathogen. Accurate measurements of mosquito abundance in time and space are required to optimize the success of such interventions. In this paper, we present a hierarchical probabilistic model for the estimation of population abundance and spatial distribution from typical mosquito MRR experiments, with direct application to the planning of these new control strategies. We perform a Bayesian analysis using the model and data from two MRR experiments performed in a neighborhood of Rio de Janeiro, Brazil, during both low- and high-dengue transmission seasons. The hierarchical model indicates that mosquito spatial distribution is clustered during the winter (0.99 mosquitoes/premise 95% CI: 0.80–1.23) and more homogeneous during the high abundance period (5.2 mosquitoes/premise 95% CI: 4.3–5.9). The hierarchical model also performed better than the commonly used Fisher-Ford’s method, when using simulated data. The proposed model provides a formal treatment of the sources of uncertainty associated with the estimation of mosquito abundance imposed by the sampling design. Our approach is useful in strategies such as population suppression or the displacement of wild vector populations by refractory Wolbachia-infected mosquitoes, since the invasion dynamics have been shown to follow threshold conditions dictated by mosquito abundance. The presence of spatially distributed abundance hotspots is also formally addressed under this modeling framework and

  3. Using spatiotemporal statistical models to estimate animal abundance and infer ecological dynamics from survey counts

    USGS Publications Warehouse

    Conn, Paul B.; Johnson, Devin S.; Ver Hoef, Jay M.; Hooten, Mevin B.; London, Joshua M.; Boveng, Peter L.

    2015-01-01

    Ecologists often fit models to survey data to estimate and explain variation in animal abundance. Such models typically require that animal density remains constant across the landscape where sampling is being conducted, a potentially problematic assumption for animals inhabiting dynamic landscapes or otherwise exhibiting considerable spatiotemporal variation in density. We review several concepts from the burgeoning literature on spatiotemporal statistical models, including the nature of the temporal structure (i.e., descriptive or dynamical) and strategies for dimension reduction to promote computational tractability. We also review several features as they specifically relate to abundance estimation, including boundary conditions, population closure, choice of link function, and extrapolation of predicted relationships to unsampled areas. We then compare a suite of novel and existing spatiotemporal hierarchical models for animal count data that permit animal density to vary over space and time, including formulations motivated by resource selection and allowing for closed populations. We gauge the relative performance (bias, precision, computational demands) of alternative spatiotemporal models when confronted with simulated and real data sets from dynamic animal populations. For the latter, we analyze spotted seal (Phoca largha) counts from an aerial survey of the Bering Sea where the quantity and quality of suitable habitat (sea ice) changed dramatically while surveys were being conducted. Simulation analyses suggested that multiple types of spatiotemporal models provide reasonable inference (low positive bias, high precision) about animal abundance, but have potential for overestimating precision. Analysis of spotted seal data indicated that several model formulations, including those based on a log-Gaussian Cox process, had a tendency to overestimate abundance. By contrast, a model that included a population closure assumption and a scale prior on total

  4. An evaluation of multipass electrofishing for estimating the abundance of stream-dwelling salmonids

    USGS Publications Warehouse

    Peterson, J.T.; Thurow, R.F.; Guzevich, J.W.

    2004-01-01

    , and those of other researchers, suggest that most electrofishing-removal-based estimates of fish abundance are likely to be biased and that these biases are related to stream characteristics, fish species, and size. We suggest that biologists regard electrofishing-removal- based estimates as biased indices and encourage them to measure and model the efficiency of their sampling methods to avoid introducing systematic errors into their data.

  5. An aerial survey method to estimate sea otter abundance

    USGS Publications Warehouse

    Bodkin, J.L.; Udevitz, M.S.

    1999-01-01

    Sea otters (Enhydra lutris) occur in shallow coastal habitats and can be highly visible on the sea surface. They generally rest in groups and their detection depends on factors that include sea conditions, viewing platform, observer technique and skill, distance, habitat and group size. While visible on the surface, they are difficult to see while diving and may dive in response to an approaching survey platform. We developed and tested an aerial survey method that uses intensive searches within portions of strip transects to adjust for availability and sightability biases. Correction factors are estimated independently for each survey and observer. In tests of our method using shore-based observers, we estimated detection probabilities of 0.52-0.72 in standard strip-transects and 0.96 in intensive searches. We used the survey method in Prince William Sound, Alaska to estimate a sea otter population size of 9,092 (SE = 1422). The new method represents an improvement over various aspects of previous methods, but additional development and testing will be required prior to its broad application.

  6. Estimating parasitic sea lamprey abundance in Lake Huron from heterogenous data sources

    USGS Publications Warehouse

    Young, Robert J.; Jones, Michael L.; Bence, James R.; McDonald, Rodney B.; Mullett, Katherine M.; Bergstedt, Roger A.

    2003-01-01

    The Great Lakes Fishery Commission uses time series of transformer, parasitic, and spawning population estimates to evaluate the effectiveness of its sea lamprey (Petromyzon marinus) control program. This study used an inverse variance weighting method to integrate Lake Huron sea lamprey population estimates derived from two estimation procedures: 1) prediction of the lake-wide spawning population from a regression model based on stream size and, 2) whole-lake mark and recapture estimates. In addition, we used a re-sampling procedure to evaluate the effect of trading off sampling effort between the regression and mark-recapture models. Population estimates derived from the regression model ranged from 132,000 to 377,000 while mark-recapture estimates of marked recently metamorphosed juveniles and parasitic sea lampreys ranged from 536,000 to 634,000 and 484,000 to 1,608,000, respectively. The precision of the estimates varied greatly among estimation procedures and years. The integrated estimate of the mark-recapture and spawner regression procedures ranged from 252,000 to 702,000 transformers. The re-sampling procedure indicated that the regression model is more sensitive to reduction in sampling effort than the mark-recapture model. Reliance on either the regression or mark-recapture model alone could produce misleading estimates of abundance of sea lampreys and the effect of the control program on sea lamprey abundance. These analyses indicate that the precision of the lakewide population estimate can be maximized by re-allocating sampling effort from marking sea lampreys to trapping additional streams.

  7. "Capture" Me if You Can: Estimating Abundance of Dolphin Populations

    ERIC Educational Resources Information Center

    Thompson, Jessica; Curran, Mary Carla; Cox, Tara

    2016-01-01

    Animal populations are monitored over time to assess the effects of environmental disaster and disease, as well as the efficacy of laws designed to protect them. Determining the abundance of a species within a defined area is one method of monitoring a population. In "Capture" Me if You Can, middle school students will use data collected…

  8. Robust Abundance Estimation in Animal Surveys with Imperfect Detection

    EPA Science Inventory

    Surveys of animal abundance are central to the conservation and management of living natural resources. However, detection uncertainty complicates the sampling process of many species. One sampling method employed to deal with this problem is depletion (or removal) surveys in whi...

  9. Estimating the abundance of mouse populations of known size: promises and pitfalls of new methods

    USGS Publications Warehouse

    Conn, P.B.; Arthur, A.D.; Bailey, L.L.; Singleton, G.R.

    2006-01-01

    Knowledge of animal abundance is fundamental to many ecological studies. Frequently, researchers cannot determine true abundance, and so must estimate it using a method such as mark-recapture or distance sampling. Recent advances in abundance estimation allow one to model heterogeneity with individual covariates or mixture distributions and to derive multimodel abundance estimators that explicitly address uncertainty about which model parameterization best represents truth. Further, it is possible to borrow information on detection probability across several populations when data are sparse. While promising, these methods have not been evaluated using mark?recapture data from populations of known abundance, and thus far have largely been overlooked by ecologists. In this paper, we explored the utility of newly developed mark?recapture methods for estimating the abundance of 12 captive populations of wild house mice (Mus musculus). We found that mark?recapture methods employing individual covariates yielded satisfactory abundance estimates for most populations. In contrast, model sets with heterogeneity formulations consisting solely of mixture distributions did not perform well for several of the populations. We show through simulation that a higher number of trapping occasions would have been necessary to achieve good estimator performance in this case. Finally, we show that simultaneous analysis of data from low abundance populations can yield viable abundance estimates.

  10. Mapping functional traits: comparing abundance and presence-absence estimates at large spatial scales.

    PubMed

    Newbold, Tim; Butchart, Stuart H M; Sekercioğlu, Cağan H; Purves, Drew W; Scharlemann, Jörn P W

    2012-01-01

    Efforts to quantify the composition of biological communities increasingly focus on functional traits. The composition of communities in terms of traits can be summarized in several ways. Ecologists are beginning to map the geographic distribution of trait-based metrics from various sources of data, but the maps have not been tested against independent data. Using data for birds of the Western Hemisphere, we test for the first time the most commonly used method for mapping community trait composition - overlaying range maps, which assumes that the local abundance of a given species is unrelated to the traits in question - and three new methods that as well as the range maps include varying degrees of information about interspecific and geographic variation in abundance. For each method, and for four traits (body mass, generation length, migratory behaviour, diet) we calculated community-weighted mean of trait values, functional richness and functional divergence. The maps based on species ranges and limited abundance data were compared with independent data on community species composition from the American Christmas Bird Count (CBC) scheme coupled with data on traits. The correspondence with observed community composition at the CBC sites was mostly positive (62/73 correlations) but varied widely depending on the metric of community composition and method used (R(2): 5.6 × 10(-7) to 0.82, with a median of 0.12). Importantly, the commonly-used range-overlap method resulted in the best fit (21/22 correlations positive; R(2): 0.004 to 0.8, with a median of 0.33). Given the paucity of data on the local abundance of species, overlaying range maps appears to be the best available method for estimating patterns of community composition, but the poor fit for some metrics suggests that local abundance data are urgently needed to allow more accurate estimates of the composition of communities.

  11. Estimating snow leopard population abundance using photography and capture-recapture techniques

    USGS Publications Warehouse

    Jackson, R.M.; Roe, J.D.; Wangchuk, R.; Hunter, D.O.

    2006-01-01

    Conservation and management of snow leopards (Uncia uncia) has largely relied on anecdotal evidence and presence-absence data due to their cryptic nature and the difficult terrain they inhabit. These methods generally lack the scientific rigor necessary to accurately estimate population size and monitor trends. We evaluated the use of photography in capture-mark-recapture (CMR) techniques for estimating snow leopard population abundance and density within Hemis National Park, Ladakh, India. We placed infrared camera traps along actively used travel paths, scent-sprayed rocks, and scrape sites within 16- to 30-km2 sampling grids in successive winters during January and March 2003-2004. We used head-on, oblique, and side-view camera configurations to obtain snow leopard photographs at varying body orientations. We calculated snow leopard abundance estimates using the program CAPTURE. We obtained a total of 66 and 49 snow leopard captures resulting in 8.91 and 5.63 individuals per 100 trap-nights during 2003 and 2004, respectively. We identified snow leopards based on the distinct pelage patterns located primarily on the forelimbs, flanks, and dorsal surface of the tail. Capture probabilities ranged from 0.33 to 0.67. Density estimates ranged from 8.49 (SE = 0.22; individuals per 100 km2 in 2003 to 4.45 (SE = 0.16) in 2004. We believe the density disparity between years is attributable to different trap density and placement rather than to an actual decline in population size. Our results suggest that photographic capture-mark-recapture sampling may be a useful tool for monitoring demographic patterns. However, we believe a larger sample size would be necessary for generating a statistically robust estimate of population density and abundance based on CMR models.

  12. A robust design mark-resight abundance estimator allowing heterogeneity in resighting probabilities

    USGS Publications Warehouse

    McClintock, B.T.; White, Gary C.; Burnham, K.P.

    2006-01-01

    This article introduces the beta-binomial estimator (BBE), a closed-population abundance mark-resight model combining the favorable qualities of maximum likelihood theory and the allowance of individual heterogeneity in sighting probability (p). The model may be parameterized for a robust sampling design consisting of multiple primary sampling occasions where closure need not be met between primary occasions. We applied the model to brown bear data from three study areas in Alaska and compared its performance to the joint hypergeometric estimator (JHE) and Bowden's estimator (BOWE). BBE estimates suggest heterogeneity levels were non-negligible and discourage the use of JHE for these data. Compared to JHE and BOWE, confidence intervals were considerably shorter for the AICc model-averaged BBE. To evaluate the properties of BBE relative to JHE and BOWE when sample sizes are small, simulations were performed with data from three primary occasions generated under both individual heterogeneity and temporal variation in p. All models remained consistent regardless of levels of variation in p. In terms of precision, the AICc model-averaged BBE showed advantages over JHE and BOWE when heterogeneity was present and mean sighting probabilities were similar between primary occasions. Based on the conditions examined, BBE is a reliable alternative to JHE or BOWE and provides a framework for further advances in mark-resight abundance estimation. ?? 2006 American Statistical Association and the International Biometric Society.

  13. Abundance estimation of long-diving animals using line transect methods.

    PubMed

    Okamura, Hiroshi; Minamikawa, Shingo; Skaug, Hans J; Kishiro, Toshiya

    2012-06-01

    Line transect sampling is one of the most widely used methods for estimating the size of wild animal populations. An assumption in standard line transect sampling is that all the animals on the trackline are detected without fail. This assumption tends to be violated for marine mammals with surfacing/diving behaviors. The detection probability on the trackline is estimated using duplicate sightings from double-platform line transect methods. The double-platform methods, however, are insufficient to estimate the abundance of long-diving animals because these animals can be completely missed while the observers pass. We developed a more flexible hazard probability model that incorporates information on surfacing/diving patterns obtained from telemetry data. The model is based on a stochastic point process and is statistically tractable. A simulation study showed that the new model provides near-unbiased abundance estimates, whereas the traditional hazard rate and hazard probability models produce considerably biased estimates. As an illustration, we applied the model to data on the Baird's beaked whale (Berardius bairdii) in the western North Pacific. PMID:21992225

  14. Hydroacoustic estimates of fish abundance. Reservoir vital signs monitoring, 1990

    SciTech Connect

    Wilson, W.K.

    1991-03-01

    Hydroacoustics, as defined in the context of this report, is the use of a scientific sonar system to determine fish densities with respect to numbers and biomass. These two parameters provide a method of monitoring reservoir fish populations and detecting gross changes in the ecosystem. With respect to southeastern reservoirs, hydroacoustic surveys represent a new method of sampling open water areas and the best technology available. The advantages of this technology are large amounts of data can be collected in a relatively short period of time allowing improved statistical interpretation and data comparison, the pelagic (open water) zone can be sampled efficiently regardless of depth, and sampling is nondestructive and noninvasive with neither injury to the fish nor alteration of the environment. Hydroacoustics cannot provide species identification and related information on species composition or length/weight relationships. Also, sampling is limited to a minimum depth of ten feet which precludes the use of this equipment for sampling shallow shoreline areas. The objective of this study is to use hydroacoustic techniques to estimate fish standing stocks (i.e., numbers and biomass) in several areas of selected Tennessee Valley Reservoirs as part of a base level monitoring program to assess long-term changes in reservoir water quality.

  15. Hankin and Reeves' Approach to Estimating Fish Abundance in Small Streams : Limitations and Potential Options.

    SciTech Connect

    Thompson, William L.

    2000-11-01

    Hankin and Reeves' (1988) approach to estimating fish abundance in small streams has been applied in stream-fish studies across North America. However, as with any method of population estimation, there are important assumptions that must be met for estimates to be minimally biased and reasonably precise. Consequently, I investigated effects of various levels of departure from these assumptions via simulation based on results from an example application in Hankin and Reeves (1988) and a spatially clustered population. Coverage of 95% confidence intervals averaged about 5% less than nominal when removal estimates equaled true numbers within sampling units, but averaged 62% - 86% less than nominal when they did not, with the exception where detection probabilities of individuals were >0.85 and constant across sampling units (95% confidence interval coverage = 90%). True total abundances averaged far (20% - 41%) below the lower confidence limit when not included within intervals, which implies large negative bias. Further, average coefficient of variation was about 1.5 times higher when removal estimates did not equal true numbers within sampling units (C{bar V} = 0.27 [SE = 0.0004]) than when they did (C{bar V} = 0.19 [SE = 0.0002]). A potential modification to Hankin and Reeves' approach is to include environmental covariates that affect detection rates of fish into the removal model or other mark-recapture model. A potential alternative is to use snorkeling in combination with line transect sampling to estimate fish densities. Regardless of the method of population estimation, a pilot study should be conducted to validate the enumeration method, which requires a known (or nearly so) population of fish to serve as a benchmark to evaluate bias and precision of population estimates.

  16. A method for estimating abundance of mobile populations using telemetry and counts of unmarked animals

    USGS Publications Warehouse

    Clement, Matthew; O'Keefe, Joy M; Walters, Brianne

    2015-01-01

    While numerous methods exist for estimating abundance when detection is imperfect, these methods may not be appropriate due to logistical difficulties or unrealistic assumptions. In particular, if highly mobile taxa are frequently absent from survey locations, methods that estimate a probability of detection conditional on presence will generate biased abundance estimates. Here, we propose a new estimator for estimating abundance of mobile populations using telemetry and counts of unmarked animals. The estimator assumes that the target population conforms to a fission-fusion grouping pattern, in which the population is divided into groups that frequently change in size and composition. If assumptions are met, it is not necessary to locate all groups in the population to estimate abundance. We derive an estimator, perform a simulation study, conduct a power analysis, and apply the method to field data. The simulation study confirmed that our estimator is asymptotically unbiased with low bias, narrow confidence intervals, and good coverage, given a modest survey effort. The power analysis provided initial guidance on survey effort. When applied to small data sets obtained by radio-tracking Indiana bats, abundance estimates were reasonable, although imprecise. The proposed method has the potential to improve abundance estimates for mobile species that have a fission-fusion social structure, such as Indiana bats, because it does not condition detection on presence at survey locations and because it avoids certain restrictive assumptions.

  17. Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest

    PubMed Central

    Ellison, Aaron M.; Jackson, Scott

    2015-01-01

    Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could

  18. Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest.

    PubMed

    Siddig, Ahmed A; Ellison, Aaron M; Jackson, Scott

    2015-01-01

    Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m(2) and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that

  19. Validation of abundance estimates from mark–recapture and removal techniques for rainbow trout captured by electrofishing in small streams

    USGS Publications Warehouse

    Rosenberger, Amanda E.; Dunham, Jason B.

    2005-01-01

    Estimation of fish abundance in streams using the removal model or the Lincoln - Peterson mark - recapture model is a common practice in fisheries. These models produce misleading results if their assumptions are violated. We evaluated the assumptions of these two models via electrofishing of rainbow trout Oncorhynchus mykiss in central Idaho streams. For one-, two-, three-, and four-pass sampling effort in closed sites, we evaluated the influences of fish size and habitat characteristics on sampling efficiency and the accuracy of removal abundance estimates. We also examined the use of models to generate unbiased estimates of fish abundance through adjustment of total catch or biased removal estimates. Our results suggested that the assumptions of the mark - recapture model were satisfied and that abundance estimates based on this approach were unbiased. In contrast, the removal model assumptions were not met. Decreasing sampling efficiencies over removal passes resulted in underestimated population sizes and overestimates of sampling efficiency. This bias decreased, but was not eliminated, with increased sampling effort. Biased removal estimates based on different levels of effort were highly correlated with each other but were less correlated with unbiased mark - recapture estimates. Stream size decreased sampling efficiency, and stream size and instream wood increased the negative bias of removal estimates. We found that reliable estimates of population abundance could be obtained from models of sampling efficiency for different levels of effort. Validation of abundance estimates requires extra attention to routine sampling considerations but can help fisheries biologists avoid pitfalls associated with biased data and facilitate standardized comparisons among studies that employ different sampling methods.

  20. Estimating abundance from repeated presence-absence data or point counts

    USGS Publications Warehouse

    Royle, J. Andrew; Nichols, J.D.

    2003-01-01

    We describe an approach for estimating occupancy rate or the proportion of area occupied when heterogeneity in detection probability exists as a result of variation in abundance of the organism under study. The key feature of such problems, which we exploit, is that variation in abundance induces variation in detection probability. Thus, heterogeneity in abundance can be modeled as heterogeneity in detection probability. Moreover, this linkage between heterogeneity in abundance and heterogeneity in detection probability allows one to exploit a heterogeneous detection probability model to estimate the underlying distribution of abundances. Therefore, our method allows estimation of abundance from repeated observations of the presence or absence of animals without having to uniquely mark individuals in the population.

  1. Bayes and empirical Bayes estimators of abundance and density from spatial capture-recapture data

    USGS Publications Warehouse

    Dorazio, Robert M.

    2013-01-01

    In capture-recapture and mark-resight surveys, movements of individuals both within and between sampling periods can alter the susceptibility of individuals to detection over the region of sampling. In these circumstances spatially explicit capture-recapture (SECR) models, which incorporate the observed locations of individuals, allow population density and abundance to be estimated while accounting for differences in detectability of individuals. In this paper I propose two Bayesian SECR models, one for the analysis of recaptures observed in trapping arrays and another for the analysis of recaptures observed in area searches. In formulating these models I used distinct submodels to specify the distribution of individual home-range centers and the observable recaptures associated with these individuals. This separation of ecological and observational processes allowed me to derive a formal connection between Bayes and empirical Bayes estimators of population abundance that has not been established previously. I showed that this connection applies to every Poisson point-process model of SECR data and provides theoretical support for a previously proposed estimator of abundance based on recaptures in trapping arrays. To illustrate results of both classical and Bayesian methods of analysis, I compared Bayes and empirical Bayes esimates of abundance and density using recaptures from simulated and real populations of animals. Real populations included two iconic datasets: recaptures of tigers detected in camera-trap surveys and recaptures of lizards detected in area-search surveys. In the datasets I analyzed, classical and Bayesian methods provided similar – and often identical – inferences, which is not surprising given the sample sizes and the noninformative priors used in the analyses.

  2. Hydroacoustic estimates of abundance and spatial distribution of pelagic prey fishes in western Lake Superior

    USGS Publications Warehouse

    Mason, Doran M.; Johnson, Timothy B.; Harvey, Chris J.; Kitchell, James F.; Schram, Stephen T.; Bronte, Charles R.; Hoff, MIchael H.; Lozano, Stephen J.; Trebitz, Anett S.; Schreiner, Donald R.; Lamon, E. Conrad; Hrabik, Thomas R.

    2005-01-01

    Lake herring (Coregonus artedi) and rainbow smelt (Osmerus mordax) are a valuable prey resource for the recovering lake trout (Salvelinus namaycush) in Lake Superior. However, prey biomass may be insufficient to support the current predator demand. In August 1997, we assessed the abundance and spatial distribution of pelagic coregonines and rainbow smelt in western Lake Superior by combining a 120 kHz split beam acoustics system with midwater trawls. Coregonines comprised the majority of the midwater trawl catches and the length distributions for trawl caught fish coincided with estimated sizes of acoustic targets. Overall mean pelagic prey fish biomass was 15.56 kg ha−1 with the greatest fish biomass occurring in the Apostle Islands region (27.98 kg ha−1), followed by the Duluth Minnesota region (20.22 kg ha−1), and with the lowest biomass occurring in the open waters of western Lake Superior (9.46 kg ha−1). Biomass estimates from hydroacoustics were typically 2–134 times greater than estimates derived from spring bottom trawl surveys. Prey fish biomass for Lake Superior is about order of magnitude less than acoustic estimates for Lakes Michigan and Ontario. Discrepancies observed between bioenergetics-based estimates of predator consumption of coregonines and earlier coregonine biomass estimates may be accounted for by our hydroacoustic estimates.

  3. Using counts to simultaneously estimate abundance and detection probabilities in a salamander community

    USGS Publications Warehouse

    Dodd, C.K.; Dorazio, R.M.

    2004-01-01

    A critical variable in both ecological and conservation field studies is determining how many individuals of a species are present within a defined sampling area. Labor intensive techniques such as capture-mark-recapture and removal sampling may provide estimates of abundance, but there are many logistical constraints to their widespread application. Many studies on terrestrial and aquatic salamanders use counts as an index of abundance, assuming that detection remains constant while sampling. If this constancy is violated, determination of detection probabilities is critical to the accurate estimation of abundance. Recently, a model was developed that provides a statistical approach that allows abundance and detection to be estimated simultaneously from spatially and temporally replicated counts. We adapted this model to estimate these parameters for salamanders sampled over a six vear period in area-constrained plots in Great Smoky Mountains National Park. Estimates of salamander abundance varied among years, but annual changes in abundance did not vary uniformly among species. Except for one species, abundance estimates were not correlated with site covariates (elevation/soil and water pH, conductivity, air and water temperature). The uncertainty in the estimates was so large as to make correlations ineffectual in predicting which covariates might influence abundance. Detection probabilities also varied among species and sometimes among years for the six species examined. We found such a high degree of variation in our counts and in estimates of detection among species, sites, and years as to cast doubt upon the appropriateness of using count data to monitor population trends using a small number of area-constrained survey plots. Still, the model provided reasonable estimates of abundance that could make it useful in estimating population size from count surveys.

  4. Chilean blue whales as a case study to illustrate methods to estimate abundance and evaluate conservation status of rare species.

    PubMed

    Williams, Rob; Hedley, Sharon L; Branch, Trevor A; Bravington, Mark V; Zerbini, Alexandre N; Findlay, Ken P

    2011-06-01

    Often abundance of rare species cannot be estimated with conventional design-based methods, so we illustrate with a population of blue whales (Balaenoptera musculus) a spatial model-based method to estimate abundance. We analyzed data from line-transect surveys of blue whales off the coast of Chile, where the population was hunted to low levels. Field protocols allowed deviation from planned track lines to collect identification photographs and tissue samples for genetic analyses, which resulted in an ad hoc sampling design with increased effort in areas of higher densities. Thus, we used spatial modeling methods to estimate abundance. Spatial models are increasingly being used to analyze data from surveys of marine, aquatic, and terrestrial species, but estimation of uncertainty from such models is often problematic. We developed a new, broadly applicable variance estimator that showed there were likely 303 whales (95% CI 176-625) in the study area. The survey did not span the whales' entire range, so this is a minimum estimate. We estimated current minimum abundance relative to pre-exploitation abundance (i.e., status) with a population dynamics model that incorporated our minimum abundance estimate, likely population growth rates from a meta-analysis of rates of increase in large baleen whales, and two alternative assumptions about historic catches. From this model, we estimated that the population was at a minimum of 9.5% (95% CI 4.9-18.0%) of pre-exploitation levels in 1998 under one catch assumption and 7.2% (CI 3.7-13.7%) of pre-exploitation levels under the other. Thus, although Chilean blue whales are probably still at a small fraction of pre-exploitation abundance, even these minimum abundance estimates demonstrate that their status is better than that of Antarctic blue whales, which are still <1% of pre-exploitation population size. We anticipate our methods will be broadly applicable in aquatic and terrestrial surveys for rarely encountered species

  5. Chilean blue whales as a case study to illustrate methods to estimate abundance and evaluate conservation status of rare species.

    PubMed

    Williams, Rob; Hedley, Sharon L; Branch, Trevor A; Bravington, Mark V; Zerbini, Alexandre N; Findlay, Ken P

    2011-06-01

    Often abundance of rare species cannot be estimated with conventional design-based methods, so we illustrate with a population of blue whales (Balaenoptera musculus) a spatial model-based method to estimate abundance. We analyzed data from line-transect surveys of blue whales off the coast of Chile, where the population was hunted to low levels. Field protocols allowed deviation from planned track lines to collect identification photographs and tissue samples for genetic analyses, which resulted in an ad hoc sampling design with increased effort in areas of higher densities. Thus, we used spatial modeling methods to estimate abundance. Spatial models are increasingly being used to analyze data from surveys of marine, aquatic, and terrestrial species, but estimation of uncertainty from such models is often problematic. We developed a new, broadly applicable variance estimator that showed there were likely 303 whales (95% CI 176-625) in the study area. The survey did not span the whales' entire range, so this is a minimum estimate. We estimated current minimum abundance relative to pre-exploitation abundance (i.e., status) with a population dynamics model that incorporated our minimum abundance estimate, likely population growth rates from a meta-analysis of rates of increase in large baleen whales, and two alternative assumptions about historic catches. From this model, we estimated that the population was at a minimum of 9.5% (95% CI 4.9-18.0%) of pre-exploitation levels in 1998 under one catch assumption and 7.2% (CI 3.7-13.7%) of pre-exploitation levels under the other. Thus, although Chilean blue whales are probably still at a small fraction of pre-exploitation abundance, even these minimum abundance estimates demonstrate that their status is better than that of Antarctic blue whales, which are still <1% of pre-exploitation population size. We anticipate our methods will be broadly applicable in aquatic and terrestrial surveys for rarely encountered species

  6. Estimating Lion Abundance using N-mixture Models for Social Species

    PubMed Central

    Belant, Jerrold L.; Bled, Florent; Wilton, Clay M.; Fyumagwa, Robert; Mwampeta, Stanslaus B.; Beyer, Dean E.

    2016-01-01

    Declining populations of large carnivores worldwide, and the complexities of managing human-carnivore conflicts, require accurate population estimates of large carnivores to promote their long-term persistence through well-informed management We used N-mixture models to estimate lion (Panthera leo) abundance from call-in and track surveys in southeastern Serengeti National Park, Tanzania. Because of potential habituation to broadcasted calls and social behavior, we developed a hierarchical observation process within the N-mixture model conditioning lion detectability on their group response to call-ins and individual detection probabilities. We estimated 270 lions (95% credible interval = 170–551) using call-ins but were unable to estimate lion abundance from track data. We found a weak negative relationship between predicted track density and predicted lion abundance from the call-in surveys. Luminosity was negatively correlated with individual detection probability during call-in surveys. Lion abundance and track density were influenced by landcover, but direction of the corresponding effects were undetermined. N-mixture models allowed us to incorporate multiple parameters (e.g., landcover, luminosity, observer effect) influencing lion abundance and probability of detection directly into abundance estimates. We suggest that N-mixture models employing a hierarchical observation process can be used to estimate abundance of other social, herding, and grouping species. PMID:27786283

  7. Horvitz-Thompson survey sample methods for estimating large-scale animal abundance

    USGS Publications Warehouse

    Samuel, M.D.; Garton, E.O.

    1994-01-01

    Large-scale surveys to estimate animal abundance can be useful for monitoring population status and trends, for measuring responses to management or environmental alterations, and for testing ecological hypotheses about abundance. However, large-scale surveys may be expensive and logistically complex. To ensure resources are not wasted on unattainable targets, the goals and uses of each survey should be specified carefully and alternative methods for addressing these objectives always should be considered. During survey design, the impoflance of each survey error component (spatial design, propofiion of detected animals, precision in detection) should be considered carefully to produce a complete statistically based survey. Failure to address these three survey components may produce population estimates that are inaccurate (biased low), have unrealistic precision (too precise) and do not satisfactorily meet the survey objectives. Optimum survey design requires trade-offs in these sources of error relative to the costs of sampling plots and detecting animals on plots, considerations that are specific to the spatial logistics and survey methods. The Horvitz-Thompson estimators provide a comprehensive framework for considering all three survey components during the design and analysis of large-scale wildlife surveys. Problems of spatial and temporal (especially survey to survey) heterogeneity in detection probabilities have received little consideration, but failure to account for heterogeneity produces biased population estimates. The goal of producing unbiased population estimates is in conflict with the increased variation from heterogeneous detection in the population estimate. One solution to this conflict is to use an MSE-based approach to achieve a balance between bias reduction and increased variation. Further research is needed to develop methods that address spatial heterogeneity in detection, evaluate the effects of temporal heterogeneity on survey

  8. Goals and strategies for estimating trends in landbird abundance

    USGS Publications Warehouse

    Bart, J.; Burnham, K.P.; Dunn, E.H.; Francis, C.M.; John, Ralph C.

    2004-01-01

    Reliable estimates of trends in population size are critical to effective management of landbirds. We propose a standard for considering that landbird populations are adequately monitored: 80% power to detect a 50% decline occuning within 20 years, using a 2-tailed test and a significance level of 0.10, and incorporating effects of potential bias. Our standard also requires that at least two-thirds of the target region be covered by the monitoring program. We recommend that the standard be achieved for species' entire ranges or for any area one-third the size of the temperate portions of Canada and the United States, whichever is smaller. We applied our approach to North American Breeding Bird Survey (BBS) data. At present, potential annual bias for the BBS is estimated at ??0.008. Further, the BBS achieves the monitoring standard for only about 42% of landbirds for which the BBS is considered the most effective monitoring approach. Achieving the proposed monitoring target for ???80% of these species would require increasing the number of BBS - or similar survey - routes by several-fold, a goal that probably is impractical. We suggest several methods for reducing potential bias and argue that if our methods are implemented, potential bias would fall to ??0.003. The required number of BBS or similar routes would then be 5,106, about 40% more than in the current BBS program. Most of the needed increases are in 15 states or provinces. Developing a comprehensive land-bird monitoring program will require increased support for coordination of the BBS (currently 2 people) and new programs for species that are poorly covered at present. Our results provide a quantitative goal for long-term land-bird monitoring and identify the sample sizes needed, within each state and province, to achieve the monitoring goal for most of the roughly 300 landbird species that are well suited to monitoring with the BBS and similar surveys.

  9. Evaluation of methods to estimate lake herring spawner abundance in Lake Superior

    USGS Publications Warehouse

    Yule, D.L.; Stockwell, J.D.; Cholwek, G.A.; Evrard, L.M.; Schram, S.; Seider, M.; Symbal, M.

    2006-01-01

    Historically, commercial fishers harvested Lake Superior lake herring Coregonus artedi for their flesh, but recently operators have targeted lake herring for roe. Because no surveys have estimated spawning female abundance, direct estimates of fishing mortality are lacking. The primary objective of this study was to determine the feasibility of using acoustic techniques in combination with midwater trawling to estimate spawning female lake herring densities in a Lake Superior statistical grid (i.e., a 10′ latitude × 10′ longitude area over which annual commercial harvest statistics are compiled). Midwater trawling showed that mature female lake herring were largely pelagic during the night in late November, accounting for 94.5% of all fish caught exceeding 250 mm total length. When calculating acoustic estimates of mature female lake herring, we excluded backscattering from smaller pelagic fishes like immature lake herring and rainbow smelt Osmerus mordax by applying an empirically derived threshold of −35.6 dB. We estimated the average density of mature females in statistical grid 1409 at 13.3 fish/ha and the total number of spawning females at 227,600 (95% confidence interval = 172,500–282,700). Using information on mature female densities, size structure, and fecundity, we estimate that females deposited 3.027 billion (109) eggs in grid 1409 (95% confidence interval = 2.356–3.778 billion). The relative estimation error of the mature female density estimate derived using a geostatistical model—based approach was low (12.3%), suggesting that the employed method was robust. Fishing mortality rates of all mature females and their eggs were estimated at 2.3% and 3.8%, respectively. The techniques described for enumerating spawning female lake herring could be used to develop a more accurate stock–recruitment model for Lake Superior lake herring.

  10. Effect of Trapping Methods, Weather, and Landscape on Estimates of the Culex Vector Mosquito Abundance

    PubMed Central

    Karki, Surendra; Hamer, Gabriel L.; Anderson, Tavis K.; Goldberg, Tony L.; Kitron, Uriel D.; Krebs, Bethany L.; Walker, Edward D.; Ruiz, Marilyn O.

    2016-01-01

    The local abundance of Culex mosquitoes is a central factor adding to the risk of West Nile virus transmission, and vector abundance data influence public health decisions. This study evaluated differences in abundance estimates from mosquitoes trapped using two common methods: CO2-baited CDC light traps and infusion-baited gravid traps in suburban, Chicago, Illinois. On a weekly basis, the two methods were modestly correlated (r = 0.219) across 71 weeks over 4 years. Lagged weather conditions of up to four weeks were associated with the number of mosquitoes collected in light and gravid traps. Collections in light traps were higher with higher temperature in the same week, higher precipitation one, two, and four weeks before the week of trapping, and lower maximum average wind speed. Collections in gravid traps were higher with higher temperature in the same week and one week earlier, lower temperature four weeks earlier, and with higher precipitation two and four weeks earlier. Culex abundance estimates from light traps were significantly higher in semi-natural areas compared to residential areas, but abundance estimates from gravid traps did not vary by the landscape type. These results highlight the importance of the surveillance methods used in the assessment of local Culex abundance estimates. Measures of risk of exposure to West Nile virus should assess carefully how mosquito abundance has been estimated and integrated into assessments of transmission risk. PMID:27375359

  11. Effect of Trapping Methods, Weather, and Landscape on Estimates of the Culex Vector Mosquito Abundance.

    PubMed

    Karki, Surendra; Hamer, Gabriel L; Anderson, Tavis K; Goldberg, Tony L; Kitron, Uriel D; Krebs, Bethany L; Walker, Edward D; Ruiz, Marilyn O

    2016-01-01

    The local abundance of Culex mosquitoes is a central factor adding to the risk of West Nile virus transmission, and vector abundance data influence public health decisions. This study evaluated differences in abundance estimates from mosquitoes trapped using two common methods: CO2-baited CDC light traps and infusion-baited gravid traps in suburban, Chicago, Illinois. On a weekly basis, the two methods were modestly correlated (r = 0.219) across 71 weeks over 4 years. Lagged weather conditions of up to four weeks were associated with the number of mosquitoes collected in light and gravid traps. Collections in light traps were higher with higher temperature in the same week, higher precipitation one, two, and four weeks before the week of trapping, and lower maximum average wind speed. Collections in gravid traps were higher with higher temperature in the same week and one week earlier, lower temperature four weeks earlier, and with higher precipitation two and four weeks earlier. Culex abundance estimates from light traps were significantly higher in semi-natural areas compared to residential areas, but abundance estimates from gravid traps did not vary by the landscape type. These results highlight the importance of the surveillance methods used in the assessment of local Culex abundance estimates. Measures of risk of exposure to West Nile virus should assess carefully how mosquito abundance has been estimated and integrated into assessments of transmission risk. PMID:27375359

  12. ELM: an Algorithm to Estimate the Alpha Abundance from Low-resolution Spectra

    NASA Astrophysics Data System (ADS)

    Bu, Yude; Zhao, Gang; Pan, Jingchang; Bharat Kumar, Yerra

    2016-01-01

    We have investigated a novel methodology using the extreme learning machine (ELM) algorithm to determine the α abundance of stars. Applying two methods based on the ELM algorithm—ELM+spectra and ELM+Lick indices—to the stellar spectra from the ELODIE database, we measured the α abundance with a precision better than 0.065 dex. By applying these two methods to the spectra with different signal-to-noise ratios (S/Ns) and different resolutions, we found that ELM+spectra is more robust against degraded resolution and ELM+Lick indices is more robust against variation in S/N. To further validate the performance of ELM, we applied ELM+spectra and ELM+Lick indices to SDSS spectra and estimated α abundances with a precision around 0.10 dex, which is comparable to the results given by the SEGUE Stellar Parameter Pipeline. We further applied ELM to the spectra of stars in Galactic globular clusters (M15, M13, M71) and open clusters (NGC 2420, M67, NGC 6791), and results show good agreement with previous studies (within 1σ). A comparison of the ELM with other widely used methods including support vector machine, Gaussian process regression, artificial neural networks, and linear least-squares regression shows that ELM is efficient with computational resources and more accurate than other methods.

  13. Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling.

    USGS Publications Warehouse

    Conroy, M.J.; Runge, J.P.; Barker, R.J.; Schofield, M.R.; Fonnesbeck, C.J.

    2008-01-01

    Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of

  14. Consideraciones para la estimacion de abundancia de poblaciones de mamiferos. [Considerations for the estimation of abundance of mammal populations.

    USGS Publications Warehouse

    Walker, R.S.; Novare, A.J.; Nichols, J.D.

    2000-01-01

    Estimation of abundance of mammal populations is essential for monitoring programs and for many ecological investigations. The first step for any study of variation in mammal abundance over space or time is to define the objectives of the study and how and why abundance data are to be used. The data used to estimate abundance are count statistics in the form of counts of animals or their signs. There are two major sources of uncertainty that must be considered in the design of the study: spatial variation and the relationship between abundance and the count statistic. Spatial variation in the distribution of animals or signs may be taken into account with appropriate spatial sampling. Count statistics may be viewed as random variables, with the expected value of the count statistic equal to the true abundance of the population multiplied by a coefficient p. With direct counts, p represents the probability of detection or capture of individuals, and with indirect counts it represents the rate of production of the signs as well as their probability of detection. Comparisons of abundance using count statistics from different times or places assume that the p are the same for all times or places being compared (p= pi). In spite of considerable evidence that this assumption rarely holds true, it is commonly made in studies of mammal abundance, as when the minimum number alive or indices based on sign counts are used to compare abundance in different habitats or times. Alternatives to relying on this assumption are to calibrate the index used by testing the assumption of p= pi, or to incorporate the estimation of p into the study design.

  15. A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data.

    PubMed

    Barker, Brandon E; Sadagopan, Narayanan; Wang, Yiping; Smallbone, Kieran; Myers, Christopher R; Xi, Hongwei; Locasale, Jason W; Gu, Zhenglong

    2015-12-01

    A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with high-throughput data including expression data, metabolomics, or DNA sequencing. The desired result is to increase predictive capability and improve our understanding of metabolism. The approach typically employed when only gene (or protein) intensities are available is the creation of tissue-specific models, which reduces the available reactions in an organism model, and does not provide an objective function for the estimation of fluxes. We develop a method, flux assignment with LAD (least absolute deviation) convex objectives and normalization (FALCON), that employs metabolic network reconstructions along with expression data to estimate fluxes. In order to use such a method, accurate measures of enzyme complex abundance are needed, so we first present an algorithm that addresses quantification of complex abundance. Our extensions to prior techniques include the capability to work with large models and significantly improved run-time performance even for smaller models, an improved analysis of enzyme complex formation, the ability to handle large enzyme complex rules that may incorporate multiple isoforms, and either maintained or significantly improved correlation with experimentally measured fluxes. FALCON has been implemented in MATLAB and ATS, and can be downloaded from: https://github.com/bbarker/FALCON. ATS is not required to compile the software, as intermediate C source code is available. FALCON requires use of the COBRA Toolbox, also implemented in MATLAB.

  16. Accuracy or precision: Implications of sample design and methodology on abundance estimation

    USGS Publications Warehouse

    Kowalewski, Lucas K.; Chizinski, Christopher J.; Powell, Larkin A.; Pope, Kevin L.; Pegg, Mark A.

    2015-01-01

    Sampling by spatially replicated counts (point-count) is an increasingly popular method of estimating population size of organisms. Challenges exist when sampling by point-count method, and it is often impractical to sample entire area of interest and impossible to detect every individual present. Ecologists encounter logistical limitations that force them to sample either few large-sample units or many small sample-units, introducing biases to sample counts. We generated a computer environment and simulated sampling scenarios to test the role of number of samples, sample unit area, number of organisms, and distribution of organisms in the estimation of population sizes using N-mixture models. Many sample units of small area provided estimates that were consistently closer to true abundance than sample scenarios with few sample units of large area. However, sample scenarios with few sample units of large area provided more precise abundance estimates than abundance estimates derived from sample scenarios with many sample units of small area. It is important to consider accuracy and precision of abundance estimates during the sample design process with study goals and objectives fully recognized, although and with consequence, consideration of accuracy and precision of abundance estimates is often an afterthought that occurs during the data analysis process.

  17. Estimating sturgeon abundance in the Carolinas using side-scan sonar

    USGS Publications Warehouse

    Flowers, H. Jared; Hightower, Joseph E.

    2015-01-01

    Sturgeons (Acipenseridae) are one of the most threatened taxa worldwide, including species in North Carolina and South Carolina. Populations of Atlantic Sturgeon Acipenser oxyrinchus in the Carolinas have been significantly reduced from historical levels by a combination of intense fishing and habitat loss. There is a need for estimates of current abundance, to describe status, and for estimates of historical abundance in order to provide realistic recovery goals. In this study we used N-mixture and distance models with data acquired from side-scan sonar surveys to estimate abundance of sturgeon in six major sturgeon rivers in North Carolina and South Carolina. Estimated abundances of sturgeon greater than 1 m TL in the Carolina distinct population segment (DPS) were 2,031 using the count model and 1,912 via the distance model. The Pee Dee River had the highest overall abundance of any river at 1,944 (count model) or 1,823 (distance model). These estimates do not account for sturgeon less than 1 m TL or occurring in riverine reaches not surveyed or in marine waters. Comparing the two models, the N-mixture model produced similar estimates using less data than the distance model with only a slight reduction of estimated precision.

  18. Filling a void: abundance estimation of North American populations of arctic geese using hunter recoveries

    USGS Publications Warehouse

    Alisauskas, R.T.; Drake, K.L.; Nichols, J.D.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael J.

    2009-01-01

    We consider use of recoveries of marked birds harvested by hunters, in conjunction with continental harvest estimates, for drawing inferences about continental abundance of a select number of goose species. We review assumptions of this method, a version of the Lincoln?Petersen approach, and consider its utility as a tool for making decisions about harvest management in comparison to current sources of information. Finally, we compare such estimates with existing count data, photographic estimates, or other abundance estimates. In most cases, Lincoln estimates are far higher than abundances assumed or perhaps accepted by many waterfowl biologists and managers. Nevertheless, depending on the geographic scope of inference, we suggest that this approach for abundance estimation of arctic geese may have usefulness for retrospective purposes or to assist with harvest management decisions for some species. Lincoln?s estimates may be as close or closer to truth than count, index, or photo data, and can be used with marking efforts currently in place for estimation of survival and harvest rates. Although there are bias issues associated with estimates of both harvest and harvest rate, some of the latter can be addressed with proper allocation of marks to spatially structured populations if subpopulations show heterogeneity in harvest rates.

  19. Using mark-recapture methods to estimate fish abundance in small mountain lakes

    USGS Publications Warehouse

    Gresswell, Robert E.; Liss, W.J.; Lomnicky, G.A.; Deimling, E.; Hoffman, Robert L.; Tyler, T.

    1997-01-01

    The majority of lacustrine fish populations in the western USA are located far from the nearest road. Although mark-recapture techniques are widely accepted for estimating population abundance, these techniques have been broadly ignored for fisheries surveys in remote mountain lakes because of restricted access and associated logistical constraints. In this study, mark recapture experiments were used to estimate fish population abundance in nine small (< 7 ha) lakes of the North Cascades National Park Service Complex. Fish in the mark sample were collected by angling, fin-clipped, and immediately released; fish were recaptured with variable mesh monofilament gill nets. A single-census Petersen estimator was used to calculate abundance in each lake, and assumptions for unbiased estimates appeared to be satisfied in most cases. Post-release mortality of angler-captured fish was low. The small size of these lakes in conjunction with the brief period of rime allotted for each individual experiment apparently reduced the probability of unequal vulnerability and mortality for marked and unmarked fish. Single-census mark-recapture experiments appeared to provide reasonable estimates of population abundance in these mountain lakes. Resulting estimates furnish a substantial increase in information when compared to more ubiquitous assessments of relative abundance, but the logistical requirements are modest. We believe that this technique may useful for survey purposes in other small, remote lakes.

  20. A comparison of abundance estimates from extended batch-marking and Jolly–Seber-type experiments

    PubMed Central

    Cowen, Laura L E; Besbeas, Panagiotis; Morgan, Byron J T; Schwarz, Carl J

    2014-01-01

    Little attention has been paid to the use of multi-sample batch-marking studies, as it is generally assumed that an individual's capture history is necessary for fully efficient estimates. However, recently, Huggins et al. (2010) present a pseudo-likelihood for a multi-sample batch-marking study where they used estimating equations to solve for survival and capture probabilities and then derived abundance estimates using a Horvitz–Thompson-type estimator. We have developed and maximized the likelihood for batch-marking studies. We use data simulated from a Jolly–Seber-type study and convert this to what would have been obtained from an extended batch-marking study. We compare our abundance estimates obtained from the Crosbie–Manly–Arnason–Schwarz (CMAS) model with those of the extended batch-marking model to determine the efficiency of collecting and analyzing batch-marking data. We found that estimates of abundance were similar for all three estimators: CMAS, Huggins, and our likelihood. Gains are made when using unique identifiers and employing the CMAS model in terms of precision; however, the likelihood typically had lower mean square error than the pseudo-likelihood method of Huggins et al. (2010). When faced with designing a batch-marking study, researchers can be confident in obtaining unbiased abundance estimators. Furthermore, they can design studies in order to reduce mean square error by manipulating capture probabilities and sample size. PMID:24558576

  1. A comparison of abundance estimates from extended batch-marking and Jolly-Seber-type experiments.

    PubMed

    Cowen, Laura L E; Besbeas, Panagiotis; Morgan, Byron J T; Schwarz, Carl J

    2014-01-01

    Little attention has been paid to the use of multi-sample batch-marking studies, as it is generally assumed that an individual's capture history is necessary for fully efficient estimates. However, recently, Huggins et al. (2010) present a pseudo-likelihood for a multi-sample batch-marking study where they used estimating equations to solve for survival and capture probabilities and then derived abundance estimates using a Horvitz-Thompson-type estimator. We have developed and maximized the likelihood for batch-marking studies. We use data simulated from a Jolly-Seber-type study and convert this to what would have been obtained from an extended batch-marking study. We compare our abundance estimates obtained from the Crosbie-Manly-Arnason-Schwarz (CMAS) model with those of the extended batch-marking model to determine the efficiency of collecting and analyzing batch-marking data. We found that estimates of abundance were similar for all three estimators: CMAS, Huggins, and our likelihood. Gains are made when using unique identifiers and employing the CMAS model in terms of precision; however, the likelihood typically had lower mean square error than the pseudo-likelihood method of Huggins et al. (2010). When faced with designing a batch-marking study, researchers can be confident in obtaining unbiased abundance estimators. Furthermore, they can design studies in order to reduce mean square error by manipulating capture probabilities and sample size.

  2. Estimating the global abundance of ground level presence of particulate matter (PM2.5).

    PubMed

    Lary, David J; Faruque, Fazlay S; Malakar, Nabin; Moore, Alex; Roscoe, Bryan; Adams, Zachary L; Eggelston, York

    2014-12-01

    With the increasing awareness of the health impacts of particulate matter, there is a growing need to comprehend the spatial and temporal variations of the global abundance of ground level airborne particulate matter with a diameter of 2.5 microns or less (PM2.5). Here we use a suite of remote sensing and meteorological data products together with ground-based observations of particulate matter from 8,329 measurement sites in 55 countries taken 1997-2014 to train a machine-learning algorithm to estimate the daily distributions of PM2.5 from 1997 to the present. In this first paper of a series, we present the methodology and global average results from this period and demonstrate that the new PM2.5 data product can reliably represent global observations of PM2.5 for epidemiological studies.

  3. Estimation and Bias Correction of Aerosol Abundance using Data-driven Machine Learning and Remote Sensing

    NASA Technical Reports Server (NTRS)

    Malakar, Nabin K.; Lary, D. L.; Moore, A.; Gencaga, D.; Roscoe, B.; Albayrak, Arif; Petrenko, Maksym; Wei, Jennifer

    2012-01-01

    Air quality information is increasingly becoming a public health concern, since some of the aerosol particles pose harmful effects to peoples health. One widely available metric of aerosol abundance is the aerosol optical depth (AOD). The AOD is the integrated light extinction coefficient over a vertical atmospheric column of unit cross section, which represents the extent to which the aerosols in that vertical profile prevent the transmission of light by absorption or scattering. The comparison between the AOD measured from the ground-based Aerosol Robotic Network (AERONET) system and the satellite MODIS instruments at 550 nm shows that there is a bias between the two data products. We performed a comprehensive analysis exploring possible factors which may be contributing to the inter-instrumental bias between MODIS and AERONET. The analysis used several measured variables, including the MODIS AOD, as input in order to train a neural network in regression mode to predict the AERONET AOD values. This not only allowed us to obtain an estimate, but also allowed us to infer the optimal sets of variables that played an important role in the prediction. In addition, we applied machine learning to infer the global abundance of ground level PM2.5 from the AOD data and other ancillary satellite and meteorology products. This research is part of our goal to provide air quality information, which can also be useful for global epidemiology studies.

  4. Derivation of safety factors for setting harvest quotas on adult walleyes from past estimates of abundance

    USGS Publications Warehouse

    Hansen, Michael J.; Staggs, Michael D.; Hoff, Michael H.

    1991-01-01

    Past population estimates of adult walleyes Stizostedion vitreum can be used to set harvest quotas, provided that temporal variability in abundance of adult walleyes is accounted for. We used a long-term data set from Escanaba Lake, Wisconsin, to evaluate the accuracy of past population estimates for setting current-year quotas for adult walleyes. The results from Escanaba Lake were corroborated by comparison with other lakes where adult walleye abundance was estimated in more than 1 year. The accuracy of estimates of adult walleye abundance declined over time from the year the estimate was obtained to the year it was used to set a harvest quota. We derived safety factors for application to past estimates of population size; these factors limit the occurrence of an exploitation rate exceeding the maximum sustainable rate (35%) to approximately 1 in 40. These safety factors declined from 35% for 1-year-old estimates to less than 20% for 10-year-old estimates.

  5. Hankin and Reeves' approach to estimating fish abundance in small streams: Limitations and alternatives

    USGS Publications Warehouse

    Thompson, W.L.

    2003-01-01

    Hankin and Reeves' (1988) approach to estimating fish abundance in small streams has been applied in stream fish studies across North America. However, their population estimator relies on two key assumptions: (1) removal estimates are equal to the true numbers of fish, and (2) removal estimates are highly correlated with snorkel counts within a subset of sampled stream units. Violations of these assumptions may produce suspect results. To determine possible sources of the assumption violations, I used data on the abundance of steelhead Oncorhynchus mykiss from Hankin and Reeves' (1988) in a simulation composed of 50,000 repeated, stratified systematic random samples from a spatially clustered distribution. The simulation was used to investigate effects of a range of removal estimates, from 75% to 100% of true fish abundance, on overall stream fish population estimates. The effects of various categories of removal-estimates-to-snorkel-count correlation levels (r = 0.75-1.0) on fish population estimates were also explored. Simulation results indicated that Hankin and Reeves' approach may produce poor results unless removal estimates exceed at least 85% of the true number of fish within sampled units and unless correlations between removal estimates and snorkel counts are at least 0.90. A potential modification to Hankin and Reeves' approach is the inclusion of environmental covariates that affect detection rates of fish into the removal model or other mark-recapture model. A potential alternative approach is to use snorkeling combined with line transect sampling to estimate fish densities within stream units. As with any method of population estimation, a pilot study should be conducted to evaluate its usefulness, which requires a known (or nearly so) population of fish to serve as a benchmark for evaluating bias and precision of estimators.

  6. A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data.

    PubMed

    Barker, Brandon E; Sadagopan, Narayanan; Wang, Yiping; Smallbone, Kieran; Myers, Christopher R; Xi, Hongwei; Locasale, Jason W; Gu, Zhenglong

    2015-12-01

    A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with high-throughput data including expression data, metabolomics, or DNA sequencing. The desired result is to increase predictive capability and improve our understanding of metabolism. The approach typically employed when only gene (or protein) intensities are available is the creation of tissue-specific models, which reduces the available reactions in an organism model, and does not provide an objective function for the estimation of fluxes. We develop a method, flux assignment with LAD (least absolute deviation) convex objectives and normalization (FALCON), that employs metabolic network reconstructions along with expression data to estimate fluxes. In order to use such a method, accurate measures of enzyme complex abundance are needed, so we first present an algorithm that addresses quantification of complex abundance. Our extensions to prior techniques include the capability to work with large models and significantly improved run-time performance even for smaller models, an improved analysis of enzyme complex formation, the ability to handle large enzyme complex rules that may incorporate multiple isoforms, and either maintained or significantly improved correlation with experimentally measured fluxes. FALCON has been implemented in MATLAB and ATS, and can be downloaded from: https://github.com/bbarker/FALCON. ATS is not required to compile the software, as intermediate C source code is available. FALCON requires use of the COBRA Toolbox, also implemented in MATLAB. PMID:26381164

  7. Estimating species occurrence, abundance, and detection probability using zero-inflated distributions

    USGS Publications Warehouse

    Wenger, S.J.; Freeman, Mary C.

    2008-01-01

    Researchers have developed methods to account for imperfect detection of species with either occupancy (presence-absence) or count data using replicated sampling. We show how these approaches can be combined to simultaneously estimate occurrence, abundance, and detection probability by specifying a zero-inflated distribution for abundance. This approach may be particularly appropriate when patterns of occurrence and abundance arise from distinct processes operating at differing spatial or temporal scales. We apply the model to two data sets: (1) previously published data for a species of duck, Anas platyrhynchos, and (2) data for a stream fish species, Etheostoma scotti. We show that in these cases, an incomplete-detection zero-inflated modeling approach yields a superior fit to the data than other models. We propose that zero-inflated abundance models accounting for incomplete detection be considered when replicate count data are available.

  8. Repeated count surveys help standardize multi-agency estimates of American Oystercatcher (Haematopus palliatus) abundance

    USGS Publications Warehouse

    Hostetter, Nathan J.; Gardner, Beth; Schweitzer, Sara H.; Boettcher, Ruth; Wilke, Alexandra L.; Addison, Lindsay; Swilling, William R.; Pollock, Kenneth H.; Simons, Theodore R.

    2015-01-01

    The extensive breeding range of many shorebird species can make integration of survey data problematic at regional spatial scales. We evaluated the effectiveness of standardized repeated count surveys coordinated across 8 agencies to estimate the abundance of American Oystercatcher (Haematopus palliatus) breeding pairs in the southeastern United States. Breeding season surveys were conducted across coastal North Carolina (90 plots) and the Eastern Shore of Virginia (3 plots). Plots were visited on 1–5 occasions during April–June 2013. N-mixture models were used to estimate abundance and detection probability in relation to survey date, tide stage, plot size, and plot location (coastal bay vs. barrier island). The estimated abundance of oystercatchers in the surveyed area was 1,048 individuals (95% credible interval: 851–1,408) and 470 pairs (384–637), substantially higher than estimates that did not account for detection probability (maximum counts of 674 individuals and 316 pairs). Detection probability was influenced by a quadratic function of survey date, and increased from mid-April (~0.60) to mid-May (~0.80), then remained relatively constant through June. Detection probability was also higher during high tide than during low, rising, or falling tides. Abundance estimates from N-mixture models were validated at 13 plots by exhaustive productivity studies (2–5 surveys wk−1). Intensive productivity studies identified 78 breeding pairs across 13 productivity plots while the N-mixture model abundance estimate was 74 pairs (62–119) using only 1–5 replicated surveys season−1. Our results indicate that standardized replicated count surveys coordinated across multiple agencies and conducted during a relatively short time window (closure assumption) provide tremendous potential to meet both agency-level (e.g., state) and regional-level (e.g., flyway) objectives in large-scale shorebird monitoring programs.

  9. Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

    USGS Publications Warehouse

    Pilliod, David S.; Goldberg, Caren S.; Arkle, Robert S.; Waits, Lisette P.

    2013-01-01

    Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.

  10. Estimating DNA coverage and abundance in metagenomes using a gamma approximation

    SciTech Connect

    Hooper, Sean D; Dalevi, Daniel; Pati, Amrita; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C

    2010-01-01

    Shotgun sequencing generates large numbers of short DNA reads from either an isolated organism or, in the case of metagenomics projects, from the aggregate genome of a microbial community. These reads are then assembled based on overlapping sequences into larger, contiguous sequences (contigs). The feasibility of assembly and the coverage achieved (reads per nucleotide or distinct sequence of nucleotides) depend on several factors: the number of reads sequenced, the read length and the relative abundances of their source genomes in the microbial community. A low coverage suggests that most of the genomic DNA in the sample has not been sequenced, but it is often difficult to estimate either the extent of the uncaptured diversity or the amount of additional sequencing that would be most efficacious. In this work, we regard a metagenome as a population of DNA fragments (bins), each of which may be covered by one or more reads. We employ a gamma distribution to model this bin population due to its flexibility and ease of use. When a gamma approximation can be found that adequately fits the data, we may estimate the number of bins that were not sequenced and that could potentially be revealed by additional sequencing. We evaluated the performance of this model using simulated metagenomes and demonstrate its applicability on three recent metagenomic datasets.

  11. Techniques and methods for estimating abundance of larval and metamorphosed sea lampreys in Great Lakes tributaries, 1995 to 2001

    USGS Publications Warehouse

    Slade, Jeffrey W.; Adams, Jean V.; Christie, Gavin C.; Cuddy, Douglas W.; Fodale, Michael F.; Heinrich, John W.; Quinlan, Henry R.; Weise, Jerry G.; Weisser, John W.; Young, Robert J.

    2003-01-01

    Before 1995, Great Lakes streams were selected for lampricide treatment based primarily on qualitative measures of the relative abundance of larval sea lampreys, Petromyzon marinus. New integrated pest management approaches required standardized quantitative measures of sea lamprey. This paper evaluates historical larval assessment techniques and data and describes how new standardized methods for estimating abundance of larval and metamorphosed sea lampreys were developed and implemented. These new methods have been used to estimate larval and metamorphosed sea lamprey abundance in about 100 Great Lakes streams annually and to rank them for lampricide treatment since 1995. Implementation of these methods has provided a quantitative means of selecting streams for treatment based on treatment cost and estimated production of metamorphosed sea lampreys, provided managers with a tool to estimate potential recruitment of sea lampreys to the Great Lakes and the ability to measure the potential consequences of not treating streams, resulting in a more justifiable allocation of resources. The empirical data produced can also be used to simulate the impacts of various control scenarios.

  12. A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples

    NASA Astrophysics Data System (ADS)

    Wu, Yu-Wei; Ye, Yuzhen

    Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. Among the computational tools recently developed for metagenomic sequence analysis, binning tools attempt to classify all (or most) of the sequences in a metagenomic dataset into different bins (i.e., species), based on various DNA composition patterns (e.g., the tetramer frequencies) of various genomes. Composition-based binning methods, however, cannot be used to classify very short fragments, because of the substantial variation of DNA composition patterns within a single genome. We developed a novel approach (AbundanceBin) for metagenomics binning by utilizing the different abundances of species living in the same environment. AbundanceBin is an application of the Lander-Waterman model to metagenomics, which is based on the l-tuple content of the reads. AbundanceBin achieved accurate, unsupervised, clustering of metagenomic sequences into different bins, such that the reads classified in a bin belong to species of identical or very similar abundances in the sample. In addition, AbundanceBin gave accurate estimations of species abundances, as well as their genome sizes - two important parameters for characterizing a microbial community. We also show that AbundanceBin performed well when the sequence lengths are very short (e.g. 75 bp) or have sequencing errors.

  13. Estimating abundances of interacting species using morphological traits, foraging guilds, and habitat

    USGS Publications Warehouse

    Dorazio, Robert M.; Connor, Edward F.

    2014-01-01

    We developed a statistical model to estimate the abundances of potentially interacting species encountered while conducting point-count surveys at a set of ecologically relevant locations - as in a metacommunity of species. In the model we assume that abundances of species with similar traits (e.g., body size) are potentially correlated and that these correlations, when present, may exist among all species or only among functionally related species (such as members of the same foraging guild). We also assume that species-specific abundances vary among locations owing to systematic and stochastic sources of heterogeneity. For example, if abundances differ among locations due to differences in habitat, then measures of habitat may be included in the model as covariates. Naturally, the quantitative effects of these covariates are assumed to differ among species. Our model also accounts for the effects of detectability on the observed counts of each species. This aspect of the model is especially important for rare or uncommon species that may be difficult to detect in community-level surveys. Estimating the detectability of each species requires sampling locations to be surveyed repeatedly using different observers or different visits of a single observer. As an illustration, we fitted models to species-specific counts of birds obtained while sampling an avian community during the breeding season. In the analysis we examined whether species abundances appeared to be correlated due to similarities in morphological measures (body mass, beak length, tarsus length, wing length, tail length) and whether these correlations existed among all species or only among species of the same foraging guild. We also used the model to estimate the effects of forested area on species abundances and the effects of sound power output (as measured by body size) on species detection probabilities.

  14. Simultaneously Sparse and Low-Rank Abundance Matrix Estimation for Hyperspectral Image Unmixing

    NASA Astrophysics Data System (ADS)

    Giampouras, Paris V.; Themelis, Konstantinos E.; Rontogiannis, Athanasios A.; Koutroumbas, Konstantinos D.

    2016-08-01

    In a plethora of applications dealing with inverse problems, e.g. in image processing, social networks, compressive sensing, biological data processing etc., the signal of interest is known to be structured in several ways at the same time. This premise has recently guided the research to the innovative and meaningful idea of imposing multiple constraints on the parameters involved in the problem under study. For instance, when dealing with problems whose parameters form sparse and low-rank matrices, the adoption of suitably combined constraints imposing sparsity and low-rankness, is expected to yield substantially enhanced estimation results. In this paper, we address the spectral unmixing problem in hyperspectral images. Specifically, two novel unmixing algorithms are introduced, in an attempt to exploit both spatial correlation and sparse representation of pixels lying in homogeneous regions of hyperspectral images. To this end, a novel convex mixed penalty term is first defined consisting of the sum of the weighted $\\ell_1$ and the weighted nuclear norm of the abundance matrix corresponding to a small area of the image determined by a sliding square window. This penalty term is then used to regularize a conventional quadratic cost function and impose simultaneously sparsity and row-rankness on the abundance matrix. The resulting regularized cost function is minimized by a) an incremental proximal sparse and low-rank unmixing algorithm and b) an algorithm based on the alternating minimization method of multipliers (ADMM). The effectiveness of the proposed algorithms is illustrated in experiments conducted both on simulated and real data.

  15. Finding a Fox: An Evaluation of Survey Methods to Estimate Abundance of a Small Desert Carnivore

    PubMed Central

    Dempsey, Steven J.; Gese, Eric M.; Kluever, Bryan M.

    2014-01-01

    The status of many carnivore species is a growing concern for wildlife agencies, conservation organizations, and the general public. Historically, kit foxes (Vulpes macrotis) were classified as abundant and distributed in the desert and semi-arid regions of southwestern North America, but is now considered rare throughout its range. Survey methods have been evaluated for kit foxes, but often in populations where abundance is high and there is little consensus on which technique is best to monitor abundance. We conducted a 2-year study to evaluate four survey methods (scat deposition surveys, scent station surveys, spotlight survey, and trapping) for detecting kit foxes and measuring fox abundance. We determined the probability of detection for each method, and examined the correlation between the relative abundance as estimated by each survey method and the known minimum kit fox abundance as determined by radio-collared animals. All surveys were conducted on 15 5-km transects during the 3 biological seasons of the kit fox. Scat deposition surveys had both the highest detection probabilities (p = 0.88) and were most closely related to minimum known fox abundance (r2 = 0.50, P = 0.001). The next best method for kit fox detection was the scent station survey (p = 0.73), which had the second highest correlation to fox abundance (r2 = 0.46, P<0.001). For detecting kit foxes in a low density population we suggest using scat deposition transects during the breeding season. Scat deposition surveys have low costs, resilience to weather, low labor requirements, and pose no risk to the study animals. The breeding season was ideal for monitoring kit fox population size, as detections consisted of the resident population and had the highest detection probabilities. Using appropriate monitoring techniques will be critical for future conservation actions for this rare desert carnivore. PMID:25148102

  16. Abundance of adult horseshoe crabs (Limulus polylphemus) in Delaware Bay estimated from a bay-wide mark-recapture study

    USGS Publications Warehouse

    Smith, D.R.; Millard, M.J.; Eyler, S.

    2006-01-01

    Estimates of the abundance of American horseshoe crabs (Limulus polyphemus) are important to determine egg production and to manage populations for the energetic needs of shorebirds that feed on horseshoe crab eggs. In 2003, over 17,500 horseshoe crabs were tagged and released throughout Delaware Bay, and recaptured crabs came from spawning surveys that were conducted during peak spawning. We used two release cohorts to test for a temporary effect of tagging on spawning behavior and we adjusted the number of releases according to relocation rates from a telemetry study. The abundance estimate was 20 million horseshoe crabs (90% confidence interval: 13-28 million), of which 6.25 million (90% CI: 4.0-8.8 million) were females. The combined harvest rate for Delaware, New Jersey, Virginia, and Maryland in 2003 was 4% (90% CI: 3-6%) of the abundance estimate. Over-wintering of adults in Delaware Bay could explain, in part, differences in estimates from ocean-trawl surveys. Based on fecundity of 88,000 eggs per female, egg production was 5.5??1011 (90% CI: 3.5??1011, 7.7??1011), but egg availability for shorebirds also depended on overlap between horseshoe crab and shorebird migrations, density-dependent bioturbation, and wave-mediated vertical transport.

  17. Estimated Rock Abundance and Thermophysical Parameters in Oppenheimer Crater on the Moon

    NASA Astrophysics Data System (ADS)

    Bauch, Karin E.; Hiesinger, Harald; Ivanov, Mikhail; van der Bogert, Carolyn H.; Pasckert, Jan-Hendrik; Weinauer, Julia

    2016-04-01

    Oppenheimer crater is located in the north-east of the South Pole-Aitken basin (SPA), the largest impact structure on the Moon [e.g., 1]. The crater is ˜215km in diameter and has an estimated age of ˜4.1 Ga [2]. The floor of Oppenheimer shows evidence of dark mantling deposits and a concentric system of graben structures close to the rim of the crater [3]. Image and topography data show that the floor is flat apart from the graben structures and subsequent impacts on the floor. Oppenheimer-U (˜40km) and -H (˜35km) are floor-fractured craters within the north-west and south-east portions of Oppenheimer crater [3]. Dark mantling deposits on the floor are associated with the graben system. [3] estimated an age between ˜3.98Ga and ˜3.66Ga for the pyroclastic activity, based on crater size-frequency distribution (CSFD) measurements on Lunar Reconnaissance Orbiter (LRO) WAC and NAC images. In this study we compare the mapping results of [3] with temperature data of the LRO Diviner experiment [4] using a numerical model [5, 6]. Nighttime temperature variations are directly influenced by the surface and subsurface thermophysical properties, namely bulk density, heat capacity, and thermal conductivity [7, 8]. These properties can be summarized to a thermal inertia, which represents the ability to conduct and store heat [8]. Low thermal inertia units, such as dust and other fine grained material, quickly respond to temperature changes, which results in large temperature amplitudes between the lunar day and night. On the other hand, high thermal inertia material, e.g. rocks or bedrock, take more time to heat up during the day and reradiate the heat during the night [8]. Relative rock abundances are derived from temperature measurements of the same location at different wavelengths. Brightness temperatures are a function of wavelength and increase with decreasing wavelength [9, 10]. This nonlinearity of the Planck radiance can be used to determine the amount of

  18. A new device to estimate abundance of moist-soil plant seeds

    USGS Publications Warehouse

    Penny, E.J.; Kaminski, R.M.; Reinecke, K.J.

    2006-01-01

    Methods to sample the abundance of moist-soil seeds efficiently and accurately are critical for evaluating management practices and determining food availability. We adapted a portable, gasoline-powered vacuum to estimate abundance of seeds on the surface of a moist-soil wetland in east-central Mississippi and evaluated the sampler by simulating conditions that researchers and managers may experience when sampling moist-soil areas for seeds. We measured the percent recovery of known masses of seeds by the vacuum sampler in relation to 4 experimentally controlled factors (i.e., seed-size class, sample mass, soil moisture class, and vacuum time) with 2-4 levels per factor. We also measured processing time of samples in the laboratory. Across all experimental factors, seed recovery averaged 88.4% and varied little (CV = 0.68%, n = 474). Overall, mean time to process a sample was 30.3 ? 2.5 min (SE, n = 417). Our estimate of seed recovery rate (88%) may be used to adjust estimates for incomplete seed recovery, or project-specific correction factors may be developed by investigators. Our device was effective for estimating surface abundance of moist-soil plant seeds after dehiscence and before habitats were flooded.

  19. Estimation of occupancy, breeding success, and predicted abundance of golden eagles (Aquila chrysaetos) in the Diablo Range, California, 2014

    USGS Publications Warehouse

    Wiens, J. David; Kolar, Patrick S.; Fuller, Mark R.; Hunt, W. Grainger; Hunt, Teresa

    2015-01-01

    We used a multistate occupancy sampling design to estimate occupancy, breeding success, and abundance of territorial pairs of golden eagles (Aquila chrysaetos) in the Diablo Range, California, in 2014. This method uses the spatial pattern of detections and non-detections over repeated visits to survey sites to estimate probabilities of occupancy and successful reproduction while accounting for imperfect detection of golden eagles and their young during surveys. The estimated probability of detecting territorial pairs of golden eagles and their young was less than 1 and varied with time of the breeding season, as did the probability of correctly classifying a pair’s breeding status. Imperfect detection and breeding classification led to a sizeable difference between the uncorrected, naïve estimate of the proportion of occupied sites where successful reproduction was observed (0.20) and the model-based estimate (0.30). The analysis further indicated a relatively high overall probability of landscape occupancy by pairs of golden eagles (0.67, standard error = 0.06), but that areas with the greatest occupancy and reproductive potential were patchily distributed. We documented a total of 138 territorial pairs of golden eagles during surveys completed in the 2014 breeding season, which represented about one-half of the 280 pairs we estimated to occur in the broader 5,169-square kilometer region sampled. The study results emphasize the importance of accounting for imperfect detection and spatial heterogeneity in studies of site occupancy, breeding success, and abundance of golden eagles.

  20. Estimating abundance and density of Amur tigers along the Sino-Russian border.

    PubMed

    Xiao, Wenhong; Feng, Limin; Mou, Pu; Miquelle, Dale G; Hebblewhite, Mark; Goldberg, Joshua F; Robinson, Hugh S; Zhao, Xiaodan; Zhou, Bo; Wang, Tianming; Ge, Jianping

    2016-07-01

    As an apex predator the Amur tiger (Panthera tigris altaica) could play a pivotal role in maintaining the integrity of forest ecosystems in Northeast Asia. Due to habitat loss and harvest over the past century, tigers rapidly declined in China and are now restricted to the Russian Far East and bordering habitat in nearby China. To facilitate restoration of the tiger in its historical range, reliable estimates of population size are essential to assess effectiveness of conservation interventions. Here we used camera trap data collected in Hunchun National Nature Reserve from April to June 2013 and 2014 to estimate tiger density and abundance using both maximum likelihood and Bayesian spatially explicit capture-recapture (SECR) methods. A minimum of 8 individuals were detected in both sample periods and the documentation of marking behavior and reproduction suggests the presence of a resident population. Using Bayesian SECR modeling within the 11 400 km(2) state space, density estimates were 0.33 and 0.40 individuals/100 km(2) in 2013 and 2014, respectively, corresponding to an estimated abundance of 38 and 45 animals for this transboundary Sino-Russian population. In a maximum likelihood framework, we estimated densities of 0.30 and 0.24 individuals/100 km(2) corresponding to abundances of 34 and 27, in 2013 and 2014, respectively. These density estimates are comparable to other published estimates for resident Amur tiger populations in the Russian Far East. This study reveals promising signs of tiger recovery in Northeast China, and demonstrates the importance of connectivity between the Russian and Chinese populations for recovering tigers in Northeast China.

  1. Estimating abundance and density of Amur tigers along the Sino-Russian border.

    PubMed

    Xiao, Wenhong; Feng, Limin; Mou, Pu; Miquelle, Dale G; Hebblewhite, Mark; Goldberg, Joshua F; Robinson, Hugh S; Zhao, Xiaodan; Zhou, Bo; Wang, Tianming; Ge, Jianping

    2016-07-01

    As an apex predator the Amur tiger (Panthera tigris altaica) could play a pivotal role in maintaining the integrity of forest ecosystems in Northeast Asia. Due to habitat loss and harvest over the past century, tigers rapidly declined in China and are now restricted to the Russian Far East and bordering habitat in nearby China. To facilitate restoration of the tiger in its historical range, reliable estimates of population size are essential to assess effectiveness of conservation interventions. Here we used camera trap data collected in Hunchun National Nature Reserve from April to June 2013 and 2014 to estimate tiger density and abundance using both maximum likelihood and Bayesian spatially explicit capture-recapture (SECR) methods. A minimum of 8 individuals were detected in both sample periods and the documentation of marking behavior and reproduction suggests the presence of a resident population. Using Bayesian SECR modeling within the 11 400 km(2) state space, density estimates were 0.33 and 0.40 individuals/100 km(2) in 2013 and 2014, respectively, corresponding to an estimated abundance of 38 and 45 animals for this transboundary Sino-Russian population. In a maximum likelihood framework, we estimated densities of 0.30 and 0.24 individuals/100 km(2) corresponding to abundances of 34 and 27, in 2013 and 2014, respectively. These density estimates are comparable to other published estimates for resident Amur tiger populations in the Russian Far East. This study reveals promising signs of tiger recovery in Northeast China, and demonstrates the importance of connectivity between the Russian and Chinese populations for recovering tigers in Northeast China. PMID:27136188

  2. Estimating the abundance of the Southern Hudson Bay polar bear subpopulation with aerial surveys

    USGS Publications Warehouse

    Obbard, Martyn E.; Stapleton, Seth P.; Middel, Kevin R.; Thibault, Isabelle; Brodeur, Vincent; Jutras, Charles

    2015-01-01

    The Southern Hudson Bay (SH) polar bear subpopulation occurs at the southern extent of the species’ range. Although capture–recapture studies indicate abundance was likely unchanged between 1986 and 2005, declines in body condition and survival occurred during the period, possibly foreshadowing a future decrease in abundance. To obtain a current estimate of abundance, we conducted a comprehensive line transect aerial survey of SH during 2011–2012. We stratified the study site by anticipated densities and flew coastal contour transects and systematically spaced inland transects in Ontario and on Akimiski Island and large offshore islands in 2011. Data were collected with double-observer and distance sampling protocols. We surveyed small islands in James Bay and eastern Hudson Bay and flew a comprehensive transect along the Québec coastline in 2012. We observed 667 bears in Ontario and on Akimiski Island and nearby islands in 2011, and we sighted 80 bears on offshore islands during 2012. Mark–recapture distance sampling and sight–resight models yielded an estimate of 860 (SE = 174) for the 2011 study area. Our estimate of abundance for the entire SH subpopulation (943; SE = 174) suggests that abundance is unlikely to have changed significantly since 1986. However, this result should be interpreted cautiously because of the methodological differences between historical studies (physical capture–recapture) and this survey. A conservative management approach is warranted given previous increases in duration of the ice-free season, which are predicted to continue in the future, and previously documented declines in body condition and vital rates.

  3. Estimating abundance of the Southern Hudson Bay polar bear subpopulation using aerial surveys, 2011 and 2012

    USGS Publications Warehouse

    Obbard, Martyn E.; Middel, Kevin R.; Stapleton, Seth P.; Thibault, Isabelle; Brodeur, Vincent; Jutras, Charles

    2013-01-01

    The Southern Hudson Bay (SH) polar bear subpopulation occurs at the southern extent of the species’ range. Although capture-recapture studies indicate that abundance remained stable between 1986 and 2005, declines in body condition and survival were documented during the period, possibly foreshadowing a future decrease in abundance. To obtain a current estimate of abundance, we conducted a comprehensive line transect aerial survey of SH during 2011–2012. We stratified the study site by anticipated densities and flew coastal contour transects and systematically spaced inland transects in Ontario and on Akimiski Island and large offshore islands in 2011. Data were collected with double observer and distance sampling protocols. We also surveyed small islands in Hudson Bay and James Bay and flew a comprehensive transect along the Québec coastline in 2012. We observed 667 bears in Ontario and on Akimiski Island and nearby islands in 2011, and we sighted 80 bears on offshore islands during 2012. Mark-recapture distance sampling and sightresight models yielded a model-averaged estimate of 868 (SE: 177) for the 2011 study area. Our estimate of abundance for the entire SH subpopulation (951; SE: 177) suggests that abundance has remained unchanged. However, this result should be interpreted cautiously because of the methodological differences between historical studies (physical capture) and this survey. A conservative management approach is warranted given the previous increases in the duration of the ice-free season, which are predicted to continue in the future, and previously documented declines in body condition and vital rates.

  4. Estimating abundance while accounting for rarity, correlated behavior, and other sources of variation in counts

    USGS Publications Warehouse

    Dorazio, Robert M.; Martin, Juulien; Edwards, Holly H.

    2013-01-01

    The class of N-mixture models allows abundance to be estimated from repeated, point count surveys while adjusting for imperfect detection of individuals. We developed an extension of N-mixture models to account for two commonly observed phenomena in point count surveys: rarity and lack of independence induced by unmeasurable sources of variation in the detectability of individuals. Rarity increases the number of locations with zero detections in excess of those expected under simple models of abundance (e.g., Poisson or negative binomial). Correlated behavior of individuals and other phenomena, though difficult to measure, increases the variation in detection probabilities among surveys. Our extension of N-mixture models includes a hurdle model of abundance and a beta-binomial model of detectability that accounts for additional (extra-binomial) sources of variation in detections among surveys. As an illustration, we fit this model to repeated point counts of the West Indian manatee, which was observed in a pilot study using aerial surveys. Our extension of N-mixture models provides increased flexibility. The effects of different sets of covariates may be estimated for the probability of occurrence of a species, for its mean abundance at occupied locations, and for its detectability.

  5. Estimating abundance while accounting for rarity, correlated behavior, and other sources of variation in counts.

    PubMed

    Dorazio, Robert M; Martin, Julien; Edwards, Holly H

    2013-07-01

    The class of N-mixture models allows abundance to be estimated from repeated, point count surveys while adjusting for imperfect detection of individuals. We developed an extension of N-mixture models to account for two commonly observed phenomena in point count surveys: rarity and lack of independence induced by unmeasurable sources of variation in the detectability of individuals. Rarity increases the number of locations with zero detections in excess of those expected under simple models of abundance (e.g., Poisson or negative binomial). Correlated behavior of individuals and other phenomena, though difficult to measure, increases the variation in detection probabilities among surveys. Our extension of N-mixture models includes a hurdle model of abundance and a beta-binomial model of detectability that accounts for additional (extra-binomial) sources of variation in detections among surveys. As an illustration, we fit this model to repeated point counts of the West Indian manatee, which was observed in a pilot study using aerial surveys. Our extension of N-mixture models provides increased flexibility. The effects of different sets of covariates may be estimated for the probability of occurrence of a species, for its mean abundance at occupied locations, and for its detectability. PMID:23951707

  6. A double-observer approach for estimating detection probability and abundance from point counts

    USGS Publications Warehouse

    Nichols, J.D.; Hines, J.E.; Sauer, J.R.; Fallon, F.W.; Fallon, J.E.; Heglund, P.J.

    2000-01-01

    Although point counts are frequently used in ornithological studies, basic assumptions about detection probabilities often are untested. We apply a double-observer approach developed to estimate detection probabilities for aerial surveys (Cook and Jacobson 1979) to avian point counts. At each point count, a designated 'primary' observer indicates to another ('secondary') observer all birds detected. The secondary observer records all detections of the primary observer as well as any birds not detected by the primary observer. Observers alternate primary and secondary roles during the course of the survey. The approach permits estimation of observer-specific detection probabilities and bird abundance. We developed a set of models that incorporate different assumptions about sources of variation (e.g. observer, bird species) in detection probability. Seventeen field trials were conducted, and models were fit to the resulting data using program SURVIV. Single-observer point counts generally miss varying proportions of the birds actually present, and observer and bird species were found to be relevant sources of variation in detection probabilities. Overall detection probabilities (probability of being detected by at least one of the two observers) estimated using the double-observer approach were very high (>0.95), yielding precise estimates of avian abundance. We consider problems with the approach and recommend possible solutions, including restriction of the approach to fixed-radius counts to reduce the effect of variation in the effective radius of detection among various observers and to provide a basis for using spatial sampling to estimate bird abundance on large areas of interest. We believe that most questions meriting the effort required to carry out point counts also merit serious attempts to estimate detection probabilities associated with the counts. The double-observer approach is a method that can be used for this purpose.

  7. Variability in abundance of temperate reef fishes estimated by visual census.

    PubMed

    Irigoyen, Alejo J; Galván, David E; Venerus, Leonardo A; Parma, Ana M

    2013-01-01

    Identifying sources of sampling variation and quantifying their magnitude is critical to the interpretation of ecological field data. Yet, most monitoring programs of reef fish populations based on underwater visual censuses (UVC) consider only a few of the factors that may influence fish counts, such as the diver or census methodology. Recent studies, however, have drawn attention to a broader range of processes that introduce variability at different temporal scales. This study analyzes the magnitude of different sources of variation in UVCs of temperate reef fishes off Patagonia (Argentina). The variability associated with time-of-day, tidal state, and time elapsed between censuses (minutes, days, weeks and months) was quantified for censuses conducted on the five most conspicuous and common species: Pinguipes brasilianus, Pseudopercis semifasciata, Sebastes oculatus, Acanthistius patachonicus and Nemadactylus bergi. Variance components corresponding to spatial heterogeneity and to the different temporal scales were estimated using nested random models. The levels of variability estimated for the different species were related to their life history attributes and behavior. Neither time-of-day nor tidal state had a significant effect on counts, except for the influence of tide on P. brasilianus. Spatial heterogeneity was the dominant source of variance in all but one species. Among the temporal scales, the intra-annual variation was the highest component for most species due to marked seasonal fluctuations in abundance, followed by the weekly and the instantaneous variation; the daily component was not significant. The variability between censuses conducted at different tidal levels and time-of-day was similar in magnitude to the instantaneous variation, reinforcing the conclusion that stochastic variation at very short time scales is non-negligible and should be taken into account in the design of monitoring programs and experiments. The present study provides

  8. Variability in Abundance of Temperate Reef Fishes Estimated by Visual Census

    PubMed Central

    Irigoyen, Alejo J.; Galván, David E.; Venerus, Leonardo A.; Parma, Ana M.

    2013-01-01

    Identifying sources of sampling variation and quantifying their magnitude is critical to the interpretation of ecological field data. Yet, most monitoring programs of reef fish populations based on underwater visual censuses (UVC) consider only a few of the factors that may influence fish counts, such as the diver or census methodology. Recent studies, however, have drawn attention to a broader range of processes that introduce variability at different temporal scales. This study analyzes the magnitude of different sources of variation in UVCs of temperate reef fishes off Patagonia (Argentina). The variability associated with time-of-day, tidal state, and time elapsed between censuses (minutes, days, weeks and months) was quantified for censuses conducted on the five most conspicuous and common species: Pinguipes brasilianus, Pseudopercis semifasciata, Sebastes oculatus, Acanthistius patachonicus and Nemadactylus bergi. Variance components corresponding to spatial heterogeneity and to the different temporal scales were estimated using nested random models. The levels of variability estimated for the different species were related to their life history attributes and behavior. Neither time-of-day nor tidal state had a significant effect on counts, except for the influence of tide on P. brasilianus. Spatial heterogeneity was the dominant source of variance in all but one species. Among the temporal scales, the intra-annual variation was the highest component for most species due to marked seasonal fluctuations in abundance, followed by the weekly and the instantaneous variation; the daily component was not significant. The variability between censuses conducted at different tidal levels and time-of-day was similar in magnitude to the instantaneous variation, reinforcing the conclusion that stochastic variation at very short time scales is non-negligible and should be taken into account in the design of monitoring programs and experiments. The present study provides

  9. Use of the robust design to estimate seasonal abundance and demographic parameters of a coastal bottlenose dolphin (Tursiops aduncus) population.

    PubMed

    Smith, Holly C; Pollock, Ken; Waples, Kelly; Bradley, Stuart; Bejder, Lars

    2013-01-01

    As delphinid populations become increasingly exposed to human activities we rely on our capacity to produce accurate abundance estimates upon which to base management decisions. This study applied mark-recapture methods following the Robust Design to estimate abundance, demographic parameters, and temporary emigration rates of an Indo-Pacific bottlenose dolphin (Tursiops aduncus) population off Bunbury, Western Australia. Boat-based photo-identification surveys were conducted year-round over three consecutive years along pre-determined transect lines to create a consistent sampling effort throughout the study period and area. The best fitting capture-recapture model showed a population with a seasonal Markovian temporary emigration with time varying survival and capture probabilities. Abundance estimates were seasonally dependent with consistently lower numbers obtained during winter and higher during summer and autumn across the three-year study period. Specifically, abundance estimates for all adults and juveniles (combined) varied from a low of 63 (95% CI 59 to 73) in winter of 2007 to a high of 139 (95% CI 134 to148) in autumn of 2009. Temporary emigration rates (γ') for animals absent in the previous period ranged from 0.34 to 0.97 (mean  =  0.54; ±SE 0.11) with a peak during spring. Temporary emigration rates for animals present during the previous period (γ'') were lower, ranging from 0.00 to 0.29, with a mean of 0.16 (± SE 0.04). This model yielded a mean apparent survival estimate for juveniles and adults (combined) of 0.95 (± SE 0.02) and a capture probability from 0.07 to 0.51 with a mean of 0.30 (± SE 0.04). This study demonstrates the importance of incorporating temporary emigration to accurately estimate abundance of coastal delphinids. Temporary emigration rates were high in this study, despite the large area surveyed, indicating the challenges of sampling highly mobile animals which range over large spatial areas. PMID:24130781

  10. A multimodal detection model of dolphins to estimate abundance validated by field experiments.

    PubMed

    Akamatsu, Tomonari; Ura, Tamaki; Sugimatsu, Harumi; Bahl, Rajendar; Behera, Sandeep; Panda, Sudarsan; Khan, Muntaz; Kar, S K; Kar, C S; Kimura, Satoko; Sasaki-Yamamoto, Yukiko

    2013-09-01

    Abundance estimation of marine mammals requires matching of detection of an animal or a group of animal by two independent means. A multimodal detection model using visual and acoustic cues (surfacing and phonation) that enables abundance estimation of dolphins is proposed. The method does not require a specific time window to match the cues of both means for applying mark-recapture method. The proposed model was evaluated using data obtained in field observations of Ganges River dolphins and Irrawaddy dolphins, as examples of dispersed and condensed distributions of animals, respectively. The acoustic detection probability was approximately 80%, 20% higher than that of visual detection for both species, regardless of the distribution of the animals in present study sites. The abundance estimates of Ganges River dolphins and Irrawaddy dolphins fairly agreed with the numbers reported in previous monitoring studies. The single animal detection probability was smaller than that of larger cluster size, as predicted by the model and confirmed by field data. However, dense groups of Irrawaddy dolphins showed difference in cluster sizes observed by visual and acoustic methods. Lower detection probability of single clusters of this species seemed to be caused by the clumped distribution of this species.

  11. Comparison of visual survey and seining methods for estimating abundance of an endangered, benthic stream fish

    USGS Publications Warehouse

    Jordan, F.; Jelks, H.L.; Bortone, S.A.; Dorazio, R.M.

    2008-01-01

    We compared visual survey and seining methods for estimating abundance of endangered Okaloosa darters, Etheostoma okaloosae, in 12 replicate stream reaches during August 2001. For each 20-m stream reach, two divers systematically located and marked the position of darters and then a second crew of three to five people came through with a small-mesh seine and exhaustively sampled the same area. Visual surveys required little extra time to complete. Visual counts (24.2 ?? 12.0; mean ?? one SD) considerably exceeded seine captures (7.4 ?? 4.8), and counts from the two methods were uncorrelated. Visual surveys, but not seines, detected the presence of Okaloosa darters at one site with low population densities. In 2003, we performed a depletion removal study in 10 replicate stream reaches to assess the accuracy of the visual survey method. Visual surveys detected 59% of Okaloosa darters present, and visual counts and removal estimates were positively correlated. Taken together, our comparisons indicate that visual surveys more accurately and precisely estimate abundance of Okaloosa darters than seining and more reliably detect presence at low population densities. We recommend evaluation of visual survey methods when designing programs to monitor abundance of benthic fishes in clear streams, especially for threatened and endangered species that may be sensitive to handling and habitat disturbance. ?? 2007 Springer Science+Business Media, Inc.

  12. Assessing small mammal abundance with track-tube indices and mark-recapture population estimates

    USGS Publications Warehouse

    Wiewel, A.S.; Clark, W.R.; Sovada, M.A.

    2007-01-01

    We compared track-tube sampling with mark-recapture livetrapping and evaluated a track-tube index, defined as the number of track tubes with identifiable small mammal tracks during a 4-night period, as a predictor of small mammal abundance estimates in North Dakota grasslands. Meadow voles (Microtus pennsylvanicus) were the most commonly recorded species by both methods, but were underrepresented in track-tube sampling, whereas 13-lined ground squirrels (Spermophilus tridecemlineatus) and Franklin's ground squirrels (S. franklinii) were overrepresented in track-tube sampling. Estimates of average species richness were lower from track tubes than from livetrapping. Regression models revealed that the track-tube index was at best a moderately good predictor of small mammal population estimates because both the form (linear versus curvilinear) and slope of the relationship varied between years. In addition, 95% prediction intervals indicated low precision when predicting population estimates from new track-tube index observations. Track tubes required less time and expense than mark-recapture and eliminated handling of small mammals. Using track tubes along with mark-recapture in a double sampling for regression framework would have potential value when attempting to estimate abundance of small mammals over large areas. ?? 2007 American Society of Mammalogists.

  13. Modelling community dynamics based on species-level abundance models from detection/nondetection data

    USGS Publications Warehouse

    Yamaura, Yuichi; Royle, J. Andrew; Kuboi, Kouji; Tada, Tsuneo; Ikeno, Susumu; Makino, Shun'ichi

    2011-01-01

    1. In large-scale field surveys, a binary recording of each species' detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species-, functional group-, and community-levels from such binary data. 2. We developed a novel hierarchical multi-species abundance model based on species-level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species-level detection/nondetection is linked to species- level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9-year dataset composed of the detection/nondetection of forest birds, at a single post-fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post-fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications. Understanding and prediction of large-scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species-, functional group-, and community-levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance-based diversity and similarity

  14. Estimating Sonoran pronghorn abundance and survival with fecal DNA and capture-recapture methods.

    PubMed

    Woodruff, Susannah P; Lukacs, Paul M; Christianson, David; Waits, Lisette P

    2016-10-01

    Population abundance estimates are important for management but can be challenging to determine in low-density, wide-ranging, and endangered species, such as Sonoran pronghorn (Antilocapra americana sonoriensis). The Sonoran pronghorn population has been increasing; however, population estimates are currently derived from a biennial aerial count that does not provide survival or recruitment estimates. We identified individuals through noninvasively collected fecal DNA and used robust-design capture-recapture to estimate abundance and survival for Sonoran pronghorn in the United States from 2013 to 2014. In 2014 we generated separate population estimates for pronghorn gathered near 13 different artificial water holes and for pronghorn not near water holes. The population using artificial water holes had 116 (95% CI 102-131) and 121 individuals (95% CI 112-132) in 2013 and 2014, respectively. For all locations, we estimated there were 144 individuals (95% CI 132-157). Adults had higher annual survival probabilities (0.83, 95% CI 0.69-0.92) than fawns (0.41, 95% CI 0.21-0.65). Our use of targeted noninvasive genetic sampling and capture-recapture with Sonoran pronghorn fecal DNA was an effective method for monitoring a large proportion of the population. Our results provided the first survival estimates for this population in over 2 decades and precise estimates of the population using artificial water holes. Our method could be used for targeted sampling of broadly distributed species in other systems, such as in African savanna ecosystems, where many species congregate at watering sites. PMID:26918820

  15. Estimating Sonoran pronghorn abundance and survival with fecal DNA and capture-recapture methods.

    PubMed

    Woodruff, Susannah P; Lukacs, Paul M; Christianson, David; Waits, Lisette P

    2016-10-01

    Population abundance estimates are important for management but can be challenging to determine in low-density, wide-ranging, and endangered species, such as Sonoran pronghorn (Antilocapra americana sonoriensis). The Sonoran pronghorn population has been increasing; however, population estimates are currently derived from a biennial aerial count that does not provide survival or recruitment estimates. We identified individuals through noninvasively collected fecal DNA and used robust-design capture-recapture to estimate abundance and survival for Sonoran pronghorn in the United States from 2013 to 2014. In 2014 we generated separate population estimates for pronghorn gathered near 13 different artificial water holes and for pronghorn not near water holes. The population using artificial water holes had 116 (95% CI 102-131) and 121 individuals (95% CI 112-132) in 2013 and 2014, respectively. For all locations, we estimated there were 144 individuals (95% CI 132-157). Adults had higher annual survival probabilities (0.83, 95% CI 0.69-0.92) than fawns (0.41, 95% CI 0.21-0.65). Our use of targeted noninvasive genetic sampling and capture-recapture with Sonoran pronghorn fecal DNA was an effective method for monitoring a large proportion of the population. Our results provided the first survival estimates for this population in over 2 decades and precise estimates of the population using artificial water holes. Our method could be used for targeted sampling of broadly distributed species in other systems, such as in African savanna ecosystems, where many species congregate at watering sites.

  16. Integrating acoustic telemetry into mark-recapture models to improve the precision of apparent survival and abundance estimates.

    PubMed

    Dudgeon, Christine L; Pollock, Kenneth H; Braccini, J Matias; Semmens, Jayson M; Barnett, Adam

    2015-07-01

    Capture-mark-recapture models are useful tools for estimating demographic parameters but often result in low precision when recapture rates are low. Low recapture rates are typical in many study systems including fishing-based studies. Incorporating auxiliary data into the models can improve precision and in some cases enable parameter estimation. Here, we present a novel application of acoustic telemetry for the estimation of apparent survival and abundance within capture-mark-recapture analysis using open population models. Our case study is based on simultaneously collecting longline fishing and acoustic telemetry data for a large mobile apex predator, the broadnose sevengill shark (Notorhynchus cepedianus), at a coastal site in Tasmania, Australia. Cormack-Jolly-Seber models showed that longline data alone had very low recapture rates while acoustic telemetry data for the same time period resulted in at least tenfold higher recapture rates. The apparent survival estimates were similar for the two datasets but the acoustic telemetry data showed much greater precision and enabled apparent survival parameter estimation for one dataset, which was inestimable using fishing data alone. Combined acoustic telemetry and longline data were incorporated into Jolly-Seber models using a Monte Carlo simulation approach. Abundance estimates were comparable to those with longline data only; however, the inclusion of acoustic telemetry data increased precision in the estimates. We conclude that acoustic telemetry is a useful tool for incorporating in capture-mark-recapture studies in the marine environment. Future studies should consider the application of acoustic telemetry within this framework when setting up the study design and sampling program.

  17. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA.

    PubMed

    Lodge, David M; Turner, Cameron R; Jerde, Christopher L; Barnes, Matthew A; Chadderton, Lindsay; Egan, Scott P; Feder, Jeffrey L; Mahon, Andrew R; Pfrender, Michael E

    2012-06-01

    Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, 'early detection and rapid response'; (ii) for conserving imperilled native species, 'protection of biodiversity hotspots'; and (iii) for assessing biosecurity risk, 'an ounce of prevention equals a pound of cure.' However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism's DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next-generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.

  18. Estimating population abundance and mapping distribution of wintering sea ducks in coastal waters of the mid-Atlantic

    USGS Publications Warehouse

    Koneff, M.D.; Royle, J. Andrew; Forsell, D.J.; Wortham, J.S.; Boomer, G.S.; Perry, M.C.

    2005-01-01

    Survey design for wintering scoters (Melanitta sp.) and other sea ducks that occur in offshore waters is challenging because these species have large ranges, are subject to distributional shifts among years and within a season, and can occur in aggregations. Interest in winter sea duck population abundance surveys has grown in recent years. This interest stems from concern over the population status of some sea ducks, limitations of extant breeding waterfowl survey programs in North America and logistical challenges and costs of conducting surveys in northern breeding regions, high winter area philopatry in some species and potential conservation implications, and increasing concern over offshore development and other threats to sea duck wintering habitats. The efficiency and practicality of statistically-rigorous monitoring strategies for mobile, aggregated wintering sea duck populations have not been sufficiently investigated. This study evaluated a 2-phase adaptive stratified strip transect sampling plan to estimate wintering population size of scoters, long-tailed ducks (Clangua hyemalis), and other sea ducks and provide information on distribution. The sampling plan results in an optimal allocation of a fixed sampling effort among offshore strata in the U.S. mid-Atlantic coast region. Phase I transect selection probabilities were based on historic distribution and abundance data, while Phase 2 selection probabilities were based on observations made during Phase 1 flights. Distance sampling methods were used to estimate detection rates. Environmental variables thought to affect detection rates were recorded during the survey and post-stratification and covariate modeling were investigated to reduce the effect of heterogeneity on detection estimation. We assessed cost-precision tradeoffs under a number of fixed-cost sampling scenarios using Monte Carlo simulation. We discuss advantages and limitations of this sampling design for estimating wintering sea duck

  19. Chemical abundances of damped Ly alpha systems:. A new method for estimating dust depletion effects

    NASA Astrophysics Data System (ADS)

    Vladilo, G.

    2002-08-01

    A new method is presented for recovering the abundances of Damped Ly alpha systems (DLAs) taking into account the effects of dust depletion. For the first time, possible variations of the chemical composition of the dust are taken into account in estimating the depletions. No prior assumptions on the extinction properties of the dust are required. The method requires a set of abundances measured in the gas and a set of parameters describing the chemical properties of the dust. A large subset of these parameters is determined from interstellar observations; the others are free parameters for which an educated guess can be made. The method is able to recover the abundances of the SMC starting from SMC interstellar measurements apparently discrepant from the stellar ones. Application of the method to 22 DLAs with available [Fe/H] and [Si/Fe] measurements gives the following results: (1) the mean metallicity of the corrected data is < [Fe/H]> =~ -1.0 dex, about 0.5 dex higher than that of the original data; (2) the slope of the [Fe/H] versus redshift relation is steeper for the corrected data (m =~ -0.3 dex) than for the original ones (m =~ -0.2 dex); (3) the corrected [Si/Fe] ratios are less enhanced, on average, than those found in Galactic stars of similar, low metallicity; (4) a decrease of the [Si/Fe] versus [Fe/H] ratios, expected by ``time delay'' models of chemical evolution, is found for the corrected data; (5) the [Si/Fe] ratios tend to increase with redshift once corrected; (6) consistency between [Si/Fe] and [S/Zn] measurements, two independent estimators of the alpha /Fe ratio, is found only for the corrected abundances.

  20. Mnemiopsis leidyi (Ctenophora) in Narragansett Bay, 1975-1979: Abundance, size composition and estimation of grazing

    NASA Astrophysics Data System (ADS)

    Deason, Ellen E.

    1982-08-01

    Surveys of the distribution, abundance and size of the ctenophore Mnemiopsis leidyi were carried out in Narragansett Bay, R.I. over a 5-year period, 1975-1979. Yearly variations were observed in time of initiation of the ctenophore increase and maximum abundance. Biomass maxima ranged from 0·2 to 3 g dry weight m -3 at Station 2 in lower Narragansett Bay while maximum abundance varied from 20 to 100 animals m -3. Ctenophores less than 1 cm in length generally composed up to 50% of the biomass and 95% of the numerical abundance during the peak of the M. leidyi pulse. During the 1978 maxima and the declining stages of the pulse each year, 100% of the population was composed of small animals. M. leidyi populations increased earlier, reached greater maximum abundances, and were more highly dominated by small animals in the upper bay than toward the mouth of the bay. The averageclearance rate of M. leidyi larvae feeding on A. tonsa at 22°C was 0·36 l mg -1 dry weight day -1, with apparent selection for nauplii relative to copepodites. Predation and excretion rates applied to ctenophore biomass estimated for Narragansett Bay indicated that M. leidyi excretion is minor but predation removed a bay-wide mean of 20% of the zooplankton standing stock daily during August of 1975 and 1976. Variation in M. leidyi predation at Station 2 was inversely related to mean zooplankton biomass during August and September, which increased 4-fold during the 5-year period.

  1. Effects of prior detections on estimates of detection probability, abundance, and occupancy

    USGS Publications Warehouse

    Riddle, Jason D.; Mordecai, Rua S.; Pollock, Kenneth H.; Simons, Theodore R.

    2010-01-01

    Survey methods that account for detection probability often require repeated detections of individual birds or repeated visits to a site to conduct Counts or collect presence-absence data. Initial encounters with individual species or individuals of a species could influence detection probabilities for subsequent encounters. For example, observers may be more likely to redetect a species or individual once they are aware of the presence of that species or individual at a particular site. Not accounting for these effects could result in biased estimators of detection probability, abundance, and occupancy. We tested for effects of prior detections in three data sets that differed dramatically by species, geographic location, and method of counting birds. We found strong support (AIC weights from 83% to 100%) for models that allowed for the effects of prior detections. These models produced estimates of detection probability, abundance, and occupancy that differed substantially from those produced by models that ignored the effects of prior detections. We discuss the consequences of the effects of prior detections on estimation for several sampling methods and provide recommendations for avoiding these effects through survey design or by modeling them when they cannot be avoided. 

  2. READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    PubMed Central

    Rashid, Mamoon; Pain, Arnab

    2013-01-01

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: arnab.pain@kaust.edu.sa or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23193222

  3. Breeding chorus indices are weakly related to estimated abundance of boreal chorus frogs

    USGS Publications Warehouse

    Corn, P.S.; Muths, E.; Kissel, A.M.; Scherer, R. D.

    2011-01-01

    Call surveys used to monitor breeding choruses of anuran amphibians generate index values that are frequently used to represent the number of male frogs present, but few studies have quantified this relationship. We compared abundance of male Boreal Chorus Frogs (Pseudacris maculata), estimated using capture–recapture methods in two populations in Colorado, to call index values derived from automated recordings. Single index values, such as might result from large monitoring efforts, were unrelated to population size. A synthetic call saturation index (CSI), the daily proportion of the maximum possible sum of index values derived from multiple recordings, was greater in larger populations, but the relationship was not highly predictive.

  4. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    DOE PAGES

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A.

    2015-05-08

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set ofmore » publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.« less

  5. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes

    SciTech Connect

    Aziz, Ramy K.; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A.

    2015-05-08

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. By adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

  6. Multidimensional metrics for estimating phage abundance, distribution, gene density, and sequence coverage in metagenomes.

    PubMed

    Aziz, Ramy K; Dwivedi, Bhakti; Akhter, Sajia; Breitbart, Mya; Edwards, Robert A

    2015-01-01

    Phages are the most abundant biological entities on Earth and play major ecological roles, yet the current sequenced phage genomes do not adequately represent their diversity, and little is known about the abundance and distribution of these sequenced genomes in nature. Although the study of phage ecology has benefited tremendously from the emergence of metagenomic sequencing, a systematic survey of phage genes and genomes in various ecosystems is still lacking, and fundamental questions about phage biology, lifestyle, and ecology remain unanswered. To address these questions and improve comparative analysis of phages in different metagenomes, we screened a core set of publicly available metagenomic samples for sequences related to completely sequenced phages using the web tool, Phage Eco-Locator. We then adopted and deployed an array of mathematical and statistical metrics for a multidimensional estimation of the abundance and distribution of phage genes and genomes in various ecosystems. Experiments using those metrics individually showed their usefulness in emphasizing the pervasive, yet uneven, distribution of known phage sequences in environmental metagenomes. Using these metrics in combination allowed us to resolve phage genomes into clusters that correlated with their genotypes and taxonomic classes as well as their ecological properties. We propose adding this set of metrics to current metaviromic analysis pipelines, where they can provide insight regarding phage mosaicism, habitat specificity, and evolution.

  7. Estimating species - area relationships by modeling abundance and frequency subject to incomplete sampling.

    PubMed

    Yamaura, Yuichi; Connor, Edward F; Royle, J Andrew; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio

    2016-07-01

    Models and data used to describe species-area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species-area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species-area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density-area relationships and occurrence probability-area relationships can alter the form of species-area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied to a

  8. Estimating species - area relationships by modeling abundance and frequency subject to incomplete sampling.

    PubMed

    Yamaura, Yuichi; Connor, Edward F; Royle, J Andrew; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio

    2016-07-01

    Models and data used to describe species-area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species-area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species-area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density-area relationships and occurrence probability-area relationships can alter the form of species-area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied to a

  9. Estimating species – area relationships by modeling abundance and frequency subject to incomplete sampling

    USGS Publications Warehouse

    Yamaura, Yuichi; Connor, Edward F.; Royle, Andy; Itoh, Katsuo; Sato, Kiyoshi; Taki, Hisatomo; Mishima, Yoshio

    2016-01-01

    Models and data used to describe species–area relationships confound sampling with ecological process as they fail to acknowledge that estimates of species richness arise due to sampling. This compromises our ability to make ecological inferences from and about species–area relationships. We develop and illustrate hierarchical community models of abundance and frequency to estimate species richness. The models we propose separate sampling from ecological processes by explicitly accounting for the fact that sampled patches are seldom completely covered by sampling plots and that individuals present in the sampling plots are imperfectly detected. We propose a multispecies abundance model in which community assembly is treated as the summation of an ensemble of species-level Poisson processes and estimate patch-level species richness as a derived parameter. We use sampling process models appropriate for specific survey methods. We propose a multispecies frequency model that treats the number of plots in which a species occurs as a binomial process. We illustrate these models using data collected in surveys of early-successional bird species and plants in young forest plantation patches. Results indicate that only mature forest plant species deviated from the constant density hypothesis, but the null model suggested that the deviations were too small to alter the form of species–area relationships. Nevertheless, results from simulations clearly show that the aggregate pattern of individual species density–area relationships and occurrence probability–area relationships can alter the form of species–area relationships. The plant community model estimated that only half of the species present in the regional species pool were encountered during the survey. The modeling framework we propose explicitly accounts for sampling processes so that ecological processes can be examined free of sampling artefacts. Our modeling approach is extensible and could be applied

  10. How should detection probability be incorporated into estimates of relative abundance?

    USGS Publications Warehouse

    MacKenzie, D.I.; Kendall, W.L.

    2002-01-01

    Determination of the relative abundance of two populations, separated by time or space, is of interest in many ecological situations. We focus on two estimators of relative abundance, which assume that the probability that an individual is detected at least once in the survey is either equal or unequal for the two populations. We present three methods for incorporating the collected information into our inference. The first method, proposed previously, is a traditional hypothesis test for evidence that detection probabilities are unequal. However, we feel that, a priori, it is more likely that detection probabilities are actually different; hence, the burden of proof should be shifted, requiring evidence that detection probabilities are practically equivalent. The second method we present, equivalence testing, is one approach to doing so. Third, we suggest that model averaging could be used by combining the two estimators according to derived model weights. These differing approaches are applied to a mark-recapture experiment on Nuttail's cottontail rabbit (Sylvilagus nuttallii) conducted in central Oregon during 1974 and 1975, which has been previously analyzed by other authors.

  11. Fitting statistical distributions to sea duck count data: implications for survey design and abundance estimation

    USGS Publications Warehouse

    Zipkin, Elise F.; Leirness, Jeffery B.; Kinlan, Brian P.; O'Connell, Allan F.; Silverman, Emily D.

    2014-01-01

    Determining appropriate statistical distributions for modeling animal count data is important for accurate estimation of abundance, distribution, and trends. In the case of sea ducks along the U.S. Atlantic coast, managers want to estimate local and regional abundance to detect and track population declines, to define areas of high and low use, and to predict the impact of future habitat change on populations. In this paper, we used a modified marked point process to model survey data that recorded flock sizes of Common eiders, Long-tailed ducks, and Black, Surf, and White-winged scoters. The data come from an experimental aerial survey, conducted by the United States Fish & Wildlife Service (USFWS) Division of Migratory Bird Management, during which east-west transects were flown along the Atlantic Coast from Maine to Florida during the winters of 2009–2011. To model the number of flocks per transect (the points), we compared the fit of four statistical distributions (zero-inflated Poisson, zero-inflated geometric, zero-inflated negative binomial and negative binomial) to data on the number of species-specific sea duck flocks that were recorded for each transect flown. To model the flock sizes (the marks), we compared the fit of flock size data for each species to seven statistical distributions: positive Poisson, positive negative binomial, positive geometric, logarithmic, discretized lognormal, zeta and Yule–Simon. Akaike’s Information Criterion and Vuong’s closeness tests indicated that the negative binomial and discretized lognormal were the best distributions for all species for the points and marks, respectively. These findings have important implications for estimating sea duck abundances as the discretized lognormal is a more skewed distribution than the Poisson and negative binomial, which are frequently used to model avian counts; the lognormal is also less heavy-tailed than the power law distributions (e.g., zeta and Yule–Simon), which are

  12. Reconciling LCROSS and Orbital Neutron Water Abundance Estimates in Cabeus Crater

    NASA Technical Reports Server (NTRS)

    Elphic, Richard; Teodoro, Luis F.; Eke, Vincent R.; Paige, David A.; Siegler, Matthew A.; Colaprete, Anthony

    2011-01-01

    The Lunar Prospector Neutron Spectrometer (LPNS) first revealed Cabeus crater (84.9 deg S, 35.5degW) as having the highest inferred hydrogen on the Moon. Because of the broad LPNS footprint (approximately 40 km FWHM), the apparent peak water-equivalent hydrogen (WEH) concentration is only approximately 0.25 wt%, but could be much higher in smaller areas than the spectrometer footprint. Earlier image reconstruction work suggested that areas within permanent shadow have abundances approximately 1 wt% WEH. However, the LCROSS impact yielded total water estimates, ice plus vapor, of between 3 and 10 wt%. The large disagreement between LCROSS and apparent orbital values imply that either the ice is buried, by perhaps as much as 50 to 100 cm; or the ice distribution within Cabeus is spatially inhomogeneous, or both. Modeling reveals that the areal extent of a "shallow permafrost zone" is far greater than the area of permanent shadow. Ice can be virtually stable for billions of years within a few tens of centimeters of the surface in these areas. However, the LCROSS impact took place in an area of permanent shadow. If stably-trapped volatiles can be found in locales that receive occasional, oblique sunlight, landed missions may target these sites and eventual resource exploitation may be done more easily. Are orbital neutron data consistent with areally-extensive, volatile-rich cold traps? Orbital epithermal neutron data over the northern half of Cabeus (near the LCROSS impact site) are consistent with 0.2 wt% WEH or less in the "permafrost zone" near the crater. On the other hand, pixon reconstructions that confine the hydrogen enhancements to permanent shadow result in higher abundance estimates -- around 1 wt% if homogeneously mixed. But if the PSR abundance is increased to 10 wt%, consistent with the sum of all H-bearing compounds seen by LCROSS, a much larger-than-observed reduction in neutron count rate would be seen from orbit. It is likely that volatiles are

  13. Iron abundance estimations of the lunar mare regions using VIS-NIR spectrometers on-board Chandrayaan-1

    NASA Astrophysics Data System (ADS)

    Bhatt, Megha; Mall, Urs; Bugiplacchi, Roberto

    2012-07-01

    We present the iron abundance estimation of the mare regions from near and farside of the Moon. Our method employs the 2-μm absorption band parameters to estimate FeO weight percentage (wt%) abundances from high resolution Near-Infrared (NIR) lunar data, as measured by the SIR-2 [1] instrument on board of the Chandrayaan-1. Our method is based on minimizing the effects of space weathering on the absorption characteristics of lunar reflectance spectra in the visible/near-infrared (VIS-NIR) wavelength range. We will report on a comparative study of mapping iron abundances using our method and methods based on the 1-μm absorption band parameters for six mare regions, including Mare Imbrium, Mare Nubium, Mare Cognitum, Mare Humorum, Oceanus Procellarum and Mare Moscoviense. Various remote sensing techniques have detected different volcanic eruptive events ranging from the early history of mare volcanism through its last major phases in Oceanus Procellarum and Mare Imbrium regions. Western mare regions are interpreted as olivine rich and iron rich based on Clementine data analysis. Recently this area was mapped for more detailed mineralogy investigation using the Moon Mineralogy Mapper (M3) [2]. Oceanus Procellarum and Mare Imbrium regions were survey by 39 SIR-2 orbits from a 100 km altitude with a ground spatial resolution of 200 m. For each study area we produced iron maps using Clementine data by applying Lucey et. al. [3] approach. We aimed to identifying and mapping the major compositional units in selected mare regions based on variations in their FeO wt%. For instance we observed a wide range of variations in FeO wt% (5 to 25) estimated for Mare Moscoviense and Mare Imbrium with the youngest mare unit in the basins with the highest FeO wt% (between 22-25). Our comparative analysis shows that iron abundance estimated using the 2-μ m absorption band parameters shares the similar trend as the FeO wt% map derived from Clementine data. However, we did not observe

  14. A spatially explicit estimate of the prewhaling abundance of the endangered North Atlantic right whale.

    PubMed

    Monsarrat, Sophie; Pennino, M Grazia; Smith, Tim D; Reeves, Randall R; Meynard, Christine N; Kaplan, David M; Rodrigues, Ana S L

    2016-08-01

    The North Atlantic right whale (NARW) (Eubalaena glacialis) is one of the world's most threatened whales. It came close to extinction after nearly a millennium of exploitation and currently persists as a population of only approximately 500 individuals. Setting appropriate conservation targets for this species requires an understanding of its historical population size, as a baseline for measuring levels of depletion and progress toward recovery. This is made difficult by the scarcity of records over this species' long whaling history. We sought to estimate the preexploitation population size of the North Atlantic right whale and understand how this species was distributed across its range. We used a spatially explicit data set on historical catches of North Pacific right whales (NPRWs) (Eubalaena japonica) to model the relationship between right whale relative density and the environment during the summer feeding season. Assuming the 2 right whale species select similar environments, we projected this model to the North Atlantic to predict how the relative abundance of NARWs varied across their range. We calibrated these relative abundances with estimates of the NPRW total prewhaling population size to obtain high and low estimates for the overall NARW population size prior to exploitation. The model predicted 9,075-21,328 right whales in the North Atlantic. The current NARW population is thus <6% of the historical North Atlantic carrying capacity and has enormous potential for recovery. According to the model, in June-September NARWs concentrated in 2 main feeding areas: east of the Grand Banks of Newfoundland and in the Norwegian Sea. These 2 areas may become important in the future as feeding grounds and may already be used more regularly by this endangered species than is thought. PMID:26632250

  15. A spatially explicit estimate of the prewhaling abundance of the endangered North Atlantic right whale.

    PubMed

    Monsarrat, Sophie; Pennino, M Grazia; Smith, Tim D; Reeves, Randall R; Meynard, Christine N; Kaplan, David M; Rodrigues, Ana S L

    2016-08-01

    The North Atlantic right whale (NARW) (Eubalaena glacialis) is one of the world's most threatened whales. It came close to extinction after nearly a millennium of exploitation and currently persists as a population of only approximately 500 individuals. Setting appropriate conservation targets for this species requires an understanding of its historical population size, as a baseline for measuring levels of depletion and progress toward recovery. This is made difficult by the scarcity of records over this species' long whaling history. We sought to estimate the preexploitation population size of the North Atlantic right whale and understand how this species was distributed across its range. We used a spatially explicit data set on historical catches of North Pacific right whales (NPRWs) (Eubalaena japonica) to model the relationship between right whale relative density and the environment during the summer feeding season. Assuming the 2 right whale species select similar environments, we projected this model to the North Atlantic to predict how the relative abundance of NARWs varied across their range. We calibrated these relative abundances with estimates of the NPRW total prewhaling population size to obtain high and low estimates for the overall NARW population size prior to exploitation. The model predicted 9,075-21,328 right whales in the North Atlantic. The current NARW population is thus <6% of the historical North Atlantic carrying capacity and has enormous potential for recovery. According to the model, in June-September NARWs concentrated in 2 main feeding areas: east of the Grand Banks of Newfoundland and in the Norwegian Sea. These 2 areas may become important in the future as feeding grounds and may already be used more regularly by this endangered species than is thought.

  16. Accounting for non-independent detection when estimating abundance of organisms with a Bayesian approach

    USGS Publications Warehouse

    Martin, Julien; Royle, J. Andrew; MacKenzie, Darryl I.; Edwards, Holly H.; Kery, Marc; Gardner, Beth

    2011-01-01

    Summary 1. Binomial mixture models use repeated count data to estimate abundance. They are becoming increasingly popular because they provide a simple and cost-effective way to account for imperfect detection. However, these models assume that individuals are detected independently of each other. This assumption may often be violated in the field. For instance, manatees (Trichechus manatus latirostris) may surface in turbid water (i.e. become available for detection during aerial surveys) in a correlated manner (i.e. in groups). However, correlated behaviour, affecting the non-independence of individual detections, may also be relevant in other systems (e.g. correlated patterns of singing in birds and amphibians). 2. We extend binomial mixture models to account for correlated behaviour and therefore to account for non-independent detection of individuals. We simulated correlated behaviour using beta-binomial random variables. Our approach can be used to simultaneously estimate abundance, detection probability and a correlation parameter. 3. Fitting binomial mixture models to data that followed a beta-binomial distribution resulted in an overestimation of abundance even for moderate levels of correlation. In contrast, the beta-binomial mixture model performed considerably better in our simulation scenarios. We also present a goodness-of-fit procedure to evaluate the fit of beta-binomial mixture models. 4. We illustrate our approach by fitting both binomial and beta-binomial mixture models to aerial survey data of manatees in Florida. We found that the binomial mixture model did not fit the data, whereas there was no evidence of lack of fit for the beta-binomial mixture model. This example helps illustrate the importance of using simulations and assessing goodness-of-fit when analysing ecological data with N-mixture models. Indeed, both the simulations and the goodness-of-fit procedure highlighted the limitations of the standard binomial mixture model for aerial

  17. Estimating forest species abundance through linear unmixing of CHRIS/PROBA imagery

    NASA Astrophysics Data System (ADS)

    Stagakis, Stavros; Vanikiotis, Theofilos; Sykioti, Olga

    2016-09-01

    The advancing technology of hyperspectral remote sensing offers the opportunity of accurate land cover characterization of complex natural environments. In this study, a linear spectral unmixing algorithm that incorporates a novel hierarchical Bayesian approach (BI-ICE) was applied on two spatially and temporally adjacent CHRIS/PROBA images over a forest in North Pindos National Park (Epirus, Greece). The scope is to investigate the potential of this algorithm to discriminate two different forest species (i.e. beech - Fagus sylvatica, pine - Pinus nigra) and produce accurate species-specific abundance maps. The unmixing results were evaluated in uniformly distributed plots across the test site using measured fractions of each species derived by very high resolution aerial orthophotos. Landsat-8 images were also used to produce a conventional discrete-type classification map of the test site. This map was used to define the exact borders of the test site and compare the thematic information of the two mapping approaches (discrete vs abundance mapping). The required ground truth information, regarding training and validation of the applied mapping methodologies, was collected during a field campaign across the study site. Abundance estimates reached very good overall accuracy (R2 = 0.98, RMSE = 0.06). The most significant source of error in our results was due to the shadowing effects that were very intense in some areas of the test site due to the low solar elevation during CHRIS acquisitions. It is also demonstrated that the two mapping approaches are in accordance across pure and dense forest areas, but the conventional classification map fails to describe the natural spatial gradients of each species and the actual species mixture across the test site. Overall, the BI-ICE algorithm presented increased potential to unmix challenging objects with high spectral similarity, such as different vegetation species, under real and not optimum acquisition conditions. Its

  18. Effects of sampling design on the estimation of adult mosquito abundance.

    PubMed

    Reisen, W K; Lothrop, H D

    1999-06-01

    During 1994-5, Culex tarsalis comprised 75% of the 902,643 adult female mosquitoes collected by 63 dry-ice-baited Centers for Disease Control (CDC)-style traps operated biweekly in a uniform sampling grid that covered the southern Coachella Valley, Riverside County, California. The ln(y + 1) transformation successfully controlled the variance and normalized the distribution of catch size among trap nights. When tested by analysis of variance, abundance varied significantly among months, years, and trap sites. Although the trap by months interaction was not significant, female distribution changed seasonally as larval habitats shifted from wetlands along the Salton Sea to agriculture to managed duck marshes. Conditional simulations utilized subsets of trap sites to compare sampling designs that required no (uniform, random, and transect designs) or prior (best-estimate and stratified random designs) knowledge of mosquito spatial distribution. All designs provided similar information on population seasonal trends, but a stratified random design provided the most accurate and precise simulation. A uniform trap grid that employed every 2nd trap site subsequently was adopted by the Coachella Valley Mosquito and Vector Control District to provide information on focal changes in abundance indicative of missed or newly created larval habitats or control failures. PMID:10412106

  19. A sampling design and model for estimating abundance of Nile crocodiles while accounting for heterogeneity of detectability of multiple observers

    USGS Publications Warehouse

    Shirley, Matthew H.; Dorazio, Robert M.; Abassery, Ekramy; Elhady, Amr A.; Mekki, Mohammed S.; Asran, Hosni H.

    2012-01-01

    As part of the development of a management program for Nile crocodiles in Lake Nasser, Egypt, we used a dependent double-observer sampling protocol with multiple observers to compute estimates of population size. To analyze the data, we developed a hierarchical model that allowed us to assess variation in detection probabilities among observers and survey dates, as well as account for variation in crocodile abundance among sites and habitats. We conducted surveys from July 2008-June 2009 in 15 areas of Lake Nasser that were representative of 3 main habitat categories. During these surveys, we sampled 1,086 km of lake shore wherein we detected 386 crocodiles. Analysis of the data revealed significant variability in both inter- and intra-observer detection probabilities. Our raw encounter rate was 0.355 crocodiles/km. When we accounted for observer effects and habitat, we estimated a surface population abundance of 2,581 (2,239-2,987, 95% credible intervals) crocodiles in Lake Nasser. Our results underscore the importance of well-trained, experienced monitoring personnel in order to decrease heterogeneity in intra-observer detection probability and to better detect changes in the population based on survey indices. This study will assist the Egyptian government establish a monitoring program as an integral part of future crocodile harvest activities in Lake Nasser

  20. Ground-based column abundance measurements of atmospheric hydroxyl

    NASA Technical Reports Server (NTRS)

    Burnett, Clyde R.

    1988-01-01

    The preliminary results of ground-based OH column abundance measurements from Truk, Federated States of Micronesia, are contained. These are the first OH column measurements from the tropics, and constitute a signficcant contribution to the OH data base. Comparisons of tropical OH behavior with the extensive mid-latitude observations serve as a critical test of the current understanding of the HO (sub x) photochemistry and its relationship to the other major chemical families. The quasi-biennial oscillation (QBO) in tropical stratospheric winds exerts a major influence on the Hadley cell vertical transport. Related QBOs in total O3 and in stratospheric H2O were identified, but QBO effects on other stratospheric species are still unknown. The solar tide in the tropics produces a diurnal surface pressure variation of 2 to 3 mb; its effect on OH photochemistry in the stratosphere may be significant.

  1. Ground-based column abundance measurements of atmospheric hydroxyl

    NASA Astrophysics Data System (ADS)

    Burnett, Clyde R.

    1988-04-01

    The preliminary results of ground-based OH column abundance measurements from Truk, Federated States of Micronesia, are contained. These are the first OH column measurements from the tropics, and constitute a signficcant contribution to the OH data base. Comparisons of tropical OH behavior with the extensive mid-latitude observations serve as a critical test of the current understanding of the HO (sub x) photochemistry and its relationship to the other major chemical families. The quasi-biennial oscillation (QBO) in tropical stratospheric winds exerts a major influence on the Hadley cell vertical transport. Related QBOs in total O3 and in stratospheric H2O were identified, but QBO effects on other stratospheric species are still unknown. The solar tide in the tropics produces a diurnal surface pressure variation of 2 to 3 mb; its effect on OH photochemistry in the stratosphere may be significant.

  2. Re-constructing historical Adélie penguin abundance estimates by retrospectively accounting for detection bias.

    PubMed

    Southwell, Colin; Emmerson, Louise; Newbery, Kym; McKinlay, John; Kerry, Knowles; Woehler, Eric; Ensor, Paul

    2015-01-01

    Seabirds and other land-breeding marine predators are considered to be useful and practical indicators of the state of marine ecosystems because of their dependence on marine prey and the accessibility of their populations at breeding colonies. Historical counts of breeding populations of these higher-order marine predators are one of few data sources available for inferring past change in marine ecosystems. However, historical abundance estimates derived from these population counts may be subject to unrecognised bias and uncertainty because of variable attendance of birds at breeding colonies and variable timing of past population surveys. We retrospectively accounted for detection bias in historical abundance estimates of the colonial, land-breeding Adélie penguin through an analysis of 222 historical abundance estimates from 81 breeding sites in east Antarctica. The published abundance estimates were de-constructed to retrieve the raw count data and then re-constructed by applying contemporary adjustment factors obtained from remotely operating time-lapse cameras. The re-construction process incorporated spatial and temporal variation in phenology and attendance by using data from cameras deployed at multiple sites over multiple years and propagating this uncertainty through to the final revised abundance estimates. Our re-constructed abundance estimates were consistently higher and more uncertain than published estimates. The re-constructed estimates alter the conclusions reached for some sites in east Antarctica in recent assessments of long-term Adélie penguin population change. Our approach is applicable to abundance data for a wide range of colonial, land-breeding marine species including other penguin species, flying seabirds and marine mammals.

  3. Re-Constructing Historical Adélie Penguin Abundance Estimates by Retrospectively Accounting for Detection Bias

    PubMed Central

    Southwell, Colin; Emmerson, Louise; Newbery, Kym; McKinlay, John; Kerry, Knowles; Woehler, Eric; Ensor, Paul

    2015-01-01

    Seabirds and other land-breeding marine predators are considered to be useful and practical indicators of the state of marine ecosystems because of their dependence on marine prey and the accessibility of their populations at breeding colonies. Historical counts of breeding populations of these higher-order marine predators are one of few data sources available for inferring past change in marine ecosystems. However, historical abundance estimates derived from these population counts may be subject to unrecognised bias and uncertainty because of variable attendance of birds at breeding colonies and variable timing of past population surveys. We retrospectively accounted for detection bias in historical abundance estimates of the colonial, land-breeding Adélie penguin through an analysis of 222 historical abundance estimates from 81 breeding sites in east Antarctica. The published abundance estimates were de-constructed to retrieve the raw count data and then re-constructed by applying contemporary adjustment factors obtained from remotely operating time-lapse cameras. The re-construction process incorporated spatial and temporal variation in phenology and attendance by using data from cameras deployed at multiple sites over multiple years and propagating this uncertainty through to the final revised abundance estimates. Our re-constructed abundance estimates were consistently higher and more uncertain than published estimates. The re-constructed estimates alter the conclusions reached for some sites in east Antarctica in recent assessments of long-term Adélie penguin population change. Our approach is applicable to abundance data for a wide range of colonial, land-breeding marine species including other penguin species, flying seabirds and marine mammals. PMID:25909636

  4. Re-constructing historical Adélie penguin abundance estimates by retrospectively accounting for detection bias.

    PubMed

    Southwell, Colin; Emmerson, Louise; Newbery, Kym; McKinlay, John; Kerry, Knowles; Woehler, Eric; Ensor, Paul

    2015-01-01

    Seabirds and other land-breeding marine predators are considered to be useful and practical indicators of the state of marine ecosystems because of their dependence on marine prey and the accessibility of their populations at breeding colonies. Historical counts of breeding populations of these higher-order marine predators are one of few data sources available for inferring past change in marine ecosystems. However, historical abundance estimates derived from these population counts may be subject to unrecognised bias and uncertainty because of variable attendance of birds at breeding colonies and variable timing of past population surveys. We retrospectively accounted for detection bias in historical abundance estimates of the colonial, land-breeding Adélie penguin through an analysis of 222 historical abundance estimates from 81 breeding sites in east Antarctica. The published abundance estimates were de-constructed to retrieve the raw count data and then re-constructed by applying contemporary adjustment factors obtained from remotely operating time-lapse cameras. The re-construction process incorporated spatial and temporal variation in phenology and attendance by using data from cameras deployed at multiple sites over multiple years and propagating this uncertainty through to the final revised abundance estimates. Our re-constructed abundance estimates were consistently higher and more uncertain than published estimates. The re-constructed estimates alter the conclusions reached for some sites in east Antarctica in recent assessments of long-term Adélie penguin population change. Our approach is applicable to abundance data for a wide range of colonial, land-breeding marine species including other penguin species, flying seabirds and marine mammals. PMID:25909636

  5. Uncommon or cryptic? Challenges in estimating leopard seal abundance by conventional but state-of-the-art methods

    NASA Astrophysics Data System (ADS)

    Southwell, Colin; Paxton, Charles G. M.; Borchers, David; Boveng, Peter; Rogers, Tracey; de la Mare, William K.

    2008-04-01

    The method traditionally used to estimate pack-ice seal abundance employs sighting surveys from ships or aircraft to estimate the number of seals hauled out on the ice, combined with studies of haul-out behaviour to estimate the proportion of time spent on the ice. Application of this approach has been improved in recent times by developments in survey methodology and satellite technology that theoretically allow biases in the estimation of hauled-out abundance and haul-out behaviour to be accounted for that previously could not be addressed. A survey using these conventional but state-of-the-art methods was undertaken in the summer of 1999/2000 off east Antarctica between longitudes 64°E and 150°E to estimate the abundance of leopard ( Hydrurga leptonyx) and other pack-ice seal species. Because they are either uncommon or very cryptic, very few leopard seals were encountered despite a large survey effort. This presented challenges in both application of the methods and analysis of the data. Abundance estimates were derived using a number of plausible predictive models. The model considered as the most reliable returned best estimates of 7300 and 12,100 for definite and definite plus probable leopard seal sightings, respectively, with 95% confidence intervals of 3700-14,500 and 7100-23,400. These estimates are likely to be negatively biased and should be treated as minimum estimates only.

  6. Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry.

    PubMed

    Ahrné, Erik; Martinez-Segura, Amalia; Syed, Afzal Pasha; Vina-Vilaseca, Arnau; Gruber, Andreas J; Marguerat, Samuel; Schmidt, Alexander

    2015-09-01

    The generation of dynamic models of biological processes critically depends on the determination of precise cellular concentrations of biomolecules. Measurements of system-wide absolute protein levels are particularly valuable information in systems biology. Recently, mass spectrometry based proteomics approaches have been developed to estimate protein concentrations on a proteome-wide scale. However, for very complex proteomes, fractionation steps are required, increasing samples number and instrument analysis time. As a result, the number of full proteomes that can be routinely analyzed is limited. Here we combined absolute quantification strategies with the multiplexing capabilities of isobaric tandem mass tags to determine cellular protein abundances in a high throughput and proteome-wide scale even for highly complex biological systems, such as a whole human cell line. We generated two independent data sets to demonstrate the power of the approach regarding sample throughput, dynamic range, quantitative precision and accuracy as well as proteome coverage in comparison to existing mass spectrometry based strategies.

  7. Trap Array Configuration Influences Estimates and Precision of Black Bear Density and Abundance

    PubMed Central

    Wilton, Clay M.; Puckett, Emily E.; Beringer, Jeff; Gardner, Beth; Eggert, Lori S.; Belant, Jerrold L.

    2014-01-01

    Spatial capture-recapture (SCR) models have advanced our ability to estimate population density for wide ranging animals by explicitly incorporating individual movement. Though these models are more robust to various spatial sampling designs, few studies have empirically tested different large-scale trap configurations using SCR models. We investigated how extent of trap coverage and trap spacing affects precision and accuracy of SCR parameters, implementing models using the R package secr. We tested two trapping scenarios, one spatially extensive and one intensive, using black bear (Ursus americanus) DNA data from hair snare arrays in south-central Missouri, USA. We also examined the influence that adding a second, lower barbed-wire strand to snares had on quantity and spatial distribution of detections. We simulated trapping data to test bias in density estimates of each configuration under a range of density and detection parameter values. Field data showed that using multiple arrays with intensive snare coverage produced more detections of more individuals than extensive coverage. Consequently, density and detection parameters were more precise for the intensive design. Density was estimated as 1.7 bears per 100 km2 and was 5.5 times greater than that under extensive sampling. Abundance was 279 (95% CI = 193–406) bears in the 16,812 km2 study area. Excluding detections from the lower strand resulted in the loss of 35 detections, 14 unique bears, and the largest recorded movement between snares. All simulations showed low bias for density under both configurations. Results demonstrated that in low density populations with non-uniform distribution of population density, optimizing the tradeoff among snare spacing, coverage, and sample size is of critical importance to estimating parameters with high precision and accuracy. With limited resources, allocating available traps to multiple arrays with intensive trap spacing increased the amount of information

  8. Use of miniroutes and Breeding Bird Survey data to estimate abundance

    USGS Publications Warehouse

    Robbins, C.S.; Dowell, B.A.

    1986-01-01

    1. Information on relative abundance is easily obtained and adds greatly to the value of an atlas project. 2. The Breeding Bird Survey (BBS) provides annual counts (birds per 50 roadside stops) that can be used to: (1) map relative abundance by physiographic region within a state or province, (2) map relative abundance on a more local scale by using results from individual routes, or (3) compute estimates of total state populations of a species. Where BBS coverage is too scanty to permit mapping, extra temporary routes may be established to provide additional information for the atlas. Or, if continuing coverage is anticipated, additional permanent random routes can be assigned by the U. S. Fish and Wildlife Service. 3. Miniroutes of 15 or more stops can be established in individual atlas blocks to serve the dual purposes of providing efficient uniform coverage and providing information on relative abundance. Miniroutes can also be extracted from BBS routes to supplement special atlas coverage, or vice versa; but the data from the BBS will not be confined to individual atlas blocks. 4. Advantages of 15- or 20-stop Miniroutes over 25-stop Miniroutes are several: the ability to do two per morning and the lower variability among M1niroute results. Also, many 5-km atlas blocks do not have enough secondary roads to accommodate 25 stops at one-half mile intervals. Disadvantages of 15-stop Miniroutes starting at sunrise are the smaller numbers of birds recorded, missing of the very productive dawn chorus period (Robbins 1981), and missing crepuscular species (rails, woodcock, owls, and goatsuckers). 5. Advantages of recording counts of individuals rather than checking only species presence at Miniroute stops are that: (1) relative abundance can be mapped rather than frequency only (a measure of frequency is already available in the number of blocks recording each species); (2) population change can be measured over a period of years when the next atlas is made; and (3

  9. Acoustic estimates of abundance and distribution of spawning lake trout on Sheboygan Reef in Lake Michigan

    USGS Publications Warehouse

    Warner, D.M.; Claramunt, R.M.; Janssen, J.; Jude, D.J.; Wattrus, N.

    2009-01-01

    Efforts to restore self-sustaining lake trout (Salvelinus namaycush) populations in the Laurentian Great Lakes have had widespread success in Lake Superior; but in other Great Lakes, populations of lake trout are maintained by stocking. Recruitment bottlenecks may be present at a number of stages of the reproduction process. To study eggs and fry, it is necessary to identify spawning locations, which is difficult in deep water. Acoustic sampling can be used to rapidly locate aggregations of fish (like spawning lake trout), describe their distribution, and estimate their abundance. To assess these capabilities for application to lake trout, we conducted an acoustic survey covering 22 km2 at Sheboygan Reef, a deep reef (<40 m summit) in southern Lake Michigan during fall 2005. Data collected with remotely operated vehicles (ROV) confirmed that fish were large lake trout, that lake trout were 1–2 m above bottom, and that spawning took place over specific habitat. Lake trout density exhibited a high degree of spatial structure (autocorrelation) up to a range of ~190 m, and highest lake trout and egg densities occurred over rough substrates (rubble and cobble) at the shallowest depths sampled (36–42 m). Mean lake trout density in the area surveyed (~2190 ha) was 5.8 fish/ha and the area surveyed contained an estimated 9500–16,000 large lake trout. Spatial aggregation in lake trout densities, similarity of depths and substrates at which high lake trout and egg densities occurred, and relatively low uncertainty in the lake trout density estimate indicate that acoustic sampling can be a useful complement to other sampling tools used in lake trout restoration research.

  10. Accounting for Subgroup Structure in Line-Transect Abundance Estimates of False Killer Whales (Pseudorca crassidens) in Hawaiian Waters

    PubMed Central

    Bradford, Amanda L.; Forney, Karin A.; Oleson, Erin M.; Barlow, Jay

    2014-01-01

    For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai’i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479–5,030) and 552 (CV = 1.09; 95% CI = 97–3

  11. Accounting for subgroup structure in line-transect abundance estimates of false killer whales (Pseudorca crassidens) in Hawaiian waters.

    PubMed

    Bradford, Amanda L; Forney, Karin A; Oleson, Erin M; Barlow, Jay

    2014-01-01

    For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai'i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479-5,030) and 552 (CV = 1.09; 95% CI = 97

  12. Accounting for subgroup structure in line-transect abundance estimates of false killer whales (Pseudorca crassidens) in Hawaiian waters.

    PubMed

    Bradford, Amanda L; Forney, Karin A; Oleson, Erin M; Barlow, Jay

    2014-01-01

    For biological populations that form aggregations (or clusters) of individuals, cluster size is an important parameter in line-transect abundance estimation and should be accurately measured. Cluster size in cetaceans has traditionally been represented as the total number of individuals in a group, but group size may be underestimated if group members are spatially diffuse. Groups of false killer whales (Pseudorca crassidens) can comprise numerous subgroups that are dispersed over tens of kilometers, leading to a spatial mismatch between a detected group and the theoretical framework of line-transect analysis. Three stocks of false killer whales are found within the U.S. Exclusive Economic Zone of the Hawaiian Islands (Hawaiian EEZ): an insular main Hawaiian Islands stock, a pelagic stock, and a Northwestern Hawaiian Islands (NWHI) stock. A ship-based line-transect survey of the Hawaiian EEZ was conducted in the summer and fall of 2010, resulting in six systematic-effort visual sightings of pelagic (n = 5) and NWHI (n = 1) false killer whale groups. The maximum number and spatial extent of subgroups per sighting was 18 subgroups and 35 km, respectively. These sightings were combined with data from similar previous surveys and analyzed within the conventional line-transect estimation framework. The detection function, mean cluster size, and encounter rate were estimated separately to appropriately incorporate data collected using different methods. Unlike previous line-transect analyses of cetaceans, subgroups were treated as the analytical cluster instead of groups because subgroups better conform to the specifications of line-transect theory. Bootstrap values (n = 5,000) of the line-transect parameters were randomly combined to estimate the variance of stock-specific abundance estimates. Hawai'i pelagic and NWHI false killer whales were estimated to number 1,552 (CV = 0.66; 95% CI = 479-5,030) and 552 (CV = 1.09; 95% CI = 97

  13. New method for estimating bacterial cell abundances in natural samples by use of sublimation

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Cleaves, H. James; Schubert, Michael; Aubrey, Andrew; Bada, Jeffrey L.

    2004-01-01

    We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500 degrees C for several seconds under reduced pressure. The sublimate was collected on a cold finger, and the amount of adenine released from the samples was then determined by high-performance liquid chromatography with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from approximately 10(5) to 10(9) E. coli cell equivalents per gram. For most of these samples, the sublimation-based cell counts were in agreement with total bacterial counts obtained by traditional DAPI (4,6-diamidino-2-phenylindole) staining.

  14. New method for estimating bacterial cell abundances in natural samples by use of sublimation.

    PubMed

    Glavin, Daniel P; Cleaves, H James; Schubert, Michael; Aubrey, Andrew; Bada, Jeffrey L

    2004-10-01

    We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500 degrees C for several seconds under reduced pressure. The sublimate was collected on a cold finger, and the amount of adenine released from the samples was then determined by high-performance liquid chromatography with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from approximately 10(5) to 10(9) E. coli cell equivalents per gram. For most of these samples, the sublimation-based cell counts were in agreement with total bacterial counts obtained by traditional DAPI (4,6-diamidino-2-phenylindole) staining.

  15. \\Space: A new code to estimate \\temp, \\logg, and elemental abundances

    NASA Astrophysics Data System (ADS)

    Boeche, C.

    2016-09-01

    \\Space is a FORTRAN95 code that derives stellar parameters and elemental abundances from stellar spectra. To derive these parameters, \\Space does not measure equivalent widths of lines nor it uses templates of synthetic spectra, but it employs a new method based on a library of General Curve-Of-Growths. To date \\Space works on the wavelength range 5212-6860 Å and 8400-8921 Å, and at the spectral resolution R=2000-20000. Extensions of these limits are possible. \\Space is a highly automated code suitable for application to large spectroscopic surveys. A web front end to this service is publicly available at http://dc.g-vo.org/SP_ACE together with the library and the binary code.

  16. RVC-CAL library for endmember and abundance estimation in hyperspectral image analysis

    NASA Astrophysics Data System (ADS)

    Lazcano López, R.; Madroñal Quintín, D.; Juárez Martínez, E.; Sanz Álvaro, C.

    2015-10-01

    Hyperspectral imaging (HI) collects information from across the electromagnetic spectrum, covering a wide range of wavelengths. Although this technology was initially developed for remote sensing and earth observation, its multiple advantages - such as high spectral resolution - led to its application in other fields, as cancer detection. However, this new field has shown specific requirements; for instance, it needs to accomplish strong time specifications, since all the potential applications - like surgical guidance or in vivo tumor detection - imply real-time requisites. Achieving this time requirements is a great challenge, as hyperspectral images generate extremely high volumes of data to process. Thus, some new research lines are studying new processing techniques, and the most relevant ones are related to system parallelization. In that line, this paper describes the construction of a new hyperspectral processing library for RVC-CAL language, which is specifically designed for multimedia applications and allows multithreading compilation and system parallelization. This paper presents the development of the required library functions to implement two of the four stages of the hyperspectral imaging processing chain--endmember and abundances estimation. The results obtained show that the library achieves speedups of 30%, approximately, comparing to an existing software of hyperspectral images analysis; concretely, the endmember estimation step reaches an average speedup of 27.6%, which saves almost 8 seconds in the execution time. It also shows the existence of some bottlenecks, as the communication interfaces among the different actors due to the volume of data to transfer. Finally, it is shown that the library considerably simplifies the implementation process. Thus, experimental results show the potential of a RVC-CAL library for analyzing hyperspectral images in real-time, as it provides enough resources to study the system performance.

  17. The effect of animal movement on line transect estimates of abundance.

    PubMed

    Glennie, Richard; Buckland, Stephen T; Thomas, Len

    2015-01-01

    Line transect sampling is a distance sampling method for estimating the abundance of wild animal populations. One key assumption of this method is that all animals are detected at their initial location. Animal movement independent of the transect and observer can thus cause substantial bias. We present an analytic expression for this bias when detection within the transect is certain (strip transect sampling) and use simulation to quantify bias when detection falls off with distance from the line (line transect sampling). We also explore the non-linear relationship between bias, detection, and animal movement by varying detectability and movement type. We consider animals that move in randomly orientated straight lines, which provides an upper bound on bias, and animals that are constrained to a home range of random radius. We find that bias is reduced when animal movement is constrained, and bias is considerably smaller in line transect sampling than strip transect sampling provided that mean animal speed is less than observer speed. By contrast, when mean animal speed exceeds observer speed the bias in line transect sampling becomes comparable with, and may exceed, that of strip transect sampling. Bias from independent animal movement is reduced by the observer searching further perpendicular to the transect, searching a shorter distance ahead and by ignoring animals that may overtake the observer from behind. However, when animals move in response to the observer, the standard practice of searching further ahead should continue as the bias from responsive movement is often greater than that from independent movement.

  18. Bayesian network for estimating the interaction between ecological health and waterfowl abundance

    NASA Astrophysics Data System (ADS)

    Teng, Te Hui; Fang, Wei Ta; Yu, Hwa Lung

    2013-04-01

    The serious decrease of biodiversity which is mainly induced by Habitat disappear is important issue of species field and in the world. The study area chooses Tauyuan County at subtropical area because of the most artificial farm ponds in Taiwan where the total area includes 27 km2. The effectiveness of these ponds is storage and irrigation and also supplies all kinds of environment like refuges for migratory birds, especially for water birds. Due to human development, farm ponds in this city not only suffer from largely disappear recent year, but also lead to the habitat and bird species reduce. Biological research usually contains incomplete and uncertain information, therefore, this study adopts Bayesian Network model to analyze interaction between land use and water birds. The habitat parameters include elevation, urbanization, building area, farm area, reconsolidation, forest area, irrigation area, farm pond area and lawn area; the biological factors have reproductive capacity, habitat condition, hydrological condition and food source. Using this structure can estimate the interaction of spatiotemporal abundance distribution between habitat parameter and biological parameter. In addition, the former results can define all the reasonable relationship of all hidden states and provide decision-makers with reasonable evaluation.

  19. Mark-recapture and mark-resight methods for estimating abundance with remote cameras: a carnivore case study.

    PubMed

    Alonso, Robert S; McClintock, Brett T; Lyren, Lisa M; Boydston, Erin E; Crooks, Kevin R

    2015-01-01

    Abundance estimation of carnivore populations is difficult and has prompted the use of non-invasive detection methods, such as remotely-triggered cameras, to collect data. To analyze photo data, studies focusing on carnivores with unique pelage patterns have utilized a mark-recapture framework and studies of carnivores without unique pelage patterns have used a mark-resight framework. We compared mark-resight and mark-recapture estimation methods to estimate bobcat (Lynx rufus) population sizes, which motivated the development of a new "hybrid" mark-resight model as an alternative to traditional methods. We deployed a sampling grid of 30 cameras throughout the urban southern California study area. Additionally, we physically captured and marked a subset of the bobcat population with GPS telemetry collars. Since we could identify individual bobcats with photos of unique pelage patterns and a subset of the population was physically marked, we were able to use traditional mark-recapture and mark-resight methods, as well as the new "hybrid" mark-resight model we developed to estimate bobcat abundance. We recorded 109 bobcat photos during 4,669 camera nights and physically marked 27 bobcats with GPS telemetry collars. Abundance estimates produced by the traditional mark-recapture, traditional mark-resight, and "hybrid" mark-resight methods were similar, however precision differed depending on the models used. Traditional mark-recapture and mark-resight estimates were relatively imprecise with percent confidence interval lengths exceeding 100% of point estimates. Hybrid mark-resight models produced better precision with percent confidence intervals not exceeding 57%. The increased precision of the hybrid mark-resight method stems from utilizing the complete encounter histories of physically marked individuals (including those never detected by a camera trap) and the encounter histories of naturally marked individuals detected at camera traps. This new estimator may be

  20. Mark-recapture and mark-resight methods for estimating abundance with remote cameras: a carnivore case study.

    PubMed

    Alonso, Robert S; McClintock, Brett T; Lyren, Lisa M; Boydston, Erin E; Crooks, Kevin R

    2015-01-01

    Abundance estimation of carnivore populations is difficult and has prompted the use of non-invasive detection methods, such as remotely-triggered cameras, to collect data. To analyze photo data, studies focusing on carnivores with unique pelage patterns have utilized a mark-recapture framework and studies of carnivores without unique pelage patterns have used a mark-resight framework. We compared mark-resight and mark-recapture estimation methods to estimate bobcat (Lynx rufus) population sizes, which motivated the development of a new "hybrid" mark-resight model as an alternative to traditional methods. We deployed a sampling grid of 30 cameras throughout the urban southern California study area. Additionally, we physically captured and marked a subset of the bobcat population with GPS telemetry collars. Since we could identify individual bobcats with photos of unique pelage patterns and a subset of the population was physically marked, we were able to use traditional mark-recapture and mark-resight methods, as well as the new "hybrid" mark-resight model we developed to estimate bobcat abundance. We recorded 109 bobcat photos during 4,669 camera nights and physically marked 27 bobcats with GPS telemetry collars. Abundance estimates produced by the traditional mark-recapture, traditional mark-resight, and "hybrid" mark-resight methods were similar, however precision differed depending on the models used. Traditional mark-recapture and mark-resight estimates were relatively imprecise with percent confidence interval lengths exceeding 100% of point estimates. Hybrid mark-resight models produced better precision with percent confidence intervals not exceeding 57%. The increased precision of the hybrid mark-resight method stems from utilizing the complete encounter histories of physically marked individuals (including those never detected by a camera trap) and the encounter histories of naturally marked individuals detected at camera traps. This new estimator may be

  1. Mark-recapture and mark-resight methods for estimating abundance with remote cameras: a carnivore case study

    USGS Publications Warehouse

    Alanso, Robert S.; McClintock, Brett T.; Lyren, Lisa M.; Boydston, Erin E.; Crooks, Kevin R.

    2015-01-01

    Abundance estimation of carnivore populations is difficult and has prompted the use of non-invasive detection methods, such as remotely-triggered cameras, to collect data. To analyze photo data, studies focusing on carnivores with unique pelage patterns have utilized a mark-recapture framework and studies of carnivores without unique pelage patterns have used a mark-resight framework. We compared mark-resight and mark-recapture estimation methods to estimate bobcat (Lynx rufus) population sizes, which motivated the development of a new "hybrid" mark-resight model as an alternative to traditional methods. We deployed a sampling grid of 30 cameras throughout the urban southern California study area. Additionally, we physically captured and marked a subset of the bobcat population with GPS telemetry collars. Since we could identify individual bobcats with photos of unique pelage patterns and a subset of the population was physically marked, we were able to use traditional mark-recapture and mark-resight methods, as well as the new “hybrid” mark-resight model we developed to estimate bobcat abundance. We recorded 109 bobcat photos during 4,669 camera nights and physically marked 27 bobcats with GPS telemetry collars. Abundance estimates produced by the traditional mark-recapture, traditional mark-resight, and “hybrid” mark-resight methods were similar, however precision differed depending on the models used. Traditional mark-recapture and mark-resight estimates were relatively imprecise with percent confidence interval lengths exceeding 100% of point estimates. Hybrid mark-resight models produced better precision with percent confidence intervals not exceeding 57%. The increased precision of the hybrid mark-resight method stems from utilizing the complete encounter histories of physically marked individuals (including those never detected by a camera trap) and the encounter histories of naturally marked individuals detected at camera traps. This new estimator

  2. Estimating vocal repertoire size is like collecting coupons: a theoretical framework with heterogeneity in signal abundance.

    PubMed

    Kershenbaum, Arik; Freeberg, Todd M; Gammon, David E

    2015-05-21

    Vocal repertoire size is an important behavioural measure in songbirds and mammals with complex vocal communication systems, and has traditionally been used as an indicator of individual fitness, cognitive ability, and social structure. Estimates of asymptotic repertoire size have typically been made using curve fitting techniques. However, the exponential model usually applied in these techniques has never been provided with a theoretical justification based on probability theory, and the model has led to inaccurate estimates. We derived the precise expression for the expected number of distinct signal types observed for a fixed sampling effort: a variation of what is known in the statistical literature as the "Coupon Collector׳s problem". We used empirical data from three species (northern mockingbird, Carolina chickadee, and rock hyrax) to assess the performance of the Coupon Collector model compared to commonly used techniques, such as exponential fitting and repertoire enumeration, and also tested the different models against simulated artificial data sets with the statistical properties of the empirical data. We found that when signal probabilities are dissimilar, the Coupon Collector model provides far more accurate estimates of repertoire size than traditional techniques. Enumeration and exponential curve fitting greatly underestimated repertoire size, despite appearing to have reached saturation. Application of the Coupon Collector model can generate more accurate estimates of repertoire size than the commonly used exponential model of repertoire discovery, and could go a long way towards re-establishing repertoire size as a useful indicator in animal communication research.

  3. A New Method for Estimating Bacterial Abundances in Natural Samples using Sublimation

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Cleaves, H. James; Schubert, Michael; Aubrey, Andrew; Bada, Jeffrey L.

    2004-01-01

    We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert were heated to a temperature of 500 C for several seconds under reduced pressure. The sublimate was collected on a cold finger and the amount of adenine released from the samples then determined by high performance liquid chromatography (HPLC) with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from approx. l0(exp 5) to l0(exp 9) E. coli cell equivalents per gram. For most of these samples, the sublimation based cell counts were in agreement with total bacterial counts obtained by traditional DAPI staining. The simplicity and robustness of the sublimation technique compared to the DAPI staining method makes this approach particularly attractive for use by spacecraft instrumentation. NASA is currently planning to send a lander to Mars in 2009 in order to assess whether or not organic compounds, especially those that might be associated with life, are present in Martian surface samples. Based on our analyses of the Atacama Desert soil samples, several million bacterial cells per gam of Martian soil should be detectable using this sublimation technique.

  4. Estimated abundance of wild burros surveyed on Bureau of Land Management Lands in 2014

    USGS Publications Warehouse

    Griffin, Paul C.

    2015-01-01

    The Bureau of Land Management (BLM) requires accurate estimates of the numbers of wild horses (Equus ferus caballus) and burros (Equus asinus) living on the lands it manages. For over ten years, BLM in Arizona has used the simultaneous double-observer method of recording wild burros during aerial surveys and has reported population estimates for those surveys that come from two formulations of a Lincoln-Petersen type of analysis (Graham and Bell, 1989). In this report, I provide those same two types of burro population analysis for 2014 aerial survey data from six herd management areas (HMAs) in Arizona, California, Nevada, and Utah. I also provide burro population estimates based on a different form of simultaneous double-observer analysis, now in widespread use for wild horse surveys that takes into account the potential effects on detection probability of sighting covariates including group size, distance, vegetative cover, and other factors (Huggins, 1989, 1991). The true number of burros present in the six areas surveyed was not known, so population estimates made with these three types of analyses cannot be directly tested for accuracy in this report. I discuss theoretical reasons why the Huggins (1989, 1991) type of analysis should provide less biased estimates of population size than the Lincoln-Petersen analyses and why estimates from all forms of double-observer analyses are likely to be lower than the true number of animals present in the surveyed areas. I note reasons why I suggest using burro observations made at all available distances in analyses, not only those within 200 meters of the flight path. For all analytical methods, small sample sizes of observed groups can be problematic, but that sample size can be increased over time for Huggins (1989, 1991) analyses by pooling observations. I note ways by which burro population estimates could be tested for accuracy when there are radio-collared animals in the population or when there are simultaneous

  5. A likelihood framework for joint estimation of salmon abundance and migratory timing using telemetric mark-recapture

    USGS Publications Warehouse

    Bromaghin, Jeffrey; Gates, Kenneth S.; Palmer, Douglas E.

    2010-01-01

    Many fisheries for Pacific salmon Oncorhynchus spp. are actively managed to meet escapement goal objectives. In fisheries where the demand for surplus production is high, an extensive assessment program is needed to achieve the opposing objectives of allowing adequate escapement and fully exploiting the available surplus. Knowledge of abundance is a critical element of such assessment programs. Abundance estimation using mark—recapture experiments in combination with telemetry has become common in recent years, particularly within Alaskan river systems. Fish are typically captured and marked in the lower river while migrating in aggregations of individuals from multiple populations. Recapture data are obtained using telemetry receivers that are co-located with abundance assessment projects near spawning areas, which provide large sample sizes and information on population-specific mark rates. When recapture data are obtained from multiple populations, unequal mark rates may reflect a violation of the assumption of homogeneous capture probabilities. A common analytical strategy is to test the hypothesis that mark rates are homogeneous and combine all recapture data if the test is not significant. However, mark rates are often low, and a test of homogeneity may lack sufficient power to detect meaningful differences among populations. In addition, differences among mark rates may provide information that could be exploited during parameter estimation. We present a temporally stratified mark—recapture model that permits capture probabilities and migratory timing through the capture area to vary among strata. Abundance information obtained from a subset of populations after the populations have segregated for spawning is jointly modeled with telemetry distribution data by use of a likelihood function. Maximization of the likelihood produces estimates of the abundance and timing of individual populations migrating through the capture area, thus yielding

  6. Oxygen abundance distributions in six late-type galaxies based on SALT spectra of H II regions

    NASA Astrophysics Data System (ADS)

    Zinchenko, I. A.; Kniazev, A. Y.; Grebel, E. K.; Pilyugin, L. S.

    2015-10-01

    Spectra of 34 H ii regions in the late-type galaxies NGC 1087, NGC 2967, NGC 3023, NGC 4030, NGC 4123, and NGC 4517A were observed with the South African Large Telescope (SALT). In all 34 H ii regions, oxygen abundances were determined through the "counterpart" method (C method). Additionally, in two H ii regions in which we detected auroral lines, we measured oxygen abundances with the classic Te method. We also estimated the abundances in our H ii regions using the O3N2 and N2 calibrations and compared those with the C-based abundances. With these data, we examined the radial abundance distributions in the disks of our target galaxies. We derived surface-brightness profiles and other characteristics of the disks (the surface brightness at the disk center and the disk scale length) in three photometric bands for each galaxy using publicly available photometric imaging data. The radial distributions of the oxygen abundances predicted by the relation between abundance and disk surface brightness in the W1 band obtained for spiral galaxies in our previous study are close to the radial distributions of the oxygen abundances determined from the analysis of the emission line spectra for four galaxies where this relation is applicable. Hence, when the surface-brightness profile of a late-type galaxy is known, this parametric relation can be used to estimate the likely present-day oxygen abundance in the disk of the galaxy. Based on observations made with the Southern African Large Telescope, programs 2012-1-RSA_OTH-001, 2012-2-RSA_OTH-003 and 2013-1-RSA_OTH-005.

  7. Asteroseismic estimate of helium abundance of a solar analog binary system

    SciTech Connect

    Verma, Kuldeep; Antia, H. M.; Faria, João P.; Monteiro, Mário J. P. F. G.; Basu, Sarbani; Mazumdar, Anwesh; Appourchaux, Thierry; Chaplin, William J.; García, Rafael A.

    2014-08-01

    16 Cyg A and B are among the brightest stars observed by Kepler. What makes these stars more interesting is that they are solar analogs. 16 Cyg A and B exhibit solar-like oscillations. In this work we use oscillation frequencies obtained using 2.5 yr of Kepler data to determine the current helium abundance of these stars. For this we use the fact that the helium ionization zone leaves a signature on the oscillation frequencies and that this signature can be calibrated to determine the helium abundance of that layer. By calibrating the signature of the helium ionization zone against models of known helium abundance, the helium abundance in the envelope of 16 Cyg A is found to lie in the range of 0.231 to 0.251 and that of 16 Cyg B lies in the range of 0.218 to 0.266.

  8. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree.

    PubMed

    Qiu, Yu-Qing; Tian, Xue; Zhang, Shihua

    2015-01-01

    Metagenomic research uses sequencing technologies to investigate the genetic biodiversity of microbiomes presented in various ecosystems or animal tissues. The composition of a microbial community is highly associated with the environment in which the organisms exist. As large amount of sequencing short reads of microorganism genomes obtained, accurately estimating the abundance of microorganisms within a metagenomic sample is becoming an increasing challenge in bioinformatics. In this paper, we describe a hierarchical taxonomy tree-based mixture model (HTTMM) for estimating the abundance of taxon within a microbial community by incorporating the structure of the taxonomy tree. In this model, genome-specific short reads and homologous short reads among genomes can be distinguished and represented by leaf and intermediate nodes in the taxonomy tree, respectively. We adopt an expectation-maximization algorithm to solve this model. Using simulated and real-world data, we demonstrate that the proposed method is superior to both flat mixture model and lowest common ancestry-based methods. Moreover, this model can reveal previously unaddressed homologous genomes.

  9. [A Method to Estimate Metal Abundance from Stellar Spectra Using Ca Line Index].

    PubMed

    Pan, Jing-chang; Luo, A-li; Li, Xiang-ru; Wei, Peng

    2015-09-01

    This paper presents a method to estimate stellar metallicity based on BP neural network and Ca line index. This method trains a BP ANN model from SDSS/SEGUE stellar spectra and parameters provided by SSPP. The values of Teff and the line index of Ca lines are the input of network while the [Fe/H] values are the oputput of the network. A set of samples are resampled from the set of all and then a network model is trained. The network can be used to predict the stellar metallicity from low-resolution spsectra. The experiment shows that the proposed method can accurately and effectively measure the [Fe/H] from the stellar spectra. PMID:26669184

  10. The relative accuracy of standard estimators for macrofaunal abundance and species richness derived from selected intertidal transect designs used to sample exposed sandy beaches

    NASA Astrophysics Data System (ADS)

    Schoeman, transect designs used to sample exposed sandy beaches D. S.; Wheeler, M.; Wait, M.

    2003-10-01

    In order to ensure that patterns detected in field samples reflect real ecological processes rather than methodological idiosyncrasies, it is important that researchers attempt to understand the consequences of the sampling and analytical designs that they select. This is especially true for sandy beach ecology, which has lagged somewhat behind ecological studies of other intertidal habitats. This paper investigates the performance of routine estimators of macrofaunal abundance and species richness, which are variables that have been widely used to infer predictable patterns of biodiversity across a gradient of beach types. To do this, a total of six shore-normal strip transects were sampled on three exposed, oceanic sandy beaches in the Eastern Cape, South Africa. These transects comprised contiguous quadrats arranged linearly between the spring high and low water marks. Using simple Monte Carlo simulation techniques, data collected from the strip transects were used to assess the accuracy of parameter estimates from different sampling strategies relative to their true values (macrofaunal abundance ranged 595-1369 individuals transect -1; species richness ranged 12-21 species transect -1). Results indicated that estimates from the various transect methods performed in a similar manner both within beaches and among beaches. Estimates for macrofaunal abundance tended to be negatively biased, especially at levels of sampling effort most commonly reported in the literature, and accuracy decreased with decreasing sampling effort. By the same token, estimates for species richness were always negatively biased and were also characterised by low precision. Furthermore, triplicate transects comprising a sampled area in the region of 4 m 2 (as has been previously recommended) are expected to miss more than 30% of the species that occur on the transect. Surprisingly, for both macrofaunal abundance and species richness, estimates based on data from transects sampling quadrats

  11. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic

    USGS Publications Warehouse

    Sillett, Scott T.; Chandler, Richard B.; Royle, J. Andrew; Kéry, Marc; Morrison, Scott A.

    2012-01-01

    Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural

  12. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic.

    PubMed

    Sillett, T Scott; Chandler, Richard B; Royle, J Andrew; Kery, Marc; Morrison, Scott A

    2012-10-01

    Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural

  13. Mark-Recapture and Mark-Resight Methods for Estimating Abundance with Remote Cameras: A Carnivore Case Study

    PubMed Central

    Alonso, Robert S.; McClintock, Brett T.; Lyren, Lisa M.; Boydston, Erin E.; Crooks, Kevin R.

    2015-01-01

    Abundance estimation of carnivore populations is difficult and has prompted the use of non-invasive detection methods, such as remotely-triggered cameras, to collect data. To analyze photo data, studies focusing on carnivores with unique pelage patterns have utilized a mark-recapture framework and studies of carnivores without unique pelage patterns have used a mark-resight framework. We compared mark-resight and mark-recapture estimation methods to estimate bobcat (Lynx rufus) population sizes, which motivated the development of a new "hybrid" mark-resight model as an alternative to traditional methods. We deployed a sampling grid of 30 cameras throughout the urban southern California study area. Additionally, we physically captured and marked a subset of the bobcat population with GPS telemetry collars. Since we could identify individual bobcats with photos of unique pelage patterns and a subset of the population was physically marked, we were able to use traditional mark-recapture and mark-resight methods, as well as the new “hybrid” mark-resight model we developed to estimate bobcat abundance. We recorded 109 bobcat photos during 4,669 camera nights and physically marked 27 bobcats with GPS telemetry collars. Abundance estimates produced by the traditional mark-recapture, traditional mark-resight, and “hybrid” mark-resight methods were similar, however precision differed depending on the models used. Traditional mark-recapture and mark-resight estimates were relatively imprecise with percent confidence interval lengths exceeding 100% of point estimates. Hybrid mark-resight models produced better precision with percent confidence intervals not exceeding 57%. The increased precision of the hybrid mark-resight method stems from utilizing the complete encounter histories of physically marked individuals (including those never detected by a camera trap) and the encounter histories of naturally marked individuals detected at camera traps. This new estimator

  14. Estimation of the Hydrogen Abundance in the Cabeus and Shoemaker Craters

    NASA Astrophysics Data System (ADS)

    Sanin, Anton; Mitrofanov, Igor; Litvak, Maxim; Boynton, William; Chin, Gordon; Evans, Larry; Garvin, James; Golovin, Dmitry; Harshman, Karl; Mcclanahan, Timothy; Malakhov, Alexey; Milikh, Gennady; Mokrousov, Maxim; Sagdeev, Roald; Starr, Richard

    2013-04-01

    The galactic cosmic rays produce in regolith high energy neutrons (with energies about 1 - 20 MeV). These neutrons are moderate to epithermal energies by multiple collisions with nuclei of regolith before they are able to escape from the surface and may be detected by a neutron detector on orbit. The leakage flux of epithermal neutrons depends on the concentration of hydrogen in the regolith, because more collisions with hydrogen nuclei lead to faster moderation and thermalization of neutrons before they can escape. Neutron spectrometer LEND (Lunar Exploration Neutron Detector) launched into lunar orbit onboard the Lunar Reconnaissance Orbiter (LRO) mission has a task to test the presence of a hydrogen bearing regolith in the lunar polar regions. Due to the neutron collimation module LEND can provide resolution ~10 km from 50 km orbit during mapping phase of LRO mission. In addition to the well-known reductions of epithermal neutron fluxes in both lunar polar regions poleward of 70°S and 70°N latitudes (observed by both Lunar Prospector Neutron Spectrometer and LEND) several local spots of epithermal neutron flux suppression in comparison with surrounding areas were found from analysis of LEND data. These suppressions mark enhanced content of hydrogen or water in the regolith. It was found that epithermal neutron flux from most of PSRs is not significantly different in comparison with neutron emissions from surrounding areas. Only PSRs in Cabeus and Shoemaker craters near the South pole show a significant suppression. On the other hand several spots of epithermal flux suppression were found completely or particularly outside of any large PSRs. We would like to present results of estimations of hydrogen concentration in regolith in South polar regions at vicinity of Cabeus and Shoemaker craters. These estimations are based on the analysis of LEND collimated detectors data accumulated from September 15, 2009 till December 20, 2012 and on numerical simulations of

  15. Bacterioplankton in antarctic ocean waters during late austral winter: abundance, frequency of dividing cells, and estimates of production.

    PubMed

    Hanson, R B; Shafer, D; Ryan, T; Pope, D H; Lowery, H K

    1983-05-01

    Bacterioplankton productivity in Antarctic waters of the eastern South Pacific Ocean and Drake Passage was estimated by direct counts and frequency of dividing cells (FDC). Total bacterioplankton assemblages were enumerated by epifluorescent microscopy. The experimentally determined relationship between in situ FDC and the potential instantaneous growth rate constant (mu) is best described by the regression equation ln mu = 0.081 FDC - 3.73. In the eastern South Pacific Ocean, bacterioplankton abundance (2 x 10 to 3.5 x 10 cells per ml) and FDC (11%) were highest at the Polar Front (Antarctic Convergence). North of the Subantarctic Front, abundance and FDC were between 1 x 10 to 2 x 10 cells per ml and 3 to 5%, respectively, and were vertically homogeneous to a depth of 600 m. In Drake Passage, abundance (10 x 10 cells per ml) and FDC (16%) were highest in waters south of the Polar Front and near the sea ice. Subantarctic waters in Drake Passage contained 4 x 10 cells per ml with 4 to 5% FDC. Instantaneous growth rate constants ranged between 0.029 and 0.088 h. Using estimates of potential mu and measured standing stocks, we estimated productivity to range from 0.62 mug of C per liter . day in the eastern South Pacific Ocean to 17.1 mug of C per liter . day in the Drake Passage near the sea ice. PMID:16346297

  16. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    PubMed

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains.

  17. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    PubMed

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains. PMID:22567089

  18. Use of portable antennas to estimate abundance of PIT-tagged fish in small streams: Factors affecting detection probability

    USGS Publications Warehouse

    O'Donnell, Matthew J.; Horton, Gregg E.; Letcher, Benjamin H.

    2010-01-01

    Portable passive integrated transponder (PIT) tag antenna systems can be valuable in providing reliable estimates of the abundance of tagged Atlantic salmon Salmo salar in small streams under a wide range of conditions. We developed and employed PIT tag antenna wand techniques in two controlled experiments and an additional case study to examine the factors that influenced our ability to estimate population size. We used Pollock's robust-design capture–mark–recapture model to obtain estimates of the probability of first detection (p), the probability of redetection (c), and abundance (N) in the two controlled experiments. First, we conducted an experiment in which tags were hidden in fixed locations. Although p and c varied among the three observers and among the three passes that each observer conducted, the estimates of N were identical to the true values and did not vary among observers. In the second experiment using free-swimming tagged fish, p and c varied among passes and time of day. Additionally, estimates of N varied between day and night and among age-classes but were within 10% of the true population size. In the case study, we used the Cormack–Jolly–Seber model to examine the variation in p, and we compared counts of tagged fish found with the antenna wand with counts collected via electrofishing. In that study, we found that although p varied for age-classes, sample dates, and time of day, antenna and electrofishing estimates of N were similar, indicating that population size can be reliably estimated via PIT tag antenna wands. However, factors such as the observer, time of day, age of fish, and stream discharge can influence the initial and subsequent detection probabilities.

  19. Constrained Maximum Likelihood Estimation of Relative Abundances of Protein Conformation in a Heterogeneous Mixture from Small Angle X-Ray Scattering Intensity Measurements

    PubMed Central

    Onuk, A. Emre; Akcakaya, Murat; Bardhan, Jaydeep P.; Erdogmus, Deniz; Brooks, Dana H.; Makowski, Lee

    2015-01-01

    In this paper, we describe a model for maximum likelihood estimation (MLE) of the relative abundances of different conformations of a protein in a heterogeneous mixture from small angle X-ray scattering (SAXS) intensities. To consider cases where the solution includes intermediate or unknown conformations, we develop a subset selection method based on k-means clustering and the Cramér-Rao bound on the mixture coefficient estimation error to find a sparse basis set that represents the space spanned by the measured SAXS intensities of the known conformations of a protein. Then, using the selected basis set and the assumptions on the model for the intensity measurements, we show that the MLE model can be expressed as a constrained convex optimization problem. Employing the adenylate kinase (ADK) protein and its known conformations as an example, and using Monte Carlo simulations, we demonstrate the performance of the proposed estimation scheme. Here, although we use 45 crystallographically determined experimental structures and we could generate many more using, for instance, molecular dynamics calculations, the clustering technique indicates that the data cannot support the determination of relative abundances for more than 5 conformations. The estimation of this maximum number of conformations is intrinsic to the methodology we have used here. PMID:26924916

  20. A visual survey technique for deep-water fishes: estimating anglerfish Lophius spp. abundance in closed areas.

    PubMed

    McIntyre, F D; Collie, N; Stewart, M; Scala, L; Fernandes, P G

    2013-10-01

    A visual survey technique was employed to estimate the abundance and distribution of anglerfish Lophius spp. in areas where destructive sampling methods, such as trawling, are unacceptable. To enable visual surveying at depths of over 300 m, a deep towed vehicle was developed equipped with video, lights and other sensors and was towed at speeds of up to 1·5 m s⁻¹ and altitudes of up to 10 m (from the seabed) to survey large areas of the seabed around the Rockall Bank in the north-west Atlantic Ocean. The system allowed for areas up to 125 000 m² to be surveyed, a substantial area comparable to that surveyed by demersal-trawl sampling. Lophius spp. densities ranged from 15 to 736 fish km⁻²; these are comparable to estimated Lophius spp. densities determined by trawl surveys in adjacent areas. Estimates of Lophius spp. abundance in the closed areas ranged between 99,855 and 176,887 for the time series considered (2007-2011). PMID:24090546

  1. Benthic flagellates and ciliates in fine freshwater sediments: Calibration of a live counting procedure and estimation of their abundances.

    PubMed

    Gasol, J M

    1993-05-01

    Despite the recognized importance of protozoans (flagellates and ciliates) as predators of bacteria, there are very few estimates of their abundance in fine sediments of freshwater lakes. This is due, in part, to the lack of a standard methodology. Because of the low concentration of protists in relation to particles, epifluorescence counts can not always be used. Instead, dilution followed by live counting was used to solve the masking by sediment particles. One to twenty μ1 sample aliquots were diluted with filtered lake water in a Palmer-Maloney counting slide. Four to eight replicates were sufficient to minimize the counting error, while minimizing effort. The method is highly replicable and could potentially be calibrated for different sediment types because sediment masking depends on the mean particle size of the sediment. When this method was applied in a survey of benthic sites in Quebec lakes, flagellate abundances were found to range from 100 to 180,000 cells ml(-1), while ciliate numbers ranged from 26 to 11,000 cells ml(-1). Bacteria are 105 to 10(7) times more abundant than protists and, thus, the impact of these protists on sediment bacterial dynamics is likely to be minimal.

  2. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.

    PubMed

    Nayfach, Stephen; Bradley, Patrick H; Wyman, Stacia K; Laurent, Timothy J; Williams, Alex; Eisen, Jonathan A; Pollard, Katherine S; Sharpton, Thomas J

    2015-11-01

    Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn's disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. PMID:26565399

  3. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

    PubMed Central

    Nayfach, Stephen; Bradley, Patrick H.; Wyman, Stacia K.; Laurent, Timothy J.; Williams, Alex; Eisen, Jonathan A.; Pollard, Katherine S.; Sharpton, Thomas J.

    2015-01-01

    Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn’s disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. PMID:26565399

  4. Inconsistencies in Estimates of Near-Surface Water Abundance are Resolved by the Volcanic Origin of Martian Outflow Channels

    NASA Astrophysics Data System (ADS)

    Leverington, D. W.

    2010-12-01

    A long-standing problem in the study of Mars has been the incompatibility between 1) geochemically-based expectations for low near-surface water abundance; and 2) the large water volumes required of aqueous interpretations of the outflow channels. On the basis of the compositions of SNC meteorites and the current Martian atmosphere, the early water content of Mars has been estimated by several groups to be equivalent to a global layer of ~6 to 200 m thickness, only a proportion of which would have been outgassed to the near-surface environment. In contrast, previous estimates of the minimum near-surface water volume required if the Martian outflow channels formed through aqueous mechanisms are equivalent to a global water layer of 300-500 m thickness, assuming unrealistic sediment loads of 40% and an absence of infiltration or evaporation during flow, and ignoring volumes such as those required of hypothesized cryospheric seals. Under more realistic outflow scenarios, required volumes are likely to be equivalent to an Earth-like global layer of at least several kilometers thickness, even assuming the past operation of a vigorous hydrological cycle. Some workers have suggested that disagreement between geochemical and geomorphological estimates of near-surface water volumes on Mars might be resolved if the amount of water outgassed by the planet was greater than expected, or if especially large volumes of water were contributed to the surface by impacts of volatile-rich bodies late in the heavy bombardment of Mars. However, resolution is instead likely to follow from changes in perspectives regarding outflow channel origins. Though most workers currently accept aqueous interpretations, recent work has indicated that the outflow channels of Mars are very likely to be the products of volcanic processes involving incision by low-viscosity mafic lavas. Volcanic interpretations are consistent with numerous considerations, including the absence of channel deposits of

  5. Field trials of line transect methods applied to estimation of desert tortoise abundance

    USGS Publications Warehouse

    Anderson, David R.; Burnham, Kenneth P.; Lubow, Bruce C.; Thomas, L. E. N.; Corn, Paul Stephen; Medica, Philip A.; Marlow, R.W.

    2001-01-01

    We examine the degree to which field observers can meet the assumptions underlying line transect sampling to monitor populations of desert tortoises (Gopherus agassizii). We present the results of 2 field trials using artificial tortoise models in 3 size classes. The trials were conducted on 2 occasions on an area south of Las Vegas, Nevada, where the density of the test population was known. In the first trials, conducted largely by experienced biologists who had been involved in tortoise surveys for many years, the density of adult tortoise models was well estimated (-3.9% bias), while the bias was higher (-20%) for subadult tortoise models. The bias for combined data was -12.0%. The bias was largely attributed to the failure to detect all tortoise models on or near the transect centerline. The second trials were conducted with a group of largely inexperienced student volunteers and used somewhat different searching methods, and the results were similar to the first trials. Estimated combined density of subadult and adult tortoise models had a negative bias (-7.3%), again attributable to failure to detect some models on or near the centerline. Experience in desert tortoise biology, either comparing the first and second trials or in the second trial with 2 experienced biologists versus 16 novices, did not have an apparent effect on the quality of the data or the accuracy of the estimates. Observer training, specific to line transect sampling, and field testing are important components of a reliable survey. Line transect sampling represents a viable method for large-scale monitoring of populations of desert tortoise; however, field protocol must be improved to assure the key assumptions are met.

  6. Estimating number of species and relative abundances in stream-fish communities: effects of sampling effort and discontinuous spatial distributions

    USGS Publications Warehouse

    Angermeier, Paul L.; Smogor, Roy A.

    1995-01-01

    We sampled fishes and measured microhabitat in series of contiguous habitat units (riffles, runs, pools) in three Virginia streams. We used Monte Carlo simulations to construct hypothetical series of habitat units, then examined how number of species, similarity in relative abundances, and number of microhabitats accumulated with increasing number of habitat units (i.e., sampling effort). Proportions of all species and microhabitats represented were relatively low and variable at low sampling effort, but increased asymptotically and became less variable with greater sampling effort. To facilitate comparisons among streams, we fitted simulation results to negative exponential curves. The curves indicated that 90% of the species present were usually found by sampling 5 to 14 habitat units (stream length of 22–67 stream widths). Estimates of species relative abundances required less sampling effort for a given accuracy than estimates of number of species. Rates of species accumulation (with effort) varied among streams and reflected discontinuity in species distributions among habitat units. Most discontinuity seemed to be due to low population density rather than to habitat selectivity. Results from an Illinois stream corroborated our findings from Virginia, and suggested that greater sampling effort is needed to characterize fish community structure in more homogeneous stream reaches.

  7. Estimating mineral abundances of clay and gypsum mixtures using radiative transfer models applied to visible-near infrared reflectance spectra

    NASA Astrophysics Data System (ADS)

    Robertson, K. M.; Milliken, R. E.; Li, S.

    2016-10-01

    Quantitative mineral abundances of lab derived clay-gypsum mixtures were estimated using a revised Hapke VIS-NIR and Shkuratov radiative transfer model. Montmorillonite-gypsum mixtures were used to test the effectiveness of the model in distinguishing between subtle differences in minor absorption features that are diagnostic of mineralogy in the presence of strong H2O absorptions that are not always diagnostic of distinct phases or mineral abundance. The optical constants (k-values) for both endmembers were determined from bi-directional reflectance spectra measured in RELAB as well as on an ASD FieldSpec3 in a controlled laboratory setting. Multiple size fractions were measured in order to derive a single k-value from optimization of the optical path length in the radiative transfer models. It is shown that with careful experimental conditions, optical constants can be accurately determined from powdered samples using a field spectrometer, consistent with previous studies. Variability in the montmorillonite hydration level increased the uncertainties in the derived k-values, but estimated modal abundances for the mixtures were still within 5% of the measured values. Results suggest that the Hapke model works well in distinguishing between hydrated phases that have overlapping H2O absorptions and it is able to detect gypsum and montmorillonite in these simple mixtures where they are present at levels of ∼10%. Care must be taken however to derive k-values from a sample with appropriate H2O content relative to the modeled spectra. These initial results are promising for the potential quantitative analysis of orbital remote sensing data of hydrated minerals, including more complex clay and sulfate assemblages such as mudstones examined by the Curiosity rover in Gale crater.

  8. Double-observer approach to estimating egg mass abundance of vernal pool breeding amphibians

    USGS Publications Warehouse

    Grant, E.H.C.; Jung, R.E.; Nichols, J.D.; Hines, J.E.

    2005-01-01

    Interest in seasonally flooded pools, and the status of associated amphibian populations, has initiated programs in the northeastern United States to document and monitor these habitats. Counting egg masses is an effective way to determine the population size of pool-breeding amphibians, such as wood frogs (Rana sylvatica) and spotted salamanders (Ambystoma maculatum). However, bias is associated with counts if egg masses are missed. Counts unadjusted for the proportion missed (i.e., without adjustment for detection probability) could lead to false assessments of population trends. We used a dependent double-observer method in 2002-2003 to estimate numbers of wood frog and spotted salamander egg masses at seasonal forest pools in 13 National Wildlife Refuges, 1 National Park, 1 National Seashore, and 1 State Park in the northeastern United States. We calculated detection probabilities for egg masses and examined whether detection probabilities varied by species, observers, pools, and in relation to pool characteristics (pool area, pool maximum depth, within-pool vegetation). For the 2 years, model selection indicated that no consistent set of variables explained the variation in data sets from individual Refuges and Parks. Because our results indicated that egg mass detection probabilities vary spatially and temporally, we conclude that it is essential to use estimation procedures, such as double-observer methods with egg mass surveys, to determine population sizes and trends of these species.

  9. Estimating Dungeness crab (Cancer magister) abundance: Crab pots and dive transects compared

    USGS Publications Warehouse

    Taggart, S.J.; O'Clair, C. E.; Shirley, T.C.; Mondragon, J.

    2004-01-01

    Dungeness crabs (Cancer magister) were sampled with commercial pots and counted by scuba divers on benthic transects at eight sites near Glacier Bay, Alaska. Catch per unit of effort (CPUE) from pots was compared to the density estimates from dives to evaluate the bias and power of the two techniques. Yearly sampling was conducted in two seasons: April and September, from 1992 to 2000. Male CPUE estimates from pots were significantly lower in April than in the following September; a step-wise regression demonstrated that season accounted for more of the variation in male CPUE than did temperature. In both April and September, pot sampling was significantly biased against females. When females were categorized as ovigerous and nonovigerous, it was clear that ovigerous females accounted for the majority of the bias because pots were not biased against nonovigerous females. We compared the power of pots and dive transects in detecting trends in populations and found that pots had much higher power than dive transects. Despite their low power, the dive transects were very useful for detecting bias in our pot sampling and in identifying the optimal times of year to sample so that pot bias could be avoided.

  10. An evaluation of the efficiency of minnow traps for estimating the abundance of minnows in desert spring systems

    USGS Publications Warehouse

    Peterson, James T.; Scheerer, Paul D.; Clements, Shaun

    2015-01-01

    Desert springs are sensitive aquatic ecosystems that pose unique challenges to natural resource managers and researchers. Among the most important of these is the need to accurately quantify population parameters for resident fish, particularly when the species are of special conservation concern. We evaluated the efficiency of baited minnow traps for estimating the abundance of two at-risk species, Foskett Speckled Dace Rhinichthys osculus ssp. and Borax Lake Chub Gila boraxobius, in desert spring systems in southeastern Oregon. We evaluated alternative sample designs using simulation and found that capture–recapture designs with four capture occasions would maximize the accuracy of estimates and minimize fish handling. We implemented the design and estimated capture and recapture probabilities using the Huggins closed-capture estimator. Trap capture probabilities averaged 23% and 26% for Foskett Speckled Dace and Borax Lake Chub, respectively, but differed substantially among sample locations, through time, and nonlinearly with fish body size. Recapture probabilities for Foskett Speckled Dace were, on average, 1.6 times greater than (first) capture probabilities, suggesting “trap-happy” behavior. Comparison of population estimates from the Huggins model with the commonly used Lincoln–Petersen estimator indicated that the latter underestimated Foskett Speckled Dace and Borax Lake Chub population size by 48% and by 20%, respectively. These biases were due to variability in capture and recapture probabilities. Simulation of fish monitoring that included the range of capture and recapture probabilities observed indicated that variability in capture and recapture probabilities in time negatively affected the ability to detect annual decreases by up to 20% in fish population size. Failure to account for variability in capture and recapture probabilities can lead to poor quality data and study inferences. Therefore, we recommend that fishery researchers and

  11. Spatio-temporal variation in male white-tailed deer harvest rates in Pennsylvania: Implications for estimating abundance

    USGS Publications Warehouse

    Norton, Andrew S.; Diefenbach, Duane R.; Wallingford, Bret D.; Rosenberry, Christopher S.

    2012-01-01

    The performance of 2 popular methods that use age-at-harvest data to estimate abundance of white-tailed deer is contingent on assumptions about variation in estimates of subadult (1.5 yr old) and adult (≥2.5 yr old) male harvest rates. Auxiliary data (e.g., estimates of survival or harvest rates from radiocollared animals) can be used to relax some assumptions, but unless these population parameters exhibit limited temporal or spatial variation, these auxiliary data may not improve accuracy. Unfortunately maintaining sufficient sample sizes of radiocollared deer for parameter estimation in every wildlife management unit (WMU) is not feasible for most state agencies. We monitored the fates of 397 subadult and 225 adult male white-tailed deer across 4 WMUs from 2002 to 2008 using radio telemetry. We investigated spatial and temporal variation in harvest rates and investigated covariates related to the patterns observed. We found that most variation in harvest rates was explained spatially and that adult harvest rates (0.36–0.69) were more variable among study areas than subadult harvest rates (0.26–0.42). We found that hunter effort during the archery and firearms season best explained variation in harvest rates of adult males among WMUs, whereas hunter effort during only the firearms season best explained harvest rates for subadult males. From a population estimation perspective, it is advantageous that most variation was spatial and explained by a readily obtained covariate (hunter effort). However, harvest rates may vary if hunting regulations or hunter behavior change, requiring additional field studies to obtain accurate estimates of harvest rates. 

  12. Establishing precise estimates of abundance in patchy habitats of the marine nearshore.

    PubMed

    Baring, Ryan J; Lester, Rebecca E; Fairweather, Peter G

    2016-09-01

    Exploratory investigations of optimal sampling designs are a critical component of the decision-making process in ecology where inherent natural variation can lead to erroneous conclusions if left unexamined. Pilot studies and exploratory analyses that investigate the precision of sampling regimes may reduce the chances of erroneous results and can be used to optimise processing time in larger ecological research programs. In our study, we calculated optimal precision estimates for sampling macroinvertebrates and ichthyofauna in surf-zone wrack accumulations by investigating the precision of the mean for sub-samples of seine nets and also for the number of replicate seine nets to guide future sampling regimes. We discovered that the processing time for individual seine net samples could be reduced by 50% using sub-sampling and that time to process replicate seine net samples could be reduced by 25% while maintaining acceptable precision. In future, we suggest that the use of pilot studies with similar exploratory approaches should be less of an exception and more a critical component of ecological investigations, particularly in under-studied or newly-developing areas of research. Further, these types of exploratory approaches are crucially important in a variety of extremely patchy environments where variability is likely to be high. PMID:27442809

  13. Purification of Vibrio cholerae fur and estimation of its intracellular abundance by antibody sandwich enzyme-linked immunosorbent assay.

    PubMed Central

    Watnick, P I; Eto, T; Takahashi, H; Calderwood, S B

    1997-01-01

    The Vibrio cholerae fur gene was previously cloned and sequenced. A putative Fur box was identified in the divergent promoters of irgA, a virulence factor of V. cholerae, and irgB, a transcriptional activator of irgA. In this work, V. cholerae Fur was overexpressed in Escherichia coli and purified to approximately 95% homogeneity. The purified protein bound a DNA fragment containing the irgA-irgB promoter in a gel shift assay. The purified protein was used to raise monoclonal and polyclonal antibodies to V. cholerae Fur, and a Fur sandwich enzyme-linked immunosorbent assay was developed to estimate the intracellular abundance of Fur under a variety of growth conditions. The number of Fur molecules per cell during exponential growth was approximately 2,500, which is higher than most measurements for other bacterial repressors but comparable to the intracellular concentration of the leucine-responsive regulatory protein. The number of Fur molecules per cell increased in the late logarithmic and stationary phases. Growth of V. cholerae in low-iron medium did not alter the intracellular abundance of Fur significantly. Growth under microaerophilic conditions resulted in a significant, approximately twofold decrease in the intracellular levels of Fur. The measurements of intracellular Fur abundance indicate that a large amount of this repressor is produced constitutively and that the concentration of Fur in the cell varies by less than a factor of 2 under the conditions studied. We hypothesize that the high constitutive expression of Fur is necessary for its role as an iron-responsive regulator. PMID:8982004

  14. Channel estimation in DCT-based OFDM.

    PubMed

    Wang, Yulin; Zhang, Gengxin; Xie, Zhidong; Hu, Jing

    2014-01-01

    This paper derives the channel estimation of a discrete cosine transform-(DCT-) based orthogonal frequency-division multiplexing (OFDM) system over a frequency-selective multipath fading channel. Channel estimation has been proved to improve system throughput and performance by allowing for coherent demodulation. Pilot-aided methods are traditionally used to learn the channel response. Least square (LS) and mean square error estimators (MMSE) are investigated. We also study a compressed sensing (CS) based channel estimation, which takes the sparse property of wireless channel into account. Simulation results have shown that the CS based channel estimation is expected to have better performance than LS. However MMSE can achieve optimal performance because of prior knowledge of the channel statistic.

  15. Forecasting contributions of lake whitefish year-classes to a Lake Superior commercial fishery from estimates of yearling abundance

    USGS Publications Warehouse

    Curtis, Gary L.; Bronte, Charles R.; Selgeby, James H.

    1993-01-01

    We developed a simple linear regression model to forecast year-class contributions of lake whitefish Coregonus clupeaformis to the commercial harvest in the Apostle Islands region of Lake Superior. We indexed year-class strength from catches of yearling fish in bottom trawl samples. Recruitment of each year-class was measured by its relative abundance in the fishery at age 6. The relation between recruitment to the commercial fishery and year-class strength indices was positive and significant (r 2 = 0.67, P < 0.01). The model produced reliable estimates of recruitment to the fishery within the range of the regression. Projected recruitment of the 1983–1987 year-classes to the fishery in 1989-1993 should be sufficient to sustain current levels of harvest through 1993.

  16. Estimating Decision Indices Based on Composite Scores

    ERIC Educational Resources Information Center

    Knupp, Tawnya Lee

    2009-01-01

    The purpose of this study was to develop an IRT model that would enable the estimation of decision indices based on composite scores. The composite scores, defined as a combination of unidimensional test scores, were either a total raw score or an average scale score. Additionally, estimation methods for the normal and compound multinomial models…

  17. Size-Based Hydroacoustic Measures of Within-Season Fish Abundance in a Boreal Freshwater Ecosystem

    PubMed Central

    Pollom, Riley A.; Rose, George A.

    2015-01-01

    Eleven sequential size-based hydroacoustic surveys conducted with a 200 kHz split-beam transducer during the summers of 2011 and 2012 were used to quantify seasonal declines in fish abundance in a boreal reservoir in Manitoba, Canada. Fish densities were sufficiently low to enable single target resolution and tracking. Target strengths converted to log2-based size-classes indicated that smaller fish were consistently more abundant than larger fish by a factor of approximately 3 for each halving of length. For all size classes, in both years, abundance (natural log) declined linearly over the summer at rates that varied from -0.067.day-1 for the smallest fish to -0.016.day-1 for the largest (R2 = 0.24–0.97). Inter-annual comparisons of size-based abundance suggested that for larger fish (>16 cm), mean winter decline rates were an order of magnitude lower (-0.001.day-1) and overall survival higher (71%) than in the main summer fishing season (mean loss rate -0.038.day-1; survival 33%). We conclude that size-based acoustic survey methods have the potential to assess within-season fish abundance dynamics, and may prove useful in long-term monitoring of productivity and hence management of boreal aquatic ecosystems. PMID:25875467

  18. Comparing Soil and Bison δ13C to Field Estimates of C4 Plant Abundances in North America

    NASA Astrophysics Data System (ADS)

    Griffith, D.; Still, C. J.; Cotton, J.; Powell, B.

    2015-12-01

    Stable carbon isotope data (i.e., δ13C) from soils and herbivore tissue are commonly used as a proxy for the relative abundance of C4 and C3 plants at a site. These data are also increasingly used to represent other climatologically relevant properties of vegetated environments, such as productivity, aridity, water use efficiency, and tree cover. The δ13C values of soils and herbivore tissues are generally assumed to resemble their source vegetation, after accounting for diverse fractionation processes during litter decomposition and tissue metabolism and turnover. However, δ13C values have rarely been compared to source vegetation at a regional to continental scale. As a result, the quality of δ13C as a proxy has not been thoroughly evaluated, and the importance of modifying factors have not been assessed at biogeographically relevant scales. To address some of these issues, we combined three multi-source datasets from North America: herbaceous C4 plant abundances from thousands of vegetation plots, hundreds of soil δ13C measurements, and hundreds of bison collagen, hair, and enamel δ13C data (tissues with different turnover rates). These datasets were resampled to common grid for comparison. A stronger relationship with C4 vegetation existed for bison as compared to soil δ13C. To determine which factors might explain deviations in the vegetation plot and isotopic data, we used statistical models to quantify the influence of soil variables, mean annual precipitation and temperature, tree cover, presence of invasives, and fire frequency in conjunction with plot-based C4 abundance data. Our bison model was only improved by the addition of invasives. In contrast, our soil model was significantly improved when accounting for tree cover (C3 vegetation and shade), precipitation, various soil parameters, and invasive grasses, suggesting that soils are more likely to be biased from source vegetation in ways that could influence interpretation as a proxy at broad

  19. View Estimation Based on Value System

    NASA Astrophysics Data System (ADS)

    Takahashi, Yasutake; Shimada, Kouki; Asada, Minoru

    Estimation of a caregiver's view is one of the most important capabilities for a child to understand the behavior demonstrated by the caregiver, that is, to infer the intention of behavior and/or to learn the observed behavior efficiently. We hypothesize that the child develops this ability in the same way as behavior learning motivated by an intrinsic reward, that is, he/she updates the model of the estimated view of his/her own during the behavior imitated from the observation of the behavior demonstrated by the caregiver based on minimizing the estimation error of the reward during the behavior. From this view, this paper shows a method for acquiring such a capability based on a value system from which values can be obtained by reinforcement learning. The parameters of the view estimation are updated based on the temporal difference error (hereafter TD error: estimation error of the state value), analogous to the way such that the parameters of the state value of the behavior are updated based on the TD error. Experiments with simple humanoid robots show the validity of the method, and the developmental process parallel to young children's estimation of its own view during the imitation of the observed behavior of the caregiver is discussed.

  20. Estimating lake-wide abundance of spawning-phase sea lampreys (Petromyzon marinus) in the Great Lakes: extrapolating from sampled streams using regression models

    USGS Publications Warehouse

    Mullett, Katherine M.; Heinrich, John W.; Adams, Jean V.; Young, Robert J.; Henson, Mary P.; McDonald, Rodney B.; Fodale, Michael F.

    2003-01-01

    Lake-wide abundance of spawning-phase sea lampreys (Petromyzon marinus) can be used as one means to evaluate sea lamprey control efforts in the Great Lakes. Lake-wide abundance in each Great Lake was the sum of estimates for all streams thought to contribute substantial numbers of sea lampreys. A subset of these streams was sampled with traps and mark-recapture studies were conducted. When sea lampreys were captured in traps, but no mark-recapture study was conducted, abundance was estimated from a relation between trap catch and mark-recapture estimates observed in other years. In non-sampled streams, a regression model that used stream drainage area, geographic region, larval sea lamprey, production potential, the number of years since the last lampricide treatment, and spawning year was used to predict abundance of spawning-phase sea lampreys. The combination of estimates from sampled and non-sampled streams provided a 20-year time series of spawning-phase sea lamprey abundance estimates in the Great Lakes.

  1. Estimating Tortuosity Coefficients Based on Hydraulic Conductivity.

    PubMed

    Carey, Grant R; McBean, Edward A; Feenstra, Stan

    2016-07-01

    While the tortuosity coefficient is commonly estimated using an expression based on total porosity, this relationship is demonstrated to not be applicable (and thus is often misapplied) over a broad range of soil textures. The fundamental basis for a correlation between the apparent diffusion tortuosity coefficient and hydraulic conductivity is demonstrated, although such a relationship is not typically considered. An empirical regression for estimating the tortuosity coefficient based on hydraulic conductivity for saturated, unconsolidated soil is derived based on results from 14 previously reported diffusion experiments performed with a broad range of soil textures. Analyses of these experimental results confirm that total porosity is a poor predictor for the tortuosity coefficient over a large range of soil textures. The apparent diffusion tortuosity coefficient is more reliably estimated based on hydraulic conductivity. PMID:27315019

  2. Molecular abundance profiles characterization of Jupiter'satmosphere using ground-based observations at 5 microns

    NASA Astrophysics Data System (ADS)

    Doriann, Blain; Fouchet, Thierry; Encrenaz, Therese A.; Drossart, Pierre; Greathouse, Thomas K.; Fletcher, Leigh N.; Orton, Glenn S.

    2016-10-01

    We report on early results of an observational campaign to support the Juno mission. At the beginning of this year, using TEXES (Texas Echelon cross-dispersed Echelle Spectrograph), mounted on the NASA Infrared Telescope Facility (IRTF), we obtained maps of Jupiter in several spectral ranges between 1800 and 2200 cm-1 which probes the atmosphere in the 1-4 bar region, with a spectral resolution of R ≈ 7000 and an angular resolution of ≈ 1.5''. This dataset is analyzed by a code which combines a line-by-line radiative transfer model with a non-linear optimal estimation inversion method. The inversion takes into account the abundance profiles of AsH3 , CO, GeH4 and H2O, as well as clouds contribution, in addtion to the abundance profiles of NH3 and PH3 . We will present the inverted abundance profiles, their significance for the understanding of Jupiter's atmospheric dynamics, and how they will be useful for the determination of water abundance up to 200 bars, which is one of the main objectives of the instrument MWR (MicroWave Radiometer) mounted on the Juno spacecraft. This work will also be useful to prepare the analysis of the JIRAM (Jovian InfraRed Auroral Mapper) 5-microns data aboard Juno.

  3. Mineral resources estimation based on block modeling

    NASA Astrophysics Data System (ADS)

    Bargawa, Waterman Sulistyana; Amri, Nur Ali

    2016-02-01

    The estimation in this paper uses three kinds of block models of nearest neighbor polygon, inverse distance squared and ordinary kriging. The techniques are weighting scheme which is based on the principle that block content is a linear combination of the grade data or the sample around the block being estimated. The case study in Pongkor area, here is gold-silver resource modeling that allegedly shaped of quartz vein as a hydrothermal process of epithermal type. Resources modeling includes of data entry, statistical and variography analysis of topography and geological model, the block model construction, estimation parameter, presentation model and tabulation of mineral resources. Skewed distribution, here isolated by robust semivariogram. The mineral resources classification generated in this model based on an analysis of the kriging standard deviation and number of samples which are used in the estimation of each block. Research results are used to evaluate the performance of OK and IDS estimator. Based on the visual and statistical analysis, concluded that the model of OK gives the estimation closer to the data used for modeling.

  4. Estimating wetland vegetation abundance from Landsat-8 operational land imager imagery: a comparison between linear spectral mixture analysis and multinomial logit modeling methods

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Gong, Zhaoning; Zhao, Wenji; Pu, Ruiliang; Liu, Ke

    2016-01-01

    Mapping vegetation abundance by using remote sensing data is an efficient means for detecting changes of an eco-environment. With Landsat-8 operational land imager (OLI) imagery acquired on July 31, 2013, both linear spectral mixture analysis (LSMA) and multinomial logit model (MNLM) methods were applied to estimate and assess the vegetation abundance in the Wild Duck Lake Wetland in Beijing, China. To improve mapping vegetation abundance and increase the number of endmembers in spectral mixture analysis, normalized difference vegetation index was extracted from OLI imagery along with the seven reflective bands of OLI data for estimating the vegetation abundance. Five endmembers were selected, which include terrestrial plants, aquatic plants, bare soil, high albedo, and low albedo. The vegetation abundance mapping results from Landsat OLI data were finally evaluated by utilizing a WorldView-2 multispectral imagery. Similar spatial patterns of vegetation abundance produced by both fully constrained LSMA algorithm and MNLM methods were observed: higher vegetation abundance levels were distributed in agricultural and riparian areas while lower levels in urban/built-up areas. The experimental results also indicate that the MNLM model outperformed the LSMA algorithm with smaller root mean square error (0.0152 versus 0.0252) and higher coefficient of determination (0.7856 versus 0.7214) as the MNLM model could handle the nonlinear reflection phenomenon better than the LSMA with mixed pixels.

  5. Comparison of mark-resight methods to estimate abundance and rabies vaccination coverage of free-roaming dogs in two urban areas of south Bhutan.

    PubMed

    Tenzin, Tenzin; McKenzie, Joanna S; Vanderstichel, Raphaël; Rai, Bir Doj; Rinzin, Karma; Tshering, Yeshey; Pem, Rinzin; Tshering, Chenga; Dahal, Narapati; Dukpa, Kinzang; Dorjee, Sithar; Wangchuk, Sonam; Jolly, Peter D; Morris, Roger; Ward, Michael P

    2015-03-01

    In Bhutan, Capture-Neuter-Vaccinate-Release (CNVR) programs have been implemented to manage the dog population and control rabies, but no detailed evaluation has been done to assess their coverage and impact. We compared estimates of the dog population using three analytical methods: Lincoln-Petersen index, the Chapman estimate, and the logit-normal mixed effects model, and a varying number of count periods at different times of the day to recommend a protocol for applying the mark-resight framework to estimate free-roaming dog population abundance. We assessed the coverage of the CNVR program by estimating the proportion of dogs that were ear-notched and visually scored the health and skin condition of free-roaming dogs in Gelephu and Phuentsholing towns in south Bhutan, bordering India, in September-October 2012. The estimated free-roaming dog population in Gelephu using the Lincoln-Petersen index and Chapman estimates ranged from 612 to 672 and 614 to 671, respectively, while the logit-normal mixed effects model estimate based on the combined two count events was 641 (95% CI: 603-682). In Phuentsholing the Lincoln-Petersen index and Chapman estimates ranged from 525 to 583 and 524 to 582, respectively, while the logit-normal mixed effects model estimate based on the combined four count events was 555 (95% CI: 526-587). The total number of dogs counted was significantly associated with the time of day (AM versus PM; P=0.007), with a 17% improvement in dog sightings during the morning counting events. We recommend to conduct a morning marking followed by one count event the next morning and estimate population size by applying the Lincoln-Peterson corrected Chapman method or conduct two morning count events and apply the logit-normal mixed model to estimate population size. The estimated proportion of vaccinated free-roaming dogs was 56% (95% CI: 52-61%) and 58% (95% CI: 53-62%) in Gelephu and Phuentsholing, respectively. Given coverage in many neighbourhoods was

  6. [Automatic Measurement of the Stellar Atmospheric Parameters Based Mass Estimation].

    PubMed

    Tu, Liang-ping; Wei, Hui-ming; Luo, A-li; Zhao, Yong-heng

    2015-11-01

    We have collected massive stellar spectral data in recent years, which leads to the research on the automatic measurement of stellar atmospheric physical parameters (effective temperature Teff, surface gravity log g and metallic abundance [Fe/ H]) become an important issue. To study the automatic measurement of these three parameters has important significance for some scientific problems, such as the evolution of the universe and so on. But the research of this problem is not very widely, some of the current methods are not able to estimate the values of the stellar atmospheric physical parameters completely and accurately. So in this paper, an automatic method to predict stellar atmospheric parameters based on mass estimation was presented, which can achieve the prediction of stellar effective temperature Teff, surface gravity log g and metallic abundance [Fe/H]. This method has small amount of computation and fast training speed. The main idea of this method is that firstly it need us to build some mass distributions, secondly the original spectral data was mapped into the mass space and then to predict the stellar parameter with the support vector regression (SVR) in the mass space. we choose the stellar spectral data from the United States SDSS-DR8 for the training and testing. We also compared the predicted results of this method with the SSPP and achieve higher accuracy. The predicted results are more stable and the experimental results show that the method is feasible and can predict the stellar atmospheric physical parameters effectively. PMID:26978937

  7. [Automatic Measurement of the Stellar Atmospheric Parameters Based Mass Estimation].

    PubMed

    Tu, Liang-ping; Wei, Hui-ming; Luo, A-li; Zhao, Yong-heng

    2015-11-01

    We have collected massive stellar spectral data in recent years, which leads to the research on the automatic measurement of stellar atmospheric physical parameters (effective temperature Teff, surface gravity log g and metallic abundance [Fe/ H]) become an important issue. To study the automatic measurement of these three parameters has important significance for some scientific problems, such as the evolution of the universe and so on. But the research of this problem is not very widely, some of the current methods are not able to estimate the values of the stellar atmospheric physical parameters completely and accurately. So in this paper, an automatic method to predict stellar atmospheric parameters based on mass estimation was presented, which can achieve the prediction of stellar effective temperature Teff, surface gravity log g and metallic abundance [Fe/H]. This method has small amount of computation and fast training speed. The main idea of this method is that firstly it need us to build some mass distributions, secondly the original spectral data was mapped into the mass space and then to predict the stellar parameter with the support vector regression (SVR) in the mass space. we choose the stellar spectral data from the United States SDSS-DR8 for the training and testing. We also compared the predicted results of this method with the SSPP and achieve higher accuracy. The predicted results are more stable and the experimental results show that the method is feasible and can predict the stellar atmospheric physical parameters effectively.

  8. Entropy Based Modelling for Estimating Demographic Trends.

    PubMed

    Li, Guoqi; Zhao, Daxuan; Xu, Yi; Kuo, Shyh-Hao; Xu, Hai-Yan; Hu, Nan; Zhao, Guangshe; Monterola, Christopher

    2015-01-01

    In this paper, an entropy-based method is proposed to forecast the demographical changes of countries. We formulate the estimation of future demographical profiles as a constrained optimization problem, anchored on the empirically validated assumption that the entropy of age distribution is increasing in time. The procedure of the proposed method involves three stages, namely: 1) Prediction of the age distribution of a country's population based on an "age-structured population model"; 2) Estimation the age distribution of each individual household size with an entropy-based formulation based on an "individual household size model"; and 3) Estimation the number of each household size based on a "total household size model". The last stage is achieved by projecting the age distribution of the country's population (obtained in stage 1) onto the age distributions of individual household sizes (obtained in stage 2). The effectiveness of the proposed method is demonstrated by feeding real world data, and it is general and versatile enough to be extended to other time dependent demographic variables. PMID:26382594

  9. A comparison of solar wind and estimated solar system xenon abundances - A test for solid/gas fractionation in the solar nebula

    NASA Technical Reports Server (NTRS)

    Wiens, Roger C.; Burnett, D. S.; Neugebauer, M.; Pepin, R. O.

    1992-01-01

    The solar Xe elemental abundance is determined here using solar wind measurements from lunar ilmenites which are normalized to Si by spacecraft data. The results are compared with estimated abundances assuming no fractionation. When corrected for solar wind/photospheric fractionation, the Xe-130 abundance given by surface layer oxidation of ilmenite from solid 71501 exposed within the last 200 m.y. is 0.24 +/- 0.09 normalized to Si = 10 exp 6. This is indistinguishable from estimates made assuming no solid/gas fractionation. Results from breccia 79035 ilmenite exposed at least 1 Gyr ago indicate that the solar wind Xe flux may have been significantly higher relative to other noble gases, perhaps due to more efficient Xe ionization. If this is true, fluxes of C and S, which have first ionization potentials similar to Xe, should also be higher in the ancient solar wind from the same time period.

  10. 2011 Kiwikiu (Maui Parrotbill) and Maui `Alauahio abundance estimates and the effect of sampling effort on power to detect a trend

    USGS Publications Warehouse

    Brinck, Kevin W.; Camp, Richard J.; Gorresen, P. Marcos; Leonard, David L.; Mounce, Hanna L.; Iknayan, Kelly J.; Paxton, Eben H.

    2012-01-01

    much of its original habitat and now occurs in forested areas of East Maui where its habitat overlaps with that of the Kiwikiu. Though they share the same habitat, the `Alauahio is much more abundant—by more than two orders of magnitude—and occurs over a wider range than the Kiwikiu. Both species appear to have no statistically significant population trend from 1980–2001, but abundance estimates vary widely from survey to survey and have wide uncertainties (Camp et al. 2009). Ideally survey design should result in estimates precise enough to be able to detect significant declines in abundance that may trigger management intervention. We wished to improve the accuracy of Kiwikiu abundance estimates and the ability to detect significant trends in abundance. To that end, in 2011, repeated point count surveys were conducted across the Kiwikiu range, excluding Haleakalā National Park (Figure 1). The increased sampling effort increases sample size and improves the precision of estimates, and repeat samples also allowed us to partition within-year and between-year variation in surveys, increasing the statistical power to detect trends.

  11. Organoheterotrophic Bacterial Abundance Associates with Zinc Removal in Lignocellulose-Based Sulfate-Reducing Systems.

    PubMed

    Drennan, Dina M; Almstrand, Robert; Lee, Ilsu; Landkamer, Lee; Figueroa, Linda; Sharp, Jonathan O

    2016-01-01

    Syntrophic relationships between fermentative and sulfate-reducing bacteria are essential to lignocellulose-based systems applied to the passive remediation of mining-influenced waters. In this study, seven pilot-scale sulfate-reducing bioreactor columns containing varying ratios of alfalfa hay, pine woodchips, and sawdust were analyzed over ∼500 days to investigate the influence of substrate composition on zinc removal and microbial community structure. Columns amended with >10% alfalfa removed significantly more sulfate and zinc than did wood-based columns. Enumeration of sulfate reducers by functional signatures (dsrA) and their putative identification from 16S rRNA genes did not reveal significant correlations with zinc removal, suggesting limitations in this directed approach. In contrast, a strong indicator of zinc removal was discerned in comparing the relative abundance of core microorganisms shared by all reactors (>80% of total community), many of which had little direct involvement in metal or sulfate respiration. The relative abundance of Desulfosporosinus, the dominant putative sulfate reducer within these reactors, correlated to representatives of this core microbiome. A subset of these clades, including Treponema, Weissella, and Anaerolinea, was associated with alfalfa and zinc removal, and the inverse was found for a second subset whose abundance was associated with wood-based columns, including Ruminococcus, Dysgonomonas, and Azospira. The construction of a putative metabolic flowchart delineated syntrophic interactions supporting sulfate reduction and suggests that the production of and competition for secondary fermentation byproducts, such as lactate scavenging, influence bacterial community composition and reactor efficacy. PMID:26605699

  12. Organoheterotrophic Bacterial Abundance Associates with Zinc Removal in Lignocellulose-Based Sulfate-Reducing Systems.

    PubMed

    Drennan, Dina M; Almstrand, Robert; Lee, Ilsu; Landkamer, Lee; Figueroa, Linda; Sharp, Jonathan O

    2016-01-01

    Syntrophic relationships between fermentative and sulfate-reducing bacteria are essential to lignocellulose-based systems applied to the passive remediation of mining-influenced waters. In this study, seven pilot-scale sulfate-reducing bioreactor columns containing varying ratios of alfalfa hay, pine woodchips, and sawdust were analyzed over ∼500 days to investigate the influence of substrate composition on zinc removal and microbial community structure. Columns amended with >10% alfalfa removed significantly more sulfate and zinc than did wood-based columns. Enumeration of sulfate reducers by functional signatures (dsrA) and their putative identification from 16S rRNA genes did not reveal significant correlations with zinc removal, suggesting limitations in this directed approach. In contrast, a strong indicator of zinc removal was discerned in comparing the relative abundance of core microorganisms shared by all reactors (>80% of total community), many of which had little direct involvement in metal or sulfate respiration. The relative abundance of Desulfosporosinus, the dominant putative sulfate reducer within these reactors, correlated to representatives of this core microbiome. A subset of these clades, including Treponema, Weissella, and Anaerolinea, was associated with alfalfa and zinc removal, and the inverse was found for a second subset whose abundance was associated with wood-based columns, including Ruminococcus, Dysgonomonas, and Azospira. The construction of a putative metabolic flowchart delineated syntrophic interactions supporting sulfate reduction and suggests that the production of and competition for secondary fermentation byproducts, such as lactate scavenging, influence bacterial community composition and reactor efficacy.

  13. Knowledge Based Estimation of Material Release Transients

    1998-07-29

    KBERT is an easy to use desktop decision support tool for estimating public and in-facility worker doses and consequences of radioactive material releases in non-reactort nuclear facilities. It automatically calculates release and respirable fractions based on published handbook data, and calculates material transport concurrently with personnel evacuation simulations. Any facility layout can be modeled easily using the intuitive graphical user interface.

  14. Estimating juvenile Chinook salmon (Oncorhynchus tshawytscha) abundance from beach seine data collected in the Sacramento–San Joaquin Delta and San Francisco Bay, California

    USGS Publications Warehouse

    Perry, Russell W.; Kirsch, Joseph E.; Hendrix, A. Noble

    2016-06-17

    Resource managers rely on abundance or density metrics derived from beach seine surveys to make vital decisions that affect fish population dynamics and assemblage structure. However, abundance and density metrics may be biased by imperfect capture and lack of geographic closure during sampling. Currently, there is considerable uncertainty about the capture efficiency of juvenile Chinook salmon (Oncorhynchus tshawytscha) by beach seines. Heterogeneity in capture can occur through unrealistic assumptions of closure and from variation in the probability of capture caused by environmental conditions. We evaluated the assumptions of closure and the influence of environmental conditions on capture efficiency and abundance estimates of Chinook salmon from beach seining within the Sacramento–San Joaquin Delta and the San Francisco Bay. Beach seine capture efficiency was measured using a stratified random sampling design combined with open and closed replicate depletion sampling. A total of 56 samples were collected during the spring of 2014. To assess variability in capture probability and the absolute abundance of juvenile Chinook salmon, beach seine capture efficiency data were fitted to the paired depletion design using modified N-mixture models. These models allowed us to explicitly test the closure assumption and estimate environmental effects on the probability of capture. We determined that our updated method allowing for lack of closure between depletion samples drastically outperformed traditional data analysis that assumes closure among replicate samples. The best-fit model (lowest-valued Akaike Information Criterion model) included the probability of fish being available for capture (relaxed closure assumption), capture probability modeled as a function of water velocity and percent coverage of fine sediment, and abundance modeled as a function of sample area, temperature, and water velocity. Given that beach seining is a ubiquitous sampling technique for

  15. Model-based estimation of knee stiffness.

    PubMed

    Pfeifer, Serge; Vallery, Heike; Hardegger, Michael; Riener, Robert; Perreault, Eric J

    2012-09-01

    During natural locomotion, the stiffness of the human knee is modulated continuously and subconsciously according to the demands of activity and terrain. Given modern actuator technology, powered transfemoral prostheses could theoretically provide a similar degree of sophistication and function. However, experimentally quantifying knee stiffness modulation during natural gait is challenging. Alternatively, joint stiffness could be estimated in a less disruptive manner using electromyography (EMG) combined with kinetic and kinematic measurements to estimate muscle force, together with models that relate muscle force to stiffness. Here we present the first step in that process, where we develop such an approach and evaluate it in isometric conditions, where experimental measurements are more feasible. Our EMG-guided modeling approach allows us to consider conditions with antagonistic muscle activation, a phenomenon commonly observed in physiological gait. Our validation shows that model-based estimates of knee joint stiffness coincide well with experimental data obtained using conventional perturbation techniques. We conclude that knee stiffness can be accurately estimated in isometric conditions without applying perturbations, which presents an important step toward our ultimate goal of quantifying knee stiffness during gait.

  16. Model-Based Estimation of Knee Stiffness

    PubMed Central

    Pfeifer, Serge; Vallery, Heike; Hardegger, Michael; Riener, Robert; Perreault, Eric J.

    2013-01-01

    During natural locomotion, the stiffness of the human knee is modulated continuously and subconsciously according to the demands of activity and terrain. Given modern actuator technology, powered transfemoral prostheses could theoretically provide a similar degree of sophistication and function. However, experimentally quantifying knee stiffness modulation during natural gait is challenging. Alternatively, joint stiffness could be estimated in a less disruptive manner using electromyography (EMG) combined with kinetic and kinematic measurements to estimate muscle force, together with models that relate muscle force to stiffness. Here we present the first step in that process, where we develop such an approach and evaluate it in isometric conditions, where experimental measurements are more feasible. Our EMG-guided modeling approach allows us to consider conditions with antagonistic muscle activation, a phenomenon commonly observed in physiological gait. Our validation shows that model-based estimates of knee joint stiffness coincide well with experimental data obtained using conventional perturbation techniques. We conclude that knee stiffness can be accurately estimated in isometric conditions without applying perturbations, which presents an important step towards our ultimate goal of quantifying knee stiffness during gait. PMID:22801482

  17. Rank-based camera spectral sensitivity estimation.

    PubMed

    Finlayson, Graham; Darrodi, Maryam Mohammadzadeh; Mackiewicz, Michal

    2016-04-01

    In order to accurately predict a digital camera response to spectral stimuli, the spectral sensitivity functions of its sensor need to be known. These functions can be determined by direct measurement in the lab-a difficult and lengthy procedure-or through simple statistical inference. Statistical inference methods are based on the observation that when a camera responds linearly to spectral stimuli, the device spectral sensitivities are linearly related to the camera rgb response values, and so can be found through regression. However, for rendered images, such as the JPEG images taken by a mobile phone, this assumption of linearity is violated. Even small departures from linearity can negatively impact the accuracy of the recovered spectral sensitivities, when a regression method is used. In our work, we develop a novel camera spectral sensitivity estimation technique that can recover the linear device spectral sensitivities from linear images and the effective linear sensitivities from rendered images. According to our method, the rank order of a pair of responses imposes a constraint on the shape of the underlying spectral sensitivity curve (of the sensor). Technically, each rank-pair splits the space where the underlying sensor might lie in two parts (a feasible region and an infeasible region). By intersecting the feasible regions from all the ranked-pairs, we can find a feasible region of sensor space. Experiments demonstrate that using rank orders delivers equal estimation to the prior art. However, the Rank-based method delivers a step-change in estimation performance when the data is not linear and, for the first time, allows for the estimation of the effective sensitivities of devices that may not even have "raw mode." Experiments validate our method. PMID:27140768

  18. Rank-based camera spectral sensitivity estimation.

    PubMed

    Finlayson, Graham; Darrodi, Maryam Mohammadzadeh; Mackiewicz, Michal

    2016-04-01

    In order to accurately predict a digital camera response to spectral stimuli, the spectral sensitivity functions of its sensor need to be known. These functions can be determined by direct measurement in the lab-a difficult and lengthy procedure-or through simple statistical inference. Statistical inference methods are based on the observation that when a camera responds linearly to spectral stimuli, the device spectral sensitivities are linearly related to the camera rgb response values, and so can be found through regression. However, for rendered images, such as the JPEG images taken by a mobile phone, this assumption of linearity is violated. Even small departures from linearity can negatively impact the accuracy of the recovered spectral sensitivities, when a regression method is used. In our work, we develop a novel camera spectral sensitivity estimation technique that can recover the linear device spectral sensitivities from linear images and the effective linear sensitivities from rendered images. According to our method, the rank order of a pair of responses imposes a constraint on the shape of the underlying spectral sensitivity curve (of the sensor). Technically, each rank-pair splits the space where the underlying sensor might lie in two parts (a feasible region and an infeasible region). By intersecting the feasible regions from all the ranked-pairs, we can find a feasible region of sensor space. Experiments demonstrate that using rank orders delivers equal estimation to the prior art. However, the Rank-based method delivers a step-change in estimation performance when the data is not linear and, for the first time, allows for the estimation of the effective sensitivities of devices that may not even have "raw mode." Experiments validate our method.

  19. Including independent estimates and uncertainty to quantify total abundance of fish migrating in a large river system: walleye (Sander vitreus) in the Maumee River, Ohio

    USGS Publications Warehouse

    Pritt, Jeremy J.; DuFour, Mark R.; Mayer, Christine M.; Kocovsky, Patrick M.; Tyson, Jeffrey T.; Weimer, Eric J.; Vandergoot, Christopher S.

    2013-01-01

    Walleye (Sander vitreus) in Lake Erie is a valuable and migratory species that spawns in tributaries. We used hydroacoustic sampling, gill net sampling, and Bayesian state-space modeling to estimate the spawning stock abundance, characterize size and sex structure, and explore environmental factors cuing migration of walleye in the Maumee River for 2011 and 2012. We estimated the spawning stock abundance to be between 431,000 and 1,446,000 individuals in 2011 and between 386,400 and 857,200 individuals in 2012 (95% Bayesian credible intervals). A back-calculation from a concurrent larval fish study produced an estimate of 78,000 to 237,000 spawners for 2011. The sex ratio was skewed towards males early in the spawning season but approached 1:1 later, and larger individuals entered the river earlier in the season than smaller individuals. Walleye migration was greater during low river discharge and intermediate temperatures. Our approach to estimating absolute abundance and uncertainty as well as characterization of the spawning stock could improve assessment and management of this species, and our methodology is applicable to other diadromous populations.

  20. Diatom species abundance and morphologically-based dissolution proxies in coastal Southern Ocean assemblages

    NASA Astrophysics Data System (ADS)

    Warnock, Jonathan P.; Scherer, Reed P.

    2015-07-01

    Taphonomic processes alter diatom assemblages in sediments, thus potentially negatively impacting paleoclimate records at various rates across space, time, and taxa. However, quantitative taphonomic data is rarely included in diatom-based paleoenvironmental reconstructions and no objective standard exists for comparing diatom dissolution in sediments recovered from marine depositional settings, including the Southern Ocean's opal belt. Furthermore, identifying changes to diatom dissolution through time can provide insight into the efficiency of both upper water column nutrient recycling and the biological pump. This is significant in that reactive metal proxies (e.g. Al, Ti) in the sediments only account for post-depositional dissolution, not the water column where the majority of dissolution occurs. In order to assess the range of variability of responses to dissolution in a typical Southern Ocean diatom community and provide a quantitative guideline for assessing taphonomic variability in diatoms recovered from core material, a sediment trap sample was subjected to controlled, serial dissolution. By evaluating dissolution-induced changes to diatom species' relative abundance, three preservational categories of diatoms have been identified: gracile, intermediate, and robust. The relative abundances of these categories can be used to establish a preservation grade for diatom assemblages. However, changes to the relative abundances of diatom species in sediment samples may reflect taphonomic or ecological factors. In order to address this complication, relative abundance changes have been tied to dissolution-induced morphological change to the areolae of Fragilariopsis curta, a significant sea-ice indicator in Southern Ocean sediments. This correlation allows differentiation between gracile species loss to dissolution versus ecological factors or sediment winnowing. These results mirror a similar morphological dissolution index from a parallel study utilizing

  1. Model-based estimation of individual fitness

    USGS Publications Warehouse

    Link, W.A.; Cooch, E.G.; Cam, E.

    2002-01-01

    Fitness is the currency of natural selection, a measure of the propagation rate of genotypes into future generations. Its various definitions have the common feature that they are functions of survival and fertility rates. At the individual level, the operative level for natural selection, these rates must be understood as latent features, genetically determined propensities existing at birth. This conception of rates requires that individual fitness be defined and estimated by consideration of the individual in a modelled relation to a group of similar individuals; the only alternative is to consider a sample of size one, unless a clone of identical individuals is available. We present hierarchical models describing individual heterogeneity in survival and fertility rates and allowing for associations between these rates at the individual level. We apply these models to an analysis of life histories of Kittiwakes (Rissa tridactyla ) observed at several colonies on the Brittany coast of France. We compare Bayesian estimation of the population distribution of individual fitness with estimation based on treating individual life histories in isolation, as samples of size one (e.g. McGraw & Caswell, 1996).

  2. Model-based estimation of individual fitness

    USGS Publications Warehouse

    Link, W.A.; Cooch, E.G.; Cam, E.

    2002-01-01

    Fitness is the currency of natural selection, a measure of the propagation rate of genotypes into future generations. Its various definitions have the common feature that they are functions of survival and fertility rates. At the individual level, the operative level for natural selection, these rates must be understood as latent features, genetically determined propensities existing at birth. This conception of rates requires that individual fitness be defined and estimated by consideration of the individual in a modelled relation to a group of similar individuals; the only alternative is to consider a sample of size one, unless a clone of identical individuals is available. We present hierarchical models describing individual heterogeneity in survival and fertility rates and allowing for associations between these rates at the individual level. We apply these models to an analysis of life histories of Kittiwakes (Rissa tridactyla) observed at several colonies on the Brittany coast of France. We compare Bayesian estimation of the population distribution of individual fitness with estimation based on treating individual life histories in isolation, as samples of size one (e.g. McGraw and Caswell, 1996).

  3. The measurement of elemental abundances above 10 exp 15 eV at a lunar base

    NASA Astrophysics Data System (ADS)

    Swordy, S. P.

    1990-03-01

    At about 10 exp 15 eV the slope of the energy spectrum of cosmic rays becomes significantly steeper than at lower energies. The measurement of relative elemental abundances at these energies is expected to provide a means to resolve the origin of this feature and greatly contribute to the understanding of the sources of cosmic rays. A moon-based detector for making well-resolved elemental measurements at these energies is described using hadronic calorimetry. This detector is particularly well suited for a site on the lunar surface because there is no overlying layer of atmosphere and the large mass required can be provided by the lunar regolith.

  4. Small-scale temporal and spatial variability in the abundance of plastic pellets on sandy beaches: Methodological considerations for estimating the input of microplastics.

    PubMed

    Moreira, Fabiana Tavares; Prantoni, Alessandro Lívio; Martini, Bruno; de Abreu, Michelle Alves; Stoiev, Sérgio Biato; Turra, Alexander

    2016-01-15

    Microplastics such as pellets have been reported for many years on sandy beaches around the globe. Nevertheless, high variability is observed in their estimates and distribution patterns across the beach environment are still to be unravelled. Here, we investigate the small-scale temporal and spatial variability in the abundance of pellets in the intertidal zone of a sandy beach and evaluate factors that can increase the variability in data sets. The abundance of pellets was estimated during twelve consecutive tidal cycles, identifying the position of the high tide between cycles and sampling drift-lines across the intertidal zone. We demonstrate that beach dynamic processes such as the overlap of strandlines and artefacts of the methods can increase the small-scale variability. The results obtained are discussed in terms of the methodological considerations needed to understand the distribution of pellets in the beach environment, with special implications for studies focused on patterns of input. PMID:26677755

  5. Small-scale temporal and spatial variability in the abundance of plastic pellets on sandy beaches: Methodological considerations for estimating the input of microplastics.

    PubMed

    Moreira, Fabiana Tavares; Prantoni, Alessandro Lívio; Martini, Bruno; de Abreu, Michelle Alves; Stoiev, Sérgio Biato; Turra, Alexander

    2016-01-15

    Microplastics such as pellets have been reported for many years on sandy beaches around the globe. Nevertheless, high variability is observed in their estimates and distribution patterns across the beach environment are still to be unravelled. Here, we investigate the small-scale temporal and spatial variability in the abundance of pellets in the intertidal zone of a sandy beach and evaluate factors that can increase the variability in data sets. The abundance of pellets was estimated during twelve consecutive tidal cycles, identifying the position of the high tide between cycles and sampling drift-lines across the intertidal zone. We demonstrate that beach dynamic processes such as the overlap of strandlines and artefacts of the methods can increase the small-scale variability. The results obtained are discussed in terms of the methodological considerations needed to understand the distribution of pellets in the beach environment, with special implications for studies focused on patterns of input.

  6. Evaluation of single and two-stage adaptive sampling designs for estimation of density and abundance of freshwater mussels in a large river

    USGS Publications Warehouse

    Smith, D.R.; Rogala, J.T.; Gray, B.R.; Zigler, S.J.; Newton, T.J.

    2011-01-01

    Reliable estimates of abundance are needed to assess consequences of proposed habitat restoration and enhancement projects on freshwater mussels in the Upper Mississippi River (UMR). Although there is general guidance on sampling techniques for population assessment of freshwater mussels, the actual performance of sampling designs can depend critically on the population density and spatial distribution at the project site. To evaluate various sampling designs, we simulated sampling of populations, which varied in density and degree of spatial clustering. Because of logistics and costs of large river sampling and spatial clustering of freshwater mussels, we focused on adaptive and non-adaptive versions of single and two-stage sampling. The candidate designs performed similarly in terms of precision (CV) and probability of species detection for fixed sample size. Both CV and species detection were determined largely by density, spatial distribution and sample size. However, designs did differ in the rate that occupied quadrats were encountered. Occupied units had a higher probability of selection using adaptive designs than conventional designs. We used two measures of cost: sample size (i.e. number of quadrats) and distance travelled between the quadrats. Adaptive and two-stage designs tended to reduce distance between sampling units, and thus performed better when distance travelled was considered. Based on the comparisons, we provide general recommendations on the sampling designs for the freshwater mussels in the UMR, and presumably other large rivers.

  7. Rapid Determination of Bacterial Abundance, Biovolume, Morphology, and Growth by Neural Network-Based Image Analysis

    PubMed Central

    Blackburn, Nicholas; Hagström, Åke; Wikner, Johan; Cuadros-Hansson, Rocio; Bjørnsen, Peter Koefoed

    1998-01-01

    Annual bacterial plankton dynamics at several depths and locations in the Baltic Sea were studied by image analysis. Individual bacteria were classified by using an artificial neural network which also effectively identified nonbacterial objects. Cell counts and frequencies of dividing cells were determined, and the data obtained agreed well with visual observations and previously published values. Cell volumes were measured accurately by comparison with bead standards. The survey included 690 images from a total of 138 samples. Each image contained approximately 200 bacteria. The images were analyzed automatically at a rate of 100 images per h. Bacterial abundance exhibited coherent patterns with time and depth, and there were distinct subsurface peaks in the summer months. Four distinct morphological classes were resolved by the image analyzer, and the dynamics of each could be visualized. The bacterial growth rates estimated from frequencies of dividing cells were different from the bacterial growth rates estimated by the thymidine incorporation method. With minor modifications, the image analysis technique described here can be used to analyze other planktonic classes. PMID:9726867

  8. Earth-abundant cocatalysts for semiconductor-based photocatalytic water splitting.

    PubMed

    Ran, Jingrun; Zhang, Jun; Yu, Jiaguo; Jaroniec, Mietek; Qiao, Shi Zhang

    2014-11-21

    Photocatalytic water splitting represents a promising strategy for clean, low-cost, and environmental-friendly production of H2 by utilizing solar energy. There are three crucial steps for the photocatalytic water splitting reaction: solar light harvesting, charge separation and transportation, and the catalytic H2 and O2 evolution reactions. While significant achievement has been made in optimizing the first two steps in the photocatalytic process, much less efforts have been put into improving the efficiency of the third step, which demands the utilization of cocatalysts. To date, cocatalysts based on rare and expensive noble metals are still required for achieving reasonable activity in most semiconductor-based photocatalytic systems, which seriously restricts their large-scale application. Therefore, seeking cheap, earth-abundant and high-performance cocatalysts is indispensable to achieve cost-effective and highly efficient photocatalytic water splitting. This review for the first time summarizes all the developed earth-abundant cocatalysts for photocatalytic H2- and O2-production half reactions as well as overall water splitting. The roles and functional mechanism of the cocatalysts are discussed in detail. Finally, this review is concluded with a summary, and remarks on some challenges and perspectives in this emerging area of research.

  9. Detection of an Abundant Plant-Based Small RNA in Healthy Consumers

    PubMed Central

    Yang, Jian; Farmer, Lisa M.; Agyekum, Abia A. A.; Elbaz-Younes, Ismail; Hirschi, Kendal D.

    2015-01-01

    The mechanisms of delivery of plant small RNAs to consumers must be investigated in order to harness this technology to positively impact biotechnology. Two groups have used honeysuckle (Lonicera japonica) feeding regimes to detect a plant-based small RNA, termed MIR2911, in sera. Meanwhile, numerous groups have failed to detect dietary plant-based small RNAs in consumers. Here we catalog levels of MIR2911 in different herbs, and suggest that in particular herb MIR2911 levels are elevated. Feeding these different herb-based diets to mice, we found MIR2911 levels in the sera and urine were associated with dietary intake levels. Abundance was not the sole determinate of apparent RNA bioavailability, as gavage-feeding large-doses of synthetic MIR2911 permitted only small transient increases in serum levels. Dietary MIR2911 were not modified in circulation by association with the host’s RNA-induced silencing complex, as the RNA did not co-immunoprecipitate with AGO2. The stability of dietary MIR2911 in circulation differed from synthesized small RNAs, as tail vein administration of various synthetic plant-based small RNAs resulted in rapid clearance. However, synthetic MIR2911 appeared to be more stable than the other plant miRNAs tested. Notably, this uptake of dietary MIR2911 was not related to perturbations in the host’s microbiome or gut permeability. We suggest dietary uptake of MIR2911 is commonplace in healthy consumers, and reproducible detection of plant-based small RNAs in consumers depends on dietary abundance, RNA stability and digestion from within the food-matrix. PMID:26335106

  10. Detection of an Abundant Plant-Based Small RNA in Healthy Consumers.

    PubMed

    Yang, Jian; Farmer, Lisa M; Agyekum, Abia A A; Elbaz-Younes, Ismail; Hirschi, Kendal D

    2015-01-01

    The mechanisms of delivery of plant small RNAs to consumers must be investigated in order to harness this technology to positively impact biotechnology. Two groups have used honeysuckle (Lonicera japonica) feeding regimes to detect a plant-based small RNA, termed MIR2911, in sera. Meanwhile, numerous groups have failed to detect dietary plant-based small RNAs in consumers. Here we catalog levels of MIR2911 in different herbs, and suggest that in particular herb MIR2911 levels are elevated. Feeding these different herb-based diets to mice, we found MIR2911 levels in the sera and urine were associated with dietary intake levels. Abundance was not the sole determinate of apparent RNA bioavailability, as gavage-feeding large-doses of synthetic MIR2911 permitted only small transient increases in serum levels. Dietary MIR2911 were not modified in circulation by association with the host's RNA-induced silencing complex, as the RNA did not co-immunoprecipitate with AGO2. The stability of dietary MIR2911 in circulation differed from synthesized small RNAs, as tail vein administration of various synthetic plant-based small RNAs resulted in rapid clearance. However, synthetic MIR2911 appeared to be more stable than the other plant miRNAs tested. Notably, this uptake of dietary MIR2911 was not related to perturbations in the host's microbiome or gut permeability. We suggest dietary uptake of MIR2911 is commonplace in healthy consumers, and reproducible detection of plant-based small RNAs in consumers depends on dietary abundance, RNA stability and digestion from within the food-matrix. PMID:26335106

  11. Particle Pollution Estimation Based on Image Analysis.

    PubMed

    Liu, Chenbin; Tsow, Francis; Zou, Yi; Tao, Nongjian

    2016-01-01

    Exposure to fine particles can cause various diseases, and an easily accessible method to monitor the particles can help raise public awareness and reduce harmful exposures. Here we report a method to estimate PM air pollution based on analysis of a large number of outdoor images available for Beijing, Shanghai (China) and Phoenix (US). Six image features were extracted from the images, which were used, together with other relevant data, such as the position of the sun, date, time, geographic information and weather conditions, to predict PM2.5 index. The results demonstrate that the image analysis method provides good prediction of PM2.5 indexes, and different features have different significance levels in the prediction. PMID:26828757

  12. Particle Pollution Estimation Based on Image Analysis

    PubMed Central

    Liu, Chenbin; Tsow, Francis; Zou, Yi; Tao, Nongjian

    2016-01-01

    Exposure to fine particles can cause various diseases, and an easily accessible method to monitor the particles can help raise public awareness and reduce harmful exposures. Here we report a method to estimate PM air pollution based on analysis of a large number of outdoor images available for Beijing, Shanghai (China) and Phoenix (US). Six image features were extracted from the images, which were used, together with other relevant data, such as the position of the sun, date, time, geographic information and weather conditions, to predict PM2.5 index. The results demonstrate that the image analysis method provides good prediction of PM2.5 indexes, and different features have different significance levels in the prediction. PMID:26828757

  13. Particle Pollution Estimation Based on Image Analysis.

    PubMed

    Liu, Chenbin; Tsow, Francis; Zou, Yi; Tao, Nongjian

    2016-01-01

    Exposure to fine particles can cause various diseases, and an easily accessible method to monitor the particles can help raise public awareness and reduce harmful exposures. Here we report a method to estimate PM air pollution based on analysis of a large number of outdoor images available for Beijing, Shanghai (China) and Phoenix (US). Six image features were extracted from the images, which were used, together with other relevant data, such as the position of the sun, date, time, geographic information and weather conditions, to predict PM2.5 index. The results demonstrate that the image analysis method provides good prediction of PM2.5 indexes, and different features have different significance levels in the prediction.

  14. Global distribution of microbial abundance and biomass in subseafloor sediment

    PubMed Central

    Kallmeyer, Jens; Pockalny, Robert; Adhikari, Rishi Ram; Smith, David C.; D’Hondt, Steven

    2012-01-01

    The global geographic distribution of subseafloor sedimentary microbes and the cause(s) of that distribution are largely unexplored. Here, we show that total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. This variation is strongly correlated with mean sedimentation rate and distance from land. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9⋅1029 cells [corresponding to 4.1 petagram (Pg) C and ∼0.6% of Earth’s total living biomass]. This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate Earth’s total number of microbes and total living biomass to be, respectively, 50–78% and 10–45% lower than previous estimates. PMID:22927371

  15. Detecting horizontally transferred and essential genes based on dinucleotide relative abundance.

    PubMed

    Baran, Robert H; Ko, Hanseok

    2008-10-01

    Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes.

  16. A trait based perspective on the biogeography of common and abundant marine bacterioplankton clades.

    PubMed

    Brown, Mark V; Ostrowski, Martin; Grzymski, Joseph J; Lauro, Federico M

    2014-06-01

    Marine microbial communities provide much of the energy upon which all higher trophic levels depend, particularly in open-ocean and oligotrophic systems, and play a pivotal role in biogeochemical cycling. How and why species are distributed in the global oceans, and whether net ecosystem function can be accurately predicted from community composition are fundamental questions for marine scientists. Many of the most abundant clades of marine bacteria, including the Prochlorococcus, Synechococcus, SAR11, SAR86 and Roseobacter, have a very broad, if not a cosmopolitan distribution. However this is not reflected in an underlying genetic identity. Rather, widespread distribution in these organisms is achieved by the existence of closely related but discrete ecotypes that display niche adaptations. Closely related ecotypes display specific nutritional or energy generating mechanisms and are adapted to different physical parameters including temperature, salinity, and hydrostatic pressure. Furthermore, biotic phenomena such as selective grazing and viral loss contribute to the success or failure of ecotypes allowing some to compete effectively in particular marine provinces but not in others. An additional layer of complexity is added by ocean currents and hydrodynamic specificity of water body masses that bound microbial dispersal and immigration. These vary in space and time with respect to intensity and direction, making the definition of large biogeographic provinces problematic. A deterministic theory aimed at understanding how all these factors shape microbial life in the oceans can only proceed through analysis of microbial traits, rather than pure phylogenetic assessments. Trait based approaches seek mechanistic explanations for the observed temporal and spatial patterns. This review will present successful recent advances in phylogenetic and trait based biogeographic analyses in some of the most abundant marine taxa. PMID:24662471

  17. Lakewide estimates of alewife biomass and Chinook salmon abundance and consumption in Lake Ontario, 1989–2005: implications for prey fish sustainability

    USGS Publications Warehouse

    Murry, Brent A.; Connerton, Michael J.; O'Gorman, Robert; Stewart, Donald J.; Ringlerd, Neil H.

    2010-01-01

    Stocking levels of Chinook salmon Oncorhynchus tshawytscha for Lake Ontario have been highly controversial since the early 1990s, largely because of uncertainties about lakewide abundance and rates of prey consumption. Previous estimates have focused on years before 1995; since then, however, the Lake Ontario ecosystem has undergone substantial changes, and there is new evidence of extensive natural recruitment. Presented here are new abundance estimates of Chinook salmon and alewives Alosa pseudoharengus in Lake Ontario and a reevaluation of the potential risk of alewife population collapse. We found that Lake Ontario has been supporting, on average (1989–2005), 1.83 × 106 (range, 1.08 × 106 to 3.24 × 106) Chinook salmon of ages 1–4, amounting to a mean annual biomass of 11.33 × 103 metric tons (range, 5.83 × 103 to 23.04 × 103 metric tons). During the same period (1989–2005), the lake supported an alewife biomass of 173.66 × 103 metric tons (range, 62.37 × 103 to 345.49 × 103 metric tons); Chinook salmon of ages 1–4 consumed, on average, 22% (range, 11–44%) of the alewife biomass annually. Because our estimates probably underestimate total consumption and because Chinook salmon are only one of several salmonine species that depend on alewives, predation pressure on the Lake Ontario alewife population may be high enough to raise concerns about long-term stability of this predator–prey system.

  18. Radar Based Quantitative Precipitation Estimation in Taiwan

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Zhang, J.; Chang, P.

    2012-12-01

    Accurate high-resolution radar quantitative precipitation estimation (QPE) has shown increasing values in hydrological predictions in the last decade. Such QPEs are especially valuable in complex terrain where rain gauge network is sparse and hard to maintain while flash floods and mudslides are common hazards. Taiwan Central Weather Bureau has deployed four S-band radars to support their flood warning operations in recent years, and a real-time multi-radar QPE system was developed. Evaluations of the real-time system over one-year revealed some underestimation issues in the radar QPE. The current work investigates these issues and develops a series of refinements to the system. The refinements include replacing the general R-Z relationships used in the old system with the local ones, mitigating non-standard beam blockage artifacts based on long-term accumulations, and applying vertical profile of reflectivity (VPR) corrections. The local R-Z relationships were derived from 2D video disdrometer observations of winter stratiform precipitation, meiyu fronts, local convective storms, and typhoons. The VPR correction was applied to reduce radar QPE errors in severely blocked area near the Central Mountain Range (CMR). The new radar QPE system was tested using different precipitation events and showed significant improvements over the old system especially along the CMR.

  19. Phylogenetic analysis of microalgae based on highly abundant proteins using mass spectrometry.

    PubMed

    Lee, Hae-Won; Roh, Seong Woon; Cho, Kichul; Kim, Kil-Nam; Cha, In-Tae; Yim, Kyung June; Song, Hye Seon; Nam, Young-Do; Oda, Tatsuya; Chung, Young-Ho; Kim, Soo Jung; Choi, Jong-Soon; Kim, Daekyung

    2015-01-01

    The blooms of toxic phototrophic microorganisms, such as microalgae and cyanobacteria, which are typically found in freshwater and marine environments, are becoming more frequent and problematic in aquatic systems. Due to accumulation of toxic algae, harmful algal blooms (HABs) exert negative effects on aquatic systems. Therefore, rapid detection of harmful microalgae is important for monitoring the occurrence of HABs. Mass spectrometry-based methods have become sensitive, specific techniques for the identification and characterization of microorganisms. Matrix-assisted laser desorption/ionization (MALDI) with time-of-flight (TOF) mass spectrometry (MS) allows us to measure a unique molecular fingerprint of highly abundant proteins in a microorganism and has been used for the rapid, accurate identification of bacteria and fungi in clinical microbiology. Here, we tested the specificity of MALDI-TOF MS using microalgal strains (Heterocapsa, Alexandrium, Nannochloropsis, Chaetoceros, Chlorella, and Dunaliella spp.). Our research suggested that this method was comparable in terms of the rapid identification of microalgea to conventional methods based on genetic information and morphology. Thus, this efficient mass spectrometry-based technique may have applications in the rapid identification of harmful microorganisms from aquatic environmental samples.

  20. Phylogenetic analysis of microalgae based on highly abundant proteins using mass spectrometry.

    PubMed

    Lee, Hae-Won; Roh, Seong Woon; Cho, Kichul; Kim, Kil-Nam; Cha, In-Tae; Yim, Kyung June; Song, Hye Seon; Nam, Young-Do; Oda, Tatsuya; Chung, Young-Ho; Kim, Soo Jung; Choi, Jong-Soon; Kim, Daekyung

    2015-01-01

    The blooms of toxic phototrophic microorganisms, such as microalgae and cyanobacteria, which are typically found in freshwater and marine environments, are becoming more frequent and problematic in aquatic systems. Due to accumulation of toxic algae, harmful algal blooms (HABs) exert negative effects on aquatic systems. Therefore, rapid detection of harmful microalgae is important for monitoring the occurrence of HABs. Mass spectrometry-based methods have become sensitive, specific techniques for the identification and characterization of microorganisms. Matrix-assisted laser desorption/ionization (MALDI) with time-of-flight (TOF) mass spectrometry (MS) allows us to measure a unique molecular fingerprint of highly abundant proteins in a microorganism and has been used for the rapid, accurate identification of bacteria and fungi in clinical microbiology. Here, we tested the specificity of MALDI-TOF MS using microalgal strains (Heterocapsa, Alexandrium, Nannochloropsis, Chaetoceros, Chlorella, and Dunaliella spp.). Our research suggested that this method was comparable in terms of the rapid identification of microalgea to conventional methods based on genetic information and morphology. Thus, this efficient mass spectrometry-based technique may have applications in the rapid identification of harmful microorganisms from aquatic environmental samples. PMID:25476355

  1. Contour-based object orientation estimation

    NASA Astrophysics Data System (ADS)

    Alpatov, Boris; Babayan, Pavel

    2016-04-01

    Real-time object orientation estimation is an actual problem of computer vision nowadays. In this paper we propose an approach to estimate an orientation of objects lacking axial symmetry. Proposed algorithm is intended to estimate orientation of a specific known 3D object, so 3D model is required for learning. The proposed orientation estimation algorithm consists of 2 stages: learning and estimation. Learning stage is devoted to the exploring of studied object. Using 3D model we can gather set of training images by capturing 3D model from viewpoints evenly distributed on a sphere. Sphere points distribution is made by the geosphere principle. It minimizes the training image set. Gathered training image set is used for calculating descriptors, which will be used in the estimation stage of the algorithm. The estimation stage is focusing on matching process between an observed image descriptor and the training image descriptors. The experimental research was performed using a set of images of Airbus A380. The proposed orientation estimation algorithm showed good accuracy (mean error value less than 6°) in all case studies. The real-time performance of the algorithm was also demonstrated.

  2. Regulation of NEIL1 protein abundance by RAD9 is important for efficient base excision repair.

    PubMed

    Panigrahi, Sunil K; Hopkins, Kevin M; Lieberman, Howard B

    2015-05-19

    RAD9 participates in DNA damage-induced cell cycle checkpoints and DNA repair. As a member of the RAD9-HUS1-RAD1 (9-1-1) complex, it can sense DNA damage and recruit ATR to damage sites. RAD9 binding can enhance activities of members of different DNA repair pathways, including NEIL1 DNA glycosylase, which initiates base excision repair (BER) by removing damaged DNA bases. Moreover, RAD9 can act independently of 9-1-1 as a gene-specific transcription factor. Herein, we show that mouse Rad9(-/-) relative to Rad9(+/+) embryonic stem (ES) cells have reduced levels of Neil1 protein. Also, human prostate cancer cells, DU145 and PC-3, knocked down for RAD9 demonstrate reduced NEIL1 abundance relative to controls. We found that Rad9 is required for Neil1 protein stability in mouse ES cells, whereas it regulates NEIL1 transcription in the human cells. RAD9 depletion enhances sensitivity to UV, gamma rays and menadione, but ectopic expression of RAD9 or NEIL1 restores resistance. Glycosylase/apurinic lyase activity was reduced in Rad9(-/-) mouse ES and RAD9 knocked-down human prostate cancer whole cell extracts, relative to controls. Neil1 or Rad9 addition restored this incision activity. Thus, we demonstrate that RAD9 regulates BER by controlling NEIL1 protein levels, albeit by different mechanisms in human prostate cancer versus mouse ES cells.

  3. Spectrum-based estimators of the bivariate Hurst exponent

    NASA Astrophysics Data System (ADS)

    Kristoufek, Ladislav

    2014-12-01

    We discuss two alternate spectrum-based estimators of the bivariate Hurst exponent in the power-law cross-correlations setting, the cross-periodogram and local X -Whittle estimators, as generalizations of their univariate counterparts. As the spectrum-based estimators are dependent on a part of the spectrum taken into consideration during estimation, a simulation study showing performance of the estimators under varying bandwidth parameter as well as correlation between processes and their specification is provided as well. These estimators are less biased than the already existent averaged periodogram estimator, which, however, has slightly lower variance. The spectrum-based estimators can serve as a good complement to the popular time domain estimators.

  4. ESTIMATION OF THE NEON/OXYGEN ABUNDANCE RATIO AT THE HELIOSPHERIC TERMINATION SHOCK AND IN THE LOCAL INTERSTELLAR MEDIUM FROM IBEX OBSERVATIONS

    SciTech Connect

    Bochsler, P.; Petersen, L.; Moebius, E.; Schwadron, N. A.; Wurz, P.; Scheer, J. A.; Fuselier, S. A.; McComas, D. J.; Bzowski, M.; Frisch, P. C.

    2012-02-01

    We report the first direct measurement of the Ne/O abundance ratio of the interstellar neutral gas flowing into the inner heliosphere. From the first year of Interstellar Boundary Explorer IBEX data collected in spring 2009, we derive the fluxes of interstellar neutral oxygen and neon. Using the flux ratio at the location of IBEX at 1 AU at the time of the observations, and using the ionization rates of neon and oxygen prevailing in the heliosphere during the period of solar minimum, we estimate the neon/oxygen ratios at the heliospheric termination shock and in the gas phase of the inflowing local interstellar medium. Our estimate is (Ne/O){sub gas,ISM} = 0.27 {+-} 0.10, which is-within the large given uncertainties-consistent with earlier measurements from pickup ions. Our value is larger than the solar abundance ratio, possibly indicating that a significant fraction of oxygen in the local interstellar medium is hidden in grains and/or ices.

  5. A Monte Carlo method for variance estimation for estimators based on induced smoothing

    PubMed Central

    Jin, Zhezhen; Shao, Yongzhao; Ying, Zhiliang

    2015-01-01

    An important issue in statistical inference for semiparametric models is how to provide reliable and consistent variance estimation. Brown and Wang (2005. Standard errors and covariance matrices for smoothed rank estimators. Biometrika 92, 732–746) proposed a variance estimation procedure based on an induced smoothing for non-smooth estimating functions. Herein a Monte Carlo version is developed that does not require any explicit form for the estimating function itself, as long as numerical evaluation can be carried out. A general convergence theory is established, showing that any one-step iteration leads to a consistent variance estimator and continuation of the iterations converges at an exponential rate. The method is demonstrated through the Buckley–James estimator and the weighted log-rank estimators for censored linear regression, and rank estimation for multiple event times data. PMID:24812418

  6. Effect of aggregation of horn fly populations within cattle herds and consequences for sampling to obtain unbiased estimates of abundance.

    PubMed

    Lysyk, T J; Steelman, C D

    2004-07-01

    Reanalysis of counts of horn fly, Hematobia irritans (L.), obtained from a variety of cattle herds indicated that aggregation of the flies within herds decreased as mean fly density increased. Aggregation was also related to the proportion of fly-resistant and fly-susceptible cattle in a herd. Herds were grouped according to their degree of horn fly aggregation. Low aggregation herds included larger framed Angus, Horned Hereford, Polled Hereford, and Red Poll breeds. Moderate aggregation occurred with Brahman, Charolais, small-framed Angus, mixed cows, and Hereford x Charolais cross. High aggregation occurred with Chianina and mixed herds. Relationships between the sample means and variances varied among aggregation groups. A resampling approach was used to determine the influence of random sampling of a herd on the proportion of horn fly population estimates within fixed percentages of the true mean. The proportion of sample means within +/- 5, 10, 15, and 20% of the true means varied with the proportion of the herd sampled, the mean and variance of fly density, and herd size. Recommendations for obtaining sample size to estimate fly density within a fixed percentage of the true mean are given.

  7. Effect of aggregation of horn fly populations within cattle herds and consequences for sampling to obtain unbiased estimates of abundance.

    PubMed

    Lysyk, T J; Steelman, C D

    2004-07-01

    Reanalysis of counts of horn fly, Hematobia irritans (L.), obtained from a variety of cattle herds indicated that aggregation of the flies within herds decreased as mean fly density increased. Aggregation was also related to the proportion of fly-resistant and fly-susceptible cattle in a herd. Herds were grouped according to their degree of horn fly aggregation. Low aggregation herds included larger framed Angus, Horned Hereford, Polled Hereford, and Red Poll breeds. Moderate aggregation occurred with Brahman, Charolais, small-framed Angus, mixed cows, and Hereford x Charolais cross. High aggregation occurred with Chianina and mixed herds. Relationships between the sample means and variances varied among aggregation groups. A resampling approach was used to determine the influence of random sampling of a herd on the proportion of horn fly population estimates within fixed percentages of the true mean. The proportion of sample means within +/- 5, 10, 15, and 20% of the true means varied with the proportion of the herd sampled, the mean and variance of fly density, and herd size. Recommendations for obtaining sample size to estimate fly density within a fixed percentage of the true mean are given. PMID:15311450

  8. Abundance, Distribution and Estimated Consumption (kg fish) of Piscivorous Birds Along the Yakima River, Washington State; Implications for Fisheries Management, 2002 Annual Report.

    SciTech Connect

    Major, III, Walter; Grassley, James M.; Ryding, Kristen E.

    2003-05-01

    This report is divided into two chapters. The abstract for chapter one is--Understanding of the abundance and spatial and temporal distributions of piscivorous birds and their potential consumption of fish is an increasingly important aspect of fisheries management. During 1999-2002, we determined the abundance and distribution and estimated the maximum consumption (kg biomass) of fish-eating birds along the length of the Yakima River in Washington State. Sixteen different species were observed during the 4-yr study, but only half of those were observed during all years. Abundance and estimated consumption of fish within the upper and middle sections of the river were dominated by common mergansers (Mergus merganser) which are known to breed in those reaches. Common mergansers accounted for 78 to 94% of the estimated total fish take for the upper river or approximately 28,383 {+-} 1,041 kg over the 4 yrs. A greater diversity of avian piscivores occurred in the lower river and potential impacts to fish populations was more evenly distributed among the species. In 1999-2000, great blue herons potentially accounted for 29 and 36% of the fish consumed, whereas in 2001-2002 American white pelicans accounted for 53 and 55%. We estimated that approximately 75,878 {+-} 6,616 kg of fish were consumed by piscivorous birds in the lower sections of the river during the study. Bird assemblages differed spatially along the river with a greater abundance of colonial nesting species within the lower sections of the river, especially during spring and the nesting season. The abundance of avian piscivores and consumption estimates are discussed within the context of salmonid supplementation efforts on the river and juvenile out-migration. The abstract for chapter two is--Consumption of fish by piscivorous birds may be a significant constraint on efforts to enhance salmonid populations within tributaries to the Columbia River in Washington State. During 1999-2002, we determined the

  9. Microclimate Data Improve Predictions of Insect Abundance Models Based on Calibrated Spatiotemporal Temperatures

    PubMed Central

    Rebaudo, François; Faye, Emile; Dangles, Olivier

    2016-01-01

    A large body of literature has recently recognized the role of microclimates in controlling the physiology and ecology of species, yet the relevance of fine-scale climatic data for modeling species performance and distribution remains a matter of debate. Using a 6-year monitoring of three potato moth species, major crop pests in the tropical Andes, we asked whether the spatiotemporal resolution of temperature data affect the predictions of models of moth performance and distribution. For this, we used three different climatic data sets: (i) the WorldClim dataset (global dataset), (ii) air temperature recorded using data loggers (weather station dataset), and (iii) air crop canopy temperature (microclimate dataset). We developed a statistical procedure to calibrate all datasets to monthly and yearly variation in temperatures, while keeping both spatial and temporal variances (air monthly temperature at 1 km² for the WorldClim dataset, air hourly temperature for the weather station, and air minute temperature over 250 m radius disks for the microclimate dataset). Then, we computed pest performances based on these three datasets. Results for temperature ranging from 9 to 11°C revealed discrepancies in the simulation outputs in both survival and development rates depending on the spatiotemporal resolution of the temperature dataset. Temperature and simulated pest performances were then combined into multiple linear regression models to compare predicted vs. field data. We used an additional set of study sites to test the ability of the results of our model to be extrapolated over larger scales. Results showed that the model implemented with microclimatic data best predicted observed pest abundances for our study sites, but was less accurate than the global dataset model when performed at larger scales. Our simulations therefore stress the importance to consider different temperature datasets depending on the issue to be solved in order to accurately predict species

  10. Microclimate Data Improve Predictions of Insect Abundance Models Based on Calibrated Spatiotemporal Temperatures.

    PubMed

    Rebaudo, François; Faye, Emile; Dangles, Olivier

    2016-01-01

    A large body of literature has recently recognized the role of microclimates in controlling the physiology and ecology of species, yet the relevance of fine-scale climatic data for modeling species performance and distribution remains a matter of debate. Using a 6-year monitoring of three potato moth species, major crop pests in the tropical Andes, we asked whether the spatiotemporal resolution of temperature data affect the predictions of models of moth performance and distribution. For this, we used three different climatic data sets: (i) the WorldClim dataset (global dataset), (ii) air temperature recorded using data loggers (weather station dataset), and (iii) air crop canopy temperature (microclimate dataset). We developed a statistical procedure to calibrate all datasets to monthly and yearly variation in temperatures, while keeping both spatial and temporal variances (air monthly temperature at 1 km² for the WorldClim dataset, air hourly temperature for the weather station, and air minute temperature over 250 m radius disks for the microclimate dataset). Then, we computed pest performances based on these three datasets. Results for temperature ranging from 9 to 11°C revealed discrepancies in the simulation outputs in both survival and development rates depending on the spatiotemporal resolution of the temperature dataset. Temperature and simulated pest performances were then combined into multiple linear regression models to compare predicted vs. field data. We used an additional set of study sites to test the ability of the results of our model to be extrapolated over larger scales. Results showed that the model implemented with microclimatic data best predicted observed pest abundances for our study sites, but was less accurate than the global dataset model when performed at larger scales. Our simulations therefore stress the importance to consider different temperature datasets depending on the issue to be solved in order to accurately predict species

  11. Web-based Interspecies Correlation Estimation

    EPA Science Inventory

    Web-ICE estimates acute toxicity (LC50/LD50) of a chemical to a species, genus, or family from the known toxicity of the chemical to a surrogate species. Web-ICE has modules to predict acute toxicity to aquatic (fish and invertebrates) and wildlife (birds and mammals) taxa for us...

  12. Using GIS mapping of the extent of nearshore rocky reefs to estimate the abundance and reproductive output of important fishery species.

    PubMed

    Claisse, Jeremy T; Pondella, Daniel J; Williams, Jonathan P; Sadd, James

    2012-01-01

    Kelp Bass (Paralabrax clathratus) and California Sheephead (Semicossyphus pulcher) are economically and ecologically valuable rocky reef fishes in southern California, making them likely indicator species for evaluating resource management actions. Multiple spatial datasets, aerial and satellite photography, underwater observations and expert judgment were used to produce a comprehensive map of nearshore natural rocky reef habitat for the Santa Monica Bay region (California, USA). It was then used to examine the relative contribution of individual reefs to a regional estimate of abundance and reproductive potential of the focal species. For the reefs surveyed for fishes (i.e. 18 out of the 22 in the region, comprising 82% the natural rocky reef habitat <30 m depth, with a total area of 1850 ha), total abundance and annual egg production of California Sheephead were 451 thousand fish (95% CI: 369 to 533 thousand) and 203 billion eggs (95% CI: 135 to 272 billion). For Kelp Bass, estimates were 805 thousand fish (95% CI: 669 to 941 thousand) and 512 billion eggs (95% CI: 414 to 610 billion). Size structure and reef area were key factors in reef-specific contributions to the regional egg production. The size structures of both species illustrated impacts from fishing, and results demonstrate the potential that relatively small increases in the proportion of large females on larger reefs could have on regional egg production. For California Sheephead, a substantial proportion of the regional egg production estimate (>30%) was produced from a relatively small proportion of the regional reef area (c. 10%). Natural nearshore rocky reefs make up only 11% of the area in the newly designated MPAs in this region, but results provide some optimism that regional fisheries could benefit through an increase in overall reproductive output, if adequate increases in size structure of targeted species are realized.

  13. Using GIS Mapping of the Extent of Nearshore Rocky Reefs to Estimate the Abundance and Reproductive Output of Important Fishery Species

    PubMed Central

    Claisse, Jeremy T.; Pondella, Daniel J.; Williams, Jonathan P.; Sadd, James

    2012-01-01

    Kelp Bass (Paralabrax clathratus) and California Sheephead (Semicossyphus pulcher) are economically and ecologically valuable rocky reef fishes in southern California, making them likely indicator species for evaluating resource management actions. Multiple spatial datasets, aerial and satellite photography, underwater observations and expert judgment were used to produce a comprehensive map of nearshore natural rocky reef habitat for the Santa Monica Bay region (California, USA). It was then used to examine the relative contribution of individual reefs to a regional estimate of abundance and reproductive potential of the focal species. For the reefs surveyed for fishes (i.e. 18 out of the 22 in the region, comprising 82% the natural rocky reef habitat <30 m depth, with a total area of 1850 ha), total abundance and annual egg production of California Sheephead were 451 thousand fish (95% CI: 369 to 533 thousand) and 203 billion eggs (95% CI: 135 to 272 billion). For Kelp Bass, estimates were 805 thousand fish (95% CI: 669 to 941thousand) and 512 billion eggs (95% CI: 414 to 610 billion). Size structure and reef area were key factors in reef-specific contributions to the regional egg production. The size structures of both species illustrated impacts from fishing, and results demonstrate the potential that relatively small increases in the proportion of large females on larger reefs could have on regional egg production. For California Sheephead, a substantial proportion of the regional egg production estimate (>30%) was produced from a relatively small proportion of the regional reef area (c. 10%). Natural nearshore rocky reefs make up only 11% of the area in the newly designated MPAs in this region, but results provide some optimism that regional fisheries could benefit through an increase in overall reproductive output, if adequate increases in size structure of targeted species are realized. PMID:22272326

  14. Using GIS mapping of the extent of nearshore rocky reefs to estimate the abundance and reproductive output of important fishery species.

    PubMed

    Claisse, Jeremy T; Pondella, Daniel J; Williams, Jonathan P; Sadd, James

    2012-01-01

    Kelp Bass (Paralabrax clathratus) and California Sheephead (Semicossyphus pulcher) are economically and ecologically valuable rocky reef fishes in southern California, making them likely indicator species for evaluating resource management actions. Multiple spatial datasets, aerial and satellite photography, underwater observations and expert judgment were used to produce a comprehensive map of nearshore natural rocky reef habitat for the Santa Monica Bay region (California, USA). It was then used to examine the relative contribution of individual reefs to a regional estimate of abundance and reproductive potential of the focal species. For the reefs surveyed for fishes (i.e. 18 out of the 22 in the region, comprising 82% the natural rocky reef habitat <30 m depth, with a total area of 1850 ha), total abundance and annual egg production of California Sheephead were 451 thousand fish (95% CI: 369 to 533 thousand) and 203 billion eggs (95% CI: 135 to 272 billion). For Kelp Bass, estimates were 805 thousand fish (95% CI: 669 to 941 thousand) and 512 billion eggs (95% CI: 414 to 610 billion). Size structure and reef area were key factors in reef-specific contributions to the regional egg production. The size structures of both species illustrated impacts from fishing, and results demonstrate the potential that relatively small increases in the proportion of large females on larger reefs could have on regional egg production. For California Sheephead, a substantial proportion of the regional egg production estimate (>30%) was produced from a relatively small proportion of the regional reef area (c. 10%). Natural nearshore rocky reefs make up only 11% of the area in the newly designated MPAs in this region, but results provide some optimism that regional fisheries could benefit through an increase in overall reproductive output, if adequate increases in size structure of targeted species are realized. PMID:22272326

  15. Abundance- and functional-based mechanisms of plant diversity loss with fertilization in the presence and absence of herbivores.

    PubMed

    Yang, Zhongling; Hautier, Yann; Borer, Elizabeth T; Zhang, Chunhui; Du, Guozhen

    2015-09-01

    Nutrient supply and herbivores can regulate plant species composition, biodiversity and functioning of terrestrial ecosystems. Nutrient enrichment frequently increases plant productivity and decreases diversity while herbivores tend to maintain plant diversity in productive systems. However, the mechanisms by which nutrient enrichment and herbivores regulate plant diversity remain unclear. Abundance-based mechanisms propose that fertilization leads to the extinction of rare species due to random loss of individuals of all species. In contrast, functional-based mechanisms propose that species exclusion is based on functional traits which are disadvantageous under fertilized conditions. We tested mechanistic links between fertilization and diversity loss in the presence or absence of consumers using data from a 4-year fertilization and fencing experiment in an alpine meadow. We found that both abundance- and functional-based mechanisms simultaneously affected species loss in the absence of herbivores while only abundance-based mechanisms affected species loss in the presence of herbivores. Our results indicate that an abundance-based mechanism may consistently play a role in the loss of plant diversity with fertilization, and that diversity decline is driven primarily by the loss of rare species regardless of a plant's functional traits and whether or not herbivores are present. Increasing efforts to conserve rare species in the context of ecosystem eutrophication is a central challenge for grazed grassland ecosystems.

  16. Statistical approach to meteoroid shape estimation based on recovered meteorites

    NASA Astrophysics Data System (ADS)

    Vinnikov, V.; Gritsevich, M.; Turchak, L.

    2014-07-01

    Each meteorite sample can provide data on the chemical and physical properties of interplanetary matter. The set of recovered fragments within one meteorite fall can give additional information on the history of its parent asteroid. A reliably estimated meteoroid shape is a valuable input parameter for the atmospheric entry scenario, since the pre-entry mass, terminal meteorite mass, and fireball luminosity are proportional to the pre-entry shape factor of the meteoroid to the power of 3 [1]. We present a statistical approach to the estimation of meteoroid pre-entry shape [2], applied to the detailed data on recovered meteorite fragments. This is a development of our recent study on the fragment mass distribution functions for the Košice meteorite fall [3]. The idea of the shape estimation technique is based on experiments that show that brittle fracturing produces multiple fragments of sizes smaller than or equal to the smallest dimension of the body [2]. Such shattering has fractal properties similar to many other natural phenomena [4]. Thus, this self-similarity for scaling mass sequences can be described by the power law statistical expressions [5]. The finite mass and the number of fragments N are represented via an exponential cutoff for the maximum fragment mass m_U. The undersampling of tiny unrecoverable fragments is handled via an additional constraint on the minimum fragment mass m_L. The complementary cumulative distribution function has the form F( m)={N-j}/{m_j}( {m}/{m_j})^{-β_0}exp( {m-m_j}/{m_U}). The resulting parameters sought (scaling exponent β_0 and mass limits) are computed to fit the empirical fragment mass distribution: S(β_0, j, m_U) = sum_{i=j}^{N}[F(m_i)-{N-j}/{m_j}]^2, m_j = m_L. The scaling exponent correlates with the dimensionless shape parameter d [2]: 0.13d^2-0.21d+1.1-β=0, which, in turn, is expressed via the ratio of the linear dimensions a, b, c of the shattering body [2]: d = 1+2(ab+ac+bc)(a^2+b^2+c^2)^{-1}. We apply the

  17. Inferring recent historic abundance from current genetic diversity.

    PubMed

    Palsbøll, Per J; Zachariah Peery, M; Olsen, Morten T; Beissinger, Steven R; Bérubé, Martine

    2013-01-01

    Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only. PMID:23181682

  18. Distributed Damage Estimation for Prognostics based on Structural Model Decomposition

    NASA Technical Reports Server (NTRS)

    Daigle, Matthew; Bregon, Anibal; Roychoudhury, Indranil

    2011-01-01

    Model-based prognostics approaches capture system knowledge in the form of physics-based models of components, and how they fail. These methods consist of a damage estimation phase, in which the health state of a component is estimated, and a prediction phase, in which the health state is projected forward in time to determine end of life. However, the damage estimation problem is often multi-dimensional and computationally intensive. We propose a model decomposition approach adapted from the diagnosis community, called possible conflicts, in order to both improve the computational efficiency of damage estimation, and formulate a damage estimation approach that is inherently distributed. Local state estimates are combined into a global state estimate from which prediction is performed. Using a centrifugal pump as a case study, we perform a number of simulation-based experiments to demonstrate the approach.

  19. THE SOLAR FLARE IRON ABUNDANCE

    SciTech Connect

    Phillips, K. J. H.; Dennis, B. R. E-mail: Brian.R.Dennis@nasa.gov

    2012-03-20

    The abundance of iron is measured from emission line complexes at 6.65 keV (Fe line) and 8 keV (Fe/Ni line) in RHESSI X-ray spectra during solar flares. Spectra during long-duration flares with steady declines were selected, with an isothermal assumption and improved data analysis methods over previous work. Two spectral fitting models give comparable results, viz., an iron abundance that is lower than previous coronal values but higher than photospheric values. In the preferred method, the estimated Fe abundance is A(Fe) = 7.91 {+-} 0.10 (on a logarithmic scale, with A(H) = 12) or 2.6 {+-} 0.6 times the photospheric Fe abundance. Our estimate is based on a detailed analysis of 1898 spectra taken during 20 flares. No variation from flare to flare is indicated. This argues for a fractionation mechanism similar to quiet-Sun plasma. The new value of A(Fe) has important implications for radiation loss curves, which are estimated.

  20. The Origin and Evolution of the Halo PN BoBn 1: From a Viewpoint of Chemical Abundances Based on Multiwavelength Spectra

    NASA Astrophysics Data System (ADS)

    Otsuka, Masaaki; Tajitsu, Akito; Hyung, Siek; Izumiura, Hideyuki

    2010-11-01

    We have performed a comprehensive chemical abundance analysis of the extremely metal-poor ([Ar/H] < -2) halo planetary nebula (PN) BoBn 1 based on International Ultraviolet Explorer archive data, Subaru/High-Dispersion Spectrograph spectra, VLT/UVES archive data, and Spitzer/IRS spectra. We have detected over 600 lines in total and calculated ionic and elemental abundances of 13 elements using detected optical recombination lines (ORLs) and collisionally excited lines (CELs). The estimations of C, N, O, and Ne abundances from the ORLs and Kr, Xe, and Ba from the CELs are done the first for this nebula, empirically and theoretically. The C, N, O, and Ne abundances from ORLs are systematically larger than those from CELs. The abundance discrepancies apart from O could be explained by a temperature fluctuation model, and that of O might be by a hydrogen-deficient cold component model. We have detected five fluorine and several slow neutron capture elements (the s-process). The amounts of [F/H], [Kr/H], and [Xe/H] suggest that BoBn 1 is the most F-rich among F-detected PNe and is a heavy s-process element rich PN. We have confirmed dust in the nebula that is composed of amorphous carbon and polycyclic aromatic hydrocarbons with a total mass of 5.8 × 10-6 M sun. The photoionization models built with non-LTE theoretical stellar atmospheres indicate that the progenitor was a 1-1.5 M sun star that would evolve into a white dwarf with an ~0.62 M sun core mass and ~0.09 M sun ionized nebula. We have measured a heliocentric radial velocity of +191.6 ±1.3 km s-1 and expansion velocity 2V exp of 40.5 ± 3.3 km s-1 from an average over 300 lines. The derived elemental abundances have been reviewed from the standpoint of theoretical nucleosynthesis models. It is likely that the elemental abundances except N could be explained either by a 1.5 M sun single star model or by a binary model composed of 0.75 M sun + 1.5 M sun stars. Careful examination implies that BoBn 1 has evolved

  1. Abundance analysis of the supergiant stars HD 80057 and HD 80404 based on their UVES Spectra

    NASA Astrophysics Data System (ADS)

    Tanrıverdi, T.; Baştürk, Ö.

    2016-08-01

    This study presents elemental abundances of the early A-type supergiant HD 80057 and the late A-type supergiant HD 80404. High resolution and high signal-to-noise ratio spectra published by the UVES Paranal Observatory Project (Bagnulo et al., 2003)1

  2. Model-based Small Area Estimates of Cancer Risk Factors and Screening Behaviors - Small Area Estimates

    Cancer.gov

    These model-based estimates use two surveys, the Behavioral Risk Factor Surveillance System (BRFSS) and the National Health Interview Survey (NHIS). The two surveys are combined using novel statistical methodology.

  3. Combining split-beam and dual-frequency identification sonars to estimate abundance of anadromous fishes in the Roanoke River, North Carolina

    USGS Publications Warehouse

    Hughes, Jacob B.; Hightower, Joseph E.

    2015-01-01

    Riverine hydroacoustic techniques are an effective method for evaluating abundance of upstream migrating anadromous fishes. To use these methods in the Roanoke River, North Carolina, at a wide site with uneven bottom topography, we used a combination of split-beam sonar and dual-frequency identification sonar (DIDSON) deployments. We aimed a split-beam sonar horizontally to monitor midchannel and near-bottom zones continuously over the 3-month spring monitoring periods in 2010 and 2011. The DIDSON was rotated between seven cross-channel locations (using a vertical aim) and nearshore regions (using horizontal aims). Vertical deployment addressed blind spots in split-beam coverage along the bottom and provided reliable information about the cross-channel and vertical distributions of upstream migrants. Using a Bayesian framework, we modeled sonar counts within four cross-channel strata and apportioned counts by species using species proportions from boat electrofishing and gill netting. Modeled estimates (95% credible intervals [CIs]) of total upstream migrants in 2010 and 2011 were 2.5 million (95% CI, 2.4–2.6 million) and 3.6 million (95% CI, 3.4–3.9 million), respectively. Results indicated that upstream migrants are extremely shore- and bottom-oriented, suggesting nearshore DIDSON monitoring improved the accuracy and precision of our estimates. This monitoring protocol and model may be widely applicable to river systems regardless of their cross-sectional width or profile.

  4. Sample Based Unit Liter Dose Estimates

    SciTech Connect

    JENSEN, L.

    2000-04-13

    The Tank Waste Characterization Program has taken many core samples, grab samples, and auger samples from the single-shell and double-shell tanks during the past 10 years. Consequently, the amount of sample data available has increased, both in terms of quantity of sample results and the number of tanks characterized. More and better data is available than when the current radiological and toxicological source terms used in the Basis for Interim Operation (BIO) (FDH 1999a) and the Final Safety Analysis Report (FSAR) (FDH 1999b) were developed. The Nuclear Safety and Licensing (NS and L) organization wants to use the new data to upgrade the radiological and toxicological source terms used in the BIO and FSAR. The NS and L organization requested assistance in producing a statistically based process for developing the source terms. This report describes the statistical techniques used and the assumptions made to support the development of a new radiological source term for liquid and solid wastes stored in single-shell and double-shell tanks. The results given in this report are a revision to similar results given in an earlier version of the document (Jensen and Wilmarth 1999). The main difference between the results in this document and the earlier version is that the dose conversion factors (DCF) for converting {mu}Ci/g or {mu}Ci/L to Sv/L (sieverts per liter) have changed. There are now two DCFs, one based on ICRP-68 and one based on ICW-71 (Brevick 2000).

  5. Estimation of treatment effects based on possibly misspecified Cox regression.

    PubMed

    Hattori, Satoshi; Henmi, Masayuki

    2012-10-01

    In randomized clinical trials, a treatment effect on a time-to-event endpoint is often estimated by the Cox proportional hazards model. The maximum partial likelihood estimator does not make sense if the proportional hazard assumption is violated. Xu and O'Quigley (Biostatistics 1:423-439, 2000) proposed an estimating equation, which provides an interpretable estimator for the treatment effect under model misspecification. Namely it provides a consistent estimator for the log-hazard ratio among the treatment groups if the model is correctly specified, and it is interpreted as an average log-hazard ratio over time even if misspecified. However, the method requires the assumption that censoring is independent of treatment group, which is more restricted than that for the maximum partial likelihood estimator and is often violated in practice. In this paper, we propose an alternative estimating equation. Our method provides an estimator of the same property as that of Xu and O'Quigley under the usual assumption for the maximum partial likelihood estimation. We show that our estimator is consistent and asymptotically normal, and derive a consistent estimator of the asymptotic variance. If the proportional hazards assumption holds, the efficiency of the estimator can be improved by applying the covariate adjustment method based on the semiparametric theory proposed by Lu and Tsiatis (Biometrika 95:679-694, 2008). PMID:22527680

  6. Wireless Solar Water Splitting Using Silicon-Based Semiconductors and Earth-Abundant Catalysts

    SciTech Connect

    Reece, SY; Hamel, JA; Sung, K; Jarvi, TD; Esswein, AJ; Pijpers, JJH; Nocera, DG

    2011-11-03

    We describe the development of solar water-splitting cells comprising earth-abundant elements that operate in near-neutral pH conditions, both with and without connecting wires. The cells consist of a triple junction, amorphous silicon photovoltaic interfaced to hydrogen- and oxygen-evolving catalysts made from an alloy of earth-abundant metals and a cobalt|borate catalyst, respectively. The devices described here carry out the solar-driven water-splitting reaction at efficiencies of 4.7% for a wired configuration and 2.5% for a wireless configuration when illuminated with 1 sun (100 milliwatts per square centimeter) of air mass 1.5 simulated sunlight. Fuel-forming catalysts interfaced with light-harvesting semiconductors afford a pathway to direct solar-to-fuels conversion that captures many of the basic functional elements of a leaf.

  7. GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater.

    PubMed

    Bayer, Kristina; Moitinho-Silva, Lucas; Brümmer, Franz; Cannistraci, Carlo V; Ravasi, Timothy; Hentschel, Ute

    2014-12-01

    The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

  8. Statistical amplitude scale estimation for quantization-based watermarking

    NASA Astrophysics Data System (ADS)

    Shterev, Ivo D.; Lagendijk, Reginald L.; Heusdens, Richard

    2004-06-01

    Quantization-based watermarking schemes are vulnerable to amplitude scaling. Therefore the scaling factor has to be accounted for either at the encoder, or at the decoder, prior to watermark decoding. In this paper we derive the marginal probability density model for the watermarked and attacked data, when the attack channel consists of amplitude scaling followed by additive noise. The encoder is Quantization Index Modulation with Distortion Compensation. Based on this model we obtain two estimation procedures for the scale parameter. The first approach is based on Fourier Analysis of the probability density function. The estimation of the scaling parameter relies on the structure of the received data. The second approach that we obtain is the Maximum Likelihood estimator of the scaling factor. We study the performance of the estimation procedures theoretically and experimentally with real audio signals, and compare them to other well known approaches for amplitude scale estimation in the literature.

  9. Localized Dictionaries Based Orientation Field Estimation for Latent Fingerprints.

    PubMed

    Xiao Yang; Jianjiang Feng; Jie Zhou

    2014-05-01

    Dictionary based orientation field estimation approach has shown promising performance for latent fingerprints. In this paper, we seek to exploit stronger prior knowledge of fingerprints in order to further improve the performance. Realizing that ridge orientations at different locations of fingerprints have different characteristics, we propose a localized dictionaries-based orientation field estimation algorithm, in which noisy orientation patch at a location output by a local estimation approach is replaced by real orientation patch in the local dictionary at the same location. The precondition of applying localized dictionaries is that the pose of the latent fingerprint needs to be estimated. We propose a Hough transform-based fingerprint pose estimation algorithm, in which the predictions about fingerprint pose made by all orientation patches in the latent fingerprint are accumulated. Experimental results on challenging latent fingerprint datasets show the proposed method outperforms previous ones markedly.

  10. Vision-based range estimation using helicopter flight data

    NASA Technical Reports Server (NTRS)

    Smith, Phillip N.; Sridhar, Banavar; Hussien, Bassam

    1992-01-01

    Pilot aiding during low-altitude flight depends on the ability to detect and locate obstacles near the helicopter's intended flightpath. Computer-vision-based methods provide one general approach for obstacle detection and range estimation. Several algorithms have been developed for this purpose, but have not been tested with actual flight data. This paper presents results obtained using helicopter flight data with a feature-based range estimation algorithm. A method for recursively estimating range using a Kalman filter with a monocular sequence of images and knowledge of the camera's motion is described. The helicopter flight experiment and four resulting datasets are discussed. Finally the performance of the range estimation algorithm is explored in detail based on comparison of the range estimates with true range measurements collected during the flight experiment.

  11. Vision-based range estimation using helicopter flight data

    NASA Technical Reports Server (NTRS)

    Smith, Phillip N.; Sridhar, Banavar; Hussein, Bassam

    1992-01-01

    Pilot aiding during low-altitude flight depends on the ability to detect and locate obstacles near the helicopter's intended flightpath. Computer-vision-based methods provide one general approach for obstacle detection and range estimation. Several algorithms have been developed for this purpose, but have not been tested with actual flight data. This paper presents results obtained using helicopter flight data with a feature-based range estimation algorithm. A method for recursively estimating range using a Kalman filter with a monocular sequence of images and knowledge of the camera's motion is described. The helicopter flight experiment and one of four resulting datasets is briefly discussed. Finally the performance of the range estimation algorithm is explored based on comparison of the range estimates with true range measurements collected during the flight experiment.

  12. Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.

    PubMed

    Roehe, Rainer; Dewhurst, Richard J; Duthie, Carol-Anne; Rooke, John A; McKain, Nest; Ross, Dave W; Hyslop, Jimmy J; Waterhouse, Anthony; Freeman, Tom C; Watson, Mick; Wallace, R John

    2016-02-01

    Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism

  13. Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

    PubMed Central

    Roehe, Rainer; Dewhurst, Richard J.; Duthie, Carol-Anne; Rooke, John A.; McKain, Nest; Ross, Dave W.; Hyslop, Jimmy J.; Waterhouse, Anthony; Freeman, Tom C.

    2016-01-01

    Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism

  14. Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.

    PubMed

    Roehe, Rainer; Dewhurst, Richard J; Duthie, Carol-Anne; Rooke, John A; McKain, Nest; Ross, Dave W; Hyslop, Jimmy J; Waterhouse, Anthony; Freeman, Tom C; Watson, Mick; Wallace, R John

    2016-02-01

    Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism

  15. Raft and floating radio frequency identification (RFID) antenna systems for detecting and estimating abundance of PIT-tagged fish in rivers

    USGS Publications Warehouse

    Fetherman, Eric R.; Avila, Brian W.; Winkelman, Dana L.

    2016-01-01

    Portable radio frequency identification (RFID) PIT tag antenna systems are increasingly being used in studies examining aquatic animal movement, survival, and habitat use, and their design flexibility permits application in a wide variety of settings. We describe the construction, use, and performance of two portable floating RFID PIT tag antenna systems designed to detect fish that were unavailable for recapture using stationary antennas or electrofishing. A raft antenna system was designed to detect and locate PIT-tagged fish in relatively long (i.e., ≥10 km) river reaches, and consisted of two antennas: (1) a horizontal antenna (4 × 1.2 m) installed on the bottom of the raft and used to detect fish in shallower river reaches (<1 m), and (2) a vertical antenna (2.7 × 1.2 m) for detecting fish in deeper pools (≥1 m). Detection distances of the horizontal antenna were between 0.7 and 1.0 m, and detection probability was 0.32 ± 0.02 (mean ± SE) in a field test using rocks marked with 32-mm PIT tags. Detection probability of PIT-tagged fish in the Cache la Poudre River, Colorado, using the raft antenna system, which covered 21% of the wetted area, was 0.14 ± 0.14. A shore-deployed floating antenna (14.6 × 0.6 m), which covered 100% of the wetted area, was designed for use by two operators for detecting and locating PIT-tagged fish in shorter (i.e., <2 km) river reaches. Detection distances of the shore-deployed floating antenna were between 0.7 and 0.8 m, and detection probabilities during field deployment in the St. Vrain River exceeded 0.52. The shore-deployed floating antenna was also used to estimate abundance of PIT-tagged fish. Results suggest that the shore-deployed floating antenna could be used as an alternative to estimating abundance using traditional sampling methods such as electrofishing.

  16. Improved Noise-Power Estimators Based On Order Statistics

    NASA Technical Reports Server (NTRS)

    Zimmerman, George A.

    1995-01-01

    Technique based on order statistics enables design of improved noise-power estimators. In original intended application, noise-power estimators part of microwave-signal-processing system of Search for Extraterrestrial Intelligence project. Involves limiting dynamic range of value to be estimated; making it possible to achieve performance of order-statistical estimator with simple algorithms and equipment and with only one pass over input data. Technique also applicable to other signal-detection systems and to image-detection systems required to exhibit constant false-alarm rates.

  17. Frequency Estimator Performance for a Software-Based Beacon Receiver

    NASA Technical Reports Server (NTRS)

    Zemba, Michael J.; Morse, Jacquelynne Rose; Nessel, James A.; Miranda, Felix

    2014-01-01

    As propagation terminals have evolved, their design has trended more toward a software-based approach that facilitates convenient adjustment and customization of the receiver algorithms. One potential improvement is the implementation of a frequency estimation algorithm, through which the primary frequency component of the received signal can be estimated with a much greater resolution than with a simple peak search of the FFT spectrum. To select an estimator for usage in a QV-band beacon receiver, analysis of six frequency estimators was conducted to characterize their effectiveness as they relate to beacon receiver design.

  18. Frequency Estimator Performance for a Software-Based Beacon Receiver

    NASA Technical Reports Server (NTRS)

    Zemba, Michael J.; Morse, Jacquelynne R.; Nessel, James A.

    2014-01-01

    As propagation terminals have evolved, their design has trended more toward a software-based approach that facilitates convenient adjustment and customization of the receiver algorithms. One potential improvement is the implementation of a frequency estimation algorithm, through which the primary frequency component of the received signal can be estimated with a much greater resolution than with a simple peak search of the FFT spectrum. To select an estimator for usage in a Q/V-band beacon receiver, analysis of six frequency estimators was conducted to characterize their effectiveness as they relate to beacon receiver design.

  19. Vision-based recursive estimation of rotorcraft obstacle locations

    NASA Technical Reports Server (NTRS)

    Leblanc, D. J.; Mcclamroch, N. H.

    1992-01-01

    The authors address vision-based passive ranging during nap-of-the-earth (NOE) rotorcraft flight. They consider the problem of estimating the relative location of identifiable features on nearby obstacles, assuming a sequence of noisy camera images and imperfect measurements of the camera's translation and rotation. An iterated extended Kalman filter is used to provide recursive range estimation. The correspondence problem is simplified by predicting and tracking each feature's image within the Kalman filter framework. Simulation results are presented which show convergent estimates and generally successful feature point tracking. Estimation performance degrades for features near the optical axis and for accelerating motions. Image tracking is also sensitive to angular rate.

  20. Estimation of Radiation Dose in CT Based on Projection Data.

    PubMed

    Tian, Xiaoyu; Yin, Zhye; De Man, Bruno; Samei, Ehsan

    2016-10-01

    Managing and optimizing radiation dose has become a core problem for the CT community. As a fundamental step for dose optimization, accurate and computationally efficient dose estimates are crucial. The purpose of this study was to devise a computationally efficient projection-based dose metric. The absorbed energy and object mass were individually modeled using the projection data. The absorbed energy was estimated using the difference between intensity of the primary photon and the exit photon. The mass was estimated using the volume under the attenuation profile. The feasibility of the approach was evaluated across phantoms with a broad size range, various kVp settings, and two bowtie filters, using a simulation tool, the Computer Assisted Tomography SIMulator (CATSIM) software. The accuracy of projection-based dose estimation was validated against Monte Carlo (MC) simulations. The relationship between projection-based dose metric and MC dose estimate was evaluated using regression models. The projection-based dose metric showed a strong correlation with Monte Carlo dose estimates (R (2) > 0.94). The prediction errors for the projection-based dose metric were all below 15 %. This study demonstrated the feasibility of computationally efficient dose estimation requiring only the projection data.

  1. Reexamining Sample Size Requirements for Multivariate, Abundance-Based Community Research: When Resources are Limited, the Research Does Not Have to Be.

    PubMed

    Forcino, Frank L; Leighton, Lindsey R; Twerdy, Pamela; Cahill, James F

    2015-01-01

    Community ecologists commonly perform multivariate techniques (e.g., ordination, cluster analysis) to assess patterns and gradients of taxonomic variation. A critical requirement for a meaningful statistical analysis is accurate information on the taxa found within an ecological sample. However, oversampling (too many individuals counted per sample) also comes at a cost, particularly for ecological systems in which identification and quantification is substantially more resource consuming than the field expedition itself. In such systems, an increasingly larger sample size will eventually result in diminishing returns in improving any pattern or gradient revealed by the data, but will also lead to continually increasing costs. Here, we examine 396 datasets: 44 previously published and 352 created datasets. Using meta-analytic and simulation-based approaches, the research within the present paper seeks (1) to determine minimal sample sizes required to produce robust multivariate statistical results when conducting abundance-based, community ecology research. Furthermore, we seek (2) to determine the dataset parameters (i.e., evenness, number of taxa, number of samples) that require larger sample sizes, regardless of resource availability. We found that in the 44 previously published and the 220 created datasets with randomly chosen abundances, a conservative estimate of a sample size of 58 produced the same multivariate results as all larger sample sizes. However, this minimal number varies as a function of evenness, where increased evenness resulted in increased minimal sample sizes. Sample sizes as small as 58 individuals are sufficient for a broad range of multivariate abundance-based research. In cases when resource availability is the limiting factor for conducting a project (e.g., small university, time to conduct the research project), statistically viable results can still be obtained with less of an investment.

  2. Estimator Based Controller for High Speed Flywheel Magnetic Bearing System

    NASA Technical Reports Server (NTRS)

    Dever, Timothy P.; Brown, Gerald V.; Jansen, Ralph H.

    2002-01-01

    A flywheel system and its operator interface are described. Measurements of magnetic bearing negative stiffness are performed. Two digital magnetic bearing control algorithms (PD and estimator based) are defined and their implementations are described. Tuning of each controller is discussed. Comparison of the two controllers' stability, damping noise, and operating current are described. Results describing the superiority of the estimator-based controller are presented and discussed.

  3. Modelling occurrence and abundance of species when detection is imperfect

    USGS Publications Warehouse

    Royle, J. Andrew; Nichols, J.D.; Kery, M.

    2005-01-01

    Relationships between species abundance and occupancy are of considerable interest in metapopulation biology and in macroecology. Such relationships may be described concisely using probability models that characterize variation in abundance of a species. However, estimation of the parameters of these models in most ecological problems is impaired by imperfect detection. When organisms are detected imperfectly, observed counts are biased estimates of true abundance, and this induces bias in stated occupancy or occurrence probability. In this paper we consider a class of models that enable estimation of abundance/occupancy relationships from counts of organisms that result from surveys in which detection is imperfect. Under such models, parameter estimation and inference are based on conventional likelihood methods. We provide an application of these models to geographically extensive breeding bird survey data in which alternative models of abundance are considered that include factors that influence variation in abundance and detectability. Using these models, we produce estimates of abundance and occupancy maps that honor important sources of spatial variation in avian abundance and provide clearly interpretable characterizations of abundance and occupancy adjusted for imperfect detection.

  4. A Laplacian-based MMSE estimator for speech enhancement

    PubMed Central

    Chen, Bin; Loizou, Philipos C.

    2007-01-01

    This paper focuses on optimal estimators of the magnitude spectrum for speech enhancement. We present an analytical solution for estimating in the MMSE sense the magnitude spectrum when the clean speech DFT coefficients are modeled by a Laplacian distribution and the noise DFT coefficients are modeled by a Gaussian distribution. Furthermore, we derive the MMSE estimator under speech presence uncertainty and a Laplacian statistical model. Results indicated that the Laplacian-based MMSE estimator yielded less residual noise in the enhanced speech than the traditional Gaussian-based MMSE estimator. Overall, the present study demonstrates that the assumed distribution of the DFT coefficients can have a significant effect on the quality of the enhanced speech. PMID:18037977

  5. Model-based estimation for dynamic cardiac studies using ECT

    SciTech Connect

    Chiao, P.C.; Rogers, W.L.; Clinthorne, N.H.; Fessler, J.A.; Hero, A.O. . Div. of Nuclear Medicine)

    1994-06-01

    In this paper, the authors develop a strategy for joint estimation of physiological parameters and myocardial boundaries using ECT (Emission Computed Tomography). The authors construct an observation model to relate parameters of interest to the projection data and to account for limited ECT system resolution and measurement noise. The authors then use a maximum likelihood (ML) estimator to jointly estimate all the parameters directly from the projection data without reconstruction of intermediate images. The authors also simulate myocardial perfusion studies based on a simplified heart model to evaluate the performance of the model-based joint ML estimator and compare this performance to the Cramer-Rao lower bound. Finally, model assumptions and potential uses of the joint estimation strategy are discussed.

  6. Understanding Long-Term Changes in Species Abundance Using a Niche-Based Approach

    PubMed Central

    Helaouët, Pierre; Beaugrand, Grégory; Edwards, Martin

    2013-01-01

    One of the major challenges to understanding population changes in ecology for assessment purposes is the difficulty in evaluating the suitability of an area for a given species. Here we used a new simple approach able to faithfully predict through time the abundance of two key zooplanktonic species by focusing on the relationship between the species’ environmental preferences and their observed abundances. The approach is applied to the marine copepods Calanus finmarchicus and C. helgolandicus as a case study characterising the multidecadal dynamics of the North Sea ecosystem. We removed all North Sea data from the Continuous Plankton Recorder (CPR) dataset and described for both species a simplified ecological niche using Sea Surface Temperature (SST) and CPR Phytoplankton Colour Index (PCI). We then modelled the dynamics of each species by associating the North Sea’s environmental parameters to the species’ ecological niches, thus creating a method to assess the suitability of this area. By using both C. finmarchicus and C. helgolandicus as indicators, the procedure reproduces the documented switches from cold to warm temperate states observed in the North Sea. PMID:24265757

  7. Recursive least square vehicle mass estimation based on acceleration partition

    NASA Astrophysics Data System (ADS)

    Feng, Yuan; Xiong, Lu; Yu, Zhuoping; Qu, Tong

    2014-05-01

    Vehicle mass is an important parameter in vehicle dynamics control systems. Although many algorithms have been developed for the estimation of mass, none of them have yet taken into account the different types of resistance that occur under different conditions. This paper proposes a vehicle mass estimator. The estimator incorporates road gradient information in the longitudinal accelerometer signal, and it removes the road grade from the longitudinal dynamics of the vehicle. Then, two different recursive least square method (RLSM) schemes are proposed to estimate the driving resistance and the mass independently based on the acceleration partition under different conditions. A 6 DOF dynamic model of four In-wheel Motor Vehicle is built to assist in the design of the algorithm and in the setting of the parameters. The acceleration limits are determined to not only reduce the estimated error but also ensure enough data for the resistance estimation and mass estimation in some critical situations. The modification of the algorithm is also discussed to improve the result of the mass estimation. Experiment data on a sphalt road, plastic runway, and gravel road and on sloping roads are used to validate the estimation algorithm. The adaptability of the algorithm is improved by using data collected under several critical operating conditions. The experimental results show the error of the estimation process to be within 2.6%, which indicates that the algorithm can estimate mass with great accuracy regardless of the road surface and gradient changes and that it may be valuable in engineering applications. This paper proposes a recursive least square vehicle mass estimation method based on acceleration partition.

  8. Influence of observers and stream flow on northern two-lined salamander (Eurycea bislineata bislineata) relative abundance estimates in Acadia and Shenandoah National Parks, USA

    USGS Publications Warehouse

    Crocker, J.B.; Bank, M.S.; Loftin, C.S.; Jung Brown, R.E.

    2007-01-01

    We investigated effects of observers and stream flow on Northern Two-Lined Salamander (Eurycea bislineata bislineata) counts in streams in Acadia (ANP) and Shenandoah National Parks (SNP). We counted salamanders in 22 ANP streams during high flow (May to June 2002) and during low flow (July 2002). We also counted salamanders in SNP in nine streams during high flow (summer 2003) and 11 streams during low flow (summers 2001?02, 2004). In 2002, we used a modified cover-controlled active search method with a first and second observer. In succession, observers turned over 100 rocks along five 1-m belt transects across the streambed. The difference between observers in total salamander counts was not significant. We counted fewer E. b. bislineata during high flow conditions, confirming that detection of this species is reduced during high flow periods and that assessment of stream salamander relative abundance is likely more reliable during low or base flow conditions.

  9. Process-based Cost Estimation for Ramjet/Scramjet Engines

    NASA Technical Reports Server (NTRS)

    Singh, Brijendra; Torres, Felix; Nesman, Miles; Reynolds, John

    2003-01-01

    Process-based cost estimation plays a key role in effecting cultural change that integrates distributed science, technology and engineering teams to rapidly create innovative and affordable products. Working together, NASA Glenn Research Center and Boeing Canoga Park have developed a methodology of process-based cost estimation bridging the methodologies of high-level parametric models and detailed bottoms-up estimation. The NASA GRC/Boeing CP process-based cost model provides a probabilistic structure of layered cost drivers. High-level inputs characterize mission requirements, system performance, and relevant economic factors. Design alternatives are extracted from a standard, product-specific work breakdown structure to pre-load lower-level cost driver inputs and generate the cost-risk analysis. As product design progresses and matures the lower level more detailed cost drivers can be re-accessed and the projected variation of input values narrowed, thereby generating a progressively more accurate estimate of cost-risk. Incorporated into the process-based cost model are techniques for decision analysis, specifically, the analytic hierarchy process (AHP) and functional utility analysis. Design alternatives may then be evaluated not just on cost-risk, but also user defined performance and schedule criteria. This implementation of full-trade study support contributes significantly to the realization of the integrated development environment. The process-based cost estimation model generates development and manufacturing cost estimates. The development team plans to expand the manufacturing process base from approximately 80 manufacturing processes to over 250 processes. Operation and support cost modeling is also envisioned. Process-based estimation considers the materials, resources, and processes in establishing cost-risk and rather depending on weight as an input, actually estimates weight along with cost and schedule.

  10. Can Nonexperimental Estimates Replicate Estimates Based on Random Assignment in Evaluations of School Choice? A Within-Study Comparison

    ERIC Educational Resources Information Center

    Bifulco, Robert

    2012-01-01

    The ability of nonexperimental estimators to match impact estimates derived from random assignment is examined using data from the evaluation of two interdistrict magnet schools. As in previous within-study comparisons, nonexperimental estimates differ from estimates based on random assignment when nonexperimental estimators are implemented…

  11. MetaBAT: Metagenome Binning based on Abundance and Tetranucleotide frequence

    SciTech Connect

    Kang, Dongwan; Froula, Jeff; Egan, Rob; Wang, Zhong

    2014-03-21

    Grouping large fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Here we developed automated metagenome binning software, called MetaBAT, which integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. On synthetic datasets MetaBAT on average achieves 98percent precision and 90percent recall at the strain level with 281 near complete unique genomes. Applying MetaBAT to a human gut microbiome data set we recovered 176 genome bins with 92percent precision and 80percent recall. Further analyses suggest MetaBAT is able to recover genome fragments missed in reference genomes up to 19percent, while 53 genome bins are novel. In summary, we believe MetaBAT is a powerful tool to facilitate comprehensive understanding of complex microbial communities.

  12. Prediction of novel, Earth abundant Cu2O based alloys for PV applications

    NASA Astrophysics Data System (ADS)

    Stevanovic, Vladan; Lany, Stephan

    2014-03-01

    Tuning the opto-electronic properties of semiconductors through alloying is essential for semiconductor industry. Currently, mostly isovalent and isostructural alloys are used (e.g. Si/Ge, GaN/InN or CdTe/ZnTe), but a vast and unexplored space of novel functional materials is conceivable when considering more complex alloys by mixing aliovalent and heterostructural constituents. The real challenge lies in the quantitative property prediction for such complex alloys to guide their experimental exploration. In our work we demonstrate how an Earth abundant p-type oxide Cu2O, can be engineered through alloying into a technologically useful absorber material. We use non-local external potentials (NLEP) fitted to GW calculations for correcting the DFT electronic structure and compute absorption coefficient of different alloy compositions and configurations. Work supported by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Next Generation Photovoltaics II (SunShot initiative).

  13. Fast model-based estimation of ancestry in unrelated individuals.

    PubMed

    Alexander, David H; Novembre, John; Lange, Kenneth

    2009-09-01

    Population stratification has long been recognized as a confounding factor in genetic association studies. Estimated ancestries, derived from multi-locus genotype data, can be used to perform a statistical correction for population stratification. One popular technique for estimation of ancestry is the model-based approach embodied by the widely applied program structure. Another approach, implemented in the program EIGENSTRAT, relies on Principal Component Analysis rather than model-based estimation and does not directly deliver admixture fractions. EIGENSTRAT has gained in popularity in part owing to its remarkable speed in comparison to structure. We present a new algorithm and a program, ADMIXTURE, for model-based estimation of ancestry in unrelated individuals. ADMIXTURE adopts the likelihood model embedded in structure. However, ADMIXTURE runs considerably faster, solving problems in minutes that take structure hours. In many of our experiments, we have found that ADMIXTURE is almost as fast as EIGENSTRAT. The runtime improvements of ADMIXTURE rely on a fast block relaxation scheme using sequential quadratic programming for block updates, coupled with a novel quasi-Newton acceleration of convergence. Our algorithm also runs faster and with greater accuracy than the implementation of an Expectation-Maximization (EM) algorithm incorporated in the program FRAPPE. Our simulations show that ADMIXTURE's maximum likelihood estimates of the underlying admixture coefficients and ancestral allele frequencies are as accurate as structure's Bayesian estimates. On real-world data sets, ADMIXTURE's estimates are directly comparable to those from structure and EIGENSTRAT. Taken together, our results show that ADMIXTURE's computational speed opens up the possibility of using a much larger set of markers in model-based ancestry estimation and that its estimates are suitable for use in correcting for population stratification in association studies.

  14. Model-based approach for elevator performance estimation

    NASA Astrophysics Data System (ADS)

    Esteban, E.; Salgado, O.; Iturrospe, A.; Isasa, I.

    2016-02-01

    In this paper, a dynamic model for an elevator installation is presented in the state space domain. The model comprises both the mechanical and the electrical subsystems, including the electrical machine and a closed-loop field oriented control. The proposed model is employed for monitoring the condition of the elevator installation. The adopted model-based approach for monitoring employs the Kalman filter as an observer. A Kalman observer estimates the elevator car acceleration, which determines the elevator ride quality, based solely on the machine control signature and the encoder signal. Finally, five elevator key performance indicators are calculated based on the estimated car acceleration. The proposed procedure is experimentally evaluated, by comparing the key performance indicators calculated based on the estimated car acceleration and the values obtained from actual acceleration measurements in a test bench. Finally, the proposed procedure is compared with the sliding mode observer.

  15. Vehicle lateral state estimation based on measured tyre forces.

    PubMed

    Tuononen, Ari J

    2009-01-01

    Future active safety systems need more accurate information about the state of vehicles. This article proposes a method to evaluate the lateral state of a vehicle based on measured tyre forces. The tyre forces of two tyres are estimated from optically measured tyre carcass deflections and transmitted wirelessly to the vehicle body. The two remaining tyres are so-called virtual tyre sensors, the forces of which are calculated from the real tyre sensor estimates. The Kalman filter estimator for lateral vehicle state based on measured tyre forces is presented, together with a simple method to define adaptive measurement error covariance depending on the driving condition of the vehicle. The estimated yaw rate and lateral velocity are compared with the validation sensor measurements. PMID:22291535

  16. Vehicle Lateral State Estimation Based on Measured Tyre Forces

    PubMed Central

    Tuononen, Ari J.

    2009-01-01

    Future active safety systems need more accurate information about the state of vehicles. This article proposes a method to evaluate the lateral state of a vehicle based on measured tyre forces. The tyre forces of two tyres are estimated from optically measured tyre carcass deflections and transmitted wirelessly to the vehicle body. The two remaining tyres are so-called virtual tyre sensors, the forces of which are calculated from the real tyre sensor estimates. The Kalman filter estimator for lateral vehicle state based on measured tyre forces is presented, together with a simple method to define adaptive measurement error covariance depending on the driving condition of the vehicle. The estimated yaw rate and lateral velocity are compared with the validation sensor measurements. PMID:22291535

  17. Improving Quantum State Estimation with Mutually Unbiased Bases

    NASA Astrophysics Data System (ADS)

    Adamson, R. B. A.; Steinberg, A. M.

    2010-07-01

    When used in quantum state estimation, projections onto mutually unbiased bases have the ability to maximize information extraction per measurement and to minimize redundancy. We present the first experimental demonstration of quantum state tomography of two-qubit polarization states to take advantage of mutually unbiased bases. We demonstrate improved state estimation as compared to standard measurement strategies and discuss how this can be understood from the structure of the measurements we use. We experimentally compared our method to the standard state estimation method for three different states and observe that the infidelity was up to 1.84±0.06 times lower by using our technique than it was by using standard state estimation methods.

  18. Virtual Estimator for Piecewise Linear Systems Based on Observability Analysis

    PubMed Central

    Morales-Morales, Cornelio; Adam-Medina, Manuel; Cervantes, Ilse; Vela-Valdés and, Luis G.; García Beltrán, Carlos Daniel

    2013-01-01

    This article proposes a virtual sensor for piecewise linear systems based on observability analysis that is in function of a commutation law related with the system's outpu. This virtual sensor is also known as a state estimator. Besides, it presents a detector of active mode when the commutation sequences of each linear subsystem are arbitrary and unknown. For the previous, this article proposes a set of virtual estimators that discern the commutation paths of the system and allow estimating their output. In this work a methodology in order to test the observability for piecewise linear systems with discrete time is proposed. An academic example is presented to show the obtained results. PMID:23447007

  19. Estimation of Ultrafilter Performance Based on Characterization Data

    SciTech Connect

    Peterson, Reid A.; Geeting, John GH; Daniel, Richard C.

    2007-08-02

    Due to limited availability of test data with actual waste samples, a method was developed to estimate expected filtration performance based on physical characterization data for the Hanford Waste Treatment and Immobilization Plant. A test with simulated waste was analyzed to demonstrate that filtration of this class of waste is consistent with a concentration polarization model. Subsequently, filtration data from actual waste samples were analyzed to demonstrate that centrifuged solids concentrations provide a reasonable estimate of the limiting concentration for filtration.

  20. Optical Enhancement of Exoskeleton-Based Estimation of Glenohumeral Angles.

    PubMed

    Cortés, Camilo; Unzueta, Luis; de Los Reyes-Guzmán, Ana; Ruiz, Oscar E; Flórez, Julián

    2016-01-01

    In Robot-Assisted Rehabilitation (RAR) the accurate estimation of the patient limb joint angles is critical for assessing therapy efficacy. In RAR, the use of classic motion capture systems (MOCAPs) (e.g., optical and electromagnetic) to estimate the Glenohumeral (GH) joint angles is hindered by the exoskeleton body, which causes occlusions and magnetic disturbances. Moreover, the exoskeleton posture does not accurately reflect limb posture, as their kinematic models differ. To address the said limitations in posture estimation, we propose installing the cameras of an optical marker-based MOCAP in the rehabilitation exoskeleton. Then, the GH joint angles are estimated by combining the estimated marker poses and exoskeleton Forward Kinematics. Such hybrid system prevents problems related to marker occlusions, reduced camera detection volume, and imprecise joint angle estimation due to the kinematic mismatch of the patient and exoskeleton models. This paper presents the formulation, simulation, and accuracy quantification of the proposed method with simulated human movements. In addition, a sensitivity analysis of the method accuracy to marker position estimation errors, due to system calibration errors and marker drifts, has been carried out. The results show that, even with significant errors in the marker position estimation, method accuracy is adequate for RAR. PMID:27403044

  1. Optical Enhancement of Exoskeleton-Based Estimation of Glenohumeral Angles

    PubMed Central

    Cortés, Camilo; Unzueta, Luis; de los Reyes-Guzmán, Ana; Ruiz, Oscar E.; Flórez, Julián

    2016-01-01

    In Robot-Assisted Rehabilitation (RAR) the accurate estimation of the patient limb joint angles is critical for assessing therapy efficacy. In RAR, the use of classic motion capture systems (MOCAPs) (e.g., optical and electromagnetic) to estimate the Glenohumeral (GH) joint angles is hindered by the exoskeleton body, which causes occlusions and magnetic disturbances. Moreover, the exoskeleton posture does not accurately reflect limb posture, as their kinematic models differ. To address the said limitations in posture estimation, we propose installing the cameras of an optical marker-based MOCAP in the rehabilitation exoskeleton. Then, the GH joint angles are estimated by combining the estimated marker poses and exoskeleton Forward Kinematics. Such hybrid system prevents problems related to marker occlusions, reduced camera detection volume, and imprecise joint angle estimation due to the kinematic mismatch of the patient and exoskeleton models. This paper presents the formulation, simulation, and accuracy quantification of the proposed method with simulated human movements. In addition, a sensitivity analysis of the method accuracy to marker position estimation errors, due to system calibration errors and marker drifts, has been carried out. The results show that, even with significant errors in the marker position estimation, method accuracy is adequate for RAR. PMID:27403044

  2. Optical Enhancement of Exoskeleton-Based Estimation of Glenohumeral Angles.

    PubMed

    Cortés, Camilo; Unzueta, Luis; de Los Reyes-Guzmán, Ana; Ruiz, Oscar E; Flórez, Julián

    2016-01-01

    In Robot-Assisted Rehabilitation (RAR) the accurate estimation of the patient limb joint angles is critical for assessing therapy efficacy. In RAR, the use of classic motion capture systems (MOCAPs) (e.g., optical and electromagnetic) to estimate the Glenohumeral (GH) joint angles is hindered by the exoskeleton body, which causes occlusions and magnetic disturbances. Moreover, the exoskeleton posture does not accurately reflect limb posture, as their kinematic models differ. To address the said limitations in posture estimation, we propose installing the cameras of an optical marker-based MOCAP in the rehabilitation exoskeleton. Then, the GH joint angles are estimated by combining the estimated marker poses and exoskeleton Forward Kinematics. Such hybrid system prevents problems related to marker occlusions, reduced camera detection volume, and imprecise joint angle estimation due to the kinematic mismatch of the patient and exoskeleton models. This paper presents the formulation, simulation, and accuracy quantification of the proposed method with simulated human movements. In addition, a sensitivity analysis of the method accuracy to marker position estimation errors, due to system calibration errors and marker drifts, has been carried out. The results show that, even with significant errors in the marker position estimation, method accuracy is adequate for RAR.

  3. Estimation of Thermal Sensation Based on Wrist Skin Temperatures.

    PubMed

    Sim, Soo Young; Koh, Myung Jun; Joo, Kwang Min; Noh, Seungwoo; Park, Sangyun; Kim, Youn Ho; Park, Kwang Suk

    2016-01-01

    Thermal comfort is an essential environmental factor related to quality of life and work effectiveness. We assessed the feasibility of wrist skin temperature monitoring for estimating subjective thermal sensation. We invented a wrist band that simultaneously monitors skin temperatures from the wrist (i.e., the radial artery and ulnar artery regions, and upper wrist) and the fingertip. Skin temperatures from eight healthy subjects were acquired while thermal sensation varied. To develop a thermal sensation estimation model, the mean skin temperature, temperature gradient, time differential of the temperatures, and average power of frequency band were calculated. A thermal sensation estimation model using temperatures of the fingertip and wrist showed the highest accuracy (mean root mean square error [RMSE]: 1.26 ± 0.31). An estimation model based on the three wrist skin temperatures showed a slightly better result to the model that used a single fingertip skin temperature (mean RMSE: 1.39 ± 0.18). When a personalized thermal sensation estimation model based on three wrist skin temperatures was used, the mean RMSE was 1.06 ± 0.29, and the correlation coefficient was 0.89. Thermal sensation estimation technology based on wrist skin temperatures, and combined with wearable devices may facilitate intelligent control of one's thermal environment. PMID:27023538

  4. Estimation of Thermal Sensation Based on Wrist Skin Temperatures.

    PubMed

    Sim, Soo Young; Koh, Myung Jun; Joo, Kwang Min; Noh, Seungwoo; Park, Sangyun; Kim, Youn Ho; Park, Kwang Suk

    2016-03-23

    Thermal comfort is an essential environmental factor related to quality of life and work effectiveness. We assessed the feasibility of wrist skin temperature monitoring for estimating subjective thermal sensation. We invented a wrist band that simultaneously monitors skin temperatures from the wrist (i.e., the radial artery and ulnar artery regions, and upper wrist) and the fingertip. Skin temperatures from eight healthy subjects were acquired while thermal sensation varied. To develop a thermal sensation estimation model, the mean skin temperature, temperature gradient, time differential of the temperatures, and average power of frequency band were calculated. A thermal sensation estimation model using temperatures of the fingertip and wrist showed the highest accuracy (mean root mean square error [RMSE]: 1.26 ± 0.31). An estimation model based on the three wrist skin temperatures showed a slightly better result to the model that used a single fingertip skin temperature (mean RMSE: 1.39 ± 0.18). When a personalized thermal sensation estimation model based on three wrist skin temperatures was used, the mean RMSE was 1.06 ± 0.29, and the correlation coefficient was 0.89. Thermal sensation estimation technology based on wrist skin temperatures, and combined with wearable devices may facilitate intelligent control of one's thermal environment.

  5. Estimation of Cometary Rotation Parameters Based on Camera Images

    NASA Technical Reports Server (NTRS)

    Spindler, Karlheinz

    2007-01-01

    The purpose of the Rosetta mission is the in situ analysis of a cometary nucleus using both remote sensing equipment and scientific instruments delivered to the comet surface by a lander and transmitting measurement data to the comet-orbiting probe. Following a tour of planets including one Mars swing-by and three Earth swing-bys, the Rosetta probe is scheduled to rendezvous with comet 67P/Churyumov-Gerasimenko in May 2014. The mission poses various flight dynamics challenges, both in terms of parameter estimation and maneuver planning. Along with spacecraft parameters, the comet's position, velocity, attitude, angular velocity, inertia tensor and gravitatonal field need to be estimated. The measurements on which the estimation process is based are ground-based measurements (range and Doppler) yielding information on the heliocentric spacecraft state and images taken by an on-board camera yielding informaton on the comet state relative to the spacecraft. The image-based navigation depends on te identification of cometary landmarks (whose body coordinates also need to be estimated in the process). The paper will describe the estimation process involved, focusing on the phase when, after orbit insertion, the task arises to estimate the cometary rotational motion from camera images on which individual landmarks begin to become identifiable.

  6. Pros, Cons, and Alternatives to Weight Based Cost Estimating

    NASA Technical Reports Server (NTRS)

    Joyner, Claude R.; Lauriem, Jonathan R.; Levack, Daniel H.; Zapata, Edgar

    2011-01-01

    Many cost estimating tools use weight as a major parameter in projecting the cost. This is often combined with modifying factors such as complexity, technical maturity of design, environment of operation, etc. to increase the fidelity of the estimate. For a set of conceptual designs, all meeting the same requirements, increased weight can be a major driver in increased cost. However, once a design is fixed, increased weight generally decreases cost, while decreased weight generally increases cost - and the relationship is not linear. Alternative approaches to estimating cost without using weight (except perhaps for materials costs) have been attempted to try to produce a tool usable throughout the design process - from concept studies through development. This paper will address the pros and cons of using weight based models for cost estimating, using liquid rocket engines as the example. It will then examine approaches that minimize the impct of weight based cost estimating. The Rocket Engine- Cost Model (RECM) is an attribute based model developed internally by Pratt & Whitney Rocketdyne for NASA. RECM will be presented primarily to show a successful method to use design and programmatic parameters instead of weight to estimate both design and development costs and production costs. An operations model developed by KSC, the Launch and Landing Effects Ground Operations model (LLEGO), will also be discussed.

  7. Estimation of Thermal Sensation Based on Wrist Skin Temperatures

    PubMed Central

    Sim, Soo Young; Koh, Myung Jun; Joo, Kwang Min; Noh, Seungwoo; Park, Sangyun; Kim, Youn Ho; Park, Kwang Suk

    2016-01-01

    Thermal comfort is an essential environmental factor related to quality of life and work effectiveness. We assessed the feasibility of wrist skin temperature monitoring for estimating subjective thermal sensation. We invented a wrist band that simultaneously monitors skin temperatures from the wrist (i.e., the radial artery and ulnar artery regions, and upper wrist) and the fingertip. Skin temperatures from eight healthy subjects were acquired while thermal sensation varied. To develop a thermal sensation estimation model, the mean skin temperature, temperature gradient, time differential of the temperatures, and average power of frequency band were calculated. A thermal sensation estimation model using temperatures of the fingertip and wrist showed the highest accuracy (mean root mean square error [RMSE]: 1.26 ± 0.31). An estimation model based on the three wrist skin temperatures showed a slightly better result to the model that used a single fingertip skin temperature (mean RMSE: 1.39 ± 0.18). When a personalized thermal sensation estimation model based on three wrist skin temperatures was used, the mean RMSE was 1.06 ± 0.29, and the correlation coefficient was 0.89. Thermal sensation estimation technology based on wrist skin temperatures, and combined with wearable devices may facilitate intelligent control of one’s thermal environment. PMID:27023538

  8. A novel SURE-based criterion for parametric PSF estimation.

    PubMed

    Xue, Feng; Blu, Thierry

    2015-02-01

    We propose an unbiased estimate of a filtered version of the mean squared error--the blur-SURE (Stein's unbiased risk estimate)--as a novel criterion for estimating an unknown point spread function (PSF) from the degraded image only. The PSF is obtained by minimizing this new objective functional over a family of Wiener processings. Based on this estimated blur kernel, we then perform nonblind deconvolution using our recently developed algorithm. The SURE-based framework is exemplified with a number of parametric PSF, involving a scaling factor that controls the blur size. A typical example of such parametrization is the Gaussian kernel. The experimental results demonstrate that minimizing the blur-SURE yields highly accurate estimates of the PSF parameters, which also result in a restoration quality that is very similar to the one obtained with the exact PSF, when plugged into our recent multi-Wiener SURE-LET deconvolution algorithm. The highly competitive results obtained outline the great potential of developing more powerful blind deconvolution algorithms based on SURE-like estimates.

  9. A novel SURE-based criterion for parametric PSF estimation.

    PubMed

    Xue, Feng; Blu, Thierry

    2015-02-01

    We propose an unbiased estimate of a filtered version of the mean squared error--the blur-SURE (Stein's unbiased risk estimate)--as a novel criterion for estimating an unknown point spread function (PSF) from the degraded image only. The PSF is obtained by minimizing this new objective functional over a family of Wiener processings. Based on this estimated blur kernel, we then perform nonblind deconvolution using our recently developed algorithm. The SURE-based framework is exemplified with a number of parametric PSF, involving a scaling factor that controls the blur size. A typical example of such parametrization is the Gaussian kernel. The experimental results demonstrate that minimizing the blur-SURE yields highly accurate estimates of the PSF parameters, which also result in a restoration quality that is very similar to the one obtained with the exact PSF, when plugged into our recent multi-Wiener SURE-LET deconvolution algorithm. The highly competitive results obtained outline the great potential of developing more powerful blind deconvolution algorithms based on SURE-like estimates. PMID:25531950

  10. Natural Abundance 17O Nuclear Magnetic Resonance and Computational Modeling Studies of Lithium Based Liquid Electrolytes

    SciTech Connect

    Deng, Xuchu; Hu, Mary Y.; Wei, Xiaoliang; Wang, Wei; Chen, Zhong; Liu, Jun; Hu, Jian Z.

    2015-07-01

    Natural abundance 17O NMR measurements were conducted on electrolyte solutions consisting of Li[CF3SO2NSO2CF3] (LiTFSI) dissolved in the solvents of ethylene carbonate (EC), propylene carbonate (PC), ethyl methyl carbonate (EMC), and their mixtures at various concentrations. It was observed that 17O chemical shifts of solvent molecules change with the concentration of LiTFSI. The chemical shift displacements of carbonyl oxygen are evidently greater than those of ethereal oxygen, strongly indicating that Li+ ion is coordinated with carbonyl oxygen rather than ethereal oxygen. To understand the detailed molecular interaction, computational modeling of 17O chemical shifts was carried out on proposed solvation structures. By comparing the predicted chemical shifts with the experimental values, it is found that a Li+ ion is coordinated with four double bond oxygen atoms from EC, PC, EMC and TFSI- anion. In the case of excessive amount of solvents of EC, PC and EMC the Li+ coordinated solvent molecules are undergoing quick exchange with bulk solvent molecules, resulting in average 17O chemical shifts. Several kinds of solvation structures are identified, where the proportion of each structure in the liquid electrolytes investigated depends on the concentration of LiTFSI.

  11. MUlti-Dimensional Spline-Based Estimator (MUSE) for motion estimation: algorithm development and initial results.

    PubMed

    Viola, Francesco; Coe, Ryan L; Owen, Kevin; Guenther, Drake A; Walker, William F

    2008-12-01

    Image registration and motion estimation play central roles in many fields, including RADAR, SONAR, light microscopy, and medical imaging. Because of its central significance, estimator accuracy, precision, and computational cost are of critical importance. We have previously presented a highly accurate, spline-based time delay estimator that directly determines sub-sample time delay estimates from sampled data. The algorithm uses cubic splines to produce a continuous representation of a reference signal and then computes an analytical matching function between this reference and a delayed signal. The location of the minima of this function yields estimates of the time delay. In this paper we describe the MUlti-dimensional Spline-based Estimator (MUSE) that allows accurate and precise estimation of multi-dimensional displacements/strain components from multi-dimensional data sets. We describe the mathematical formulation for two- and three-dimensional motion/strain estimation and present simulation results to assess the intrinsic bias and standard deviation of this algorithm and compare it to currently available multi-dimensional estimators. In 1000 noise-free simulations of ultrasound data we found that 2D MUSE exhibits maximum bias of 2.6 x 10(-4) samples in range and 2.2 x 10(-3) samples in azimuth (corresponding to 4.8 and 297 nm, respectively). The maximum simulated standard deviation of estimates in both dimensions was comparable at roughly 2.8 x 10(-3) samples (corresponding to 54 nm axially and 378 nm laterally). These results are between two and three orders of magnitude better than currently used 2D tracking methods. Simulation of performance in 3D yielded similar results to those observed in 2D. We also present experimental results obtained using 2D MUSE on data acquired by an Ultrasonix Sonix RP imaging system with an L14-5/38 linear array transducer operating at 6.6 MHz. While our validation of the algorithm was performed using ultrasound data, MUSE is

  12. Ground-based measurements of HF total column abundances in the stratosphere near St. Petersburg (2009-2013)

    NASA Astrophysics Data System (ADS)

    Polyakov, A. V.; Timofeev, Yu. M.; Virolainen, Ya. A.; Poberovskii, A. V.

    2014-11-01

    An analysis of ground-based spectroscopic measurements of hydrogen fluoride total column abundances (HF TCAs) near St. Petersburg for a 4-year period (2009-2013) is performed. The average HF TCA is 1.93 × 1015 cm-2, and the RMS variation (natural variability) for the measurement ensemble is about 20%. The data are in good agreement with measurements collected at the NDACC stations (Bremen and Harestua), taking into account the differences in latitude. The monthly average HF TCAs show seasonal variation with peaks in late winter and early spring and troughs in the period from November to January. The variability of the monthly averages is at a maximum in winter and spring. A comparison of the HF TCAs from ground-based measurements with those from ACE-FTS solar occultation measurements shows that the total abundances from the ground-based data are 12% lower than those from the ACE-FTS data, and the RMS differences depend on the version of the satellite data processing system, being 13 and 16% for versions 2.2 and 3.0, respectively. The calculated ratio between HCl and HF total column abundances is significantly lower in late winter and spring. The linear trend of this ratio is 2.5% per year. Although the trend statistics is insufficient due to the short observation period, the pattern is explained both by the decrease in the stratospheric HCl content and the small increase in HF TCAs over the studied period and is consistent with literature data.

  13. Fuzzy case based reasoning in sports facilities unit cost estimating

    NASA Astrophysics Data System (ADS)

    Zima, Krzysztof

    2016-06-01

    This article presents an example of estimating costs in the early phase of the project using fuzzy case-based reasoning. The fragment of database containing descriptions and unit cost of sports facilities was shown. The formulas used in Case Based Reasoning method were presented, too. The article presents similarity measurement using a few formulas, including fuzzy similarity. The outcome of cost calculations based on CBR method was presented as a fuzzy number of unit cost of construction work.

  14. A Channelization-Based DOA Estimation Method for Wideband Signals.

    PubMed

    Guo, Rui; Zhang, Yue; Lin, Qianqiang; Chen, Zengping

    2016-01-01

    In this paper, we propose a novel direction of arrival (DOA) estimation method for wideband signals with sensor arrays. The proposed method splits the wideband array output into multiple frequency sub-channels and estimates the signal parameters using a digital channelization receiver. Based on the output sub-channels, a channelization-based incoherent signal subspace method (Channelization-ISM) and a channelization-based test of orthogonality of projected subspaces method (Channelization-TOPS) are proposed. Channelization-ISM applies narrowband signal subspace methods on each sub-channel independently. Then the arithmetic mean or geometric mean of the estimated DOAs from each sub-channel gives the final result. Channelization-TOPS measures the orthogonality between the signal and the noise subspaces of the output sub-channels to estimate DOAs. The proposed channelization-based method isolates signals in different bandwidths reasonably and improves the output SNR. It outperforms the conventional ISM and TOPS methods on estimation accuracy and dynamic range, especially in real environments. Besides, the parallel processing architecture makes it easy to implement on hardware. A wideband digital array radar (DAR) using direct wideband radio frequency (RF) digitization is presented. Experiments carried out in a microwave anechoic chamber with the wideband DAR are presented to demonstrate the performance. The results verify the effectiveness of the proposed method. PMID:27384566

  15. CALIBRATING C-IV-BASED BLACK HOLE MASS ESTIMATORS

    SciTech Connect

    Park, Daeseong; Woo, Jong-Hak; Shin, Jaejin; Denney, Kelly D. E-mail: woo@astro.snu.ac.kr E-mail: kelly@dark-cosmology.dk

    2013-06-20

    We present the single-epoch black hole mass estimators based on the C IV {lambda}1549 broad emission line, using the updated sample of the reverberation-mapped active galactic nuclei and high-quality UV spectra. By performing multi-component spectral fitting analysis, we measure the C IV line widths (FWHM{sub C{sub IV}} and line dispersion, {sigma}{sub C{sub IV}}) and the continuum luminosity at 1350 A (L{sub 1350}) to calibrate the C-IV-based mass estimators. By comparing with the H{beta} reverberation-based masses, we provide new mass estimators with the best-fit relationships, i.e., M{sub BH}{proportional_to}L{sub 1350}{sup 0.50{+-}0.07}{sigma}{sub C{sub IV}{sup 2}} and M{sub BH}{proportional_to}L{sub 1350}{sup 0.52{+-}0.09} FWHM{sub C{sub IV}{sup 0.56{+-}0.48}}. The new C-IV-based mass estimators show significant mass-dependent systematic difference compared to the estimators commonly used in the literature. Using the published Sloan Digital Sky Survey QSO catalog, we show that the black hole mass of high-redshift QSOs decreases on average by {approx}0.25 dex if our recipe is adopted.

  16. A Channelization-Based DOA Estimation Method for Wideband Signals

    PubMed Central

    Guo, Rui; Zhang, Yue; Lin, Qianqiang; Chen, Zengping

    2016-01-01

    In this paper, we propose a novel direction of arrival (DOA) estimation method for wideband signals with sensor arrays. The proposed method splits the wideband array output into multiple frequency sub-channels and estimates the signal parameters using a digital channelization receiver. Based on the output sub-channels, a channelization-based incoherent signal subspace method (Channelization-ISM) and a channelization-based test of orthogonality of projected subspaces method (Channelization-TOPS) are proposed. Channelization-ISM applies narrowband signal subspace methods on each sub-channel independently. Then the arithmetic mean or geometric mean of the estimated DOAs from each sub-channel gives the final result. Channelization-TOPS measures the orthogonality between the signal and the noise subspaces of the output sub-channels to estimate DOAs. The proposed channelization-based method isolates signals in different bandwidths reasonably and improves the output SNR. It outperforms the conventional ISM and TOPS methods on estimation accuracy and dynamic range, especially in real environments. Besides, the parallel processing architecture makes it easy to implement on hardware. A wideband digital array radar (DAR) using direct wideband radio frequency (RF) digitization is presented. Experiments carried out in a microwave anechoic chamber with the wideband DAR are presented to demonstrate the performance. The results verify the effectiveness of the proposed method. PMID:27384566

  17. Bootstrap-based intercomparison of regional flood estimation procedures

    SciTech Connect

    Ouarda, T.B.M.J.; Ashkar, F.

    1995-12-31

    The present paper describes a methodology, based on the regional bootstrap procedure, for the intercomparison of some of the most frequently used regional flood frequency estimation models. The results of the application of this methodology, with Canadian flood data, for comparing the different regional estimation models are also presented. A regional model C{sub ij} = [DRH]{sub i} x [MER]{sub j} (i=1,...,L ; j=1,...,M) is obtained by combining a methodology for the delineation of homogeneous regions [DRH]{sub i} and a regional estimation method [MER]{sub j}. These regional models are compared with respect to their ability to provide reliable estimates of certain flood quantiles (floods with return periods of 10 and 100 years). Two types of bootstrapping have been applied within the framework of this project: the classical scalar bootstrap used in at-site estimation, and the vector (or regional) bootstrap procedure applied in the intercomparison between the different regional models. This last technique is illustrated with an example, and all the details of the procedure are presented. The performance indices that were employed for the purpose of the intercomparison are also detailed. One important feature of regional bootstrapping is that it preserves the regional dependence structure between annual flood values at the different sites of an {open_quote}homogeneous{close_quote} region. Three versions of the regional bootstrap algorithm are presented and applied to the three cases of estimation-regional estimation for ungauged sites, regional estimation for gauged sites with a short record, and at-site estimation. It will be shown how at-site estimates can be used as basis for the intercomparison between the regional models. Results of the application of the bootstrap procedure, with flood data from the Provinces of Quebec and Ontario, are presented in the final section of the paper.

  18. Single-View Food Portion Estimation Based on Geometric Models

    PubMed Central

    Fang, Shaobo; Liu, Chang; Zhu, Fengqing; Delp, Edward J.; Boushey, Carol J.

    2016-01-01

    In this paper we present a food portion estimation technique based on a single-view food image used for the estimation of the amount of energy (in kilocalories) consumed at a meal. Unlike previous methods we have developed, the new technique is capable of estimating food portion without manual tuning of parameters. Although single-view 3D scene reconstruction is in general an ill-posed problem, the use of geometric models such as the shape of a container can help to partially recover 3D parameters of food items in the scene. Based on the estimated 3D parameters of each food item and a reference object in the scene, the volume of each food item in the image can be determined. The weight of each food can then be estimated using the density of the food item. We were able to achieve an error of less than 6% for energy estimation of an image of a meal assuming accurate segmentation and food classification. PMID:27672682

  19. Support vector based battery state of charge estimator

    NASA Astrophysics Data System (ADS)

    Hansen, Terry; Wang, Chia-Jiu

    This paper investigates the use of a support vector machine (SVM) to estimate the state-of-charge (SOC) of a large-scale lithium-ion-polymer (LiP) battery pack. The SOC of a battery cannot be measured directly and must be estimated from measurable battery parameters such as current and voltage. The coulomb counting SOC estimator has been used in many applications but it has many drawbacks [S. Piller, M. Perrin, Methods for state-of-charge determination and their application, J. Power Sources 96 (2001) 113-120]. The proposed SVM based solution not only removes the drawbacks of the coulomb counting SOC estimator but also produces accurate SOC estimates, using industry standard US06 [V.H. Johnson, A.A. Pesaran, T. Sack, Temperature-dependent battery models for high-power lithium-ion batteries, in: Presented at the 17th Annual Electric Vehicle Symposium Montreal, Canada, October 15-18, 2000. The paper is downloadable at website http://www.nrel.gov/docs/fy01osti/28716.pdf] aggressive driving cycle test procedures. The proposed SOC estimator extracts support vectors from a battery operation history then uses only these support vectors to estimate SOC, resulting in minimal computation load and suitable for real-time embedded system applications.

  20. Monitoring Butterfly Abundance: Beyond Pollard Walks

    PubMed Central

    Pellet, Jérôme; Bried, Jason T.; Parietti, David; Gander, Antoine; Heer, Patrick O.; Cherix, Daniel; Arlettaz, Raphaël

    2012-01-01

    Most butterfly monitoring protocols rely on counts along transects (Pollard walks) to generate species abundance indices and track population trends. It is still too often ignored that a population count results from two processes: the biological process (true abundance) and the statistical process (our ability to properly quantify abundance). Because individual detectability tends to vary in space (e.g., among sites) and time (e.g., among years), it remains unclear whether index counts truly reflect population sizes and trends. This study compares capture-mark-recapture (absolute abundance) and count-index (relative abundance) monitoring methods in three species (Maculinea nausithous and Iolana iolas: Lycaenidae; Minois dryas: Satyridae) in contrasted habitat types. We demonstrate that intraspecific variability in individual detectability under standard monitoring conditions is probably the rule rather than the exception, which questions the reliability of count-based indices to estimate and compare specific population abundance. Our results suggest that the accuracy of count-based methods depends heavily on the ecology and behavior of the target species, as well as on the type of habitat in which surveys take place. Monitoring programs designed to assess the abundance and trends in butterfly populations should incorporate a measure of detectability. We discuss the relative advantages and inconveniences of current monitoring methods and analytical approaches with respect to the characteristics of the species under scrutiny and resources availability. PMID:22859980

  1. Adaptive Estimation of Intravascular Shear Rate Based on Parameter Optimization

    NASA Astrophysics Data System (ADS)

    Nitta, Naotaka; Takeda, Naoto

    2008-05-01

    The relationships between the intravascular wall shear stress, controlled by flow dynamics, and the progress of arteriosclerosis plaque have been clarified by various studies. Since the shear stress is determined by the viscosity coefficient and shear rate, both factors must be estimated accurately. In this paper, an adaptive method for improving the accuracy of quantitative shear rate estimation was investigated. First, the parameter dependence of the estimated shear rate was investigated in terms of the differential window width and the number of averaged velocity profiles based on simulation and experimental data, and then the shear rate calculation was optimized. The optimized result revealed that the proposed adaptive method of shear rate estimation was effective for improving the accuracy of shear rate calculation.

  2. A phase match based frequency estimation method for sinusoidal signals

    NASA Astrophysics Data System (ADS)

    Shen, Yan-Lin; Tu, Ya-Qing; Chen, Lin-Jun; Shen, Ting-Ao

    2015-04-01

    Accurate frequency estimation affects the ranging precision of linear frequency modulated continuous wave (LFMCW) radars significantly. To improve the ranging precision of LFMCW radars, a phase match based frequency estimation method is proposed. To obtain frequency estimation, linear prediction property, autocorrelation, and cross correlation of sinusoidal signals are utilized. The analysis of computational complex shows that the computational load of the proposed method is smaller than those of two-stage autocorrelation (TSA) and maximum likelihood. Simulations and field experiments are performed to validate the proposed method, and the results demonstrate the proposed method has better performance in terms of frequency estimation precision than methods of Pisarenko harmonic decomposition, modified covariance, and TSA, which contribute to improving the precision of LFMCW radars effectively.

  3. Nonlinear transform for robust dense block-based motion estimation.

    PubMed

    Xu, Rui; Taubman, David; Naman, Aous Thabit

    2014-05-01

    We present a noniterative multiresolution motion estimation strategy, involving block-based comparisons in each detail band of a Laplacian pyramid. A novel matching score is developed and analyzed. The proposed matching score is based on a class of nonlinear transformations of Laplacian detail bands, yielding 1-bit or 2-bit representations. The matching score is evaluated in a dense full-search motion estimation setting, with synthetic video frames and an optical flow data set. Together with a strategy for combining the matching scores across resolutions, the proposed method is shown to produce smoother and more robust estimates than mean square error (MSE) in each detail band and combined. It tolerates more of nontranslational motion, such as rotation, validating the analysis, while providing much better localization of the motion discontinuities. We also provide an efficient implementation of the motion estimation strategy and show that the computational complexity of the approach is closely related to the traditional MSE block-based full-search motion estimation procedure.

  4. Breast surface estimation for radar-based breast imaging systems.

    PubMed

    Williams, Trevor C; Sill, Jeff M; Fear, Elise C

    2008-06-01

    Radar-based microwave breast-imaging techniques typically require the antennas to be placed at a certain distance from or on the breast surface. This requires prior knowledge of the breast location, shape, and size. The method proposed in this paper for obtaining this information is based on a modified tissue sensing adaptive radar algorithm. First, a breast surface detection scan is performed. Data from this scan are used to localize the breast by creating an estimate of the breast surface. If required, the antennas may then be placed at specified distances from the breast surface for a second tumor-sensing scan. This paper introduces the breast surface estimation and antenna placement algorithms. Surface estimation and antenna placement results are demonstrated on three-dimensional breast models derived from magnetic resonance images.

  5. Magnetotelluric Response Function Estimation Based on Hilbert-Huang Transform

    NASA Astrophysics Data System (ADS)

    Cai, Jian-hua

    2013-11-01

    Magnetotelluric (MT) data series are non-stationary random signals that do not meet the basic requirements of conventional methods based on the Fourier transform. To minimize the estimation bias errors brought about by the non-stationary characteristics of MT data, a new method, based on the Hilbert-Huang transform (HHT), is proposed for the first time for estimating the MT response functions from a time series of electromagnetic field variations. With the HHT method, the amplitude of data series are expressed as a function of frequency and time and then response functions are estimated statistically from the time-frequency spectrum. Mathematical model and calculation processes are introduced and some simulated data are analyzed to verify the correctness of the method. Finally, the measured MT data is facilitated by applying the HHT to assess the ability of HHT method to quantify meaningful geologic information.

  6. Linear Frequency Estimation Technique for Reducing Frequency Based Signals

    PubMed Central

    Woodbridge, Jonathan; Bui, Alex; Sarrafzadeh, Majid

    2016-01-01

    This paper presents a linear frequency estimation (LFE) technique for data reduction of frequency-based signals. LFE converts a signal to the frequency domain by utilizing the Fourier transform and estimates both the real and imaginary parts with a series of vectors much smaller than the original signal size. The estimation is accomplished by selecting optimal points from the frequency domain and interpolating data between these points with a first order approximation. The difficulty of such a problem lies in determining which points are most significant. LFE is unique in the fact that it is generic to a wide variety of frequency-based signals such as electromyography (EMG), voice, and electrocardiography (ECG). The only requirement is that spectral coefficients are spatially correlated. This paper presents the algorithm and results from both EMG and voice data. We complete the paper with a description of how this method can be applied to pattern types of recognition, signal indexing, and compression.

  7. Coverage estimation-based system design in wireless communications

    NASA Astrophysics Data System (ADS)

    Aktul, Kavas

    2004-04-01

    A coverage estimation based cellular system design in microcell structure under shadowing and multipath conditions is presented. The effect of the signal weakening conditions is examined by log-normal shadowing/Rayleigh fading distribution. By taking the application values of GSM operating systems and cellular phones, area reliability and cell radius are calculated and reliable RF coverage is investigated.

  8. Automatic activity estimation based on object behaviour signature

    NASA Astrophysics Data System (ADS)

    Martínez-Pérez, F. E.; González-Fraga, J. A.; Tentori, M.

    2010-08-01

    Automatic estimation of human activities is a topic widely studied. However the process becomes difficult when we want to estimate activities from a video stream, because human activities are dynamic and complex. Furthermore, we have to take into account the amount of information that images provide, since it makes the modelling and estimation activities a hard work. In this paper we propose a method for activity estimation based on object behavior. Objects are located in a delimited observation area and their handling is recorded with a video camera. Activity estimation can be done automatically by analyzing the video sequences. The proposed method is called "signature recognition" because it considers a space-time signature of the behaviour of objects that are used in particular activities (e.g. patients' care in a healthcare environment for elder people with restricted mobility). A pulse is produced when an object appears in or disappears of the observation area. This means there is a change from zero to one or vice versa. These changes are produced by the identification of the objects with a bank of nonlinear correlation filters. Each object is processed independently and produces its own pulses; hence we are able to recognize several objects with different patterns at the same time. The method is applied to estimate three healthcare-related activities of elder people with restricted mobility.

  9. Age estimation based on Kvaal's technique using digital panoramic radiographs

    PubMed Central

    Mittal, Samta; Nagendrareddy, Suma Gundareddy; Sharma, Manisha Lakhanpal; Agnihotri, Poornapragna; Chaudhary, Sunil; Dhillon, Manu

    2016-01-01

    Introduction: Age estimation is important for administrative and ethical reasons and also because of legal consequences. Dental pulp undergoes regression in size with increasing age due to secondary dentin deposition and can be used as a parameter of age estimation even beyond 25 years of age. Kvaal et al. developed a method for chronological age estimation based on the pulp size using periapical dental radiographs. There is a need for testing this method of age estimation in the Indian population using simple tools like digital imaging on living individuals not requiring extraction of teeth. Aims and Objectives: Estimation of the chronological age of subjects by Kvaal's method using digital panoramic radiographs and also testing the validity of regression equations as given by Kvaal et al. Materials and Methods: The study sample included a total of 152 subjects in the age group of 14-60 years. Measurements were performed on the standardized digital panoramic radiographs based on Kvaal's method. Different regression formulae were derived and the age was assessed. The assessed age was then correlated to the actual age of the patient using Student's t-test. Results: No significant difference between the mean of the chronological age and the estimated age was observed. However, the values of the mean age estimated by using regression equations as given previously in the study of Kvaal et al. significantly underestimated the chronological age in the present study sample. Conclusion: The results of the study give an inference for the feasibility of this technique by calculation of regression equations on digital panoramic radiographs. However, it negates the applicability of same regression equations as given by Kvaal et al. on the study population. PMID:27555738

  10. Detection of an abundant plant-based small RNA in consumers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mechanisms of delivery of plant small RNAs to consumers must be addressed in order to harness this technology to positively impact agbiotechnology. Two groups have used honeysuckle (Lonicera japonica) feeding regimes to detect a plant-based small RNA, termed MIR2911, in sera. Meanwhile, numerous gro...

  11. Fast, moment-based estimation methods for delay network tomography

    SciTech Connect

    Lawrence, Earl Christophre; Michailidis, George; Nair, Vijayan N

    2008-01-01

    Consider the delay network tomography problem where the goal is to estimate distributions of delays at the link-level using data on end-to-end delays. These measurements are obtained using probes that are injected at nodes located on the periphery of the network and sent to other nodes also located on the periphery. Much of the previous literature deals with discrete delay distributions by discretizing the data into small bins. This paper considers more general models with a focus on computationally efficient estimation. The moment-based schemes presented here are designed to function well for larger networks and for applications like monitoring that require speedy solutions.

  12. Synchronous Generator Model Parameter Estimation Based on Noisy Dynamic Waveforms

    NASA Astrophysics Data System (ADS)

    Berhausen, Sebastian; Paszek, Stefan

    2016-01-01

    In recent years, there have occurred system failures in many power systems all over the world. They have resulted in a lack of power supply to a large number of recipients. To minimize the risk of occurrence of power failures, it is necessary to perform multivariate investigations, including simulations, of power system operating conditions. To conduct reliable simulations, the current base of parameters of the models of generating units, containing the models of synchronous generators, is necessary. In the paper, there is presented a method for parameter estimation of a synchronous generator nonlinear model based on the analysis of selected transient waveforms caused by introducing a disturbance (in the form of a pseudorandom signal) in the generator voltage regulation channel. The parameter estimation was performed by minimizing the objective function defined as a mean square error for deviations between the measurement waveforms and the waveforms calculated based on the generator mathematical model. A hybrid algorithm was used for the minimization of the objective function. In the paper, there is described a filter system used for filtering the noisy measurement waveforms. The calculation results of the model of a 44 kW synchronous generator installed on a laboratory stand of the Institute of Electrical Engineering and Computer Science of the Silesian University of Technology are also given. The presented estimation method can be successfully applied to parameter estimation of different models of high-power synchronous generators operating in a power system.

  13. Estimating evaporative vapor generation from automobiles based on parking activities.

    PubMed

    Dong, Xinyi; Tschantz, Michael; Fu, Joshua S

    2015-07-01

    A new approach is proposed to quantify the evaporative vapor generation based on real parking activity data. As compared to the existing methods, two improvements are applied in this new approach to reduce the uncertainties: First, evaporative vapor generation from diurnal parking events is usually calculated based on estimated average parking duration for the whole fleet, while in this study, vapor generation rate is calculated based on parking activities distribution. Second, rather than using the daily temperature gradient, this study uses hourly temperature observations to derive the hourly incremental vapor generation rates. The parking distribution and hourly incremental vapor generation rates are then adopted with Wade-Reddy's equation to estimate the weighted average evaporative generation. We find that hourly incremental rates can better describe the temporal variations of vapor generation, and the weighted vapor generation rate is 5-8% less than calculation without considering parking activity.

  14. Estimation of Characteristic Period for Energy Based Seismic Design

    SciTech Connect

    Hancloglu, Baykal; Polat, Zekeriya; Kircil, Murat Serdar

    2008-07-08

    Estimation of input energy using approximate methods has been always a considerable research topic of energy based seismic design. Therefore several approaches have been proposed by many researchers to estimate the energy input to SDOF systems in the last decades. The characteristic period is the key parameter of most of these approaches and it is defined as the period at which the peak value of the input energy occurs. In this study an equation is proposed for estimating the characteristic period considering an extensive earthquake ground motion database which includes a total of 268 far-field records, two horizontal components from 134 recording stations located on both soft and firm soil sites. For this purpose statistical regression analyses are performed to develop an equation in terms of a number of structural parameters, and it is found that the developed equation yields satisfactory results comparing the characteristic periods calculated from time history analyses of SDOF systems.

  15. Robust disparity estimation based on color monogenic curvature phase.

    PubMed

    Zang, Di; Li, Jie; Zhang, Dongdong; Zhang, Junqi

    2012-07-01

    Disparity estimation for binocular images is an important problem for many visual tasks such as 3D environment reconstruction, digital hologram, virtual reality, robot navigation, etc. Conventional approaches are based on brightness constancy assumption to establish spatial correspondences between a pair of images. However, in the presence of large illumination variation and serious noisy contamination, conventional approaches fail to generate accurate disparity maps. To have robust disparity estimation in these situations, we first propose a model - color monogenic curvature phase to describe local features of color images by embedding the monogenic curvature signal into the quaternion representation. Then a multiscale framework to estimate disparities is proposed by coupling the advantages of the color monogenic curvature phase and mutual information. Both indoor and outdoor images with large brightness variation are used in the experiments, and the results demonstrate that our approach can achieve a good performance even in the conditions of large illumination change and serious noisy contamination. PMID:22772192

  16. Optical flow based velocity estimation for mobile robots

    NASA Astrophysics Data System (ADS)

    Li, Xiuzhi; Zhao, Guanrong; Jia, Songmin; Qin, Baoling; Yang, Ailin

    2015-02-01

    This paper presents an optical flow based novel technique to perceive the instant motion velocity of mobile robots. The primary focus of this study is to determine the robot's ego-motion using displacement field in temporally consecutive image pairs. In contrast to most previous approaches for estimating velocity, we employ a polynomial expansion based dense optical flow approach and propose a quadratic model based RANSAC refinement of flow fields to render our method more robust with respect to noise and outliers. Accordingly, techniques for geometrical transformation and interpretation of the inter-frame motion are presented. Advantages of our proposal are validated by real experimental results conducted on Pioneer robot.

  17. Oxygen abundance maps of CALIFA galaxies

    NASA Astrophysics Data System (ADS)

    Zinchenko, I. A.; Pilyugin, L. S.; Grebel, E. K.; Sánchez, S. F.; Vílchez, J. M.

    2016-11-01

    We construct maps of the oxygen abundance distribution across the discs of 88 galaxies using Calar Alto Legacy Integral Field Area survey (CALIFA) Data Release 2 (DR2) spectra. The position of the centre of a galaxy (coordinates on the plate) was also taken from the CALIFA DR2. The galaxy inclination, the position angle of the major axis, and the optical radius were determined from the analysis of the surface brightnesses in the Sloan Digital Sky Survey (SDSS) g and r bands of the photometric maps of SDSS Data Release 9. We explore the global azimuthal abundance asymmetry in the discs of the CALIFA galaxies and the presence of a break in the radial oxygen abundance distribution. We found that there is no significant global azimuthal asymmetry for our sample of galaxies, i.e. the asymmetry is small, usually lower than 0.05 dex. The scatter in oxygen abundances around the abundance gradient has a comparable value, ≲0.05 dex. A significant (possibly dominant) fraction of the asymmetry can be attributed to the uncertainties in the geometrical parameters of these galaxies. There is evidence for a flattening of the radial abundance gradient in the central part of 18 galaxies. We also estimated the geometric parameters (coordinates of the centre, the galaxy inclination and the position angle of the major axis) of our galaxies from the analysis of the abundance map. The photometry-map-based and the abundance-map-based geometrical parameters are relatively close to each other for the majority of the galaxies but the discrepancy is large for a few galaxies with a flat radial abundance gradient.

  18. Ensemble Kalman filter implementations based on shrinkage covariance matrix estimation

    NASA Astrophysics Data System (ADS)

    Nino-Ruiz, Elias D.; Sandu, Adrian

    2015-11-01

    This paper develops efficient ensemble Kalman filter (EnKF) implementations based on shrinkage covariance estimation. The forecast ensemble members at each step are used to estimate the background error covariance matrix via the Rao-Blackwell Ledoit and Wolf estimator, which has been specifically developed to approximate high-dimensional covariance matrices using a small number of samples. Two implementations are considered: in the EnKF full-space (EnKF-FS) approach, the assimilation process is performed in the model space, while the EnKF reduce-space (EnKF-RS) formulation performs the analysis in the subspace spanned by the ensemble members. In the context of EnKF-RS, additional samples are taken from the normal distribution described by the background ensemble mean and the estimated background covariance matrix, in order to increase the size of the ensemble and reduce the sampling error of the filter. This increase in the size of the ensemble is obtained without running the forward model. After the assimilation step, the additional samples are discarded and only the model-based ensemble members are propagated further. Methodologies to reduce the impact of spurious correlations and under-estimation of sample variances in the context of the EnKF-FS and EnKF-RS implementations are discussed. An adjoint-free four-dimensional extension of EnKF-RS is also discussed. Numerical experiments carried out with the Lorenz-96 model and a quasi-geostrophic model show that the use of shrinkage covariance matrix estimation can mitigate the impact of spurious correlations during the assimilation process.

  19. Parallel implementation of a hyperspectral data geometry-based estimation of number of endmembers algorithm

    NASA Astrophysics Data System (ADS)

    Bernabé, Sergio; Martin, Gabriel; Botella, Guillermo; Prieto-Matias, Manuel; Plaza, Antonio

    2016-04-01

    In the last years, hyperspectral analysis have been applied in many remote sensing applications. In fact, hyperspectral unmixing has been a challenging task in hyperspectral data exploitation. This process consists of three stages: (i) estimation of the number of pure spectral signatures or endmembers, (ii) automatic identification of the estimated endmembers, and (iii) estimation of the fractional abundance of each endmember in each pixel of the scene. However, unmixing algorithms can be computationally very expensive, a fact that compromises their use in applications under real-time constraints. In recent years, several techniques have been proposed to solve the aforementioned problem but until now, most works have focused on the second and third stages. The execution cost of the first stage is usually lower than the other stages. Indeed, it can be optional if we known a priori this estimation. However, its acceleration on parallel architectures is still an interesting and open problem. In this paper we have addressed this issue focusing on the GENE algorithm, a promising geometry-based proposal introduced in.1 We have evaluated our parallel implementation in terms of both accuracy and computational performance through Monte Carlo simulations for real and synthetic data experiments. Performance results on a modern GPU shows satisfactory 16x speedup factors, which allow us to expect that this method could meet real-time requirements on a fully operational unmixing chain.

  20. MRI-based intelligence quotient (IQ) estimation with sparse learning.

    PubMed

    Wang, Liye; Wee, Chong-Yaw; Suk, Heung-Il; Tang, Xiaoying; Shen, Dinggang

    2015-01-01

    In this paper, we propose a novel framework for IQ estimation using Magnetic Resonance Imaging (MRI) data. In particular, we devise a new feature selection method based on an extended dirty model for jointly considering both element-wise sparsity and group-wise sparsity. Meanwhile, due to the absence of large dataset with consistent scanning protocols for the IQ estimation, we integrate multiple datasets scanned from different sites with different scanning parameters and protocols. In this way, there is large variability in these different datasets. To address this issue, we design a two-step procedure for 1) first identifying the possible scanning site for each testing subject and 2) then estimating the testing subject's IQ by using a specific estimator designed for that scanning site. We perform two experiments to test the performance of our method by using the MRI data collected from 164 typically developing children between 6 and 15 years old. In the first experiment, we use a multi-kernel Support Vector Regression (SVR) for estimating IQ values, and obtain an average correlation coefficient of 0.718 and also an average root mean square error of 8.695 between the true IQs and the estimated ones. In the second experiment, we use a single-kernel SVR for IQ estimation, and achieve an average correlation coefficient of 0.684 and an average root mean square error of 9.166. All these results show the effectiveness of using imaging data for IQ prediction, which is rarely done in the field according to our knowledge.

  1. MRI-Based Intelligence Quotient (IQ) Estimation with Sparse Learning

    PubMed Central

    Wang, Liye; Wee, Chong-Yaw; Suk, Heung-Il; Tang, Xiaoying; Shen, Dinggang

    2015-01-01

    In this paper, we propose a novel framework for IQ estimation using Magnetic Resonance Imaging (MRI) data. In particular, we devise a new feature selection method based on an extended dirty model for jointly considering both element-wise sparsity and group-wise sparsity. Meanwhile, due to the absence of large dataset with consistent scanning protocols for the IQ estimation, we integrate multiple datasets scanned from different sites with different scanning parameters and protocols. In this way, there is large variability in these different datasets. To address this issue, we design a two-step procedure for 1) first identifying the possible scanning site for each testing subject and 2) then estimating the testing subject’s IQ by using a specific estimator designed for that scanning site. We perform two experiments to test the performance of our method by using the MRI data collected from 164 typically developing children between 6 and 15 years old. In the first experiment, we use a multi-kernel Support Vector Regression (SVR) for estimating IQ values, and obtain an average correlation coefficient of 0.718 and also an average root mean square error of 8.695 between the true IQs and the estimated ones. In the second experiment, we use a single-kernel SVR for IQ estimation, and achieve an average correlation coefficient of 0.684 and an average root mean square error of 9.166. All these results show the effectiveness of using imaging data for IQ prediction, which is rarely done in the field according to our knowledge. PMID:25822851

  2. Channel mismatch estimation in time-interleaved ADCs based on input dependent estimating model

    NASA Astrophysics Data System (ADS)

    Liu, Sujuan; Wang, Junshan; Qi, Peipei; Chen, Jianxin

    2012-04-01

    Time-interleaved Analog-to-Digital Converter (TIADC) is an efficient way to achieve higher sampling rates for medium-to-high resolution applications. However, the performance of a TIADC suffers from mismatch errors among the sub-channels. This paper presents a method to estimate the channel mismatch errors using the sub-channels' output data. The proposed method introduces an input dependent estimating model (IDEM) based on an equivalent transfer function including the mismatch errors to calculate the standard deviation of the mismatch errors. The spurious-free dynamic range (SFDR) is then evaluated by applying multi-tone sinusoids signal to input. The simulated results show that the method in this work can get about 45dB SFDR enhancement.

  3. Neuromorphic Event-Based 3D Pose Estimation

    PubMed Central

    Reverter Valeiras, David; Orchard, Garrick; Ieng, Sio-Hoi; Benosman, Ryad B.

    2016-01-01

    Pose estimation is a fundamental step in many artificial vision tasks. It consists of estimating the 3D pose of an object with respect to a camera from the object's 2D projection. Current state of the art implementations operate on images. These implementations are computationally expensive, especially for real-time applications. Scenes with fast dynamics exceeding 30–60 Hz can rarely be processed in real-time using conventional hardware. This paper presents a new method for event-based 3D object pose estimation, making full use of the high temporal resolution (1 μs) of asynchronous visual events output from a single neuromorphic camera. Given an initial estimate of the pose, each incoming event is used to update the pose by combining both 3D and 2D criteria. We show that the asynchronous high temporal resolution of the neuromorphic camera allows us to solve the problem in an incremental manner, achieving real-time performance at an update rate of several hundreds kHz on a conventional laptop. We show that the high temporal resolution of neuromorphic cameras is a key feature for performing accurate pose estimation. Experiments are provided showing the performance of the algorithm on real data, including fast moving objects, occlusions, and cases where the neuromorphic camera and the object are both in motion. PMID:26834547

  4. Wireless capsule endoscopy video reduction based on camera motion estimation.

    PubMed

    Liu, Hong; Pan, Ning; Lu, Heng; Song, Enmin; Wang, Qian; Hung, Chih-Cheng

    2013-04-01

    Wireless capsule endoscopy (WCE) is a novel technology aiming for investigating the diseases and abnormalities in small intestine. The major drawback of WCE examination is that it takes a long time to examine the whole WCE video. In this paper, we present a new reduction scheme for WCE video to reduce the examination time. To achieve this task, a WCE video motion model is proposed. Under this motion model, the WCE imaging motion is estimated in two stages (the coarse level and the fine level). In the coarse level, the WCE camera motion is estimated with a combination of Bee Algorithm and Mutual Information. In the fine level, the local gastrointestinal tract motion is estimated with SIFT flow. Based on the result of WCE imaging motion estimation, the reduction scheme preserves key images in WCE video with scene changes. From experimental results, we notice that the proposed motion model is suitable for the motion estimation in successive WCE images. Through the comparison with APRS and FCM-NMF scheme, our scheme can produce an acceptable reduction sequence for browsing and examination. PMID:22868484

  5. Neuromorphic Event-Based 3D Pose Estimation.

    PubMed

    Reverter Valeiras, David; Orchard, Garrick; Ieng, Sio-Hoi; Benosman, Ryad B

    2015-01-01

    Pose estimation is a fundamental step in many artificial vision tasks. It consists of estimating the 3D pose of an object with respect to a camera from the object's 2D projection. Current state of the art implementations operate on images. These implementations are computationally expensive, especially for real-time applications. Scenes with fast dynamics exceeding 30-60 Hz can rarely be processed in real-time using conventional hardware. This paper presents a new method for event-based 3D object pose estimation, making full use of the high temporal resolution (1 μs) of asynchronous visual events output from a single neuromorphic camera. Given an initial estimate of the pose, each incoming event is used to update the pose by combining both 3D and 2D criteria. We show that the asynchronous high temporal resolution of the neuromorphic camera allows us to solve the problem in an incremental manner, achieving real-time performance at an update rate of several hundreds kHz on a conventional laptop. We show that the high temporal resolution of neuromorphic cameras is a key feature for performing accurate pose estimation. Experiments are provided showing the performance of the algorithm on real data, including fast moving objects, occlusions, and cases where the neuromorphic camera and the object are both in motion.

  6. Uav-Based Automatic Tree Growth Measurement for Biomass Estimation

    NASA Astrophysics Data System (ADS)

    Karpina, M.; Jarząbek-Rychard, M.; Tymków, P.; Borkowski, A.

    2016-06-01

    Manual in-situ measurements of geometric tree parameters for the biomass volume estimation are time-consuming and economically non-effective. Photogrammetric techniques can be deployed in order to automate the measurement procedure. The purpose of the presented work is an automatic tree growth estimation based on Unmanned Aircraft Vehicle (UAV) imagery. The experiment was conducted in an agriculture test field with scots pine canopies. The data was collected using a Leica Aibotix X6V2 platform equipped with a Nikon D800 camera. Reference geometric parameters of selected sample plants were measured manually each week. In situ measurements were correlated with the UAV data acquisition. The correlation aimed at the investigation of optimal conditions for a flight and parameter settings for image acquisition. The collected images are processed in a state of the art tool resulting in a generation of dense 3D point clouds. The algorithm is developed in order to estimate geometric tree parameters from 3D points. Stem positions and tree tops are identified automatically in a cross section, followed by the calculation of tree heights. The automatically derived height values are compared to the reference measurements performed manually. The comparison allows for the evaluation of automatic growth estimation process. The accuracy achieved using UAV photogrammetry for tree heights estimation is about 5cm.

  7. Neuromorphic Event-Based 3D Pose Estimation.

    PubMed

    Reverter Valeiras, David; Orchard, Garrick; Ieng, Sio-Hoi; Benosman, Ryad B

    2015-01-01

    Pose estimation is a fundamental step in many artificial vision tasks. It consists of estimating the 3D pose of an object with respect to a camera from the object's 2D projection. Current state of the art implementations operate on images. These implementations are computationally expensive, especially for real-time applications. Scenes with fast dynamics exceeding 30-60 Hz can rarely be processed in real-time using conventional hardware. This paper presents a new method for event-based 3D object pose estimation, making full use of the high temporal resolution (1 μs) of asynchronous visual events output from a single neuromorphic camera. Given an initial estimate of the pose, each incoming event is used to update the pose by combining both 3D and 2D criteria. We show that the asynchronous high temporal resolution of the neuromorphic camera allows us to solve the problem in an incremental manner, achieving real-time performance at an update rate of several hundreds kHz on a conventional laptop. We show that the high temporal resolution of neuromorphic cameras is a key feature for performing accurate pose estimation. Experiments are provided showing the performance of the algorithm on real data, including fast moving objects, occlusions, and cases where the neuromorphic camera and the object are both in motion. PMID:26834547

  8. Tyre pressure monitoring using a dynamical model-based estimator

    NASA Astrophysics Data System (ADS)

    Reina, Giulio; Gentile, Angelo; Messina, Arcangelo

    2015-04-01

    In the last few years, various control systems have been investigated in the automotive field with the aim of increasing the level of safety and stability, avoid roll-over, and customise handling characteristics. One critical issue connected with their integration is the lack of state and parameter information. As an example, vehicle handling depends to a large extent on tyre inflation pressure. When inflation pressure drops, handling and comfort performance generally deteriorate. In addition, it results in an increase in fuel consumption and in a decrease in lifetime. Therefore, it is important to keep tyres within the normal inflation pressure range. This paper introduces a model-based approach to estimate online tyre inflation pressure. First, basic vertical dynamic modelling of the vehicle is discussed. Then, a parameter estimation framework for dynamic analysis is presented. Several important vehicle parameters including tyre inflation pressure can be estimated using the estimated states. This method aims to work during normal driving using information from standard sensors only. On the one hand, the driver is informed about the inflation pressure and he is warned for sudden changes. On the other hand, accurate estimation of the vehicle states is available as possible input to onboard control systems.

  9. Wireless capsule endoscopy video reduction based on camera motion estimation.

    PubMed

    Liu, Hong; Pan, Ning; Lu, Heng; Song, Enmin; Wang, Qian; Hung, Chih-Cheng

    2013-04-01

    Wireless capsule endoscopy (WCE) is a novel technology aiming for investigating the diseases and abnormalities in small intestine. The major drawback of WCE examination is that it takes a long time to examine the whole WCE video. In this paper, we present a new reduction scheme for WCE video to reduce the examination time. To achieve this task, a WCE video motion model is proposed. Under this motion model, the WCE imaging motion is estimated in two stages (the coarse level and the fine level). In the coarse level, the WCE camera motion is estimated with a combination of Bee Algorithm and Mutual Information. In the fine level, the local gastrointestinal tract motion is estimated with SIFT flow. Based on the result of WCE imaging motion estimation, the reduction scheme preserves key images in WCE video with scene changes. From experimental results, we notice that the proposed motion model is suitable for the motion estimation in successive WCE images. Through the comparison with APRS and FCM-NMF scheme, our scheme can produce an acceptable reduction sequence for browsing and examination.

  10. Adenovirus type 2 early nuclear and mRNA: kinetic estimation of l anf r DNA strand fractions complementary to different abundance classes of viral RNA.

    PubMed

    Wold, W S; Green, M; Brackmann, K H; Devine, C; Cartas, M A

    1977-09-01

    RNA from unfractionated cells, nuclei, and polyribosomes was extracted from adenovirus 2 (Ad2)-infected KB cells early in infection and annealed in vast excess in liquid to purified Ad2 l (heavy) and r (light) [(32)P]DNA strands (specific activity, 3 x 10(6) to 1.5 x 10(7) cpm/mug). The number of abundance classes of Ad2 RNA, their relative concentrations, and the strand fraction from which they arose were determined by a computer-assisted nonlinear regression analysis of hybridization kinetic data. Whole-cell RNA and nuclear RNA annealed to 60 and 40%, respectively, of l and r strands. Well-defined abundance (kinetic) classes were identified: abundant and scarce classes were complementary to 15 to 17 and 40 to 45%, respectively, of l strand, and to 11 to 16 and 17 to 23%, respectively, of r strand. In whole-cell RNA and nuclear RNA the abundant classes were 57 to 208 and 13 to 27 times more concentrated, respectively, than scarce classes. RNA-RNA hybrids were isolated that annealed to about 70% of both strands, indicating that whole-cell RNA and nuclear RNA hybridization values were minimal. Polyribosomal RNA appeared to anneal as three abundance classes to each DNA strand; abundant, scarce, and very scarce classes, respectively, hybridized to 6, 5, and about 10% of l strand and 7 (6 to 8), 10 (8 to 13), and about 19% of r strand. The abundant classes were 41 (11 to 67) times more concentrated than the scarce classes and 10(3) times more concentrated than the very scarce classes. Although the biological significance of these classes is not known, the very scarce classes probably represent nuclear RNA contaminants of polyribosomal RNA. The abundant and scarce classes may comprise mRNA, because together they are complementary to about the same fraction of each DNA strand (11% [10 to 12%] and 17% [14 to 20%] of l and r strands) known to be expressed as early mRNA. Thus, nuclear RNA contains Ad2 RNA sequences not found on polyribosomes; most or all of both DNA strands

  11. Statistical properties of Fourier-based time-lag estimates

    NASA Astrophysics Data System (ADS)

    Epitropakis, A.; Papadakis, I. E.

    2016-06-01

    Context. The study of X-ray time-lag spectra in active galactic nuclei (AGN) is currently an active research area, since it has the potential to illuminate the physics and geometry of the innermost region (i.e. close to the putative super-massive black hole) in these objects. To obtain reliable information from these studies, the statistical properties of time-lags estimated from data must be known as accurately as possible. Aims: We investigated the statistical properties of Fourier-based time-lag estimates (i.e. based on the cross-periodogram), using evenly sampled time series with no missing points. Our aim is to provide practical "guidelines" on estimating time-lags that are minimally biased (i.e. whose mean is close to their intrinsic value) and have known errors. Methods: Our investigation is based on both analytical work and extensive numerical simulations. The latter consisted of generating artificial time series with various signal-to-noise ratios and sampling patterns/durations similar to those offered by AGN observations with present and past X-ray satellites. We also considered a range of different model time-lag spectra commonly assumed in X-ray analyses of compact accreting systems. Results: Discrete sampling, binning and finite light curve duration cause the mean of the time-lag estimates to have a smaller magnitude than their intrinsic values. Smoothing (i.e. binning over consecutive frequencies) of the cross-periodogram can add extra bias at low frequencies. The use of light curves with low signal-to-noise ratio reduces the intrinsic coherence, and can introduce a bias to the sample coherence, time-lag estimates, and their predicted error. Conclusions: Our results have direct implications for X-ray time-lag studies in AGN, but can also be applied to similar studies in other research fields. We find that: a) time-lags should be estimated at frequencies lower than ≈ 1/2 the Nyquist frequency to minimise the effects of discrete binning of the

  12. Neural Net Gains Estimation Based on an Equivalent Model.

    PubMed

    Aguilar Cruz, Karen Alicia; Medel Juárez, José de Jesús; Fernández Muñoz, José Luis; Esmeralda Vigueras Velázquez, Midory

    2016-01-01

    A model of an Equivalent Artificial Neural Net (EANN) describes the gains set, viewed as parameters in a layer, and this consideration is a reproducible process, applicable to a neuron in a neural net (NN). The EANN helps to estimate the NN gains or parameters, so we propose two methods to determine them. The first considers a fuzzy inference combined with the traditional Kalman filter, obtaining the equivalent model and estimating in a fuzzy sense the gains matrix A and the proper gain K into the traditional filter identification. The second develops a direct estimation in state space, describing an EANN using the expected value and the recursive description of the gains estimation. Finally, a comparison of both descriptions is performed; highlighting the analytical method describes the neural net coefficients in a direct form, whereas the other technique requires selecting into the Knowledge Base (KB) the factors based on the functional error and the reference signal built with the past information of the system.

  13. Neural Net Gains Estimation Based on an Equivalent Model.

    PubMed

    Aguilar Cruz, Karen Alicia; Medel Juárez, José de Jesús; Fernández Muñoz, José Luis; Esmeralda Vigueras Velázquez, Midory

    2016-01-01

    A model of an Equivalent Artificial Neural Net (EANN) describes the gains set, viewed as parameters in a layer, and this consideration is a reproducible process, applicable to a neuron in a neural net (NN). The EANN helps to estimate the NN gains or parameters, so we propose two methods to determine them. The first considers a fuzzy inference combined with the traditional Kalman filter, obtaining the equivalent model and estimating in a fuzzy sense the gains matrix A and the proper gain K into the traditional filter identification. The second develops a direct estimation in state space, describing an EANN using the expected value and the recursive description of the gains estimation. Finally, a comparison of both descriptions is performed; highlighting the analytical method describes the neural net coefficients in a direct form, whereas the other technique requires selecting into the Knowledge Base (KB) the factors based on the functional error and the reference signal built with the past information of the system. PMID:27366146

  14. Neural Net Gains Estimation Based on an Equivalent Model

    PubMed Central

    Aguilar Cruz, Karen Alicia; Medel Juárez, José de Jesús; Fernández Muñoz, José Luis; Esmeralda Vigueras Velázquez, Midory

    2016-01-01

    A model of an Equivalent Artificial Neural Net (EANN) describes the gains set, viewed as parameters in a layer, and this consideration is a reproducible process, applicable to a neuron in a neural net (NN). The EANN helps to estimate the NN gains or parameters, so we propose two methods to determine them. The first considers a fuzzy inference combined with the traditional Kalman filter, obtaining the equivalent model and estimating in a fuzzy sense the gains matrix A and the proper gain K into the traditional filter identification. The second develops a direct estimation in state space, describing an EANN using the expected value and the recursive description of the gains estimation. Finally, a comparison of both descriptions is performed; highlighting the analytical method describes the neural net coefficients in a direct form, whereas the other technique requires selecting into the Knowledge Base (KB) the factors based on the functional error and the reference signal built with the past information of the system. PMID:27366146

  15. Evidence-based estimates of the demand for radiotherapy.

    PubMed

    Delaney, G P; Barton, M B

    2015-02-01

    There are different methods that may be used to estimate the future demand for radiotherapy services in a population ranging from expert opinion through to complex modelling techniques. This manuscript describes the use of evidence-based treatment guidelines to determine indications for radiotherapy. It also uses epidemiological data to estimate the proportion of the population who have attributes that suggest a benefit from radiotherapy in order to calculate the overall proportion of a population of new cases of cancer who appropriately could be recommended to undergo radiotherapy. Evidence-based methods are transparent and adaptable to different populations but require extensive information about the indications for radiotherapy and the proportion of cancer cases with those indications in the population. In 2003 this method produced an estimate that 52.4% of patients with a registered cancer-type had an indication for radiotherapy. The model was updated in 2012 because of changes in cancer incidence, stage distributions and indications for radiotherapy. The new estimate of the optimal radiotherapy utilisation rate was 48.3%. The decrease was due to changes in the relative frequency of cancer types and some changes in indications for radiotherapy. Actual rates of radiotherapy utilisation in most populations still fall well below this benchmark. PMID:25455408

  16. MODIS Based Estimation of Forest Aboveground Biomass in China

    PubMed Central

    Sun, Yan; Wang, Tao; Zeng, Zhenzhong; Piao, Shilong

    2015-01-01

    Accurate estimation of forest biomass C stock is essential to understand carbon cycles. However, current estimates of Chinese forest biomass are mostly based on inventory-based timber volumes and empirical conversion factors at the provincial scale, which could introduce large uncertainties in forest biomass estimation. Here we provide a data-driven estimate of Chinese forest aboveground biomass from 2001 to 2013 at a spatial resolution of 1 km by integrating a recently reviewed plot-level ground-measured forest aboveground biomass database with geospatial information from 1-km Moderate-Resolution Imaging Spectroradiometer (MODIS) dataset in a machine learning algorithm (the model tree ensemble, MTE). We show that Chinese forest aboveground biomass is 8.56 Pg C, which is mainly contributed by evergreen needle-leaf forests and deciduous broadleaf forests. The mean forest aboveground biomass density is 56.1 Mg C ha−1, with high values observed in temperate humid regions. The responses of forest aboveground biomass density to mean annual temperature are closely tied to water conditions; that is, negative responses dominate regions with mean annual precipitation less than 1300 mm y−1 and positive responses prevail in regions with mean annual precipitation higher than 2800 mm y−1. During the 2000s, the forests in China sequestered C by 61.9 Tg C y−1, and this C sink is mainly distributed in north China and may be attributed to warming climate, rising CO2 concentration, N deposition, and growth of young forests. PMID:26115195

  17. MODIS Based Estimation of Forest Aboveground Biomass in China.

    PubMed

    Yin, Guodong; Zhang, Yuan; Sun, Yan; Wang, Tao; Zeng, Zhenzhong; Piao, Shilong

    2015-01-01

    Accurate estimation of forest biomass C stock is essential to understand carbon cycles. However, current estimates of Chinese forest biomass are mostly based on inventory-based timber volumes and empirical conversion factors at the provincial scale, which could introduce large uncertainties in forest biomass estimation. Here we provide a data-driven estimate of Chinese forest aboveground biomass from 2001 to 2013 at a spatial resolution of 1 km by integrating a recently reviewed plot-level ground-measured forest aboveground biomass database with geospatial information from 1-km Moderate-Resolution Imaging Spectroradiometer (MODIS) dataset in a machine learning algorithm (the model tree ensemble, MTE). We show that Chinese forest aboveground biomass is 8.56 Pg C, which is mainly contributed by evergreen needle-leaf forests and deciduous broadleaf forests. The mean forest aboveground biomass density is 56.1 Mg C ha-1, with high values observed in temperate humid regions. The responses of forest aboveground biomass density to mean annual temperature are closely tied to water conditions; that is, negative responses dominate regions with mean annual precipitation less than 1300 mm y-1 and positive responses prevail in regions with mean annual precipitation higher than 2800 mm y-1. During the 2000s, the forests in China sequestered C by 61.9 Tg C y-1, and this C sink is mainly distributed in north China and may be attributed to warming climate, rising CO2 concentration, N deposition, and growth of young forests. PMID:26115195

  18. MODIS Based Estimation of Forest Aboveground Biomass in China.

    PubMed

    Yin, Guodong; Zhang, Yuan; Sun, Yan; Wang, Tao; Zeng, Zhenzhong; Piao, Shilong

    2015-01-01

    Accurate estimation of forest biomass C stock is essential to understand carbon cycles. However, current estimates of Chinese forest biomass are mostly based on inventory-based timber volumes and empirical conversion factors at the provincial scale, which could introduce large uncertainties in forest biomass estimation. Here we provide a data-driven estimate of Chinese forest aboveground biomass from 2001 to 2013 at a spatial resolution of 1 km by integrating a recently reviewed plot-level ground-measured forest aboveground biomass database with geospatial information from 1-km Moderate-Resolution Imaging Spectroradiometer (MODIS) dataset in a machine learning algorithm (the model tree ensemble, MTE). We show that Chinese forest aboveground biomass is 8.56 Pg C, which is mainly contributed by evergreen needle-leaf forests and deciduous broadleaf forests. The mean forest aboveground biomass density is 56.1 Mg C ha-1, with high values observed in temperate humid regions. The responses of forest aboveground biomass density to mean annual temperature are closely tied to water conditions; that is, negative responses dominate regions with mean annual precipitation less than 1300 mm y-1 and positive responses prevail in regions with mean annual precipitation higher than 2800 mm y-1. During the 2000s, the forests in China sequestered C by 61.9 Tg C y-1, and this C sink is mainly distributed in north China and may be attributed to warming climate, rising CO2 concentration, N deposition, and growth of young forests.

  19. CO component estimation based on the independent component analysis

    SciTech Connect

    Ichiki, Kiyotomo; Kaji, Ryohei; Yamamoto, Hiroaki; Takeuchi, Tsutomu T.; Fukui, Yasuo

    2014-01-01

    Fast Independent Component Analysis (FastICA) is a component separation algorithm based on the levels of non-Gaussianity. Here we apply FastICA to the component separation problem of the microwave background, including carbon monoxide (CO) line emissions that are found to contaminate the PLANCK High Frequency Instrument (HFI) data. Specifically, we prepare 100 GHz, 143 GHz, and 217 GHz mock microwave sky maps, which include galactic thermal dust, NANTEN CO line, and the cosmic microwave background (CMB) emissions, and then estimate the independent components based on the kurtosis. We find that FastICA can successfully estimate the CO component as the first independent component in our deflection algorithm because its distribution has the largest degree of non-Gaussianity among the components. Thus, FastICA can be a promising technique to extract CO-like components without prior assumptions about their distributions and frequency dependences.

  20. Robust image reconstruction enhancement based on Gaussian mixture model estimation

    NASA Astrophysics Data System (ADS)

    Zhao, Fan; Zhao, Jian; Han, Xizhen; Wang, He; Liu, Bochao

    2016-03-01

    The low quality of an image is often characterized by low contrast and blurred edge details. Gradients have a direct relationship with image edge details. More specifically, the larger the gradients, the clearer the image details become. Robust image reconstruction enhancement based on Gaussian mixture model estimation is proposed here. First, image is transformed to its gradient domain, obtaining the gradient histogram. Second, the gradient histogram is estimated and extended using a Gaussian mixture model, and the predetermined function is constructed. Then, using histogram specification technology, the gradient field is enhanced with the constraint of the predetermined function. Finally, a matrix sine transform-based method is applied to reconstruct the enhanced image from the enhanced gradient field. Experimental results show that the proposed algorithm can effectively enhance different types of images such as medical image, aerial image, and visible image, providing high-quality image information for high-level processing.

  1. Arterial stiffness estimation based photoplethysmographic pulse wave analysis

    NASA Astrophysics Data System (ADS)

    Huotari, Matti; Maatta, Kari; Kostamovaara, Juha

    2010-11-01

    Arterial stiffness is one of the indices of vascular healthiness. It is based on pulse wave analysis. In the case we decompose the pulse waveform for the estimation and determination of arterial elasticity. Firstly, optically measured with photoplethysmograph and then investigating means by four lognormal pulse waveforms for which we can find very good fit between the original and summed decomposed pulse wave. Several studies have demonstrated that these kinds of measures predict cardiovascular events. While dynamic factors, e.g., arterial stiffness, depend on fixed structural features of the vascular wall. Arterial stiffness is estimated based on pulse wave decomposition analysis in the radial and tibial arteries. Elucidation of the precise relationship between endothelial function and vascular stiffness awaits still further study.

  2. Projection-based block-matching motion estimation

    NASA Astrophysics Data System (ADS)

    Tu, Chengjie; Tran, Trac D.; Prince, Jerry L.; Topiwala, Pankaj N.

    2000-12-01

    This paper introduces a fast block-based motion estimation algorithm based on matching projections. The idea is simple: blocks cannot match well if their corresponding 1D projections do not match well. We can take advantage of this observation to translate the expensive 2D block matching problem to a simpler 1D matching one by quickly eliminating a majority of matching candidates. Our novel motion estimation algorithm offers computational scalability through a single parameter and global optimum can still be achieved. Moreover, an efficient implementation to compute projections and to buffer recyclable data is also presented. Experiments show that the proposed algorithm is several times faster than the exhaustive search algorithm with nearly identical prediction performance. With the proposed BME method, high-performance real-time all- software video encoding starts to become practical for reasonable video sizes.

  3. A Novel Rules Based Approach for Estimating Software Birthmark

    PubMed Central

    Binti Alias, Norma; Anwar, Sajid

    2015-01-01

    Software birthmark is a unique quality of software to detect software theft. Comparing birthmarks of software can tell us whether a program or software is a copy of another. Software theft and piracy are rapidly increasing problems of copying, stealing, and misusing the software without proper permission, as mentioned in the desired license agreement. The estimation of birthmark can play a key role in understanding the effectiveness of a birthmark. In this paper, a new technique is presented to evaluate and estimate software birthmark based on the two most sought-after properties of birthmarks, that is, credibility and resilience. For this purpose, the concept of soft computing such as probabilistic and fuzzy computing has been taken into account and fuzzy logic is used to estimate properties of birthmark. The proposed fuzzy rule based technique is validated through a case study and the results show that the technique is successful in assessing the specified properties of the birthmark, its resilience and credibility. This, in turn, shows how much effort will be required to detect the originality of the software based on its birthmark. PMID:25945363

  4. A novel rules based approach for estimating software birthmark.

    PubMed

    Nazir, Shah; Shahzad, Sara; Khan, Sher Afzal; Alias, Norma Binti; Anwar, Sajid

    2015-01-01

    Software birthmark is a unique quality of software to detect software theft. Comparing birthmarks of software can tell us whether a program or software is a copy of another. Software theft and piracy are rapidly increasing problems of copying, stealing, and misusing the software without proper permission, as mentioned in the desired license agreement. The estimation of birthmark can play a key role in understanding the effectiveness of a birthmark. In this paper, a new technique is presented to evaluate and estimate software birthmark based on the two most sought-after properties of birthmarks, that is, credibility and resilience. For this purpose, the concept of soft computing such as probabilistic and fuzzy computing has been taken into account and fuzzy logic is used to estimate properties of birthmark. The proposed fuzzy rule based technique is validated through a case study and the results show that the technique is successful in assessing the specified properties of the birthmark, its resilience and credibility. This, in turn, shows how much effort will be required to detect the originality of the software based on its birthmark.

  5. SPECTRAL data-based estimation of soil heat flux

    USGS Publications Warehouse

    Singh, R.K.; Irmak, A.; Walter-Shea, Elizabeth; Verma, S.B.; Suyker, A.E.

    2011-01-01

    Numerous existing spectral-based soil heat flux (G) models have shown wide variation in performance for maize and soybean cropping systems in Nebraska, indicating the need for localized calibration and model development. The objectives of this article are to develop a semi-empirical model to estimate G from a normalized difference vegetation index (NDVI) and net radiation (R n) for maize (Zea mays L.) and soybean (Glycine max L.) fields in the Great Plains, and present the suitability of the developed model to estimate G under similar and different soil and management conditions. Soil heat fluxes measured in both irrigated and rainfed fields in eastern and south-central Nebraska were used for model development and validation. An exponential model that uses NDVI and Rn was found to be the best to estimate G based on r2 values. The effect of geographic location, crop, and water management practices were used to develop semi-empirical models under four case studies. Each case study has the same exponential model structure but a different set of coefficients and exponents to represent the crop, soil, and management practices. Results showed that the semi-empirical models can be used effectively for G estimation for nearby fields with similar soil properties for independent years, regardless of differences in crop type, crop rotation, and irrigation practices, provided that the crop residue from the previous year is more than 4000 kg ha-1. The coefficients calibrated from particular fields can be used at nearby fields in order to capture temporal variation in G. However, there is a need for further investigation of the models to account for the interaction effects of crop rotation and irrigation. Validation at an independent site having different soil and crop management practices showed the limitation of the semi-empirical model in estimating G under different soil and environment conditions. ?? 2011 American Society of Agricultural and Biological Engineers ISSN 2151-0032.

  6. Validation of Satellite-based Rainfall Estimates of Hurricane

    NASA Astrophysics Data System (ADS)

    Nourozi, N.; Mahani, S.; Khanbilvardi, R.

    2006-05-01

    Severe storms such as hurricanes and tornadoes cause devastating damages, almost every year, over a large section of the United States. More accurate forecasting intensity and track of a heavy storm can help to reduce if not to prevent its damages to lives, infrastructure, and economy. Estimating accurate high resolution quantitative precipitation (QPE) from a hurricane, required to improve the forecasting and warning capabilities, is still a challenging problem because of physical characteristics of the hurricane even when it is still over the ocean. Satellite imagery seems to be a valuable source of information for estimating and forecasting heavy precipitation and also flash floods, particularly for over the oceans where the traditional ground-based gauge and radar sources cannot provide any information. To improve the capability of a rainfall retrieval algorithm for estimating QPE of severe storms, its product is evaluated in this study. High (hourly 4km x 4km) resolutions satellite infrared-based rainfall products, from the NESDIS Hydro- Estimator (HE) and also PERSIANN (Precipitation Estimation from Remotely Sensed Information using an Artificial Neural Networks) algorithms, have been tested against NEXRAD stage-IV and rain gauge observations in this project. Three strong hurricanes: Charley, Jeanne, and Frances that caused devastating damages over Florida in the summer 2004 and also from summer 2005 hurricane Katrina, hurricane Wilma, and hurricane Ophelia have been considered to be investigated. Preliminary results demonstrate that for all hurricanes except for hurricane Charley, HE tends to underestimate rain rates especially when NEXRAD shows a heavy storm. In hurricanes Frances, Jeanne, and Wilma there are picks of heavy storm, which HE shows a big underestimation on those picks. In hurricane Charley HE tends to overestimate the amount of storm in general.

  7. Estimating Evapotranspiration Using an Observation Based Terrestrial Water Budget

    NASA Technical Reports Server (NTRS)

    Rodell, Matthew; McWilliams, Eric B.; Famiglietti, James S.; Beaudoing, Hiroko K.; Nigro, Joseph

    2011-01-01

    Evapotranspiration (ET) is difficult to measure at the scales of climate models and climate variability. While satellite retrieval algorithms do exist, their accuracy is limited by the sparseness of in situ observations available for calibration and validation, which themselves may be unrepresentative of 500m and larger scale satellite footprints and grid pixels. Here, we use a combination of satellite and ground-based observations to close the water budgets of seven continental scale river basins (Mackenzie, Fraser, Nelson, Mississippi, Tocantins, Danube, and Ubangi), estimating mean ET as a residual. For any river basin, ET must equal total precipitation minus net runoff minus the change in total terrestrial water storage (TWS), in order for mass to be conserved. We make use of precipitation from two global observation-based products, archived runoff data, and TWS changes from the Gravity Recovery and Climate Experiment satellite mission. We demonstrate that while uncertainty in the water budget-based estimates of monthly ET is often too large for those estimates to be useful, the uncertainty in the mean annual cycle is small enough that it is practical for evaluating other ET products. Here, we evaluate five land surface model simulations, two operational atmospheric analyses, and a recent global reanalysis product based on our results. An important outcome is that the water budget-based ET time series in two tropical river basins, one in Brazil and the other in central Africa, exhibit a weak annual cycle, which may help to resolve debate about the strength of the annual cycle of ET in such regions and how ET is constrained throughout the year. The methods described will be useful for water and energy budget studies, weather and climate model assessments, and satellite-based ET retrieval optimization.

  8. Rectal temperature-based death time estimation in infants.

    PubMed

    Igari, Yui; Hosokai, Yoshiyuki; Funayama, Masato

    2016-03-01

    In determining the time of death in infants based on rectal temperature, the same methods used in adults are generally used. However, whether the methods for adults are suitable for infants is unclear. In this study, we examined the following 3 methods in 20 infant death cases: computer simulation of rectal temperature based on the infinite cylinder model (Ohno's method), computer-based double exponential approximation based on Marshall and Hoare's double exponential model with Henssge's parameter determination (Henssge's method), and computer-based collinear approximation based on extrapolation of the rectal temperature curve (collinear approximation). The interval between the last time the infant was seen alive and the time that he/she was found dead was defined as the death time interval and compared with the estimated time of death. In Ohno's method, 7 cases were within the death time interval, and the average deviation in the other 12 cases was approximately 80 min. The results of both Henssge's method and collinear approximation were apparently inferior to the results of Ohno's method. The corrective factor was set within the range of 0.7-1.3 in Henssge's method, and a modified program was newly developed to make it possible to change the corrective factors. Modification A, in which the upper limit of the corrective factor range was set as the maximum value in each body weight, produced the best results: 8 cases were within the death time interval, and the average deviation in the other 12 cases was approximately 80min. There was a possibility that the influence of thermal isolation on the actual infants was stronger than that previously shown by Henssge. We conclude that Ohno's method and Modification A are useful for death time estimation in infants. However, it is important to accept the estimated time of death with certain latitude considering other circumstances.

  9. Estimation of Ionospheric Conductivity Based on the Measurements by Superdarn

    NASA Astrophysics Data System (ADS)

    Lee, Eun-Ah; An, Byung-Ho; Yi, Yu

    2002-06-01

    The ionosphere plays an important role in the electrodynamics of space environment. In particular, the information on the ionospheric conductivity distribution is indispensable in understanding the electrodynamics of the magnetosphere and ionosphere coupling study. To meet such a requirement, several attempts have been made to estimate the conductivity distribution over the polar ionosphere. As one of such attempts we compare the ionospheric plasma convection patterns obtained from the Super Dual Auroral Radar Network (SuperDARN), from which the electric field distribution is estimated, and the simultaneously measured ground magnetic disturbance. Specifically, the electric field measured from the Goose Bay and Stokkseyri radars and magnetic disturbance data obtained from the west coast chain of Greenland are compared. In order to estimate ionospheric conductivity distribution with these information, the overhead infinite sheet current approximation is employed. As expected, the Hall conductance, height-integrated conductivity, shows a wide enhancement along the center of the auroral electrojet. However, Pedersen conductance shows negative values over a wide portion of the auroral oval region, a physically unacceptable situation. To alleviate this problem, the effect of the field-aligned current is taken into account. As a result, the region with negative Pedersen conductance disappears significantly, suggesting that the effect of the field-aligned current should be taken into account, when one wants to estimate ionospheric conductance based on ground magnetic disturbance and electric field measurements by radars.

  10. Yield estimation of sugarcane based on agrometeorological-spectral models

    NASA Technical Reports Server (NTRS)

    Rudorff, Bernardo Friedrich Theodor; Batista, Getulio Teixeira

    1990-01-01

    This work has the objective to assess the performance of a yield estimation model for sugarcane (Succharum officinarum). The model uses orbital gathered spectral data along with yield estimated from an agrometeorological model. The test site includes the sugarcane plantations of the Barra Grande Plant located in Lencois Paulista municipality in Sao Paulo State. Production data of four crop years were analyzed. Yield data observed in the first crop year (1983/84) were regressed against spectral and agrometeorological data of that same year. This provided the model to predict the yield for the following crop year i.e., 1984/85. The model to predict the yield of subsequent years (up to 1987/88) were developed similarly, incorporating all previous years data. The yield estimations obtained from these models explained 69, 54, and 50 percent of the yield variation in the 1984/85, 1985/86, and 1986/87 crop years, respectively. The accuracy of yield estimations based on spectral data only (vegetation index model) and on agrometeorological data only (agrometeorological model) were also investigated.

  11. A novel ULA-based geometry for improving AOA estimation

    NASA Astrophysics Data System (ADS)

    Shirvani-Moghaddam, Shahriar; Akbari, Farida

    2011-12-01

    Due to relatively simple implementation, Uniform Linear Array (ULA) is a popular geometry for array signal processing. Despite this advantage, it does not have a uniform performance in all directions and Angle of Arrival (AOA) estimation performance degrades considerably in the angles close to endfire. In this article, a new configuration is proposed which can solve this problem. Proposed Array (PA) configuration adds two elements to the ULA in top and bottom of the array axis. By extending signal model of the ULA to the new proposed ULA-based array, AOA estimation performance has been compared in terms of angular accuracy and resolution threshold through two well-known AOA estimation algorithms, MUSIC and MVDR. In both algorithms, Root Mean Square Error (RMSE) of the detected angles descends as the input Signal to Noise Ratio (SNR) increases. Simulation results show that the proposed array geometry introduces uniform accurate performance and higher resolution in middle angles as well as border ones. The PA also presents less RMSE than the ULA in endfire directions. Therefore, the proposed array offers better performance for the border angles with almost the same array size and simplicity in both MUSIC and MVDR algorithms with respect to the conventional ULA. In addition, AOA estimation performance of the PA geometry is compared with two well-known 2D-array geometries: L-shape and V-shape, and acceptable results are obtained with equivalent or lower complexity.

  12. Performance-based selection of likelihood models for phylogeny estimation.

    PubMed

    Minin, Vladimir; Abdo, Zaid; Joyce, Paul; Sullivan, Jack

    2003-10-01

    Phylogenetic estimation has largely come to rely on explicitly model-based methods. This approach requires that a model be chosen and that that choice be justified. To date, justification has largely been accomplished through use of likelihood-ratio tests (LRTs) to assess the relative fit of a nested series of reversible models. While this approach certainly represents an important advance over arbitrary model selection, the best fit of a series of models may not always provide the most reliable phylogenetic estimates for finite real data sets, where all available models are surely incorrect. Here, we develop a novel approach to model selection, which is based on the Bayesian information criterion, but incorporates relative branch-length error as a performance measure in a decision theory (DT) framework. This DT method includes a penalty for overfitting, is applicable prior to running extensive analyses, and simultaneously compares all models being considered and thus does not rely on a series of pairwise comparisons of models to traverse model space. We evaluate this method by examining four real data sets and by using those data sets to define simulation conditions. In the real data sets, the DT method selects the same or simpler models than conventional LRTs. In order to lend generality to the simulations, codon-based models (with parameters estimated from the real data sets) were used to generate simulated data sets, which are therefore more complex than any of the models we evaluate. On average, the DT method selects models that are simpler than those chosen by conventional LRTs. Nevertheless, these simpler models provide estimates of branch lengths that are more accurate both in terms of relative error and absolute error than those derived using the more complex (yet still wrong) models chosen by conventional LRTs. This method is available in a program called DT-ModSel. PMID:14530134

  13. Hierarchical bilateral filtering based disparity estimation for view synthesis

    NASA Astrophysics Data System (ADS)

    Shin, Hong-Chang; Lee, Gwangsoon; Cheong, Won-Sik; Hur, Namho

    2016-06-01

    In this paper, we introduce a high efficient and practical disparity estimation using hierarchical bilateral filtering for real-time view synthesis. The proposed method is based on hierarchical stereo matching with hardware-efficient bilateral filtering. Hardware-efficient bilateral filtering is different from the exact bilateral filter. The purpose of the method is to design an edge-preserving filter that can be efficiently parallelized on hardware. The proposed hierarchical bilateral filtering based disparity estimation is essentially a coarse-to-fine use of stereo matching with bilateral filtering. It works as follows: firstly, the hierarchical image pyramid are constructed; the multi-scale algorithm then starts by applying a local stereo matching to the downsampled images at the coarsest level of the hierarchy. After the local stereo matching, the estimated disparity map is refined with the bilateral filtering. And then the refined disparity map will be adaptively upsampled to the next finer level. The upsampled disparity map used as a prior of the corresponding local stereo matching at the next level, and filtered and so on. The method we propose is essentially a combination of hierarchical stereo matching and hardware-efficient bilateral filtering. As a result, visual comparison using real-world stereoscopic video clips shows that the method gives better results than one of state-of-art methods in terms of robustness and computation time.

  14. Marker-based estimation of genetic parameters in genomics.

    PubMed

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing 'big' genomic data sets. PMID:25025305

  15. Analytical phase-tracking-based strain estimation for ultrasound elasticity.

    PubMed

    Yuan, Lili; Pedersen, Peder C

    2015-01-01

    A new strain estimator for quasi-static elastography is presented, based on tracking of the analytical signal phase as a function of the external force. Two implementations are introduced: zero-phase search with moving window (SMW) and zero-phase band tracking using connected component labeling (CCL). Low analytical signal amplitude caused by local destructive interference is associated with large error in the phase trajectories, and amplitude thresholding can thus be used to terminate the phase tracking along a particular path. Interpolation is then applied to estimate displacement in the eliminated path. The paper describes first a mathematical analysis based on 1-D multi-scatter modeling, followed by a statistical study of the displacement and strain error. Simulation and experiment with an inhomogeneous phantom indicate that SMW and CCL are capable of reliably estimating tissue displacement and strain over a larger range of deformation than standard timedomain cross-correlation (SCC). Results also show that SMW is roughly 40 times faster than SCC with comparable or even better accuracy. CCL is slower than SMW, but more noise robust. Simulation assessment at compression level 3% and 6% with SNR 20 dB demonstrates average strain error for SMW and CCL of 10%, whereas SCC achieves 18%. PMID:25585402

  16. Optimal estimation of spectral reflectance based on metamerism

    NASA Astrophysics Data System (ADS)

    Chou, Tzren-Ru; Lin, Wei-Ju

    2012-01-01

    In this paper, we proposed an accurate estimation method for spectral reflectance of objects captured in an image. The spectral reflectance is simply modeled by a linear combination of three basic spectrums of R, G, and B colors respectively, named as spectral reflective bases of objects, which are acquired by solving a linear system based on the principle of color metamerism. Some experiments were performed to evaluate the accuracy of the estimated spectral reflectance of objects. The average mean square error of 24 colors in Macbeth checker between we simulated and the measured is 0.0866, and the maximum is 0.310. In addition, the average color difference of the 24 colors is less than 1.5 under the D65 illuminant. There are 13 colors having their color difference values less than 1, and other 8 colors having the values during the range of 1 and 2. Only three colors are relatively larger, with the differences of 2.558, 4.130 and 2.569, from the colors of No. 2, No. 13, and No. 18 in Macbeth checker respectively. Furthermore, the computational cost of this spectral estimation is very low and suitable for many practical applications in real time.

  17. Mortality estimation based on Business as Usual Scenario

    NASA Astrophysics Data System (ADS)

    Pozzer, Andrea; Lelieveld, Jos; Barlas, Ceren

    2013-04-01

    Air pollution by fine particulate matter (PM2.5) and ozone (O3) has increased strongly with industrialization and urbanization. Epidemiological studies have shown that these pollutants increase lung cancer, cardiopulmonary and respiratory mortality. The atmospheric chemistry general circulation model EMAC has been used to estimate the concentration of such pollutants in recent and future years (2005, 2010, 2025 and 2050), based on a Business as Usual scenario. The emission scenario assumes that population and economic growth largely determine energy consumption and consequent pollution sources ("business as usual"). Based on the modeled pollutants concentrations and the UN estimates of population growth in the future, we assessed the premature mortality and the years of human life lost (YLL) caused by anthropogenic PM2.5 and O3 for epidemiological regions defined by the World Health Organization. The premature mortality for people of 30 years and older were estimated using a health impact function using parameters derived from epidemiological studies. Our results suggest that with a Business as Usual scenario, the ratio between mortality and population would increase of ~ 50% by 2050. This ratio, together with the increase of world population, would lead by the year 2050 to 8.9 millions premature deaths, equivalent to 79 millions of YYL.

  18. Marker-Based Estimation of Genetic Parameters in Genomics

    PubMed Central

    Hu, Zhiqiu; Yang, Rong-Cai

    2014-01-01

    Linear mixed model (LMM) analysis has been recently used extensively for estimating additive genetic variances and narrow-sense heritability in many genomic studies. While the LMM analysis is computationally less intensive than the Bayesian algorithms, it remains infeasible for large-scale genomic data sets. In this paper, we advocate the use of a statistical procedure known as symmetric differences squared (SDS) as it may serve as a viable alternative when the LMM methods have difficulty or fail to work with large datasets. The SDS procedure is a general and computationally simple method based only on the least squares regression analysis. We carry out computer simulations and empirical analyses to compare the SDS procedure with two commonly used LMM-based procedures. Our results show that the SDS method is not as good as the LMM methods for small data sets, but it becomes progressively better and can match well with the precision of estimation by the LMM methods for data sets with large sample sizes. Its major advantage is that with larger and larger samples, it continues to work with the increasing precision of estimation while the commonly used LMM methods are no longer able to work under our current typical computing capacity. Thus, these results suggest that the SDS method can serve as a viable alternative particularly when analyzing ‘big’ genomic data sets. PMID:25025305

  19. Intensity-Based Registration for Lung Motion Estimation

    NASA Astrophysics Data System (ADS)

    Cao, Kunlin; Ding, Kai; Amelon, Ryan E.; Du, Kaifang; Reinhardt, Joseph M.; Raghavan, Madhavan L.; Christensen, Gary E.

    Image registration plays an important role within pulmonary image analysis. The task of registration is to find the spatial mapping that brings two images into alignment. Registration algorithms designed for matching 4D lung scans or two 3D scans acquired at different inflation levels can catch the temporal changes in position and shape of the region of interest. Accurate registration is critical to post-analysis of lung mechanics and motion estimation. In this chapter, we discuss lung-specific adaptations of intensity-based registration methods for 3D/4D lung images and review approaches for assessing registration accuracy. Then we introduce methods for estimating tissue motion and studying lung mechanics. Finally, we discuss methods for assessing and quantifying specific volume change, specific ventilation, strain/ stretch information and lobar sliding.

  20. Estimation of Convective Momentum Fluxes Using Satellite-Based Methods

    NASA Astrophysics Data System (ADS)

    Jewett, C.; Mecikalski, J. R.

    2009-12-01

    Research and case studies have shown that convection plays a significant role in large-scale environmental circulations. Convective momentum fluxes (CMFs) have been studied for many years using in-situ and aircraft measurements, along with numerical simulations. However, despite these successes, little work has been conducted on methods that use satellite remote sensing as a tool to diagnose these fluxes. Uses of satellite data have the capability to provide continuous analysis across regions void of ground-based remote sensing. Therefore, the project's overall goal is to develop a synergistic approach for retrieving CMFs using a collection of instruments including GOES, TRMM, CloudSat, MODIS, and QuikScat. However, this particular study will focus on the work using TRMM and QuikScat, and the methodology of using CloudSat. Sound research has already been conducted for computing CMFs using the GOES instruments (Jewett and Mecikalski 2009, submitted to J. Geophys. Res.). Using satellite-derived winds, namely mesoscale atmospheric motion vectors (MAMVs) as described by Bedka and Mecikalski (2005), one can obtain the actual winds occurring within a convective environment as perturbed by convection. Surface outflow boundaries and upper-tropospheric anvil outflow will produce “perturbation” winds on smaller, convective scales. Combined with estimated vertical motion retrieved using geostationary infrared imagery, CMFs were estimated using MAMVs, with an average profile being calculated across a convective regime or a domain covered by active storms. This study involves estimating draft-tilt from TRMM PR radar reflectivity and sub-cloud base fluxes using QuikScat data. The “slope” of falling hydrometeors (relative to Earth) in data are related to u', v' and w' winds within convection. The main up- and down-drafts within convection are described by precipitation patterns (Mecikalski 2003). Vertical motion estimates are made using model results for deep convection

  1. Estimation of base station position using timing advance measurements

    NASA Astrophysics Data System (ADS)

    Raitoharju, Matti; Ali-Löytty, Simo; Wirola, Lauri

    2011-10-01

    Timing Advance is used in TDMA (Time Division Multiple Access) systems, such as GSM and LTE, to synchronize the mobile phone to the cellular BS (Base Station). Mobile phone positioning can use TA measurements if BS positions are known, but in many cases BS positions are not in the public domain. In this work we study how to use a set of TA measurements taken by mobile phones at known positions to estimate the position of a BS. This paper describes two methods -- GMF (Gaussian Mixture Filter) and PMF (Point Mass Filter) for estimation of the BS position. Positioning performance is evaluated using simulated and real measurements. In suburban field tests, TA measurements suffice to determine BS position with an error comparable to the TA granularity (550m). GMF computes BS position much faster than PMF and is only slightly less accurate.

  2. A History-based Estimation for LHCb job requirements

    NASA Astrophysics Data System (ADS)

    Rauschmayr, Nathalie

    2015-12-01

    The main goal of a Workload Management System (WMS) is to find and allocate resources for the given tasks. The more and better job information the WMS receives, the easier will be to accomplish its task, which directly translates into higher utilization of resources. Traditionally, the information associated with each job, like expected runtime, is defined beforehand by the Production Manager in best case and fixed arbitrary values by default. In the case of LHCb's Workload Management System no mechanisms are provided which automate the estimation of job requirements. As a result, much more CPU time is normally requested than actually needed. Particularly, in the context of multicore jobs this presents a major problem, since single- and multicore jobs shall share the same resources. Consequently, grid sites need to rely on estimations given by the VOs in order to not decrease the utilization of their worker nodes when making multicore job slots available. The main reason for going to multicore jobs is the reduction of the overall memory footprint. Therefore, it also needs to be studied how memory consumption of jobs can be estimated. A detailed workload analysis of past LHCb jobs is presented. It includes a study of job features and their correlation with runtime and memory consumption. Following the features, a supervised learning algorithm is developed based on a history based prediction. The aim is to learn over time how jobs’ runtime and memory evolve influenced due to changes in experiment conditions and software versions. It will be shown that estimation can be notably improved if experiment conditions are taken into account.

  3. Array-based GNSS Ionospheric Sensing: Estimability and Precision Analyses

    NASA Astrophysics Data System (ADS)

    Teunissen, Peter

    2016-04-01

    Array-based GNSS Ionospheric Sensing: Estimability and Precision Analyses PJG Teunissen1,2, A Khodabandeh1 and B Zhang1 1GNSS Research Centre, Curtin University, Perth, Australia 2Geoscience and Remote Sensing, Delft University of Technology, The Netherlands Introduction: The Global Navigation Satellite Systems (GNSS) have proved to be an effective means of measuring the Earth's ionosphere. The well-known geometry-free linear combinations of the GNSS data serve as the input of an external ionospheric model to capture both the spatial and temporal characteristics of the ionosphere. Next to the slant ionospheric delays experienced by the GNSS antennas, the geometry-free combinations also contain additional unknown delays that are caused by the presence of the carrier-phase ambiguous cycles and/or the code instrumental delays. That the geometry-free combinations, without an external ionospheric model, cannot unbiasedly determine the slant ionospheric delays reveals the lack of information content in the GNSS data. Motivation and objectives: With the advent of modernized multi-frequency signals, one is confronted with many different combinations of the GNSS data that are capable of sensing the ionosphere. Owing to such diversity and the lack of information content in the GNSS data, various estimable ionospheric delays of different interpretations (and of different precision) can therefore be formed. How such estimable ionospheric delays should be interpreted and the extent to which they contribute to the precision of the unbiased slant ionosphere are the topics of this contribution. Approach and results: In this contribution, we apply S-system theory to study the estimability and precision of the estimable slant ionospheric delays that are measured by the multi-frequency GNSS data. Two different S-systems are presented, leading to two different estimable parameters of different precision: 1) the phase-driven ionospheric delays and 2) the code-driven ionospheric delays

  4. A novel method to prioritize RNAseq data for post-hoc analysis based on absolute changes in transcript abundance.

    PubMed

    McNutt, Patrick; Gut, Ian; Hubbard, Kyle; Beske, Phil

    2015-06-01

    . These findings suggest that the large ΔT genes are not a product of random or stochastic phenomenon, but rather represent biologically meaningful changes in the transcriptional program. They furthermore imply that high abundance transcripts are associated with particularly cellular states, and as cells change in response to internal or external conditions, the relative distribution of the abundant transcripts changes accordingly. Thus, prioritization of DEGs based on the concept of metabolic cost is a simple yet powerful method to identify biologically important transcriptional changes and provide novel insights into cellular behaviors. PMID:25781714

  5. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant.

    PubMed

    Lautenschlager, Karin; Hwang, Chiachi; Ling, Fangqiong; Liu, Wen-Tso; Boon, Nico; Köster, Oliver; Egli, Thomas; Hammes, Frederik

    2014-10-01

    Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of organic carbon degradation underpinned biodegradation as the primary function of the biofilter biomass. The biomass was present in concentrations ranging between 2-5 × 10(15) cells/m(3) in all filters but was phylogenetically, enzymatically and metabolically diverse. Based on 16S rRNA gene-based 454 pyrosequencing analysis for microbial community composition, similar microbial taxa (predominantly Proteobacteria, Planctomycetes, Acidobacteria, Bacteriodetes, Nitrospira and Chloroflexi) were present in all biofilters and in their respective effluents, but the ratio of microbial taxa was different in each filter type. This change was also reflected in the cluster analysis, which revealed a change of 50-60% in microbial community composition between the different filter types. This study documents the direct influence of the filter biomass on the microbial community composition of the final drinking water, particularly when the water is distributed without post-disinfection. The results provide new insights on the complexity of indigenous bacteria colonizing drinking water systems, especially in different biofilters of a multi-step treatment plant.

  6. Estimation of biological parameters of marine organisms using linear and nonlinear acoustic scattering model-based inversion methods.

    PubMed

    Chu, Dezhang; Lawson, Gareth L; Wiebe, Peter H

    2016-05-01

    The linear inversion commonly used in fisheries and zooplankton acoustics assumes a constant inversion kernel and ignores the uncertainties associated with the shape and behavior of the scattering targets, as well as other relevant animal parameters. Here, errors of the linear inversion due to uncertainty associated with the inversion kernel are quantified. A scattering model-based nonlinear inversion method is presented that takes into account the nonlinearity of the inverse problem and is able to estimate simultaneously animal abundance and the parameters associated with the scattering model inherent to the kernel. It uses sophisticated scattering models to estimate first, the abundance, and second, the relevant shape and behavioral parameters of the target organisms. Numerical simulations demonstrate that the abundance, size, and behavior (tilt angle) parameters of marine animals (fish or zooplankton) can be accurately inferred from the inversion by using multi-frequency acoustic data. The influence of the singularity and uncertainty in the inversion kernel on the inversion results can be mitigated by examining the singular values for linear inverse problems and employing a non-linear inversion involving a scattering model-based kernel. PMID:27250181

  7. An automatic iris occlusion estimation method based on high-dimensional density estimation.

    PubMed

    Li, Yung-Hui; Savvides, Marios

    2013-04-01

    Iris masks play an important role in iris recognition. They indicate which part of the iris texture map is useful and which part is occluded or contaminated by noisy image artifacts such as eyelashes, eyelids, eyeglasses frames, and specular reflections. The accuracy of the iris mask is extremely important. The performance of the iris recognition system will decrease dramatically when the iris mask is inaccurate, even when the best recognition algorithm is used. Traditionally, people used the rule-based algorithms to estimate iris masks from iris images. However, the accuracy of the iris masks generated this way is questionable. In this work, we propose to use Figueiredo and Jain's Gaussian Mixture Models (FJ-GMMs) to model the underlying probabilistic distributions of both valid and invalid regions on iris images. We also explored possible features and found that Gabor Filter Bank (GFB) provides the most discriminative information for our goal. Finally, we applied Simulated Annealing (SA) technique to optimize the parameters of GFB in order to achieve the best recognition rate. Experimental results show that the masks generated by the proposed algorithm increase the iris recognition rate on both ICE2 and UBIRIS dataset, verifying the effectiveness and importance of our proposed method for iris occlusion estimation. PMID:22868651

  8. Estimation for sparse vegetation information in desertification region based on Tiangong-1 hyperspectral image.

    PubMed

    Wu, Jun-Jun; Gao, Zhi-Hai; Li, Zeng-Yuan; Wang, Hong-Yan; Pang, Yong; Sun, Bin; Li, Chang-Long; Li, Xu-Zhi; Zhang, Jiu-Xing

    2014-03-01

    In order to estimate the sparse vegetation information accurately in desertification region, taking southeast of Sunite Right Banner, Inner Mongolia, as the test site and Tiangong-1 hyperspectral image as the main data, sparse vegetation coverage and biomass were retrieved based on normalized difference vegetation index (NDVI) and soil adjusted vegetation index (SAVI), combined with the field investigation data. Then the advantages and disadvantages between them were compared. Firstly, the correlation between vegetation indexes and vegetation coverage under different bands combination was analyzed, as well as the biomass. Secondly, the best bands combination was determined when the maximum correlation coefficient turned up between vegetation indexes (VI) and vegetation parameters. It showed that the maximum correlation coefficient between vegetation parameters and NDVI could reach as high as 0.7, while that of SAVI could nearly reach 0.8. The center wavelength of red band in the best bands combination for NDVI was 630nm, and that of the near infrared (NIR) band was 910 nm. Whereas, when the center wavelength was 620 and 920 nm respectively, they were the best combination for SAVI. Finally, the linear regression models were established to retrieve vegetation coverage and biomass based on Tiangong-1 VIs. R2 of all models was more than 0.5, while that of the model based on SAVI was higher than that based on NDVI, especially, the R2 of vegetation coverage retrieve model based on SAVI was as high as 0.59. By intersection validation, the standard errors RMSE based on SAVI models were lower than that of the model based on NDVI. The results showed that the abundant spectral information of Tiangong-1 hyperspectral image can reflect the actual vegetaion condition effectively, and SAVI can estimate the sparse vegetation information more accurately than NDVI in desertification region.

  9. Kernel based color estimation for night vision imagery

    NASA Astrophysics Data System (ADS)

    Gu, Xiaojing; Sun, Shaoyuan; Fang, Jian'an; Zhou, Peng

    2012-04-01

    Displaying night vision (NV) imagery with colors can largely improve observer's performance of scene recognition and situational awareness comparing to the conventional monochrome representation. However, estimating colors for single-band NV imagery has two challenges: deriving an appropriate color mapping model and extracting sufficient image features required by the model. To address these, a kernel based regression model and a set of multi-scale image features are used here. The proposed method can automatically render single-band NV imagery with natural colors, even when it has abnormal luminance distribution and lacks identifiable details.

  10. Safe Maneuvering Envelope Estimation Based on a Physical Approach

    NASA Technical Reports Server (NTRS)

    Lombaerts, Thomas J. J.; Schuet, Stefan R.; Wheeler, Kevin R.; Acosta, Diana; Kaneshige, John T.

    2013-01-01

    This paper discusses a computationally efficient algorithm for estimating the safe maneuvering envelope of damaged aircraft. The algorithm performs a robust reachability analysis through an optimal control formulation while making use of time scale separation and taking into account uncertainties in the aerodynamic derivatives. This approach differs from others since it is physically inspired. This more transparent approach allows interpreting data in each step, and it is assumed that these physical models based upon flight dynamics theory will therefore facilitate certification for future real life applications.

  11. Contrasting community versus population-based estimates of grazing and virus-induced mortality of phytoplankton.

    PubMed

    Staniewski, Michael A; Short, Cindy M; Short, Steven M

    2012-07-01

    In this study, grazing and virus-induced mortality of phytoplankton was investigated in a freshwater pond at the University of Toronto Mississauga, Canada, during September 2009. The modified dilution assay, which partitions phytoplankton mortality into virus and grazing-induced fractions, was used along with newly designed, taxon-specific quantitative polymerase chain reaction (qPCR) assays that target psbA gene fragments to estimate growth and mortality rates for both the entire phytoplankton community and four distinct phytoplankton populations. Community mortality was estimated via fluorometric determination of chlorophyll a (Chl a) concentrations, whereas the relative mortality of individual phytoplankton populations was estimated via qPCR. The sources and amounts of mortality for individual phytoplankton populations differed from those of the whole community, as well as from each other. Grazing was found to be the only significant source of mortality for the community (0.32 day(-1)), and the Prymnesiales (1.65 day(-1)) and Chroococcales (2.79 day(-1)) populations studied. On the other hand, the Chlamydomonadales population examined experienced both significant grazing (1.01 day(-1)) and viral lysis (0.96 day(-1)), while the Chlorellales population only experienced significant mortality as a result of viral lysis (1.38 day(-1)). Our results demonstrate that the combination of qPCR and the modified dilution method can be used to estimate both viral lysis and grazing pressure on several individual phytoplankton populations within a community simultaneously. Further, previously noted limitations of the modified dilution method associated with the dilution of specific phytoplankton populations at low abundances can be overcome with the qPCR-based approach. Most importantly, this study demonstrates that when used alone, whole community-based methods of assessing mortality can overlook valuable information about carbon flow in aquatic microbial food webs. PMID

  12. ASTRAL: genome-scale coalescent-based species tree estimation

    PubMed Central

    Mirarab, S.; Reaz, R.; Bayzid, Md. S.; Zimmermann, T.; Swenson, M. S.; Warnow, T.

    2014-01-01

    Motivation: Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity and co-evolution between genes and species. Yet, gene trees often differ from species trees, creating challenges to species tree estimation. One of the most frequent causes for conflicting topologies between gene trees and species trees is incomplete lineage sorting (ILS), which is modelled by the multi-species coalescent. While many methods have been developed to estimate species trees from multiple genes, some which have statistical guarantees under the multi-species coalescent model, existing methods are too computationally intensive for use with genome-scale analyses or have been shown to have poor accuracy under some realistic conditions. Results: We present ASTRAL, a fast method for estimating species trees from multiple genes. ASTRAL is statistically consistent, can run on datasets with thousands of genes and has outstanding accuracy—improving on MP-EST and the population tree from BUCKy, two statistically consistent leading coalescent-based methods. ASTRAL is often more accurate than concatenation using maximum likelihood, except when ILS levels are low or there are too few gene trees. Availability and implementation: ASTRAL is available in open source form at https://github.com/smirarab/ASTRAL/. Datasets studied in this article are available at http://www.cs.utexas.edu/users/phylo/datasets/astral. Contact: warnow@illinois.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161245

  13. Time-based position estimation in monolithic scintillator detectors

    NASA Astrophysics Data System (ADS)

    Tabacchini, Valerio; Borghi, Giacomo; Schaart, Dennis R.

    2015-07-01

    Gamma-ray detectors based on bright monolithic scintillation crystals coupled to pixelated photodetectors are currently being considered for several applications in the medical imaging field. In a typical monolithic detector, both the light intensity and the time of arrival of the earliest scintillation photons can be recorded by each of the photosensor pixels every time a gamma interaction occurs. Generally, the time stamps are used to determine the gamma interaction time while the light intensities are used to estimate the 3D position of the interaction point. In this work we show that the spatio-temporal distribution of the time stamps also carries information on the location of the gamma interaction point and thus the time stamps can be used as explanatory variables for position estimation. We present a model for the spatial resolution obtainable when the interaction position is estimated using exclusively the time stamp of the first photon detected on each of the photosensor pixels. The model is shown to be in agreement with experimental measurements on a 16 mm  ×  16 mm  ×  10 mm LSO : Ce,0.2%Ca crystal coupled to a digital photon counter (DPC) array where a spatial resolution of 3 mm (root mean squared error) is obtained. Finally we discuss the effects of the main parameters such as scintillator rise and decay time, light output and photosensor single photon time resolution and pixel size.

  14. A Landmark Based Position Estimation for Pinpoint Landing on Mars

    NASA Technical Reports Server (NTRS)

    Cheng, Yang; Ansar, Adnan

    2005-01-01

    Real-time position estimation for a descent lander is a critical technological need for many of NASA's planned in situ missions including landing on a number of bodies at locations of greatest scientific interest and sample return. In particular, it enables the capability to land precisely and safely in a scientifically promising but hazardous site and is a key technology to be demonstrated by NASA in the next decade. The key challenge of pinpoint landing (PPL) is how to localize the lander by recognizing the landmarks (craters) in the landing area and match them positively to a preexisting landmark database while the spacecraft is descending. In this paper, a real-time landmark based position estimation technique for pinpoint landing is suggested. This system includes three crucial components: (1) real time landmark detection, (2) real-time landmark matching and (3) state (both position and velocity) estimation. We discuss the performance analysis of this system. Finally, we show that the suggested technology is able to deliver a spacecraft to less than 100 m from a pre-selected landing site on Mars.

  15. Estimating glomerular filtration rate in a population-based study

    PubMed Central

    Shankar, Anoop; Lee, Kristine E; Klein, Barbara EK; Muntner, Paul; Brazy, Peter C; Cruickshanks, Karen J; Nieto, F Javier; Danforth, Lorraine G; Schubert, Carla R; Tsai, Michael Y; Klein, Ronald

    2010-01-01

    Background: Glomerular filtration rate (GFR)-estimating equations are used to determine the prevalence of chronic kidney disease (CKD) in population-based studies. However, it has been suggested that since the commonly used GFR equations were originally developed from samples of patients with CKD, they underestimate GFR in healthy populations. Few studies have made side-by-side comparisons of the effect of various estimating equations on the prevalence estimates of CKD in a general population sample. Patients and methods: We examined a population-based sample comprising adults from Wisconsin (age, 43–86 years; 56% women). We compared the prevalence of CKD, defined as a GFR of <60 mL/min per 1.73 m2 estimated from serum creatinine, by applying various commonly used equations including the modification of diet in renal disease (MDRD) equation, Cockcroft–Gault (CG) equation, and the Mayo equation. We compared the performance of these equations against the CKD definition of cystatin C >1.23 mg/L. Results: We found that the prevalence of CKD varied widely among different GFR equations. Although the prevalence of CKD was 17.2% with the MDRD equation and 16.5% with the CG equation, it was only 4.8% with the Mayo equation. Only 24% of those identified to have GFR in the range of 50–59 mL/min per 1.73 m2 by the MDRD equation had cystatin C levels >1.23 mg/L; their mean cystatin C level was only 1 mg/L (interquartile range, 0.9–1.2 mg/L). This finding was similar for the CG equation. For the Mayo equation, 62.8% of those patients with GFR in the range of 50–59 mL/min per 1.73 m2 had cystatin C levels >1.23 mg/L; their mean cystatin C level was 1.3 mg/L (interquartile range, 1.2–1.5 mg/L). The MDRD and CG equations showed a false-positive rate of >10%. Discussion: We found that the MDRD and CG equations, the current standard to estimate GFR, appeared to overestimate the prevalence of CKD in a general population sample. PMID:20730018

  16. Long-term Observations of Jovian Mid-Infrared Aurora, Hydrocarbon Abundances, and Temperature: Ground-based and Space-based Comparison and Preparation for Juno

    NASA Astrophysics Data System (ADS)

    Kostiuk, T.; Hewagama, T.; Livengood, T. A.; Fast, K. E.; Bjoraker, G. L.; Carlson, R. C.; Schmuelling, F.

    2015-12-01

    With Juno's approach to Jupiter in 2016 nearing, we report on long term measurements of Jupiter's thermal infrared aurora covering spectral and altitude regions that will complement Juno observational capabilities. Previously acquired spectral data from ground-based observatories as well as by Voyager IRIS and Cassini CIRS during Jupiter flybys will be investigated using current methods and capabilities. The thermal (mid-) IR aurora from Jupiter's polar regions, hydrocarbon abundances, and thermal structure retrieved from the ground and from space-based investigations will be compared and used to illustrate the different capabilities and complementarity of the measurement platforms. We report on the reexamination and re-analysis of hydrocarbon emission spectra from Jupiter obtained using ground-based ultra-high spectral resolution infrared heterodyne spectroscopy (IRHS) and Fourier transform spectroscopy (FTS) from Cassini CIRS during its flyby of Jupiter in 2000-2001 and Voyager IRIS data obtained during flybys in 1979. Measurements with IRHS have been made over 30 years, primarily of ethane near 12 micrometer wavelength. These measurements yield fully resolved individual spectral lines whose shape provides unique information on variability of temperature and abundance. CIRS and IRIS data at coarser spectral resolution provide extended spatial distributions covering a broad spectral region, including abundances and auroral response of hydrocarbon constituents in the 8-13 micrometer spectral region (ethane, methane, ethylene, and acetylene). Analysis shows detailed spatial variability of the primary hydrocarbons in northern latitudes. Temporal changes of the ethane line emission over three solar cycles and comparison of retrievals from ethane data taken contemporaneously during the Cassini flyby by both techniques will be compared and results discussed. From these analyses, the expectation is that the thermal IR auroral emission may be low during the Juno tour at

  17. Estimating microsatellite based genetic diversity in Rhode Island Red chicken.

    PubMed

    Das, A K; Kumar, S; Rahim, A

    2015-01-01

    This study aimed to estimate microsatellite based genetic diversity in two lines (the selected RIR(S) and control line RIR(C)) of Rhode Island Red (RIR) chicken. Genomic DNA of 24 randomly selected birds maintained at Central Avian Research Institute (India) and 24 microsatellite markers were used. Microsatellite alleles were determined on 6% urea-PAGE, recorded using GelDoc system and the samples were genotyped. Nei's heterozygosity and Botstein's polymorphic information content (PIC) at each microsatellite locus were estimated. Wright's fixation indices and gene flow were estimated using POPGENE software. All the microsatellite loci were polymorphic and the estimated PIC ranged from 0.3648 (MCW0059) to 0.7819 (ADL0267) in RIR(S) and from 0.2392 (MCW0059) to 0.8620 (ADL0136) in RIR(C). Most of the loci were highly informative (PIC>0.50) in the both lines, except for five loci in RIR(S) and six loci in RIR(C) line. Nei's heterozygosity per locus ranged from 0.4800 (MCW0059) to 0.8056 (ADL0267) in RIR(S) and from 0.2778 (MCW0059) to 0.875 (ADL0136) in RIR(C). Out of 24 loci, 15 (62.5%) in RIR(S) and 14 loci (58.33%) in RIR(C) revealed moderate to high negative FIS index indicating heterozygote excess for these loci in corresponding lines, but the rest revealed positive FIS indicating heterozygosity deficiency. A mean FIS across the both lines indicated overall 10.77% heterozygosity deficit and a mean FIT indicated 17.19% inbreeding co-efficient favoring homozygosity over the two lines. The mean FST indicated that 10.18% of the microsatellite variation between the two lines was due to their genetic difference. PMID:27175188

  18. US-based Drug Cost Parameter Estimation for Economic Evaluations

    PubMed Central

    Levy, Joseph F; Meek, Patrick D; Rosenberg, Marjorie A

    2014-01-01

    Introduction In the US, more than 10% of national health expenditures are for prescription drugs. Assessing drug costs in US economic evaluation studies is not consistent, as the true acquisition cost of a drug is not known by decision modelers. Current US practice focuses on identifying one reasonable drug cost and imposing some distributional assumption to assess uncertainty. Methods We propose a set of Rules based on current pharmacy practice that account for the heterogeneity of drug product costs. The set of products derived from our Rules, and their associated costs, form an empirical distribution that can be used for more realistic sensitivity analyses, and create transparency in drug cost parameter computation. The Rules specify an algorithmic process to select clinically equivalent drug products that reduce pill burden, use an appropriate package size, and assume uniform weighting of substitutable products. Three diverse examples show derived empirical distributions and are compared with previously reported cost estimates. Results The shapes of the empirical distributions among the three drugs differ dramatically, including multiple modes and different variation. Previously published estimates differed from the means of the empirical distributions. Published ranges for sensitivity analyses did not cover the ranges of the empirical distributions. In one example using lisinopril, the empirical mean cost of substitutable products was $444 (range $23–$953) as compared to a published estimate of $305 (range $51–$523). Conclusions Our Rules create a simple and transparent approach to create cost estimates of drug products and assess their variability. The approach is easily modified to include a subset of, or different weighting for, substitutable products. The derived empirical distribution is easily incorporated into one-way or probabilistic sensitivity analyses. PMID:25532826

  19. Lunar base scenario cost estimates: Lunar base systems study task 6.1

    NASA Technical Reports Server (NTRS)

    1988-01-01

    The projected development and production costs of each of the Lunar Base's systems are described and unit costs are estimated for transporting the systems to the lunar surface and for setting up the system.

  20. Estimating Cetacean Carrying Capacity Based on Spacing Behaviour

    PubMed Central

    Braithwaite, Janelle E.; Meeuwig, Jessica J.; Jenner, K. Curt S.

    2012-01-01

    Conservation of large ocean wildlife requires an understanding of how they use space. In Western Australia, the humpback whale (Megaptera novaeangliae) population is growing at a minimum rate of 10% per year. An important consideration for conservation based management in space-limited environments, such as coastal resting areas, is the potential expansion in area use by humpback whales if the carrying capacity of existing areas is exceeded. Here we determined the theoretical carrying capacity of a known humpback resting area based on the spacing behaviour of pods, where a resting area is defined as a sheltered embayment along the coast. Two separate approaches were taken to estimate this distance. The first used the median nearest neighbour distance between pods in relatively dense areas, giving a spacing distance of 2.16 km (±0.94). The second estimated the spacing distance as the radius at which 50% of the population included no other pods, and was calculated as 1.93 km (range: 1.62–2.50 km). Using these values, the maximum number of pods able to fit into the resting area was 698 and 872 pods, respectively. Given an average observed pod size of 1.7 whales, this equates to a carrying capacity estimate of between 1187 and 1482 whales at any given point in time. This study demonstrates that whale pods do maintain a distance from each other, which may determine the number of animals that can occupy aggregation areas where space is limited. This requirement for space has implications when considering boundaries for protected areas or competition for space with the fishing and resources sectors. PMID:23236479

  1. Note: Localization based on estimated source energy homogeneity

    NASA Astrophysics Data System (ADS)

    Turkaya, Semih; Toussaint, Renaud; Eriksen, Fredrik Kvalheim; Lengliné, Olivier; Daniel, Guillaume; Flekkøy, Eirik G.; Mâløy, Knut Jørgen

    2016-09-01

    Acoustic signal localization is a complex problem with a wide range of industrial and academic applications. Herein, we propose a localization method based on energy attenuation and inverted source amplitude comparison (termed estimated source energy homogeneity, or ESEH). This inversion is tested on both synthetic (numerical) data using a Lamb wave propagation model and experimental 2D plate data (recorded with 4 accelerometers sensitive up to 26 kHz). We compare the performance of this technique with classic source localization algorithms: arrival time localization, time reversal localization, and localization based on energy amplitude. Our technique is highly versatile and out-performs the conventional techniques in terms of error minimization and cost (both computational and financial).

  2. Clustering-based redshift estimation: application to VIPERS/CFHTLS

    NASA Astrophysics Data System (ADS)

    Scottez, V.; Mellier, Y.; Granett, B. R.; Moutard, T.; Kilbinger, M.; Scodeggio, M.; Garilli, B.; Bolzonella, M.; de la Torre, S.; Guzzo, L.; Abbas, U.; Adami, C.; Arnouts, S.; Bottini, D.; Branchini, E.; Cappi, A.; Cucciati, O.; Davidzon, I.; Fritz, A.; Franzetti, P.; Iovino, A.; Krywult, J.; Le Brun, V.; Le Fèvre, O.; Maccagni, D.; Małek, K.; Marulli, F.; Polletta, M.; Pollo, A.; Tasca, L. A. M.; Tojeiro, R.; Vergani, D.; Zanichelli, A.; Bel, J.; Coupon, J.; De Lucia, G.; Ilbert, O.; McCracken, H. J.; Moscardini, L.

    2016-10-01

    We explore the accuracy of the clustering-based redshift estimation proposed by Ménard et al. when applied to VIMOS Public Extragalactic Redshift Survey (VIPERS) and Canada-France-Hawaii Telescope Legacy Survey (CFHTLS) real data. This method enables us to reconstruct redshift distributions from measurement of the angular clustering of objects using a set of secure spectroscopic redshifts. We use state-of-the-art spectroscopic measurements with iAB < 22.5 from the VIPERS as reference population to infer the redshift distribution of galaxies from the CFHTLS T0007 release. VIPERS provides a nearly representative sample to a flux limit of iAB < 22.5 at a redshift of >0.5 which allows us to test the accuracy of the clustering-based redshift distributions. We show that this method enables us to reproduce the true mean colour-redshift relation when both populations have the same magnitude limit. We also show that this technique allows the inference of redshift distributions for a population fainter than the reference and we give an estimate of the colour-redshift mapping in this case. This last point is of great interest for future large-redshift surveys which require a complete faint spectroscopic sample.

  3. Single nucleotide polymorphism-based dispersal estimates using noninvasive sampling

    PubMed Central

    Norman, Anita J; Spong, Göran

    2015-01-01

    Quantifying dispersal within wild populations is an important but challenging task. Here we present a method to estimate contemporary, individual-based dispersal distance from noninvasively collected samples using a specialized panel of 96 SNPs (single nucleotide polymorphisms). One main issue in conducting dispersal studies is the requirement for a high sampling resolution at a geographic scale appropriate for capturing the majority of dispersal events. In this study, fecal samples of brown bear (Ursus arctos) were collected by volunteer citizens, resulting in a high sampling resolution spanning over 45,000 km2 in Gävleborg and Dalarna counties in Sweden. SNP genotypes were obtained for unique individuals sampled (n = 433) and subsequently used to reconstruct pedigrees. A Mantel test for isolation by distance suggests that the sampling scale was appropriate for females but not for males, which are known to disperse long distances. Euclidean distance was estimated between mother and offspring pairs identified through the reconstructed pedigrees. The mean dispersal distance was 12.9 km (SE 3.2) and 33.8 km (SE 6.8) for females and males, respectively. These results were significantly different (Wilcoxon’s rank-sum test: P-value = 0.02) and are in agreement with the previously identified pattern of male-biased dispersal. Our results illustrate the potential of using a combination of noninvasively collected samples at high resolution and specialized SNPs for pedigree-based dispersal models. PMID:26357536

  4. Observed Variability in CO2 Column Abundances from aircraft vertical profiles: Insight into future space-based mission requirements

    NASA Astrophysics Data System (ADS)

    Choi, Y.; Kooi, S. A.; Vay, S. A.; Browell, E. V.

    2011-12-01

    This presentation discusses the use of high-resolution in-situ CO2 data to quantify the variability in tropospheric CO2 column optical depth. CO2 column abundances are derived from vertical soundings executed during several large-scale airborne campaigns over different geographic regions and seasons spanning the eastern United States (INTEX-NA summer 2004); Mexico (MILAGRO March 2006); the eastern North Pacific and Alaska (INTEX-B May 2006); the Canadian Arctic (ARCTAS spring and summer 2008); and California (CARB June 2008). Data from smaller-scale field experiments associated with the calibration/validation activities of a new active remote CO2 sensor for ASCENDS (Active Sensing of CO2 Emissions over Nights, Days, and Seasons) conducted over OK, MI, NH, VA, and CA, since 2005, are also examined. Nominal weighting functions for ASCENDS measurements of CO2 in the 1.57- and 2.0-microns regions are used to convert the observed CO2 mixing ratio profiles to column optical depths. Using statistics calculated from these optical depths, we show the variability of the CO2 columns and how it relates to the measurement requirements for future space-based missions.

  5. Models of Quantitative Estimations: Rule-Based and Exemplar-Based Processes Compared

    ERIC Educational Resources Information Center

    von Helversen, Bettina; Rieskamp, Jorg

    2009-01-01

    The cognitive processes underlying quantitative estimations vary. Past research has identified task-contingent changes between rule-based and exemplar-based processes (P. Juslin, L. Karlsson, & H. Olsson, 2008). B. von Helversen and J. Rieskamp (2008), however, proposed a simple rule-based model--the mapping model--that outperformed the exemplar…

  6. Can we use ground-based measurements of HCFCs and HFCs to derive their emissions, lifetimes, and the global OH abundance?

    NASA Astrophysics Data System (ADS)

    Liang, Q.; Chipperfield, M.; Daniel, J. S.; Burkholder, J. B.; Rigby, M. L.; Velders, G. J. M.

    2015-12-01

    The hydroxyl radical (OH) is the major oxidant in the atmosphere. Reaction with OH is the primary removal process for many non-CO2greenhouse gases (GHGs), ozone-depleting substances (ODSs) and their replacements, e.g. hydrochlorofluorocarbons (HCFCs) and hydrofluorocarbons (HFCs). Traditionally, the global OH abundance is inferred using the observed atmospheric rate of change for methyl chloroform (MCF). Due to the Montreal Protocol regulation, the atmospheric abundance of MCF has been decreasing rapidly to near-zero values. It is becoming critical to find an alternative reference compound to continue to provide quantitative information for the global OH abundance. Our model analysis using the NASA 3-D GEOS-5 Chemistry Climate Model suggests that the inter-hemispheric gradients (IHG) of the HCFCs and HFCs show a strong linear correlation with their global emissions. Therefore it is possible to use (i) the observed IHGs of HCFCs and HFCs to estimate their global emissions, and (ii) use the derived emissions and the observed long-term trend to calculate their lifetimes and to infer the global OH abundance. Preliminary analysis using a simple global two-box model (one box for each hemisphere) and information from the global 3-D model suggests that the quantitative relationship between IHG and global emissions varies slightly among individual compounds depending on their lifetime, their emissions history and emission fractions from the two hemispheres. While each compound shows different sensitivity to the above quantities, the combined suite of the HCFCs and HFCs provides a means to derive global OH abundance and the corresponding atmospheric lifetimes of long-lived gases with respect to OH (tOH). The fact that the OH partial lifetimes of these compounds are highly correlated, with the ratio of tOH equal to the reverse ratio of their OH thermal reaction rates at 272K, provides an additional constraint that can greatly reduce the uncertainty in the OH abundance and t

  7. Testing the use of a citronella-based repellent as an effective method to reduce the prevalence and abundance of biting flies in avian nests.

    PubMed

    Martínez-de la Puente, Josué; Merino, Santiago; Lobato, Elisa; Rivero-de Aguilar, Juan; del Cerro, Sara; Ruiz-de-Castañeda, Rafael

    2009-04-01

    Here, we validate the use of a citronella (natural oil) based repellent to reduce the abundance of flying blood-sucking insects in avian nests. These insects are important parasites of birds affecting them as blood feeders and as vectors of a diversity of pathogens. When nestling were 10 days old, we assigned wild great tit Parus major nests to one of two treatments, control and fumigated nests. The abundance of biting midges and blackflies captured during 3 days following the treatment application were lower in fumigated nests with respect to control ones. By contrast, the abundance of blowfly pupae measured when nestlings left their nests was not affected by the treatment. Although many experimental studies modify the abundance of nest-dweller ectoparasites, to our knowledge, this is the first one describing an easy, safe, and effective method, reducing the total abundance of both biting midges and blackflies in wild avian nests. Our results could be used in future conservation projects and experimental studies on host-parasite evolution affecting the abundance of flying blood-feeder insects under natural conditions.

  8. Abundances of light elements.

    PubMed Central

    Pagel, B E

    1993-01-01

    Recent developments in the study of abundances of light elements and their relevance to cosmological nucleosynthesis are briefly reviewed. The simplest model, based on standard cosmology and particle physics and assuming homogeneous baryon density at the relevant times, continues to stand up well. PMID:11607388

  9. Estimating peak oxygen uptake based on postexercise measurements in swimming.

    PubMed

    Chaverri, Diego; Iglesias, Xavier; Schuller, Thorsten; Hoffmann, Uwe; Rodríguez, Ferran A

    2016-06-01

    To assess the validity of postexercise measurements in estimating peak oxygen uptake (V̇O2peak) in swimming, we compared oxygen uptake (V̇O2) measurements during supramaximal exercise with various commonly adopted methods, including a recently developed heart rate - V̇O2 modelling procedure. Thirty-one elite swimmers performed a 200-m maximal swim where V̇O2 was measured breath-by-breath using a portable gas analyzer connected to a respiratory snorkel, 1 min before, during, and 3 min postexercise. V̇O2peak(-20-0) was the average of the last 20 s of effort. The following postexercise measures were compared: (i) first 20-s average (V̇O2peak(0-20)); (ii) linear backward extrapolation (BE) of the first 20 s (BE(20)), 30 s, and 3 × 20-, 4 × 20-, and 3 or 4 × 20-s averages; (iii) semilogarithmic BE at 20 s (LOG(20)) and at the other same time intervals as in linear BE; and (iv) predicted V̇O2peak using mathematical modelling (pV̇O2(0-20)]. Repeated-measures ANOVA and post-hoc Bonferroni tests compared V̇O2peak (criterion) and each estimated value. Pearson's coefficient of determination (r(2)) was used to assess correlation. Exercise V̇O2peak(-20-0) (mean ± SD 3531 ± 738 mL·min(-1)) was not different (p > 0.30) from pV̇O2(0-20) (3571 ± 735 mL·min(-1)), BE(20) (3617 ± 708 mL·min(-1)), or LOG(20) (3627 ± 746 mL·min(-1)). pV̇O2(0-20) was very strongly correlated with exercise V̇O2peak (r(2) = 0.962; p < 0.001), and showed a low standard error of the estimate (146 mL·min(-1), 4.1%) and the lowest mean difference (40 mL·min(-1); 1.1%). We confirm that the new modelling procedure based on postexercise V̇O2 and heart rate measurements is a valid and accurate procedure for estimating V̇O2peak in swimmers and avoids the estimation bias produced by other methods.

  10. Grid Based Nonlinear Filtering Revisited: Recursive Estimation & Asymptotic Optimality

    NASA Astrophysics Data System (ADS)

    Kalogerias, Dionysios S.; Petropulu, Athina P.

    2016-08-01

    We revisit the development of grid based recursive approximate filtering of general Markov processes in discrete time, partially observed in conditionally Gaussian noise. The grid based filters considered rely on two types of state quantization: The \\textit{Markovian} type and the \\textit{marginal} type. We propose a set of novel, relaxed sufficient conditions, ensuring strong and fully characterized pathwise convergence of these filters to the respective MMSE state estimator. In particular, for marginal state quantizations, we introduce the notion of \\textit{conditional regularity of stochastic kernels}, which, to the best of our knowledge, constitutes the most relaxed condition proposed, under which asymptotic optimality of the respective grid based filters is guaranteed. Further, we extend our convergence results, including filtering of bounded and continuous functionals of the state, as well as recursive approximate state prediction. For both Markovian and marginal quantizations, the whole development of the respective grid based filters relies more on linear-algebraic techniques and less on measure theoretic arguments, making the presentation considerably shorter and technically simpler.

  11. Model based estimation of image depth and displacement

    NASA Technical Reports Server (NTRS)

    Damour, Kevin T.

    1992-01-01

    Passive depth and displacement map determinations have become an important part of computer vision processing. Applications that make use of this type of information include autonomous navigation, robotic assembly, image sequence compression, structure identification, and 3-D motion estimation. With the reliance of such systems on visual image characteristics, a need to overcome image degradations, such as random image-capture noise, motion, and quantization effects, is clearly necessary. Many depth and displacement estimation algorithms also introduce additional distortions due to the gradient operations performed on the noisy intensity images. These degradations can limit the accuracy and reliability of the displacement or depth information extracted from such sequences. Recognizing the previously stated conditions, a new method to model and estimate a restored depth or displacement field is presented. Once a model has been established, the field can be filtered using currently established multidimensional algorithms. In particular, the reduced order model Kalman filter (ROMKF), which has been shown to be an effective tool in the reduction of image intensity distortions, was applied to the computed displacement fields. Results of the application of this model show significant improvements on the restored field. Previous attempts at restoring the depth or displacement fields assumed homogeneous characteristics which resulted in the smoothing of discontinuities. In these situations, edges were lost. An adaptive model parameter selection method is provided that maintains sharp edge boundaries in the restored field. This has been successfully applied to images representative of robotic scenarios. In order to accommodate image sequences, the standard 2-D ROMKF model is extended into 3-D by the incorporation of a deterministic component based on previously restored fields. The inclusion of past depth and displacement fields allows a means of incorporating the temporal

  12. Towards observation-based gridded runoff estimates for Europe

    NASA Astrophysics Data System (ADS)

    Gudmundsson, L.; Seneviratne, S. I.

    2015-06-01

    Terrestrial water variables are the key to understanding ecosystem processes, feed back on weather and climate, and are a prerequisite for human activities. To provide context for local investigations and to better understand phenomena that only emerge at large spatial scales, reliable information on continental-scale freshwater dynamics is necessary. To date streamflow is among the best-observed variables of terrestrial water systems. However, observation networks have a limited station density and often incomplete temporal coverage, limiting investigations to locations and times with observations. This paper presents a methodology to estimate continental-scale runoff on a 0.5° spatial grid with monthly resolution. The methodology is based on statistical upscaling of observed streamflow from small catchments in Europe and exploits readily available gridded atmospheric forcing data combined with the capability of machine learning techniques. The resulting runoff estimates are validated against (1) runoff from small catchments that were not used for model training, (2) river discharge from nine continental-scale river basins and (3) independent estimates of long-term mean evapotranspiration at the pan-European scale. In addition it is shown that the produced gridded runoff compares on average better to observations than a multi-model ensemble of comprehensive land surface models (LSMs), making it an ideal candidate for model evaluation and model development. In particular, the presented machine learning approach may help determining which factors are most relevant for an efficient modelling of runoff at regional scales. Finally, the resulting data product is used to derive a comprehensive runoff climatology for Europe and its potential for drought monitoring is illustrated.

  13. Global Distribution of Microbial Abundance and Biomass in Subseafloor Sediment

    NASA Astrophysics Data System (ADS)

    Kallmeyer, J.; Pockalny, R. A.; Adhikari, R. R.; Smith, D. C.; D'Hondt, S. L.

    2012-12-01

    Previously published cell counts were mostly from ocean margins and the eastern equatorial Pacific. Cell counts from these environments are generally similar from site to site and decrease logarithmically with sediment depth, although there can be sharp peaks of high cell densities in zones of anaerobic methane-oxidation. Recent counts from the South Pacific Gyre and the North Pacific Gyre are several orders of magnitude lower and show a more rapid decrease with depth than all previously published datasets. With these new data available, total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. The differences between cell counts from ocean margins and upwelling areas and cell counts from oceanic gyres raise three questions. First, how does the abundance of microbes in subseafloor sediment vary throughout the world ocean? Second, what property or properties are likely to control that variation? Third, how does this variation affect estimates of total subseafloor sedimentary biomass and Earth's total biomass? To address these questions, we compiled our cell counts from the South Pacific Gyre, the North Pacific Gyre and the eastern equatorial Pacific Ocean with previously published counts and parameterized the cell distribution at each site and determined two parameters, (i) cell concentration at 1 mbsf and (ii) rate of decrease in cell counts with depth. Both parameters are strongly correlated with mean sedimentation rate and distance to shore. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9*1029 cells (corresponding to 4.1 Pg C and ~0.6% of Earth's total living biomass). This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate

  14. Risk estimation based on chromosomal aberrations induced by radiation

    NASA Technical Reports Server (NTRS)

    Durante, M.; Bonassi, S.; George, K.; Cucinotta, F. A.

    2001-01-01

    The presence of a causal association between the frequency of chromosomal aberrations in peripheral blood lymphocytes and the risk of cancer has been substantiated recently by epidemiological studies. Cytogenetic analyses of crew members of the Mir Space Station have shown that a significant increase in the frequency of chromosomal aberrations can be detected after flight, and that such an increase is likely to be attributed to the radiation exposure. The risk of cancer can be estimated directly from the yields of chromosomal aberrations, taking into account some aspects of individual susceptibility and other factors unrelated to radiation. However, the use of an appropriate technique for the collection and analysis of chromosomes and the choice of the structural aberrations to be measured are crucial in providing sound results. Based on the fraction of aberrant lymphocytes detected before and after flight, the relative risk after a long-term Mir mission is estimated to be about 1.2-1.3. The new technique of mFISH can provide useful insights into the quantification of risk on an individual basis.

  15. A Parallax-based Distance Estimator for Spiral Arm Sources

    NASA Astrophysics Data System (ADS)

    Reid, M. J.; Dame, T. M.; Menten, K. M.; Brunthaler, A.

    2016-06-01

    The spiral arms of the Milky Way are being accurately located for the first time via trigonometric parallaxes of massive star-forming regions with the Bar and Spiral Structure Legacy Survey, using the Very Long Baseline Array and the European VLBI Network, and with the Japanese VLBI Exploration of Radio Astrometry project. Here we describe a computer program that leverages these results to significantly improve the accuracy and reliability of distance estimates to other sources that are known to follow spiral structure. Using a Bayesian approach, sources are assigned to arms based on their (l, b, v) coordinates with respect to arm signatures seen in CO and H i surveys. A source's kinematic distance, displacement from the plane, and proximity to individual parallax sources are also considered in generating a full distance probability density function. Using this program to estimate distances to large numbers of star-forming regions, we generate a realistic visualization of the Milky Way's spiral structure as seen from the northern hemisphere.

  16. SYNTHESIS OF MULTIPLE DATA STRUCTURES FOR IMPROVED ACCURACY OF ABUNDANCE AND DEMOGRAPHIC ESTIMATES FROM WHITE-TAILED DEER AT SAVANNAH RIVER SITE.

    SciTech Connect

    Conroy, Michael J.

    2014-12-08

    The goal of this study was to provide a framework for combining existing data (from camera trapping, harvest surveys, and spotlight counts) into an integrated system that produces the most accurate estimates possible for use in setting harvest goals. A summary of the key data components that were available is included.

  17. Estimating the distribution of harvested estuarine bivalves with natural-history-based habitat suitability models

    EPA Science Inventory

    Habitat suitability models are useful to forecast how environmental change may affect the abundance or distribution of species of concern. In the case of harvested bivalves, those models may be used to estimate the vulnerability of this valued ecosystem good to natural or human-...

  18. Estimating global carbon uptake by lichens and bryophytes with a process-based model

    NASA Astrophysics Data System (ADS)

    Porada, P.; Weber, B.; Elbert, W.; Pöschl, U.; Kleidon, A.

    2013-02-01

    Lichens and bryophytes are abundant globally and they may even form the dominant autotrophs in (sub)polar ecosystems, in deserts and at high altitudes. Moreover, they can be found in large amounts as epiphytes in old-growth forests. Here, we present the first process-based model which estimates the net carbon uptake by these organisms at the global scale, thus assessing their significance for biogeochemical cycles. The model uses gridded climate data and key properties of the habitat (e.g. disturbance intervals) to predict processes which control net carbon uptake, namely photosynthesis, respiration, water uptake and evaporation. It relies on equations used in many dynamical vegetation models, which are combined with concepts specific to lichens and bryophytes, such as poikilohydry or the effect of water content on CO2 diffusivity. To incorporate the great functional variation of lichens and bryophytes at the global scale, the model parameters are characterised by broad ranges of possible values instead of a single, globally uniform value. The predicted terrestrial net carbon uptake of 0.34 to 3.3 (Gt C) yr-1 and global patterns of productivity are in accordance with empirically-derived estimates. Considering that the assimilated carbon can be invested in processes such as weathering or nitrogen fixation, lichens and bryophytes may play a significant role in biogeochemical cycles.

  19. Estimating global carbon uptake by lichens and bryophytes with a process-based model

    NASA Astrophysics Data System (ADS)

    Porada, P.; Weber, B.; Elbert, W.; Pöschl, U.; Kleidon, A.

    2013-11-01

    Lichens and bryophytes are abundant globally and they may even form the dominant autotrophs in (sub)polar ecosystems, in deserts and at high altitudes. Moreover, they can be found in large amounts as epiphytes in old-growth forests. Here, we present the first process-based model which estimates the net carbon uptake by these organisms at the global scale, thus assessing their significance for biogeochemical cycles. The model uses gridded climate data and key properties of the habitat (e.g. disturbance intervals) to predict processes which control net carbon uptake, namely photosynthesis, respiration, water uptake and evaporation. It relies on equations used in many dynamical vegetation models, which are combined with concepts specific to lichens and bryophytes, such as poikilohydry or the effect of water content on CO2 diffusivity. To incorporate the great functional variation of lichens and bryophytes at the global scale, the model parameters are characterised by broad ranges of possible values instead of a single, globally uniform value. The predicted terrestrial net uptake of 0.34 to 3.3 Gt yr-1 of carbon and global patterns of productivity are in accordance with empirically-derived estimates. Considering that the assimilated carbon can be invested in processes such as weathering or nitrogen fixation, lichens and bryophytes may play a significant role in biogeochemical cycles.

  20. Porosity estimation of alumina samples based on resonant backscattering spectrometry

    NASA Astrophysics Data System (ADS)

    Mokhles Gerami, F.; Kakuee, O.; Mohammadi, S.

    2016-04-01

    In this work, columnar porous alumina samples were investigated using the 16O(α,α)16O resonance scattering at 3.045 MeV. If the incident energy is slightly above the resonance energy, a resonance peak appears in the energy spectra of the backscattered ions. The position and width of this peak for non-porous samples are mainly determined by the experimental setup, whilst for porous materials, the peak position shifts towards higher energies under certain conditions. This effect can be explained by the lower amount of material which the ions encounter along the backscattered trajectories. The energy shift of the resonance peak towards higher energies was revealed experimentally and discussed theoretically. The estimated porosities of the samples based on this energy shift were compared with those evaluated from the graphical analysis of the images obtained by field emission scanning electron microscopy.

  1. Degradation trend estimation of slewing bearing based on LSSVM model

    NASA Astrophysics Data System (ADS)

    Lu, Chao; Chen, Jie; Hong, Rongjing; Feng, Yang; Li, Yuanyuan

    2016-08-01

    A novel prediction method is proposed based on least squares support vector machine (LSSVM) to estimate the slewing bearing's degradation trend with small sample data. This method chooses the vibration signal which contains rich state information as the object of the study. Principal component analysis (PCA) was applied to fuse multi-feature vectors which could reflect the health state of slewing bearing, such as root mean square, kurtosis, wavelet energy entropy, and intrinsic mode function (IMF) energy. The degradation indicator fused by PCA can reflect the degradation more comprehensively and effectively. Then the degradation trend of slewing bearing was predicted by using the LSSVM model optimized by particle swarm optimization (PSO). The proposed method was demonstrated to be more accurate and effective by the whole life experiment of slewing bearing. Therefore, it can be applied in engineering practice.

  2. Data Sources for the Model-based Small Area Estimates of Cancer-Related Knowledge - Small Area Estimates

    Cancer.gov

    The model-based estimates of important cancer risk factors and screening behaviors are obtained by combining the responses to the Behavioral Risk Factor Surveillance System (BRFSS) and the National Health Interview Survey (NHIS).

  3. Data Sources for the Model-based Small Area Estimates of Cancer Risk Factors and Screening Behaviors - Small Area Estimates

    Cancer.gov

    The model-based estimates of important cancer risk factors and screening behaviors are obtained by combining the responses to the Behavioral Risk Factor Surveillance System (BRFSS) and the National Health Interview Survey (NHIS).

  4. Antarctic mixotrophic protist abundances by microscopy and molecular methods.

    PubMed

    Gast, Rebecca J; McKie-Krisberg, Zaid M; Fay, Scott A; Rose, Julie M; Sanders, Robert W

    2014-08-01

    Protists are traditionally described as either phototrophic or heterotrophic, but studies have indicated that mixotrophic species, organisms that combine both strategies, can have significant impacts on prey populations in marine microbial food webs. While estimates of active mixotroph abundances in environmental samples are determined microscopically by fluorescent particle ingestion, species identification is difficult. We developed SYBR-based qPCR strategies for three Antarctic algal species that we identified as mixotrophic. This method and traditional ingestion experiments were applied to determine the total mixotroph abundance in Antarctic water samples, to ascertain the abundance of known mixotrophic species, and to identify environmental variables that impact the distribution and abundance of these species. Despite differences in sampling locations and years, mixotroph distribution was strongly influenced by season. Environmental variables that best explained variation in the individual mixotroph species abundances included temperature, oxygen, date, fluorescence, conductivity, and latitude. Phosphate was identified as an additional explanatory variable when nutrients were included in the analysis. Utilizing culture-based grazing rates and qPCR abundances, the estimated summed impact on bacterial populations by the three mixotrophs was usually < 2% of the overall mixotrophic grazing, but in one sample, Pyramimonas was estimated to contribute up to 80% of mixotrophic grazing.

  5. Software Effort Estimation Accuracy: A Comparative Study of Estimations Based on Software Sizing and Development Methods

    ERIC Educational Resources Information Center

    Lafferty, Mark T.

    2010-01-01

    The number of project failures and those projects completed over cost and over schedule has been a significant issue for software project managers. Among the many reasons for failure, inaccuracy in software estimation--the basis for project bidding, budgeting, planning, and probability estimates--has been identified as a root cause of a high…

  6. Comparing remotely sensed Pictometry Web-based height estimates with in situ clinometer and laser range finder height estimates

    NASA Astrophysics Data System (ADS)

    Unger, Daniel R.; Hung, I.-Kuai; Kulhavy, David L.

    2014-01-01

    Heights of 30 light poles were measured with a telescopic height pole. Clinometer and laser range finder in situ estimated light pole height was compared to Pictometry estimated light pole height using hyperspatial 4-in. (10.2-cm) multispectral imagery within a Web-based interface. Average percent agreement between light pole height and clinometer and laser range finder estimated that light pole height ranged from 3.97% to 3.79% for clinometer and laser range finder estimated light pole height, respectively. Average percent agreement between light pole height and Pictometry estimated light pole height at image magnification factors of 100%, 125%, 150%, 200%, and 300% magnification ranged from 1.77% to 2.39%. Root-mean-square error (RMSE) between light pole height and clinometer and laser range finder estimated that light pole height ranged from 0.22 to 0.20 m for clinometer and laser range finder estimated light pole height, respectively. RMSE between light pole height and Pictometry estimated light pole height ranged from 0.10 to 0.14 m. An analysis of variance between absolute errors of light pole height estimate by different techniques indicated that Pictometry was significantly more accurate than both clinometer and laser range finder light pole height estimates.

  7. Comparison of Aquifer Recharge Estimates Based on Measured and Estimated Hydraulic Properties

    NASA Astrophysics Data System (ADS)

    Perkins, K. S.

    2003-12-01

    Because unsaturated hydraulic properties, which are used to estimate recharge, are difficult and time consuming to measure accurately, models that estimate these properties indirectly are often used. Using data from six locations in southern New Jersey that appear to have steady-state flow conditions, five hydraulic property prediction and parameterization techniques were evaluated for recharge estimation. The unsaturated zone at this site, as in many coastal plain regions, is mainly sand to sandy loam in texture, which is considered a highly favorable case for soil hydraulic property estimation. Annual recharge has been estimated for several southern New Jersey watersheds by water budget methods and ranges from 33 to 49 cm/yr. Using these estimates as a gauge of reasonable values for steady flow, several indirect methods were compared to determine which are appropriate for recharge estimation in the coastal plain environment. The methods used in this study were: (1) simple power-law and hand-drawn curve fits to measured unsaturated hydraulic conductivity, (2) measured water retention and measured unsaturated hydraulic conductivity fit using the van Genuchten-Mualem model with fixed and optimized parameter values, (3) unsaturated hydraulic conductivity estimated from measured water retention with fixed and optimized parameter values, (4) estimation of water retention and hydraulic conductivity from bulk density and minimal textural information using the Rosetta pedotransfer function model, and (5) estimation of water retention and hydraulic conductivity using high resolution particle size distributions with the Arya-Paris and van Genuchten-Mualem models. Preliminary results show that while reasonable estimates can come from directly measured unsaturated hydraulic conductivity, the curve fitting method is critical because of the extreme non-linearity of the relationship between hydraulic conductivity and water content. Even a relatively good visual fit can lead to

  8. Modeling avian abundance from replicated counts using binomial mixture models

    USGS Publications Warehouse

    Kery, M.; Royle, J. Andrew; Schmid, H.

    2005-01-01

    Abundance estimation in ecology is usually accomplished by capture-recapture, removal, or distance sampling methods. These may be hard to implement at large spatial scales. In contrast, binomial mixture models enable abundance estimation without individual identification, based simply on temporally and spatially replicated counts. Here, we evaluate mixture models using data from the national breeding bird monitoring program in Switzerland, where some 250 1-km(2) quadrats are surveyed using the territory mapping method three times during each breeding season. We chose eight species with contrasting distribution (wide-narrow), abundance (high-low), and detectability (easy-difficult). Abundance was modeled as a random effect with a Poisson or negative binomial distribution, with mean affected by forest cover, elevation, and route length. Detectability was a logit-linear function of survey date, survey date-by-elevation, and sampling effort (time per transect unit). Resulting covariate effects and parameter estimates were consistent with expectations. Detectability per territory (for three surveys) ranged from 0.66 to 0.94 (mean 0.84) for easy species, and from 0.16 to 0.83 (mean 0.53) for difficult species, depended on survey effort for two easy and all four difficult species, and changed seasonally for three easy and three difficult species. Abundance was positively related to route length in three high-abundance and one low-abundance (one easy and three difficult) species, and increased with forest cover in five forest species, decreased for two nonforest species, and was unaffected for a generalist species. Abundance estimates under the most parsimonious mixture models were between 1.1 and 8.9 (median 1.8) times greater than estimates based on territory mapping; hence, three surveys were insufficient to detect all territories for each species. We conclude that binomial mixture models are an important new approach for estimating abundance corrected for detectability

  9. Modeling avian abundance from replicated counts using binomial mixture models

    USGS Publications Warehouse

    Kery, Marc; Royle, J. Andrew; Schmid, Hans

    2005-01-01

    Abundance estimation in ecology is usually accomplished by capture–recapture, removal, or distance sampling methods. These may be hard to implement at large spatial scales. In contrast, binomial mixture models enable abundance estimation without individual identification, based simply on temporally and spatially replicated counts. Here, we evaluate mixture models using data from the national breeding bird monitoring program in Switzerland, where some 250 1-km2 quadrats are surveyed using the territory mapping method three times during each breeding season. We chose eight species with contrasting distribution (wide–narrow), abundance (high–low), and detectability (easy–difficult). Abundance was modeled as a random effect with a Poisson or negative binomial distribution, with mean affected by forest cover, elevation, and route length. Detectability was a logit-linear function of survey date, survey date-by-elevation, and sampling effort (time per transect unit). Resulting covariate effects and parameter estimates were consistent with expectations. Detectability per territory (for three surveys) ranged from 0.66 to 0.94 (mean 0.84) for easy species, and from 0.16 to 0.83 (mean 0.53) for difficult species, depended on survey effort for two easy and all four difficult species, and changed seasonally for three easy and three difficult species. Abundance was positively related to route length in three high-abundance and one low-abundance (one easy and three difficult) species, and increased with forest cover in five forest species, decreased for two nonforest species, and was unaffected for a generalist species. Abundance estimates under the most parsimonious mixture models were between 1.1 and 8.9 (median 1.8) times greater than estimates based on territory mapping; hence, three surveys were insufficient to detect all territories for each species. We conclude that binomial mixture models are an important new approach for estimating abundance corrected for

  10. Height estimations based on eye measurements throughout a gait cycle.

    PubMed

    Yang, Sylvia X M; Larsen, Peter K; Alkjær, Tine; Juul-Kristensen, Birgit; Simonsen, Erik B; Lynnerup, Niels

    2014-03-01

    Anthropometric measurements (e.g. the height to the head, nose tip, eyes or shoulders) of a perpetrator based on video material may be used in criminal cases. However, several height measurements may be difficult to assess as the perpetrators may be disguised by clothes or headwear. The eye height (EH) measurement, on the other hand, is less prone to concealment. The purpose of the present study was to investigate: (1) how the eye height varies during the gait cycle, and (2) how the eye height changes with head position. The eyes were plotted manually in APAS for 16 test subjects during a complete gait cycle. The influence of head tilt on the EH was investigated in 20 healthy men. Markers were attached to the face and the subjects were instructed to stand relaxed, tilt their head to the right, to the left, forward and backward. The marker data for the right eye were used to calculate the EH. The respective deviation and SD from the relaxed standing EH and the EH in the Frankfurt plane, left tilted, right tilted, forward tilted and backward tilted, in addition to the corresponding head tilt angles were calculated. There was no correlation between the height of the subject and the maximum vertical displacement of the EH throughout the gait cycle nor between height of the subjects and the variation of the EH throughout the gait cycle. The average maximum vertical displacement for the test subject group was 4.76 cm (± 1.56 cm). The average EH was lower when the subjects were standing in the relaxed position than in the Frankfurt plane. The average EH was higher in the relaxed position than when the subjects tilted their heads, except when they tilted their heads backwards. The subjects had a slightly larger range of motion to the right than to the left, which was not significant. The results of this study provide a range for eye height estimates and may be readily implemented in forensic case work. It can be used as a reference in height estimates in cases with height

  11. Unsupervised, Robust Estimation-based Clustering for Multispectral Images

    NASA Technical Reports Server (NTRS)

    Netanyahu, Nathan S.

    1997-01-01

    To prepare for the challenge of handling the archiving and querying of terabyte-sized scientific spatial databases, the NASA Goddard Space Flight Center's Applied Information Sciences Branch (AISB, Code 935) developed a number of characterization algorithms that rely on supervised clustering techniques. The research reported upon here has been aimed at continuing the evolution of some of these supervised techniques, namely the neural network and decision tree-based classifiers, plus extending the approach to incorporating unsupervised clustering algorithms, such as those based on robust estimation (RE) techniques. The algorithms developed under this task should be suited for use by the Intelligent Information Fusion System (IIFS) metadata extraction modules, and as such these algorithms must be fast, robust, and anytime in nature. Finally, so that the planner/schedule module of the IlFS can oversee the use and execution of these algorithms, all information required by the planner/scheduler must be provided to the IIFS development team to ensure the timely integration of these algorithms into the overall system.

  12. EEG-based workload estimation across affective contexts

    PubMed Central

    Mühl, Christian; Jeunet, Camille; Lotte, Fabien

    2014-01-01

    Workload estimation from electroencephalographic signals (EEG) offers a highly sensitive tool to adapt the human–computer interaction to the user state. To create systems that reliably work in the complexity of the real world, a robustness against contextual changes (e.g., mood), has to be achieved. To study the resilience of state-of-the-art EEG-based workload classification against stress we devise a novel experimental protocol, in which we manipulated the affective context (stressful/non-stressful) while the participant solved a task with two workload levels. We recorded self-ratings, behavior, and physiology from 24 participants to validate the protocol. We test the capability of different, subject-specific workload classifiers using either frequency-domain, time-domain, or both feature varieties to generalize across contexts. We show that the classifiers are able to transfer between affective contexts, though performance suffers independent of the used feature domain. However, cross-context training is a simple and powerful remedy allowing the extraction of features in all studied feature varieties that are more resilient to task-unrelated variations in signal characteristics. Especially for frequency-domain features, across-context training is leading to a performance comparable to within-context training and testing. We discuss the significance of the result for neurophysiology-based workload detection in particular and for the construction of reliable passive brain–computer interfaces in general. PMID:24971046

  13. Physics-based estimates of maximum magnitude of induced earthquakes

    NASA Astrophysics Data System (ADS)

    Ampuero, Jean-Paul; Galis, Martin; Mai, P. Martin

    2016-04-01

    In this study, we present new findings when integrating earthquake physics and rupture dynamics into estimates of maximum magnitude of induced seismicity (Mmax). Existing empirical relations for Mmax lack a physics-based relation between earthquake size and the characteristics of the triggering stress perturbation. To fill this gap, we extend our recent work on the nucleation and arrest of dynamic ruptures derived from fracture mechanics theory. There, we derived theoretical relations between the area and overstress of overstressed asperity and the ability of ruptures to either stop spontaneously (sub-critical ruptures) or runaway (super-critical ruptures). These relations were verified by comparison with simulation and laboratory results, namely 3D dynamic rupture simulations on faults governed by slip-weakening friction, and laboratory experiments of frictional sliding nucleated by localized stresses. Here, we apply and extend these results to situations that are representative for the induced seismicity environment. We present physics-based predictions of Mmax on a fault intersecting cylindrical reservoir. We investigate Mmax dependence on pore-pressure variations (by varying reservoir parameters), frictional parameters and stress conditions of the fault. We also derive Mmax as a function of injected volume. Our approach provides results that are consistent with observations but suggests different scaling with injected volume than that of empirical relation by McGarr, 2014.

  14. [Optimized Spectral Indices Based Estimation of Forage Grass Biomass].

    PubMed

    An, Hai-bo; Li, Fei; Zhao, Meng-li; Liu, Ya-jun

    2015-11-01

    As an important indicator of forage production, aboveground biomass will directly illustrate the growth of forage grass. Therefore, Real-time monitoring biomass of forage grass play a crucial role in performing suitable grazing and management in artificial and natural grassland. However, traditional sampling and measuring are time-consuming and labor-intensive. Recently, development of hyperspectral remote sensing provides the feasibility in timely and nondestructive deriving biomass of forage grass. In the present study, the main objectives were to explore the robustness of published and optimized spectral indices in estimating biomass of forage grass in natural and artificial pasture. The natural pasture with four grazing density (control, light grazing, moderate grazing and high grazing) was designed in desert steppe, and different forage cultivars with different N rate were conducted in artificial forage fields in Inner Mongolia. The canopy reflectance and biomass in each plot were measured during critical stages. The result showed that, due to the influence in canopy structure and biomass, the canopy reflectance have a great difference in different type of forage grass. The best performing spectral index varied in different species of forage grass with different treatments (R² = 0.00-0.69). The predictive ability of spectral indices decreased under low biomass of desert steppe, while red band based spectral indices lost sensitivity under moderate-high biomass of forage maize. When band combinations of simple ratio and normalized difference spectral indices were optimized in combined datasets of natural and artificial grassland, optimized spectral indices significant increased predictive ability and the model between biomass and optimized spectral indices had the highest R² (R² = 0.72) compared to published spectral indices. Sensitive analysis further confirmed that the optimized index had the lowest noise equivalent and were the best performing index in

  15. [Optimized Spectral Indices Based Estimation of Forage Grass Biomass].

    PubMed

    An, Hai-bo; Li, Fei; Zhao, Meng-li; Liu, Ya-jun

    2015-11-01

    As an important indicator of forage production, aboveground biomass will directly illustrate the growth of forage grass. Therefore, Real-time monitoring biomass of forage grass play a crucial role in performing suitable grazing and management in artificial and natural grassland. However, traditional sampling and measuring are time-consuming and labor-intensive. Recently, development of hyperspectral remote sensing provides the feasibility in timely and nondestructive deriving biomass of forage grass. In the present study, the main objectives were to explore the robustness of published and optimized spectral indices in estimating biomass of forage grass in natural and artificial pasture. The natural pasture with four grazing density (control, light grazing, moderate grazing and high grazing) was designed in desert steppe, and different forage cultivars with different N rate were conducted in artificial forage fields in Inner Mongolia. The canopy reflectance and biomass in each plot were measured during critical stages. The result showed that, due to the influence in canopy structure and biomass, the canopy reflectance have a great difference in different type of forage grass. The best performing spectral index varied in different species of forage grass with different treatments (R² = 0.00-0.69). The predictive ability of spectral indices decreased under low biomass of desert steppe, while red band based spectral indices lost sensitivity under moderate-high biomass of forage maize. When band combinations of simple ratio and normalized difference spectral indices were optimized in combined datasets of natural and artificial grassland, optimized spectral indices significant increased predictive ability and the model between biomass and optimized spectral indices had the highest R² (R² = 0.72) compared to published spectral indices. Sensitive analysis further confirmed that the optimized index had the lowest noise equivalent and were the best performing index in

  16. Estimating dengue vector abundance in the wet and dry season: implications for targeted vector control in urban and peri-urban Asia

    PubMed Central

    Wai, Khin Thet; Arunachalam, Natarajan; Tana, Susilowati; Espino, Fe; Kittayapong, Pattamaporn; Abeyewickreme, W; Hapangama, Dilini; Tyagi, Brij Kishore; Htun, Pe Than; Koyadun, Surachart; Kroeger, Axel; Sommerfeld, Johannes; Petzold, Max

    2012-01-01

    Background Research has shown that the classical Stegomyia indices (or “larval indices”) of the dengue vector Aedes aegypti reflect the absence or presence of the vector but do not provide accurate measures of adult mosquito density. In contrast, pupal indices as collected in pupal productivity surveys are a much better proxy indicator for adult vector abundance. However, it is unknown when it is most optimal to conduct pupal productivity surveys, in the wet or in the dry season or in both, to inform control services about the most productive water container types and if this pattern varies among different ecological settings. Methods A multi-country study in randomly selected twelve to twenty urban and peri-urban neighborhoods (“clusters”) of six Asian countries, in which all water holding containers were examined for larvae and pupae of Aedes aegypti during the dry season and the wet season and their productivity was characterized by water container types. In addition, meteorological data and information on reported dengue cases were collected. Findings The study reconfirmed the association between rainfall and dengue cases (“dengue season”) and underlined the importance of determining through pupal productivity surveys the “most productive containers types”, responsible for the majority (>70%) of adult dengue vectors. The variety of productive container types was greater during the wet than during the dry season, but included practically all container types productive in the dry season. Container types producing pupae were usually different from those infested by larvae indicating that containers with larval infestations do not necessarily foster pupal development and thus the production of adult Aedes mosquitoes. Conclusion Pupal productivity surveys conducted during the wet season will identify almost all of the most productive container types for both the dry and wet seasons and will therefore facilitate cost-effective targeted interventions

  17. Water balance-based estimation of groundwater recharge in the Lake Chad Basin

    NASA Astrophysics Data System (ADS)

    Babamaaji, R. A.; Lee, J.

    2012-12-01

    Lake Chad Basin (LCB) has experienced drastic changes of land cover and poor water management practices during the last 50 years. The successive droughts in the 1970s and 1980s resulted in the shortage of surface water and groundwater resources. This problem of drought and shortage of water has a devastating implication on the natural resources of the Basin with great consequence on food security, poverty reduction and quality of life of the inhabitants in the LCB. Therefore, understanding the change of land use and its characteristics must be a first step to find how such changes disturb the water cycle especially the groundwater in the LCB. The abundance of groundwater is affected by the climate change through the interaction with surface water, such as lakes and rivers, and vertical recharge through an infiltration process. Quantifying the impact of climate change on the groundwater resource requires not only reliable forecasting of changes in the major climatic variables, but also accurate estimation of groundwater recharge. Spatial variations in the land use/land cover, soil texture, topographic slope, and meteorological conditions should be accounted for in the recharge estimation. In this study, we employed a spatially distributed water balance model WetSpass to simulate a long-term average change of groundwater recharge in the LCB of Africa. WetSpass is a water balance-based model to estimate seasonal average spatial distribution of surface runoff, evapotranspiration, and groundwater recharge. The model is especially suitable for studying the effect of land use/land cover change on the water regime in the LCB. The present study describes the concept of the model and its application to the development of recharge map of the LCB.

  18. 48 CFR 2452.216-70 - Estimated cost, base fee and award fee.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Estimated cost, base fee... Provisions and Clauses 2452.216-70 Estimated cost, base fee and award fee. As prescribed in 2416.406(e)(1), insert the following clause in all cost-plus-award-fee contracts: Estimated Cost, Base Fee and Award...

  19. 48 CFR 2452.216-70 - Estimated cost, base fee and award fee.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 6 2011-10-01 2011-10-01 false Estimated cost, base fee... Provisions and Clauses 2452.216-70 Estimated cost, base fee and award fee. As prescribed in 2416.406(e)(1), insert the following clause in all cost-plus-award-fee contracts: Estimated Cost, Base Fee and Award...

  20. Improved image registration by sparse patch-based deformation estimation.

    PubMed

    Kim, Minjeong; Wu, Guorong; Wang, Qian; Lee, Seong-Whan; Shen, Dinggang

    2015-01-15

    Despite intensive efforts for decades, deformable image registration is still a challenging problem due to the potential large anatomical differences across individual images, which limits the registration performance. Fortunately, this issue could be alleviated if a good initial deformation can be provided for the two images under registration, which are often termed as the moving subject and the fixed template, respectively. In this work, we present a novel patch-based initial deformation prediction framework for improving the performance of existing registration algorithms. Our main idea is to estimate the initial deformation between subject and template in a patch-wise fashion by using the sparse representation technique. We argue that two image patches should follow the same deformation toward the template image if their patch-wise appearance patterns are similar. To this end, our framework consists of two stages, i.e., the training stage and the application stage. In the training stage, we register all training images to the pre-selected template, such that the deformation of each training image with respect to the template is known. In the application stage, we apply the following four steps to efficiently calculate the initial deformation field for the new test subject: (1) We pick a small number of key points in the distinctive regions of the test subject; (2) for each key point, we extract a local patch and form a coupled appearance-deformation dictionary from training images where each dictionary atom consists of the image intensity patch as well as their respective local deformations; (3) a small set of training image patches in the coupled dictionary are selected to represent the image patch of each subject key point by sparse representation. Then, we can predict the initial deformation for each subject key point by propagating the pre-estimated deformations on the selected training patches with the same sparse representation coefficients; and (4) we

  1. Stochastic physical ecohydrologic-based model for estimating irrigation requirement

    NASA Astrophysics Data System (ADS)

    Alizadeh, H.; Mousavi, S. J.

    2012-04-01

    Climate uncertainty affects both natural and managed hydrological systems. Therefore, methods which could take this kind of uncertainty into account are of primal importance for management of ecosystems, especially agricultural ecosystems. One of the famous problems in these ecosystems is crop water requirement estimation under climatic uncertainty. Both deterministic physically-based methods and stochastic time series modeling have been utilized in the literature. Like other fields of hydroclimatic sciences, there is a vast area in irrigation process modeling for developing approaches integrating physics of the process and statistics aspects. This study is about deriving closed-form expressions for probability density function (p.d.f.) of irrigation water requirement using a stochastic physically-based model, which considers important aspects of plant, soil, atmosphere and irrigation technique and policy in a coherent framework. An ecohydrologic stochastic model, building upon the stochastic differential equation of soil moisture dynamics at root zone, is employed as a basis for deriving the expressions considering temporal stochasticity of rainfall. Due to distinguished nature of stochastic processes of micro and traditional irrigation applications, two different methodologies have been used. Micro-irrigation application has been modeled through dichotomic process. Chapman-Kolomogrov equation of time integral of the dichotomic process for transient condition has been solved to derive analytical expressions for probability density function of seasonal irrigation requirement. For traditional irrigation, irrigation application during growing season has been modeled using a marked point process. Using the renewal theory, probability mass function of seasonal irrigation requirement, which is a discrete-value quantity, has been analytically derived. The methodology deals with estimation of statistical properties of the total water requirement in a growing season that

  2. Models of quantitative estimations: rule-based and exemplar-based processes compared.

    PubMed

    von Helversen, Bettina; Rieskamp, Jörg

    2009-07-01

    The cognitive processes underlying quantitative estimations vary. Past research has identified task-contingent changes between rule-based and exemplar-based processes (P. Juslin, L. Karlsson, & H. Olsson, 2008). B. von Helversen and J. Rieskamp (2008), however, proposed a simple rule-based model-the mapping model-that outperformed the exemplar model in a task thought to promote exemplar-based processing. This raised questions about the assumptions of rule-based versus exemplar-based models that underlie the notion of task contingency of cognitive processes. Rule-based models, such as the mapping model, assume the abstraction of explicit task knowledge. In contrast, exemplar models should profit if storage and activation of the exemplars is facilitated. Two studies tested the importance of the two models' assumptions. When knowledge about cues existed, the rule-based mapping model predicted quantitative estimations best. In contrast, when knowledge about the cues was difficult to gain, participants' estimations were best described by an exemplar model. The results emphasize the task contingency of cognitive processes. PMID:19586258

  3. Age Estimation Based on Children's Voice: A Fuzzy-Based Decision Fusion Strategy

    PubMed Central

    Ting, Hua-Nong

    2014-01-01

    Automatic estimation of a speaker's age is a challenging research topic in the area of speech analysis. In this paper, a novel approach to estimate a speaker's age is presented. The method features a “divide and conquer” strategy wherein the speech data are divided into six groups based on the vowel classes. There are two reasons behind this strategy. First, reduction in the complicated distribution of the processing data improves the classifier's learning performance. Second, different vowel classes contain complementary information for age estimation. Mel-frequency cepstral coefficients are computed for each group and single layer feed-forward neural networks based on self-adaptive extreme learning machine are applied to the features to make a primary decision. Subsequently, fuzzy data fusion is employed to provide an overall decision by aggregating the classifier's outputs. The results are then compared with a number of state-of-the-art age estimation methods. Experiments conducted based on six age groups including children aged between 7 and 12 years revealed that fuzzy fusion of the classifier's outputs resulted in considerable improvement of up to 53.33% in age estimation accuracy. Moreover, the fuzzy fusion of decisions aggregated the complementary information of a speaker's age from various speech sources. PMID:25006595

  4. A signal strength priority based position estimation for mobile platforms

    NASA Astrophysics Data System (ADS)

    Kalgikar, Bhargav; Akopian, David; Chen, Philip

    2010-01-01

    Global Positioning System (GPS) products help to navigate while driving, hiking, boating, and flying. GPS uses a combination of orbiting satellites to determine position coordinates. This works great in most outdoor areas, but the satellite signals are not strong enough to penetrate inside most indoor environments. As a result, a new strain of indoor positioning technologies that make use of 802.11 wireless LANs (WLAN) is beginning to appear on the market. In WLAN positioning the system either monitors propagation delays between wireless access points and wireless device users to apply trilateration techniques or it maintains the database of location-specific signal fingerprints which is used to identify the most likely match of incoming signal data with those preliminary surveyed and saved in the database. In this paper we investigate the issue of deploying WLAN positioning software on mobile platforms with typically limited computational resources. We suggest a novel received signal strength rank order based location estimation system to reduce computational loads with a robust performance. The proposed system performance is compared to conventional approaches.

  5. Disk storage management for LHCb based on Data Popularity estimator

    NASA Astrophysics Data System (ADS)

    Hushchyn, Mikhail; Charpentier, Philippe; Ustyuzhanin, Andrey

    2015-12-01

    This paper presents an algorithm providing recommendations for optimizing the LHCb data storage. The LHCb data storage system is a hybrid system. All datasets are kept as archives on magnetic tapes. The most popular datasets are kept on disks. The algorithm takes the dataset usage history and metadata (size, type, configuration etc.) to generate a recommendation report. This article presents how we use machine learning algorithms to predict future data popularity. Using these predictions it is possible to estimate which datasets should be removed from disk. We use regression algorithms and time series analysis to find the optimal number of replicas for datasets that are kept on disk. Based on the data popularity and the number of replicas optimization, the algorithm minimizes a loss function to find the optimal data distribution. The loss function represents all requirements for data distribution in the data storage system. We demonstrate how our algorithm helps to save disk space and to reduce waiting times for jobs using this data.

  6. Auto-focus algorithm based on statistical blur estimation

    NASA Astrophysics Data System (ADS)

    Kulkarni, Prajit

    2013-03-01

    Conventional auto-focus techniques in movable-lens camera systems use a measure of image sharpness to determine the lens position that brings the scene into focus. This paper presents a novel wavelet-domain approach to determine the position of best focus. In contrast to current techniques, the proposed algorithm estimates the level of blur in the captured image at each lens position. Image blur is quantified by fitting a Generalized Gaussian Density (GGD) curve to a high-pass version of the image using second-order statistics. The system then moves the lens to the position that yields the least measure of image blur. The algorithm overcomes shortcomings of sharpness-based approaches, namely, the application of large band-pass filters, sensitivity to image noise and need for calibration under different imaging conditions. Since noise has no effect on the proposed blur metric, the algorithm works with a short filter and is devoid of parameter tuning. Furthermore, the algorithm could be simplified to use a single high-pass filter to reduce complexity. These advantages, along with the optimization presented in the paper, make the proposed algorithm very attractive for hardware implementation on cell phones. Experiments prove that the algorithm performs well in the presence of noise as well as resolution and data scaling.

  7. Human Age Estimation Based on Locality and Ordinal Information.

    PubMed

    Li, Changsheng; Liu, Qingshan; Dong, Weishan; Zhu, Xiaobin; Liu, Jing; Lu, Hanqing

    2015-11-01

    In this paper, we propose a novel feature selection-based method for facial age estimation. The face aging is a typical temporal process, and facial images should have certain ordinal patterns in the aging feature space. From the geometrical perspective, a facial image can be usually seen as sampled from a low-dimensional manifold embedded in the original high-dimensional feature space. Thus, we first measure the energy of each feature in preserving the underlying local structure information and the ordinal information of the facial images, respectively, and then we intend to learn a low-dimensional aging representation that can maximally preserve both kinds of information. To further improve the performance, we try to eliminate the redundant local information and ordinal information as much as possible by minimizing nonlinear correlation and rank correlation among features. Finally, we formulate all these issues into a unified optimization problem, which is similar to linear discriminant analysis in format. Since it is expensive to collect the labeled facial aging images in practice, we extend the proposed supervised method to a semi-supervised learning mode including the semi-supervised feature selection method and the semi-supervised age prediction algorithm. Extensive experiments are conducted on the FACES dataset, the Images of Groups dataset, and the FG-NET aging dataset to show the power of the proposed algorithms, compared to the state-of-the-arts. PMID:26470062

  8. Carbon Dioxide and Methane Column Abundances Retrieved from Ground-Based Near-Infrared Solar Spectra and Comparison with In Situ Aircraft Profiles

    NASA Astrophysics Data System (ADS)

    Washenfelder, R. A.; Toon, G. C.; Blavier, J.; Wennberg, P. O.; Yang, Z.; Vay, S. A.; Sachse, G. W.; Blake, D. R.; Matross, D. M.; Gerbig, C.

    2004-12-01

    We have developed an automated observatory for measuring ground-based column abundances of CO2, CH4, CO, N2O, O2, H2O, and HF. Near-infrared spectra of the direct sun are measured between 3,900 - 15,600 cm-1 (0.67 - 2.56 μ m) by a Bruker 125HR Fourier Transform Spectrometer. This is the first laboratory in a proposed network of ground-based solar observatories that will be used for carbon cycle studies and validation of spaceborne column measurements of greenhouse gases. The laboratory was assembled in Pasadena, California and then permanently deployed to northern Wisconsin during May 2004. It is located in the heavily forested Chequamegon National Forest at the WLEF Tall Tower site, 14 km east of Park Falls, Wisconsin. This site was chosen because NOAA CMDL and other groups conduct intensive measurements in the area, including continuous monitoring of CO2 at six heights on the 447-m tall tower. CO2 and CH4 column abundances for May - November 2004 demonstrate ˜0.1% precision. The seasonal drawdown of CO2 is recognizable within the late-May column abundances. As part of the INTEX and COBRA campaigns, the DC-8 or King Air recorded in situ measurements during profiles over the WLEF site during five dates in July and August 2004. We will compare the column abundances of CO2, CH4, and CO with these in situ aircraft measurements.

  9. Methow River Studies, Washington: abundance estimates from Beaver Creek and the Chewuch River screw trap, methodology testing in the Whitefish Island side channel, and survival and detection estimates from hatchery fish releases, 2013

    USGS Publications Warehouse

    Martens, Kyle D.; Fish, Teresa M.; Watson, Grace A.; Connolly, Patrick J.

    2014-01-01

    2008, focuses on the evaluation of the M2 reach (rkm 66– 80) of the mainstem Methow River prior to restoration actions planned by Reclamation and Yakama Nation. The M2 study was designed to help understand the inter-relationships between stream habitat and the life history of various fish species to explain potential success or limitations in response to restoration actions. To help document changes derived by restoration, two reference reaches (Upper Methow between rkm 85 and 90, and Chewuch River between rkm 4 and 11) were identified based on relative lack of disturbance, proximity to the restoration reach, and relative unconfined geomorphology. A control reach (Lower Methow between rkm 57 and 64, also referred to as “Silver Reach”) was 2 identified based on its similar disturbance as the reference reach, proximity to the restoration reach, and relatively unconfined geomorphology. Products to date include Barber and others (2011), Bellmore (2011), Tibbits and others (2012), Bellmore and others (2013), Benjamin and others (2013), Romine and others (2013b), Bellmore and other (2014), Martens and others (2014), and Martens and Connolly (2014). The third phase of work has been to help with the development and to provide data for modeling efforts. Most of the planned M2 reach restoration is focused on the creation or improvement of offchannel habitat, especially side channels. The pre-restoration portion of this study has been documented by Martens and Connolly (2014). Side channel restoration actions were initiated in 2012 (Whitefish Island side channel, also referred to as SC3; rkm 76) and are planned to continue over the next several years. The Whitefish Island side channel was modified to maintain hydrological connection with the mainstem throughout the year. In addition, several log structures were installed and pools were deepened to create fish habitat. Prior to restoration, this side channel would lose hydrological connection with the mainstem Methow River

  10. Model-Based Estimation of Active Knee Stiffness

    PubMed Central

    Pfeifer, Serge; Hardegger, Michael; Vallery, Heike; List, Renate; Foresti, Mauro; Riener, Robert; Perreault, Eric J.

    2013-01-01

    Knee joint impedance varies substantially during physiological gait. Quantifying this modulation is critical for the design of transfemoral prostheses that aim to mimic physiological limb behavior. Conventional methods for quantifying joint impedance typically involve perturbing the joint in a controlled manner, and describing impedance as the dynamic relationship between applied perturbations and corresponding joint torques. These experimental techniques, however, are difficult to apply during locomotion without impeding natural movements. In this paper, we propose a method to estimate the elastic component of knee joint impedance that depends on muscle activation, often referred to as active knee stiffness. The method estimates stiffness using a musculoskeletal model of the leg and a model for activation-dependent short-range muscle stiffness. Muscle forces are estimated from measurements including limb kinematics, kinetics and muscle electromyograms. For isometric validation, we compare model estimates to measurements involving joint perturbations; measured stiffness is 17% lower than model estimates for extension, and 42% lower for flexion torques. We show that sensitivity of stiffness estimates to common approaches for estimating muscle force is small in isometric conditions. We also make initial estimates of how knee stiffness is modulated during gait, illustrating how this approach may be used to obtain parameters relevant to the design of transfemoral prostheses. PMID:22275672

  11. Ocean Color Based Estimates of Global Photochemical Rate Processes

    NASA Astrophysics Data System (ADS)

    Nelson, N. B.; Siegel, D. A.; Toole, D. A.

    2005-12-01

    The development and validation of new ocean color data products beyond chlorophyll allows for the assessment of biogeochemically relevant rate processes other than primary production, such as CO production and DMS photolysis. We present here a proof-of-concept study in which we integrate multiple global remote sensing data streams to estimate the solar irradiance absorbed by chromophoric dissolved organic matter (CDOM) in the euphotic zone. This quantity can be convolved with apparent quantum yield spectra to estimate photochemical reaction rates. In this study we use ocean color reflectance spectra from SeaWiFS and/or MODIS to estimate in-water light absorption and backscattering spectra using the Garver-Siegel-Maritorena ocean color model. These quantities were used to empirically estimate the diffuse attenuation coefficient spectrum (Kd) for surface waters, and thus depth profiles of light penetration. UV Irradiance spectra at the surface were estimated using TOMS data. We also estimated the scalar to vector irradiance ratio using information from radiative transfer modeling in conjunction with absorption and backscattering coefficient spectra. These quantities were combined to estimate the spectrum of light absorption by CDOM, or photochemically active radiation. Finally, we combined the photochemically active radiation spectra with open ocean estimates of apparent quantum yield to produce maps of photochemical production of CO. Global maps of time integrated production rates closely resemble similar maps of CDOM distribution, indicating a proximal control of photochemistry by CDOM.

  12. Abundances of volatile-bearing phases in carbonaceous chondrites and cooling rates of meteorites based on cation ordering of orthopyroxenes

    NASA Technical Reports Server (NTRS)

    Ganguly, Jibamitra

    1989-01-01

    Results of preliminary calculations of volatile abundances in carbonaceous chondrites are discussed. The method (Ganguly 1982) was refined for the calculation of cooling rate on the basis of cation ordering in orthopyroxenes, and it was applied to the derivation of cooling rates of some stony meteorites. Evaluation of cooling rate is important to the analysis of condensation, accretion, and post-accretionary metamorphic histories of meteorites. The method of orthopyroxene speedometry is widely applicable to meteorites and would be very useful in the understanding of the evolutionary histories of carbonaceous chondrites, especially since the conventional metallographic and fission track methods yield widely different results in many cases. Abstracts are given which summarize the major conclusions of the volatile abundance and cooling rate calculations.

  13. Pressure Gradient Estimation Based on Ultrasonic Blood Flow Measurement

    NASA Astrophysics Data System (ADS)

    Nitta, Naotaka; Homma, Kazuhiro; Shiina, Tsuyoshi

    2006-05-01

    Mechanical load to the blood vessel wall, such as shear stress and pressure, which oc