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Sample records for model species comparison

  1. How can model comparison help improving species distribution models?

    PubMed

    Gritti, Emmanuel Stephan; Gaucherel, Cédric; Crespo-Perez, Maria-Veronica; Chuine, Isabelle

    2013-01-01

    Today, more than ever, robust projections of potential species range shifts are needed to anticipate and mitigate the impacts of climate change on biodiversity and ecosystem services. Such projections are so far provided almost exclusively by correlative species distribution models (correlative SDMs). However, concerns regarding the reliability of their predictive power are growing and several authors call for the development of process-based SDMs. Still, each of these methods presents strengths and weakness which have to be estimated if they are to be reliably used by decision makers. In this study we compare projections of three different SDMs (STASH, LPJ and PHENOFIT) that lie in the continuum between correlative models and process-based models for the current distribution of three major European tree species, Fagussylvatica L., Quercusrobur L. and Pinussylvestris L. We compare the consistency of the model simulations using an innovative comparison map profile method, integrating local and multi-scale comparisons. The three models simulate relatively accurately the current distribution of the three species. The process-based model performs almost as well as the correlative model, although parameters of the former are not fitted to the observed species distributions. According to our simulations, species range limits are triggered, at the European scale, by establishment and survival through processes primarily related to phenology and resistance to abiotic stress rather than to growth efficiency. The accuracy of projections of the hybrid and process-based model could however be improved by integrating a more realistic representation of the species resistance to water stress for instance, advocating for pursuing efforts to understand and formulate explicitly the impact of climatic conditions and variations on these processes. PMID:23874779

  2. Reranking candidate gene models with cross-species comparison for improved gene prediction

    PubMed Central

    Liu, Qian; Crammer, Koby; Pereira, Fernando CN; Roos, David S

    2008-01-01

    Background Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models. PMID:18854050

  3. Controlled comparison of species- and community-level models across novel climates and communities.

    PubMed

    Maguire, Kaitlin C; Nieto-Lugilde, Diego; Blois, Jessica L; Fitzpatrick, Matthew C; Williams, John W; Ferrier, Simon; Lorenz, David J

    2016-03-16

    Species distribution models (SDMs) assume species exist in isolation and do not influence one another's distributions, thus potentially limiting their ability to predict biodiversity patterns. Community-level models (CLMs) capitalize on species co-occurrences to fit shared environmental responses of species and communities, and therefore may result in more robust and transferable models. Here, we conduct a controlled comparison of five paired SDMs and CLMs across changing climates, using palaeoclimatic simulations and fossil-pollen records of eastern North America for the past 21 000 years. Both SDMs and CLMs performed poorly when projected to time periods that are temporally distant and climatically dissimilar from those in which they were fit; however, CLMs generally outperformed SDMs in these instances, especially when models were fit with sparse calibration datasets. Additionally, CLMs did not over-fit training data, unlike SDMs. The expected emergence of novel climates presents a major forecasting challenge for all models, but CLMs may better rise to this challenge by borrowing information from co-occurring taxa. PMID:26962143

  4. A Rapid and Scalable Method for Multilocus Species Delimitation Using Bayesian Model Comparison and Rooted Triplets

    PubMed Central

    Fujisawa, Tomochika; Aswad, Amr; Barraclough, Timothy G.

    2016-01-01

    Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces 2 new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published, and newly generated data. Analyses of simulated data demonstrate that the combined method has favorable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases. PMID:27055648

  5. A Rapid and Scalable Method for Multilocus Species Delimitation Using Bayesian Model Comparison and Rooted Triplets.

    PubMed

    Fujisawa, Tomochika; Aswad, Amr; Barraclough, Timothy G

    2016-09-01

    Multilocus sequence data provide far greater power to resolve species limits than the single locus data typically used for broad surveys of clades. However, current statistical methods based on a multispecies coalescent framework are computationally demanding, because of the number of possible delimitations that must be compared and time-consuming likelihood calculations. New methods are therefore needed to open up the power of multilocus approaches to larger systematic surveys. Here, we present a rapid and scalable method that introduces 2 new innovations. First, the method reduces the complexity of likelihood calculations by decomposing the tree into rooted triplets. The distribution of topologies for a triplet across multiple loci has a uniform trinomial distribution when the 3 individuals belong to the same species, but a skewed distribution if they belong to separate species with a form that is specified by the multispecies coalescent. A Bayesian model comparison framework was developed and the best delimitation found by comparing the product of posterior probabilities of all triplets. The second innovation is a new dynamic programming algorithm for finding the optimum delimitation from all those compatible with a guide tree by successively analyzing subtrees defined by each node. This algorithm removes the need for heuristic searches used by current methods, and guarantees that the best solution is found and potentially could be used in other systematic applications. We assessed the performance of the method with simulated, published, and newly generated data. Analyses of simulated data demonstrate that the combined method has favorable statistical properties and scalability with increasing sample sizes. Analyses of empirical data from both eukaryotes and prokaryotes demonstrate its potential for delimiting species in real cases. PMID:27055648

  6. Comparison of model results transporting the odd nitrogen family with results transporting separate odd nitrogen species

    NASA Technical Reports Server (NTRS)

    Douglass, Anne R.; Jackman, Charles H.; Stolarski, Richard S.

    1989-01-01

    A fast two-dimensional residual circulation stratospheric family transport model, designed to minimize computer requirements, is developed. The model was used to calculate the ambient and perturbed atmospheres in which odd nitrogen species are transported as a family, and the results were compared with calculations in which HNO3, N2O5, ClONO2, and HO2NO2 are transported separately. It was found that ozone distributions computed by the two models for a present-day atmosphere are nearly identical. Good agreement was also found between calculated species concentrations and the ozone response, indicating the general applicability of the odd-nitrogen family approximations.

  7. Vertical Distributions of Sulfur Species Simulated by Large Scale Atmospheric Models in COSAM: Comparison with Observations

    SciTech Connect

    Lohmann, U.; Leaitch, W. R.; Barrie, Leonard A.; Law, K.; Yi, Y.; Bergmann, D.; Bridgeman, C.; Chin, M.; Christensen, J.; Easter, Richard C.; Feichter, J.; Jeuken, A.; Kjellstrom, E.; Koch, D.; Land, C.; Rasch, P.; Roelofs, G.-J.

    2001-11-01

    A comparison of large-scale models simulating atmospheric sulfate aerosols (COSAM) was conducted to increase our understanding of global distributions of sulfate aerosols and precursors. Earlier model comparisons focused on wet deposition measurements and sulfate aerosol concentrations in source regions at the surface. They found that different models simulated the observed sulfate surface concentrations mostly within a factor of two, but that the simulated column burdens and vertical profiles were very different amongst different models. In the COSAM exercise, one aspect is the comparison of sulfate aerosol and precursor gases above the surface. Vertical profiles of SO2, SO42-, oxidants and cloud properties were measured by aircraft during the North Atlantic Regional Experiment (NARE) experiment in August/September 1993 off the coast of Nova Scotia and during the Second Eulerian Model Evaluation Field Study (EMEFSII) in central Ontario in March/April 1990. While no single model stands out as being best or worst, the general tendency is that those models simulating the full oxidant chemistry tend to agree best with observations although differences in transport and treatment of clouds are important as well.

  8. Aspects of the comparison of stratospheric trace species measurements with photochemical models

    SciTech Connect

    Connell, P.S.; Wuebbles, D.J.

    1984-08-01

    Observation and measurement of reservoir species, including H/sub 2/O/sub 2/, ClONO/sub 2/, HNO/sub 4/, HOCl, N/sub 2/O/sub 5/ and others, can potentially test some portions of photochemical models of the stratosphere, leading to improvements and increased confidence in model predictions. But abundance measurements of a single reservoir species without accompanying values for other species do not serve, in most cases, to constrain the related model mechanism and parameters within the recognized uncertainties. This follows from the sensitivity of abundance of a species to fluctuations in its long-lived precursors from transport processes. A better test of theory would be provided by correlation studies in which precursor concentrations and photolytic fluxes are measured simultaneously and in the same air volume as the reservoir species. Three recent reported differing observations or upper limits for H/sub 2/O/sub 2/ give an example of the difficulties. All three reported values could be nearly consistent with the current LLNL one-dimensional stratospheric photochemical model, depending on the values of O/sub 3/, NO/sub x/ and H/sub 2/O appropriate to each measurement. The important precursors in each case can be identified by consideration of the appropriate kinetics and observed precursor variability. 10 references, 3 figures, 1 table.

  9. Comparison of generalized transport and Monte-Carlo models of the escape of a minor species

    NASA Technical Reports Server (NTRS)

    Demars, H. G.; Barakat, A. R.; Schunk, R. W.

    1993-01-01

    The steady-state diffusion of a minor species through a static background species is studied using a Monte Carlo model and a generalized 16-moment transport model. The two models are in excellent agreement in the collision-dominated region and in the 'transition region'. In the 'collisionless' region the 16-moment solution contains two singularities, and physical meaning cannot be assigned to the solution in their vicinity. In all regions, agreement between the models is best for the distribution function and for the lower-order moments and is less good for higher-order moments. Moments of order higher than the heat flow and hence beyond the level of description provided by the transport model have a noticeable effect on the shape of distribution functions in the collisionless region.

  10. Ecophysiology of wetland plant roots: A modelling comparison of aeration in relation to species distribution

    USGS Publications Warehouse

    Sorrell, B.K.; Mendelssohn, I.A.; McKee, K.L.; Woods, R.A.

    2000-01-01

    This study examined the potential for inter-specific differences in root aeration to determine wetland plant distribution in nature. We compared aeration in species that differ in the type of sediment and depth of water they colonize. Differences in root anatomy, structure and physiology were applied to aeration models that predicted the maximum possible aerobic lengths and development of anoxic zones in primary adventitious roots. Differences in anatomy and metabolism that provided higher axial fluxes of oxygen allowed deeper root growth in species that favour more reducing sediments and deeper water. Modelling identified factors that affected growth in anoxic soils through their effects on aeration. These included lateral root formation, which occurred at the expense of extension of the primary root because of the additional respiratory demand they imposed, reducing oxygen fluxes to the tip and stele, and the development of stelar anoxia. However, changes in sediment oxygen demand had little detectable effect on aeration in the primary roots due to their low wall permeability and high surface impedance, but appeared to reduce internal oxygen availability by accelerating loss from laterals. The development of pressurized convective gas flow in shoots and rhizomes was also found to be important in assisting root aeration, as it maintained higher basal oxygen concentrations at the rhizome-root junctions in species growing into deep water. (C) 2000 Annals of Botany Company.

  11. Titan's photochemical model: Further update, oxygen species, and comparison with Triton and Pluto

    NASA Astrophysics Data System (ADS)

    Krasnopolsky, V. A.

    2012-12-01

    The photochemical model for Titan's atmosphere and ionosphere is improved using the Troe approximation for termolecular reactions and inclusion of four radiative association reactions from those calculated by Vuitton et al. (2012). Proper fitting of eddy diffusion results in a reduction of the mean difference between 63 observed mixing ratios and their calculated values from a factor of 5 in our previous Titan's models to a factor of 3 in the current model. Oxygen chemistry on Titan is initiated by influxes of H2O from meteorites and O+ from magnetospheric interactions with the Saturn rings and Enceladus. Two versions of the model were calculated, with and without the O+ flux. Balances of CO, CO2, H2O, and H2CO are discussed in detail for both versions. The calculated model with the O+ flux agrees with the observations of CO, CO2, and H2O, including recent H2O CIRS limb observations and measurements by the Herschel Space Observatory. Major observational data and photochemical models for Triton and Pluto are briefly discussed. While the basic atmospheric species N2, CH4, and CO are similar on Triton and Pluto, properties of their atmospheres are very different with dominating atomic species and ions in Triton's upper atmosphere and ionosphere opposed to the molecular composition on Pluto. Calculations favor a transition between two types of photochemistry at the CH4 mixing ratio of ~5×10-4. Therefore the current Triton's photochemistry is still similar to that at the Voyager flyby despite the observed increase in N2 and CH4. The meteorite H2O results in precipitation of CO on Triton and CO2 on Pluto near perihelion. Main oxygen species on Titan: observations and the model. Solid lines show the model with both meteorite influx of H2O and magnetospheric flux of O+. Thin lines show the model without flux of O+. Observations: (1) CIRS (de Kok et al. 2007), (2) CIRS at 5°N (Vinatier et al. 2010), (3) ISO (Coustenis et al. 1998), (4) INMS (Cui et al., 2009), (5) CIRS

  12. Titan's photochemical model: Further update, oxygen species, and comparison with Triton and Pluto

    NASA Astrophysics Data System (ADS)

    Krasnopolsky, Vladimir A.

    2012-12-01

    My photochemical model for Titan's atmosphere and ionosphere is improved using the Troe approximation for termolecular reactions and inclusion of four radiative association reactions from those calculated by Vuitton et al. (2012). Proper fitting of eddy diffusion results in a reduction of the mean difference between 63 observed mixing ratios and their calculated values from a factor of 5 in my previous models for Titan to a factor of 3 in the current model. Oxygen chemistry on Titan is initiated by influxes of H2O from meteorites and O+ from magnetospheric interactions with the Saturn rings and Enceladus. Two versions of the model were calculated, with and without the O+ flux. Balances of CO, CO2, H2O, and H2CO are discussed in detail for both versions. The calculated model with the O+ flux agrees with the observations of CO, CO2, and H2O, including recent H2O CIRS limb observations and measurements by the Herschel Space Observatory. Major observational data and photochemical models for Triton and Pluto are briefly discussed. While the basic atmospheric species N2, CH4, and CO are similar on Triton and Pluto, properties of their atmospheres are very different with atomic species and ions dominating in Triton's upper atmosphere and ionosphere opposed to the molecular composition on Pluto. Calculations favor a transition between two types of photochemistry at the CH4 mixing ratio of ∼5×10-4. Therefore Triton's current photochemistry is still similar to that at the Voyager flyby despite the observed increase in N2 and CH4. The meteorite H2O results in precipitation of CO on Triton and CO2 on Pluto near perihelion.

  13. A comparison of neutral and charged species of one- and two-dimensional models of graphene nanoribbons using multireference theory

    SciTech Connect

    Horn, Shawn; Lischka, Hans

    2015-02-07

    This study examines the dependence of the polyradical character of charged quasi-linear n-acenes and two-dimensional periacenes used as models for graphene nanoribbons in comparison to the corresponding neutral compounds. For this purpose, high-level ab initio calculations have been performed using the multireference averaged quadratic coupled cluster theory. Vertical ionization energies and electron affinities have been computed. Systematic tests show that the dependence on chain length of these quantities can be obtained from a consideration of the π system only and that remaining contributions coming from the σ orbitals or extended basis sets remain fairly constant. Using best estimate values, the experimental values for the ionization energy of the acene series can be reproduced within 0.1 eV and the experimental electron affinities within 0.4 V. The analysis of the natural orbital occupations and related unpaired electron densities shows that the ionic species exhibit a significant decrease in polyradical character and thus an increased chemical stability as compared to the neutral state.

  14. A comparison of neutral and charged species of one- and two-dimensional models of graphene nanoribbons using multireference theory.

    PubMed

    Horn, Shawn; Lischka, Hans

    2015-02-01

    This study examines the dependence of the polyradical character of charged quasi-linear n-acenes and two-dimensional periacenes used as models for graphene nanoribbons in comparison to the corresponding neutral compounds. For this purpose, high-level ab initio calculations have been performed using the multireference averaged quadratic coupled cluster theory. Vertical ionization energies and electron affinities have been computed. Systematic tests show that the dependence on chain length of these quantities can be obtained from a consideration of the π system only and that remaining contributions coming from the σ orbitals or extended basis sets remain fairly constant. Using best estimate values, the experimental values for the ionization energy of the acene series can be reproduced within 0.1 eV and the experimental electron affinities within 0.4 V. The analysis of the natural orbital occupations and related unpaired electron densities shows that the ionic species exhibit a significant decrease in polyradical character and thus an increased chemical stability as compared to the neutral state. PMID:25662640

  15. A comparison of absolute performance of different correlative and mechanistic species distribution models in an independent area.

    PubMed

    Shabani, Farzin; Kumar, Lalit; Ahmadi, Mohsen

    2016-08-01

    To investigate the comparative abilities of six different bioclimatic models in an independent area, utilizing the distribution of eight different species available at a global scale and in Australia. Global scale and Australia. We tested a variety of bioclimatic models for eight different plant species employing five discriminatory correlative species distribution models (SDMs) including Generalized Linear Model (GLM), MaxEnt, Random Forest (RF), Boosted Regression Tree (BRT), Bioclim, together with CLIMEX (CL) as a mechanistic niche model. These models were fitted using a training dataset of available global data, but with the exclusion of Australian locations. The capabilities of these techniques in projecting suitable climate, based on independent records for these species in Australia, were compared. Thus, Australia is not used to calibrate the models and therefore it is as an independent area regarding geographic locations. To assess and compare performance, we utilized the area under the receiver operating characteristic (ROC) curves (AUC), true skill statistic (TSS), and fractional predicted areas for all SDMs. In addition, we assessed satisfactory agreements between the outputs of the six different bioclimatic models, for all eight species in Australia. The modeling method impacted on potential distribution predictions under current climate. However, the utilization of sensitivity and the fractional predicted areas showed that GLM, MaxEnt, Bioclim, and CL had the highest sensitivity for Australian climate conditions. Bioclim calculated the highest fractional predicted area of an independent area, while RF and BRT were poor. For many applications, it is difficult to decide which bioclimatic model to use. This research shows that variable results are obtained using different SDMs in an independent area. This research also shows that the SDMs produce different results for different species; for example, Bioclim may not be good for one species but works better

  16. Bounding Species Distribution Models

    NASA Technical Reports Server (NTRS)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  17. Bounding species distribution models

    USGS Publications Warehouse

    Stohlgren, T.J.; Jarnevich, C.S.; Esaias, W.E.; Morisette, J.T.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used. ?? 2011 Current Zoology.

  18. Comparison of the pathogen species-specific immune response in udder derived cell types and their models.

    PubMed

    Günther, Juliane; Koy, Mirja; Berthold, Anne; Schuberth, Hans-Joachim; Seyfert, Hans-Martin

    2016-01-01

    The outcome of an udder infection (mastitis) largely depends on the species of the invading pathogen. Gram-negative pathogens, such as Escherichia coli often elicit acute clinical mastitis while Gram-positive pathogens, such as Staphylococcus aureus tend to cause milder subclinical inflammations. It is unclear which type of the immune competent cells residing in the udder governs the pathogen species-specific physiology of mastitis and which established cell lines might provide suitable models. We therefore profiled the pathogen species-specific immune response of different cell types derived from udder and blood. Primary cultures of bovine mammary epithelial cells (pbMEC), mammary derived fibroblasts (pbMFC), and bovine monocyte-derived macrophages (boMdM) were challenged with heat-killed E. coli, S. aureus and S. uberis mastitis pathogens and their immune response was scaled against the response of established models for MEC (bovine MAC-T) and macrophages (murine RAW 264.7). Only E. coli provoked a full scale immune reaction in pbMEC, fibroblasts and MAC-T cells, as indicated by induced cytokine and chemokine expression and NF-κB activation. Weak reactions were induced by S. aureus and none by S. uberis challenges. In contrast, both models for macrophages (boMdM and RAW 264.7) reacted strongly against all the three pathogens accompanied by strong activation of NF-κB factors. Hence, the established cell models MAC-T and RAW 264.7 properly reflected key aspects of the pathogen species-specific immune response of the respective parental cell type. Our data imply that the pathogen species-specific physiology of mastitis likely relates to the respective response of MEC rather to that of professional immune cells. PMID:26830914

  19. Inter-species comparisons of carcinogenicity.

    PubMed Central

    Purchase, I. F.

    1980-01-01

    The carcinogenicity of 250 chemicals in 2 species, usually the rat and the mouse, was obtained from the published literature through 3 independent sources. Of the 250 compounds listed, 38% were non-carcinogenic in both rats and mice, and 44% were carcinogenic in both species. A total of 43 compounds had different results in the two species, 21 (8%) being carcinogenic in mice only, 17 (7%) in rats only and 5 (2%) having differing results from other species. A comparison of the major target organs affected by chemicals carcinogenic in both species revealed that 64% of the chemicals studied produced cancer at the same site. This comparison of carcinogenic activity in 2 species suggests that extrapolation from results in a single-animal study to man may be subject to substantial errors. PMID:7387835

  20. Quantitative comparisons of three modeling approaches for characterizing drought response of a highly variable, widely grown crop species

    NASA Astrophysics Data System (ADS)

    Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B. E.; Wienig, C.

    2013-12-01

    Quantifying the drought tolerance of crop species and genotypes is essential in order to predict how water stress may impact agricultural productivity. As climate models predict an increase in both frequency and severity of drought corresponding plant hydraulic and biochemical models are needed to accurately predict crop drought tolerance. Drought can result in cavitation of xylem conduits and related loss of plant hydraulic conductivity. This study tested the hypothesis that a model incorporating a plants vulnerability to cavitation would best assess drought tolerance in Brassica rapa. Four Brassica genotypes were subjected to drought conditions at a field site in Laramie, WY. Concurrent leaf gas exchange, volumetric soil moisture content and xylem pressure measurements were made during the drought period. Three models were used to access genotype specific drought tolerance. All 3 models rely on the Farquhar biochemical/biophysical model of leaf level photosynthesis, which is integrated into the Terrestrial Regional Ecosystem Exchange Simulator (TREES). The models differ in how TREES applies the environmental driving data and plant physiological mechanisms; specifically how water availability at the site of photosynthesis is derived. Model 1 established leaf water availability from a modeled soil moisture content; Model 2 input soil moisture measurements directly to establish leaf water availability; Model 3 incorporated the Sperry soil-plant transport model, which calculates flows and pressure along the soil-plant water transport pathway to establish leaf water availability. This third model incorporated measured xylem pressures thus constraining leaf water availability via genotype specific vulnerability curves. A multi-model intercomparison was made using a Bayesian approach, which assessed the interaction between uncertainty in model results and data. The three models were further evaluated by assessing model accuracy and complexity via deviance information

  1. Comparisons between satellite-derived datasets of stratospheric NOy species: using a photochemical model to account for diurnal variations

    NASA Astrophysics Data System (ADS)

    Sheese, Patrick; Walker, Kaley; McLinden, Chris; Boone, Chris; Bernath, Peter; Burrows, John; Funke, Bernd; Fussen, Didier; Manney, Gloria; Murtagh, Donal; Randall, Cora; Raspollini, Piera; Rozanov, Alexei; Russell, James; Urban, Jo; von Clarmann, Thomas; Zawodny, Joseph

    2014-05-01

    The ACE-FTS (Atmospheric Chemistry Experiment - Fourier Transform Spectrometer) instrument on the Canadian satellite SCISAT, which has been in operation now for over 10 years, has the capability of deriving stratospheric profiles of many of the NOy (NO + NO2+ NO3+ 2×N2O5+ HNO3+ HNO4+ ClONO2+ BrONO2) species. However, as a solar occultation instrument, opportunities for ACE-FTS and another given satellite instrument to observe a common air mass, can be rather limited. In the case of comparing species that exhibit significant diurnal variation, finding 'coincident' measurements can be even more difficult. In order for the measurements to be considered common-volume, the required difference between measurement times can be limitingly small. In this study, for each ACE-FTS measurement, we use a photochemical box model to simulate the diurnal variations of different NOy species over that day. The ACE-FTS NOy profiles are then scaled to the local times of coincident measurements from different satellite instruments-GOMOS, MIPAS, MLS, OSIRIS, POAM III, SAGE III, SCIAMACHY, and SMR. This allows for a much larger number of coincidences to be utilized. This study will discuss the advantages and limitations of this technique, as well as the results from comparing NO, NO2, N2O5, HNO3, and ClONO2 between ACE-FTS and other atmospheric limb sounders.

  2. Cross-species comparison of orthologous gene expression in human bladder cancer and carcinogen-induced rodent models

    PubMed Central

    Lu, Yan; Liu, Pengyuan; Wen, Weidong; Grubbs, Clinton J; Townsend, Reid R; Malone, James P; Lubet, Ronald A; You, Ming

    2011-01-01

    Genes differentially expressed by tumor cells represent promising drug targets for anti-cancer therapy. Such candidate genes need to be validated in appropriate animal models. This study examined the suitability of rodent models of bladder cancer in B6D2F1 mice and Fischer-344 rats to model clinical bladder cancer specimens in humans. Using a global gene expression approach cross-species analysis showed that 13-34% of total genes in the genome were differentially expressed between tumor and normal tissues in each of five datasets from humans, rats, and mice. About 20% of these differentially expressed genes overlapped among species, corresponding to 2.6 to 4.8% of total genes in the genome. Several genes were consistently dysregulated in bladder tumors in both humans and rodents. Notably, CNN1, MYL9, PDLIM3, ITIH5, MYH11, PCP4 and FM05 were found to commonly down-regulated; while T0P2A, CCNB2, KIF20A and RRM2 were up-regulated. These genes are likely to have conserved functions contributing to bladder carcinogenesis. Gene set enrichment analysis detected a number of molecular pathways commonly activated in both humans and rodent bladder cancer. These pathways affect the cell cycle, HIF-1 and MYC expression, and regulation of apoptosis. We also compared expression changes at mRNA and protein levels in the rat model and identified several genes/proteins exhibiting concordant changes in bladder tumors, including ANXA1, ANXA2, CA2, KRT14, LDHA, LGALS4, SERPINA1, KRT18 and LDHB. In general, rodent models of bladder cancer represent the clinical disease to an extent that will allow successful mining of target genes and permit studies on the molecular mechanisms of bladder carcinogenesis. PMID:21139803

  3. Comparison of Species Sensitivity Distributions Derived from Interspecies Correlation Models to Distributions used to Derive Water Quality Criteria

    EPA Science Inventory

    Species sensitivity distributions (SSD) require a large number of measured toxicity values to define a chemical’s toxicity to multiple species. This investigation comprehensively evaluated the accuracy of SSDs generated from toxicity values predicted from interspecies correlation...

  4. Discovery of serum protein biomarkers in the mdx mouse model and cross-species comparison to Duchenne muscular dystrophy patients.

    PubMed

    Hathout, Yetrib; Marathi, Ramya L; Rayavarapu, Sree; Zhang, Aiping; Brown, Kristy J; Seol, Haeri; Gordish-Dressman, Heather; Cirak, Sebahattin; Bello, Luca; Nagaraju, Kanneboyina; Partridge, Terry; Hoffman, Eric P; Takeda, Shin'ichi; Mah, Jean K; Henricson, Erik; McDonald, Craig

    2014-12-15

    It is expected that serum protein biomarkers in Duchenne muscular dystrophy (DMD) will reflect disease pathogenesis, progression and aid future therapy developments. Here, we describe use of quantitative in vivo stable isotope labeling in mammals to accurately compare serum proteomes of wild-type and dystrophin-deficient mdx mice. Biomarkers identified in serum from two independent dystrophin-deficient mouse models (mdx-Δ52 and mdx-23) were concordant with those identified in sera samples of DMD patients. Of the 355 mouse sera proteins, 23 were significantly elevated and 4 significantly lower in mdx relative to wild-type mice (P-value < 0.001). Elevated proteins were mostly of muscle origin: including myofibrillar proteins (titin, myosin light chain 1/3, myomesin 3 and filamin-C), glycolytic enzymes (aldolase, phosphoglycerate mutase 2, beta enolase and glycogen phosphorylase), transport proteins (fatty acid-binding protein, myoglobin and somatic cytochrome-C) and others (creatine kinase M, malate dehydrogenase cytosolic, fibrinogen and parvalbumin). Decreased proteins, mostly of extracellular origin, included adiponectin, lumican, plasminogen and leukemia inhibitory factor receptor. Analysis of sera from 1 week to 7 months old mdx mice revealed age-dependent changes in the level of these biomarkers with most biomarkers acutely elevated at 3 weeks of age. Serum analysis of DMD patients, with ages ranging from 4 to 15 years old, confirmed elevation of 20 of the murine biomarkers in DMD, with similar age-related changes. This study provides a panel of biomarkers that reflect muscle activity and pathogenesis and should prove valuable tool to complement natural history studies and to monitor treatment efficacy in future clinical trials. PMID:25027324

  5. Discovery of serum protein biomarkers in the mdx mouse model and cross-species comparison to Duchenne muscular dystrophy patients

    PubMed Central

    Hathout, Yetrib; Marathi, Ramya L.; Rayavarapu, Sree; Zhang, Aiping; Brown, Kristy J.; Seol, Haeri; Gordish-Dressman, Heather; Cirak, Sebahattin; Bello, Luca; Nagaraju, Kanneboyina; Partridge, Terry; Hoffman, Eric P.; Takeda, Shin'ichi; Mah, Jean K.; Henricson, Erik; McDonald, Craig

    2014-01-01

    It is expected that serum protein biomarkers in Duchenne muscular dystrophy (DMD) will reflect disease pathogenesis, progression and aid future therapy developments. Here, we describe use of quantitative in vivo stable isotope labeling in mammals to accurately compare serum proteomes of wild-type and dystrophin-deficient mdx mice. Biomarkers identified in serum from two independent dystrophin-deficient mouse models (mdx-Δ52 and mdx-23) were concordant with those identified in sera samples of DMD patients. Of the 355 mouse sera proteins, 23 were significantly elevated and 4 significantly lower in mdx relative to wild-type mice (P-value < 0.001). Elevated proteins were mostly of muscle origin: including myofibrillar proteins (titin, myosin light chain 1/3, myomesin 3 and filamin-C), glycolytic enzymes (aldolase, phosphoglycerate mutase 2, beta enolase and glycogen phosphorylase), transport proteins (fatty acid-binding protein, myoglobin and somatic cytochrome-C) and others (creatine kinase M, malate dehydrogenase cytosolic, fibrinogen and parvalbumin). Decreased proteins, mostly of extracellular origin, included adiponectin, lumican, plasminogen and leukemia inhibitory factor receptor. Analysis of sera from 1 week to 7 months old mdx mice revealed age-dependent changes in the level of these biomarkers with most biomarkers acutely elevated at 3 weeks of age. Serum analysis of DMD patients, with ages ranging from 4 to 15 years old, confirmed elevation of 20 of the murine biomarkers in DMD, with similar age-related changes. This study provides a panel of biomarkers that reflect muscle activity and pathogenesis and should prove valuable tool to complement natural history studies and to monitor treatment efficacy in future clinical trials. PMID:25027324

  6. Toxicity of lead (Pb) to freshwater green algae: development and validation of a bioavailability model and inter-species sensitivity comparison.

    PubMed

    De Schamphelaere, K A C; Nys, C; Janssen, C R

    2014-10-01

    model to reduce uncertainty in site-specific risk assessment. A model-based comparison with other species indicated that the sensitivity difference between P. subcapitata and two of the most chronically Pb-sensitive aquatic invertebrates (the crustacean Ceriodaphnia dubia and the snail Lymnaea stagnalis) is strongly pH dependent, with P. subcapitata becoming the most sensitive of the three at pH > 7.4. This indicates that inter-species differences in Pb bioavailability relationships should be accounted for in risk assessment and in the derivation of water quality criteria or environmental quality standards for Pb. The chronic toxicity data with three algae species and the bioavailability model presented here will help to provide a stronger scientific basis for evaluating ecological effects of Pb in the freshwater environment. PMID:25089923

  7. Predicting tree species presence and basal area in Utah: A comparison of stochastic gradient boosting, generalized additive models, and tree-based methods

    USGS Publications Warehouse

    Moisen, G.G.; Freeman, E.A.; Blackard, J.A.; Frescino, T.S.; Zimmermann, N.E.; Edwards, T.C., Jr.

    2006-01-01

    Many efforts are underway to produce broad-scale forest attribute maps by modelling forest class and structure variables collected in forest inventories as functions of satellite-based and biophysical information. Typically, variants of classification and regression trees implemented in Rulequest's?? See5 and Cubist (for binary and continuous responses, respectively) are the tools of choice in many of these applications. These tools are widely used in large remote sensing applications, but are not easily interpretable, do not have ties with survey estimation methods, and use proprietary unpublished algorithms. Consequently, three alternative modelling techniques were compared for mapping presence and basal area of 13 species located in the mountain ranges of Utah, USA. The modelling techniques compared included the widely used See5/Cubist, generalized additive models (GAMs), and stochastic gradient boosting (SGB). Model performance was evaluated using independent test data sets. Evaluation criteria for mapping species presence included specificity, sensitivity, Kappa, and area under the curve (AUC). Evaluation criteria for the continuous basal area variables included correlation and relative mean squared error. For predicting species presence (setting thresholds to maximize Kappa), SGB had higher values for the majority of the species for specificity and Kappa, while GAMs had higher values for the majority of the species for sensitivity. In evaluating resultant AUC values, GAM and/or SGB models had significantly better results than the See5 models where significant differences could be detected between models. For nine out of 13 species, basal area prediction results for all modelling techniques were poor (correlations less than 0.5 and relative mean squared errors greater than 0.8), but SGB provided the most stable predictions in these instances. SGB and Cubist performed equally well for modelling basal area for three species with moderate prediction success

  8. Comparison of Brassicaceae species for phytotoxicity testing

    EPA Science Inventory

    We compared four Brassicaceae species for potential use as test species in the EPAs Series 850 vegetative vigor test and other phytotoxicity tests to determine effects of chemicals on non-target plants. Arabidopsis thaliana var. Columbia is commonly used in plant molecular and p...

  9. Recognition of Yeast Species from Gene Sequence Comparisons

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This review discusses recognition of yeast species from gene sequence comparisons, which have been responsible for doubling the number of known yeasts over the past decade. The resolution provided by various single gene sequences is examined for both ascomycetous and basidiomycetous species, and th...

  10. SPECIES COMPARISON OF ACUTE INHALATION TOXICITY OF OZONE AND PHOSGENE

    EPA Science Inventory

    A comparison of the concentration-response effects of inhaled ozone (O3) in different species of laboratory animals was made in order to better understand the influence of the choice of species in inhalation studies of this gas. The effect of 4 hour exposure to ozone (O3) at conc...

  11. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    SciTech Connect

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  12. Retinal, functional, and morphological comparisons of two different macaque species, Macaca mulatta and Macaca fasicularis, for models of laser eye injury

    NASA Astrophysics Data System (ADS)

    DiCarlo, Cheryl D.; Hacker, Henry D.; Brown, Araceli; Cheramie, Rachael; Martinsen, Gary L.; Rockwell, Benjamin; Stuck, Bruce E.

    2005-04-01

    The past several years has seen a severe shortage of pathogen-free Indian origin rhesus macaques due to the increased requirement for this model in retroviral research. With greater than 30 years of research data accumulated using the Rhesus macaque as the model for laser eye injury there exists a need to bridge to a more readily available nonhuman primate model. Much of the data previously collected from the Rhesus monkey (Macaca mulatta) provided the basis for the American National Standards Institute (ANSI) standards for laser safety. Currently a Tri-service effort is underway to utilize the Cynomolgus monkey (Macaca fasicularis) as a replacement for the Rhesus macaque. Preliminary functional and morphological baseline data collected from multifocal electroretinography (mfERG), optical coherence tomography (OCT) and retinal cell counts were compared from a small group of monkeys and tissues to determine if significant differences existed between the species. Initial functional findings rom mfERG yielded only one difference for the n2 amplitude value which was greater in the Cynomolgus monkey. No significant differences were seen in retinal and foveal thickness, as determined by OCT scans and no significant differences were seen in ganglion cell and inner nuclear cell nuclei counts. A highly significant difference was seen in the numbers of photoreceptor nuclei with greater numbers in the Rhesus macaque. This indicates more studies should be performed to determine the impact that a model change would have on the laser bioeffects community and their ability to continue to provide minimal visible lesion data for laser safety standards. The continued goal of this project will be to provide that necessary baseline information for a seamless transition to a more readily available animal model.

  13. Humans as cucinivores: comparisons with other species.

    PubMed

    Furness, John B; Bravo, David M

    2015-12-01

    We discuss the relations of processed foods, especially cooked foods, in the human diet to digestive tract form and function. The modern consumption of over 70% of foods and beverages in highly refined form favours the diet-related classification of humans as cucinivores, rather than omnivores. Archaeological evidence indicates that humans have consumed cooked food for at least 300-400,000 years, and divergence in genes associated with human subpopulations that utilise different foods has been shown to occur over periods of 10-30,000 years. One such divergence is the greater presence of adult lactase persistence in communities that have consumed dairy products, over periods of about 8,000 years, compared to communities not consuming dairy products. We postulate that 300-400,000 years, or 10,000-14,000 generations, is sufficient time for food processing to have influenced the form and function of the human digestive tract. It is difficult to determine how long humans have prepared foods in other ways, such as pounding, grinding, drying or fermenting, but this appears to be for at least 20,000 years, which has been sufficient time to influence gene expression for digestive enzymes. Cooking and food processing expands the range of food that can be eaten, extends food availability into lean times and enhances digestibility. Cooking also detoxifies food to some extent, destroys infective agents, decreases eating time and slightly increases the efficiency of assimilation of energy substrates. On the other hand, cooking can destroy some nutrients and produce toxic products. The human digestive system is suited to a processed food diet because of its smaller volume, notably smaller colonic volume, relative to the intestines of other species, and because of differences from other primates in dentition and facial muscles that result in lower bite strength. There is no known group of humans which does not consume cooked foods, and the modern diet is dominated by processed

  14. Comparison of Decision Models

    NASA Technical Reports Server (NTRS)

    Feinberg, A.; Miles, J. R. F.; Smith, J. H.; Scheuer, E. M.

    1986-01-01

    Two methods of multiattribute decision analysis compared in report. One method employs linear utility model. Other utilizes multiplicative utility model. Report based on interviews with experts in automotive technology to obtain their preferences regarding 10 new types of vehicles.

  15. Intra-species sequence comparisons for annotating genomes

    SciTech Connect

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  16. Species comparison of acute inhalation toxicity of ozone and phosgene

    SciTech Connect

    Hatch, G.E.; Slade, R.; Stead, A.G.; Graham, J.A.

    1986-01-01

    A comparison of the concentration-response effects of inhaled ozone (O/sub 3/) in different species of laboratory animals was made in order to better understand the influence of the choice of species in inhalation studies of this gas. The effect of 4-hour exposure to ozone (O/sub 3/) at concentrations of 0.0, 0.2, 0.5, 1.0, and 2.0 ppm was determined in rabbits, guinea pigs, rats, hamsters and mice. Lavage fluid protein (LFP) accumulation 18 hr after exposure was used as the indicator of O/sub 3/-induced pulmonary edema. All species had similar basal levels of LFP (250-350 ug/ml) when a volume of saline which approximated the total lung capacity was used for lavage of the collapsed lungs. Exponential dose-response curves were seen in all species except guinea pigs, which showed significant increases in LFP at low O/sub 3/ concentrations (0.2 ppm) and a leveling off of response at the higher O/sub 3/ levels. Other species usually showed significant elevations in LFP only at concentrations greater than 0.5 ppm. Recovery of lavage fluid as a percent of the amount of injected saline varied significantly between species, and between O/sub 3/ concentrations; higher O/sub 3/ levels causing lower recovery. The time course of LFP accumulation also appeared to vary according to the species.

  17. Endangered species toxicity extrapolation using ICE models

    EPA Science Inventory

    The National Research Council’s (NRC) report on assessing pesticide risks to threatened and endangered species (T&E) included the recommendation of using interspecies correlation models (ICE) as an alternative to general safety factors for extrapolating across species. ...

  18. Comparison of laser models

    NASA Technical Reports Server (NTRS)

    Heinbockel, John H.

    1992-01-01

    The final phase of modeling solar pumped lasers considers the photodissociation of the perfloralkyl molecules n - C3F7I ,t - C4F9I, and i - C3F7I. Computer modeling was compared to laboratory data and good agreement between theory and experiment was achieved. The following is a summary of the modeling of solar pumped lasers. A perfloride gas enters a tube at a point z = 0 and travels a distance L at a velocity, W, and then exits at the point z = L. During the flow, the gas is solar pumped over the initial distance 0 less than or = z less than or = z sub 0, where z sub 0 is less than or equal to L. The perfloride gas interacts chemically with light and a chain of chemical reactions occur.

  19. Data Mining Model Comparison

    NASA Astrophysics Data System (ADS)

    Giudici, Paolo

    The aim of this contribution is to illustrate the role of statistical models and, more generally, of statistics, in choosing a Data Mining model. After a preliminary introduction on the distinction between Data Mining and statistics, we will focus on the issue of how to choose a Data Mining methodology. This well illustrates how statistical thinking can bring real added value to a Data Mining analysis, as otherwise it becomes rather difficult to make a reasoned choice. In the third part of the paper we will present, by means of a case study in credit risk management, how Data Mining and statistics can profitably interact.

  20. Comparison of alopecia areata in human and nonhuman mammalian species.

    PubMed

    McElwee, K J; Boggess, D; Olivry, T; Oliver, R F; Whiting, D; Tobin, D J; Bystryn, J C; King, L E; Sundberg, J P

    1998-01-01

    Alopecia areata (AA) is a nonscarring form of inflammatory hair loss in humans. AA-like hair loss has also been observed in other species. In recent years the Dundee experimental bald rat and the C3H/HeJ mouse have been put forward as models for human AA. AA in all species presents with a wide range of clinical features from focal, locally extensive, diffuse hair loss, to near universal alopecia. Histologically, all species have dystrophic anagen stage hair follicles associated with a peri- and intrafollicular inflammatory cell infiltrate. Autoantibodies directed against anagen stage hair follicle structures are a consistent finding. Observations on AA pathogenesis suggest nonhuman species can provide excellent models for the human disease. Ultimately, animal models will be used to determine the genetic basis of AA, potential endogenous and/or environmental trigger(s), mechanism(s) of disease initiation and progression, and allow rapid evaluation of new and improved disease treatments. PMID:9645633

  1. Modeling species-abundance relationships in multi-species collections

    USGS Publications Warehouse

    Peng, S.; Yin, Z.; Ren, H.; Guo, Q.

    2003-01-01

    Species-abundance relationship is one of the most fundamental aspects of community ecology. Since Motomura first developed the geometric series model to describe the feature of community structure, ecologists have developed many other models to fit the species-abundance data in communities. These models can be classified into empirical and theoretical ones, including (1) statistical models, i.e., negative binomial distribution (and its extension), log-series distribution (and its extension), geometric distribution, lognormal distribution, Poisson-lognormal distribution, (2) niche models, i.e., geometric series, broken stick, overlapping niche, particulate niche, random assortment, dominance pre-emption, dominance decay, random fraction, weighted random fraction, composite niche, Zipf or Zipf-Mandelbrot model, and (3) dynamic models describing community dynamics and restrictive function of environment on community. These models have different characteristics and fit species-abundance data in various communities or collections. Among them, log-series distribution, lognormal distribution, geometric series, and broken stick model have been most widely used.

  2. Caveats for correlative species distribution modeling

    USGS Publications Warehouse

    Jarnevich, Catherine S.; Stohlgren, Thomas J.; Kumar, Sunil; Morisette, Jeffrey T.; Holcombe, Tracy R.

    2015-01-01

    Correlative species distribution models are becoming commonplace in the scientific literature and public outreach products, displaying locations, abundance, or suitable environmental conditions for harmful invasive species, threatened and endangered species, or species of special concern. Accurate species distribution models are useful for efficient and adaptive management and conservation, research, and ecological forecasting. Yet, these models are often presented without fully examining or explaining the caveats for their proper use and interpretation and are often implemented without understanding the limitations and assumptions of the model being used. We describe common pitfalls, assumptions, and caveats of correlative species distribution models to help novice users and end users better interpret these models. Four primary caveats corresponding to different phases of the modeling process, each with supporting documentation and examples, include: (1) all sampling data are incomplete and potentially biased; (2) predictor variables must capture distribution constraints; (3) no single model works best for all species, in all areas, at all spatial scales, and over time; and (4) the results of species distribution models should be treated like a hypothesis to be tested and validated with additional sampling and modeling in an iterative process.

  3. Species comparison of acute inhalation toxicity of ozone and phosgene

    SciTech Connect

    Hatch, G.E.; Slade, R.; Stead, A.G.; Graham, J.A.

    1986-01-01

    A comparison of the concentration-response effects of inhaled ozone (O/sub 3/) and phosgene (COCl/sub 2/) in different species of laboratory animals was made in order to better understand the influence of the choice of species in inhalation toxicity studies. The effect of 4-h exposures to ozone at concentrations of 0.2, 0.5, 1.0, and 2.0 ppm, and to COCl/sub 2/ and 0.1, 0.2, 0.5, and 1.0 ppm was determined in rabbits, guinea pigs, rats, hamsters, and mice. Lavage fluid protein (LFP) accumulation 18-20 h after exposure was used as the indicator of O3- and COCl/sub 2/-induced pulmonary edema. All species had similar basal levels of LFP (250-350 mg/ml) when a volume of saline that approximated the total lung capacity was used to lavage the collapsed lungs. Ozone effects were most marked in guinea pigs, which showed significant effects at 0.2 ppm and above. Mice, hamsters, and rats showed effects at 1.0 ppm O3 and above, while rabbits responded only at 2.0 ppm O3. Phosgene similarly affected mice, hamsters, and rats at 0.2 ppm and above, while guinea pigs and rabbits were affected at 0.5 ppm and above. Percent recovery of lavage fluid varied significantly between species, guinea pigs having lower recovery than other species with both gases. Lavage fluid recovery was lower following exposure to higher levels of O3 but not COCl/sub 2/. Results of this study indicate that significant species differences are seen in the response to low levels of O3 and COCl/sub 2/. These differences do not appear to be related in a simple manner to body weight.

  4. MCNPX Model/Table Comparison

    SciTech Connect

    J.S. Hendricks

    2003-03-03

    MCNPX is a Monte Carlo N-Particle radiation transport code extending the capabilities of MCNP4C. As with MCNP, MCNPX uses nuclear data tables to transport neutrons, photons, and electrons. Unlike MCNP, MCNPX also uses (1) nuclear data tables to transport protons; (2) physics models to transport 30 additional particle types (deuterons, tritons, alphas, pions, muons, etc.); and (3) physics models to transport neutrons and protons when no tabular data are available or when the data are above the energy range (20 to 150 MeV) where the data tables end. MCNPX can mix and match data tables and physics models throughout a problem. For example, MCNPX can model neutron transport in a bismuth germinate (BGO) particle detector by using data tables for bismuth and oxygen and using physics models for germanium. Also, MCNPX can model neutron transport in UO{sub 2}, making the best use of physics models and data tables: below 20 MeV, data tables are used; above 150 MeV, physics models are used; between 20 and 150 MeV, data tables are used for oxygen and models are used for uranium. The mix-and-match capability became available with MCNPX2.5.b (November 2002). For the first time, we present here comparisons that calculate radiation transport in materials with various combinations of data charts and model physics. The physics models are poor at low energies (<150 MeV); thus, data tables should be used when available. Our comparisons demonstrate the importance of the mix-and-match capability and indicate how well physics models work in the absence of data tables.

  5. IDENTIFICATION AND COMPARISON OF NATURAL RUBBER FROM TWO LACTUCA SPECIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Renewed interest in the identification of alternative sources of natural rubber to Hevea brasiliensis has focused on the Compositae family. In our search for Compositae models for rubber synthesis, we extracted latex from stems of two lettuce species: Lactuca serriola, prickly lettuce, and Lactuca...

  6. Identification and comparison of natural rubber from two lactuca species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Renewed interest in the identification of alternative sources of natural rubber to Hevea brasiliensis has focused on the Compositae family. In our search for Compositae models for rubber synthesis, we extracted latex from stems of two lettuce species: Lactuca serriola, prickly lettuce, and Lactuca s...

  7. Pseudoabsence Generation Strategies for Species Distribution Models

    PubMed Central

    Hanberry, Brice B.; He, Hong S.; Palik, Brian J.

    2012-01-01

    Background Species distribution models require selection of species, study extent and spatial unit, statistical methods, variables, and assessment metrics. If absence data are not available, another important consideration is pseudoabsence generation. Different strategies for pseudoabsence generation can produce varying spatial representation of species. Methodology We considered model outcomes from four different strategies for generating pseudoabsences. We generating pseudoabsences randomly by 1) selection from the entire study extent, 2) a two-step process of selection first from the entire study extent, followed by selection for pseudoabsences from areas with predicted probability <25%, 3) selection from plots surveyed without detection of species presence, 4) a two-step process of selection first for pseudoabsences from plots surveyed without detection of species presence, followed by selection for pseudoabsences from the areas with predicted probability <25%. We used Random Forests as our statistical method and sixteen predictor variables to model tree species with at least 150 records from Forest Inventory and Analysis surveys in the Laurentian Mixed Forest province of Minnesota. Conclusions Pseudoabsence generation strategy completely affected the area predicted as present for species distribution models and may be one of the most influential determinants of models. All the pseudoabsence strategies produced mean AUC values of at least 0.87. More importantly than accuracy metrics, the two-step strategies over-predicted species presence, due to too much environmental distance between the pseudoabsences and recorded presences, whereas models based on random pseudoabsences under-predicted species presence, due to too little environmental distance between the pseudoabsences and recorded presences. Models using pseudoabsences from surveyed plots produced a balance between areas with high and low predicted probabilities and the strongest relationship between

  8. New trends in species distribution modelling

    USGS Publications Warehouse

    Zimmermann, Niklaus E.; Edwards, Thomas C., Jr.; Graham, Catherine H.; Pearman, Peter B.; Svenning, Jens-Christian

    2010-01-01

    Species distribution modelling has its origin in the late 1970s when computing capacity was limited. Early work in the field concentrated mostly on the development of methods to model effectively the shape of a species' response to environmental gradients (Austin 1987, Austin et al. 1990). The methodology and its framework were summarized in reviews 10–15 yr ago (Franklin 1995, Guisan and Zimmermann 2000), and these syntheses are still widely used as reference landmarks in the current distribution modelling literature. However, enormous advancements have occurred over the last decade, with hundreds – if not thousands – of publications on species distribution model (SDM) methodologies and their application to a broad set of conservation, ecological and evolutionary questions. With this special issue, originating from the third of a set of specialized SDM workshops (2008 Riederalp) entitled 'The Utility of Species Distribution Models as Tools for Conservation Ecology', we reflect on current trends and the progress achieved over the last decade.

  9. Measuring size and composition of species pools: a comparison of dark diversity estimates.

    PubMed

    de Bello, Francesco; Fibich, Pavel; Zelený, David; Kopecký, Martin; Mudrák, Ondřej; Chytrý, Milan; Pyšek, Petr; Wild, Jan; Michalcová, Dana; Sádlo, Jiří; Šmilauer, Petr; Lepš, Jan; Pärtel, Meelis

    2016-06-01

    Ecological theory and biodiversity conservation have traditionally relied on the number of species recorded at a site, but it is agreed that site richness represents only a portion of the species that can inhabit particular ecological conditions, that is, the habitat-specific species pool. Knowledge of the species pool at different sites enables meaningful comparisons of biodiversity and provides insights into processes of biodiversity formation. Empirical studies, however, are limited due to conceptual and methodological difficulties in determining both the size and composition of the absent part of species pools, the so-called dark diversity. We used >50,000 vegetation plots from 18 types of habitats throughout the Czech Republic, most of which served as a training dataset and 1083 as a subset of test sites. These data were used to compare predicted results from three quantitative methods with those of previously published expert estimates based on species habitat preferences: (1) species co-occurrence based on Beals' smoothing approach; (2) species ecological requirements, with envelopes around community mean Ellenberg values; and (3) species distribution models, using species environmental niches modeled by Biomod software. Dark diversity estimates were compared at both plot and habitat levels, and each method was applied in different configurations. While there were some differences in the results obtained by different methods, particularly at the plot level, there was a clear convergence, especially at the habitat level. The better convergence at the habitat level reflects less variation in local environmental conditions, whereas variation at the plot level is an effect of each particular method. The co-occurrence agreed closest the expert estimate, followed by the method based on species ecological requirements. We conclude that several analytical methods can estimate species pools of given habitats. However, the strengths and weaknesses of different methods

  10. Applying various algorithms for species distribution modelling.

    PubMed

    Li, Xinhai; Wang, Yuan

    2013-06-01

    Species distribution models have been used extensively in many fields, including climate change biology, landscape ecology and conservation biology. In the past 3 decades, a number of new models have been proposed, yet researchers still find it difficult to select appropriate models for data and objectives. In this review, we aim to provide insight into the prevailing species distribution models for newcomers in the field of modelling. We compared 11 popular models, including regression models (the generalized linear model, the generalized additive model, the multivariate adaptive regression splines model and hierarchical modelling), classification models (mixture discriminant analysis, the generalized boosting model, and classification and regression tree analysis) and complex models (artificial neural network, random forest, genetic algorithm for rule set production and maximum entropy approaches). Our objectives are: (i) to compare the strengths and weaknesses of the models, their characteristics and identify suitable situations for their use (in terms of data type and species-environment relationships) and (ii) to provide guidelines for model application, including 3 steps: model selection, model formulation and parameter estimation. PMID:23731809

  11. Species ages in neutral biodiversity models.

    PubMed

    Chisholm, Ryan A; O'Dwyer, James P

    2014-05-01

    Biogeography seeks to understand the mechanisms that drive biodiversity across long temporal and large spatial scales. Theoretical models of biogeography can be tested by comparing their predictions of quantities such as species ages against empirical estimates. It has previously been claimed that the neutral theory of biodiversity and biogeography predicts species ages that are unrealistically long. Any improved theory of biodiversity must rectify this problem, but first it is necessary to quantify the problem precisely. Here we provide analytical expressions for species ages in neutral biodiversity communities. We analyse a spatially implicit metacommunity model and solve for both the zero-sum and non-zero-sum cases. We explain why our new expressions are, in the context of biodiversity, usually more appropriate than those previously imported from neutral molecular evolution. Because of the time symmetry of the spatially implicit neutral model, our expressions also lead directly to formulas for species persistence times and species lifetimes. We use our new expressions to estimate species ages of forest trees under a neutral model and find that they are about an order of magnitude shorter than those predicted previously but still unrealistically long. In light of our results, we discuss different models of biogeography that may solve the problem of species ages. PMID:24530891

  12. Which Models Are Appropriate for Six Subtropical Forests: Species-Area and Species-Abundance Models

    PubMed Central

    Wei, Shi Guang; Li, Lin; Chen, Zhen Cheng; Lian, Ju Yu; Lin, Guo Jun; Huang, Zhong Liang; Yin, Zuo Yun

    2014-01-01

    The species-area relationship is one of the most important topic in the study of species diversity, conservation biology and landscape ecology. The species-area relationship curves describe the increase of species number with increasing area, and have been modeled by various equations. In this paper, we used detailed data from six 1-ha subtropical forest communities to fit three species-area relationship models. The coefficient of determination and F ratio of ANOVA showed all the three models fitted well to the species-area relationship data in the subtropical communities, with the logarithm model performing better than the other two models. We also used the three species-abundance distributions, namely the lognormal, logcauchy and logseries model, to fit them to the species-abundance data of six communities. In this case, the logcauchy model had the better fit based on the coefficient of determination. Our research reveals that the rare species always exist in the six communities, corroborating the neutral theory of Hubbell. Furthermore, we explained why all species-abundance figures appeared to be left-side truncated. This was due to subtropical forests have high diversity, and their large species number includes many rare species. PMID:24755956

  13. Comparison of debris flux models

    NASA Astrophysics Data System (ADS)

    Sdunnus, H.; Beltrami, P.; Klinkrad, H.; Matney, M.; Nazarenko, A.; Wegener, P.

    The availability of models to estimate the impact risk from the man-made space debris and the natural meteoroid environment is essential for both, manned and unmanned satellite missions. Various independent tools based on different approaches have been developed in the past years. Due to an increased knowledge of the debris environment and its sources e.g. from improved measurement capabilities, these models could be updated regularly, providing more detailed and more reliable simulations. This paper addresses an in-depth, quantitative comparison of widely distributed debris flux models which were recently updated, namely ESA's MASTER 2001 model, NASA's ORDEM 2000 and the Russian SDPA 2000 model. The comparison was performed in the frame of the work of the 20t h Interagency Debris Coordination (IADC) meeting held in Surrey, UK. ORDEM 2000ORDEM 2000 uses careful empirical estimates of the orbit populations based onthree primary data sources - the US Space Command Catalog, the H ystackaRadar, and the Long Duration Exposure Facility spacecraft returned surfaces.Further data (e.g. HAX and Goldstone radars, impacts on Shuttle windows andradiators, and others) were used to adjust these populations for regions in time,size, and space not covered by the primary data sets. Some interpolation andextrapolation to regions with no data (such as projections into the future) wasprovided by the EVOLVE model. MASTER 2001The ESA MASTER model offers a full three dimensional description of theterrestrial debris distribution reaching from LEO up to the GEO region. Fluxresults relative to an orbiting target or to an inertial volume can be resolved intosource terms, impactor characteristics and orbit, as well as impact velocity anddirection. All relevant debris source terms are considered by the MASTERmodel. For each simulated source, a corresponding debris generation model interms of mass/diameter distribution, additional velocities, and directionalspreading has been developed. A

  14. 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

  15. Species Tree Inference Using a Mixture Model.

    PubMed

    Ullah, Ikram; Parviainen, Pekka; Lagergren, Jens

    2015-09-01

    Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (Åkerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714-5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG (Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323-330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic

  16. Supervised DNA Barcodes species classification: analysis, comparisons and results

    PubMed Central

    2014-01-01

    Background Specific fragments, coming from short portions of DNA (e.g., mitochondrial, nuclear, and plastid sequences), have been defined as DNA Barcode and can be used as markers for organisms of the main life kingdoms. Species classification with DNA Barcode sequences has been proven effective on different organisms. Indeed, specific gene regions have been identified as Barcode: COI in animals, rbcL and matK in plants, and ITS in fungi. The classification problem assigns an unknown specimen to a known species by analyzing its Barcode. This task has to be supported with reliable methods and algorithms. Methods In this work the efficacy of supervised machine learning methods to classify species with DNA Barcode sequences is shown. The Weka software suite, which includes a collection of supervised classification methods, is adopted to address the task of DNA Barcode analysis. Classifier families are tested on synthetic and empirical datasets belonging to the animal, fungus, and plant kingdoms. In particular, the function-based method Support Vector Machines (SVM), the rule-based RIPPER, the decision tree C4.5, and the Naïve Bayes method are considered. Additionally, the classification results are compared with respect to ad-hoc and well-established DNA Barcode classification methods. Results A software that converts the DNA Barcode FASTA sequences to the Weka format is released, to adapt different input formats and to allow the execution of the classification procedure. The analysis of results on synthetic and real datasets shows that SVM and Naïve Bayes outperform on average the other considered classifiers, although they do not provide a human interpretable classification model. Rule-based methods have slightly inferior classification performances, but deliver the species specific positions and nucleotide assignments. On synthetic data the supervised machine learning methods obtain superior classification performances with respect to the traditional DNA Barcode

  17. Monotonicity-constrained species distribution models.

    PubMed

    Hofner, Benjamin; Müller, Jörg; Hothorn, Torsten

    2011-10-01

    Flexible modeling frameworks for species distribution models based on generalized additive models that allow for smooth, nonlinear effects and interactions are of increasing importance in ecology. Commonly, the flexibility of such smooth function estimates is controlled by means of penalized estimation procedures. However, the actual shape remains unspecified. In many applications, this is not desirable as researchers have a priori assumptions on the shape of the estimated effects, with monotonicity being the most important. Here we demonstrate how monotonicity constraints can be incorporated in a recently proposed flexible framework for species distribution models. Our proposal allows monotonicity constraints to be imposed on smooth effects and on ordinal, categorical variables using an additional asymmetric L2 penalty. Model estimation and variable selection for Red Kite (Milvus milvus) breeding was conducted using the flexible boosting framework implemented in R package mboost. PMID:22073780

  18. Incorporating uncertainty in predictive species distribution modelling

    PubMed Central

    Beale, Colin M.; Lennon, Jack J.

    2012-01-01

    Motivated by the need to solve ecological problems (climate change, habitat fragmentation and biological invasions), there has been increasing interest in species distribution models (SDMs). Predictions from these models inform conservation policy, invasive species management and disease-control measures. However, predictions are subject to uncertainty, the degree and source of which is often unrecognized. Here, we review the SDM literature in the context of uncertainty, focusing on three main classes of SDM: niche-based models, demographic models and process-based models. We identify sources of uncertainty for each class and discuss how uncertainty can be minimized or included in the modelling process to give realistic measures of confidence around predictions. Because this has typically not been performed, we conclude that uncertainty in SDMs has often been underestimated and a false precision assigned to predictions of geographical distribution. We identify areas where development of new statistical tools will improve predictions from distribution models, notably the development of hierarchical models that link different types of distribution model and their attendant uncertainties across spatial scales. Finally, we discuss the need to develop more defensible methods for assessing predictive performance, quantifying model goodness-of-fit and for assessing the significance of model covariates. PMID:22144387

  19. Identification of Simple Sequence Repeat Biomarkers through Cross-Species Comparison in a Tag Cloud Representation

    PubMed Central

    2014-01-01

    Simple sequence repeats (SSRs) are not only applied as genetic markers in evolutionary studies but they also play an important role in gene regulatory activities. Efficient identification of conserved and exclusive SSRs through cross-species comparison is helpful for understanding the evolutionary mechanisms and associations between specific gene groups and SSR motifs. In this paper, we developed an online cross-species comparative system and integrated it with a tag cloud visualization technique for identifying potential SSR biomarkers within fourteen frequently used model species. Ultraconserved or exclusive SSRs among cross-species orthologous genes could be effectively retrieved and displayed through a friendly interface design. Four different types of testing cases were applied to demonstrate and verify the retrieved SSR biomarker candidates. Through statistical analysis and enhanced tag cloud representation on defined functional related genes and cross-species clusters, the proposed system can correctly represent the patterns, loci, colors, and sizes of identified SSRs in accordance with gene functions, pattern qualities, and conserved characteristics among species. PMID:24800246

  20. Cross-species and interassay comparisons of phytoestrogen action.

    PubMed Central

    Whitten, P L; Patisaul, H B

    2001-01-01

    This paper compiles animal and human data on the biologic effects and exposure levels of phytoestrogens in order to identify areas of research in which direct species comparisons can be made. In vitro and in vivo assays of phytoestrogen action and potency are reviewed and compared to actions, dose-response relationships, and estimates of exposure in human subjects. Binding studies show that the isoflavonoid phytoestrogens are high-affinity ligands for estrogen receptors (ERs), especially ER beta, but have lower potency in whole-cell assays, perhaps because of interactions with binding proteins. Many other enzymatic actions require concentrations higher than those normally seen in plasma. In vivo data show that phytoestrogens have a wide range of biologic effects at doses and plasma concentrations seen with normal human diets. Significant in vivoresponses have been observed in animal and human tests for bone, breast, ovary, pituitary, vasculature, prostate, and serum lipids. The doses reported to be biologically active in humans (0.4--10 mg/kg body weight/day) are lower than the doses generally reported to be active in rodents (10--100 mg/kg body weight/day), although some studies have reported rodent responses at lower doses. However, available estimates of bioavailability and peak plasma levels in rodents and humans are more similar. Steroidogenesis and the hypothalamic-pituitary-gonadal axis appear to be important loci of phytoestrogen actions, but these inferences must be tentative because good dose-response data are not available for many end points. The similarity of reported proliferative and antiproliferative doses illustrates the need for fuller examination of dose-response relationships and multiple end points in assessing phytoestrogen actions. PMID:11250801

  1. Nonindigenous vs. native species: A comparison of preferred niche breadth

    EPA Science Inventory

    To successfully invade and expand their populations, nonindigenous species must be able to physiologically cope with their new environment. Given this, species that tolerate a wide array of environmental conditions are often predicted to be better at establishing populations in ...

  2. Cross-species models of human melanoma.

    PubMed

    van der Weyden, Louise; Patton, E Elizabeth; Wood, Geoffrey A; Foote, Alastair K; Brenn, Thomas; Arends, Mark J; Adams, David J

    2016-01-01

    Although transformation of melanocytes to melanoma is rare, the rapid growth, systemic spread, as well as the chemoresistance of melanoma present significant challenges for patient care. Here we review animal models of melanoma, including murine, canine, equine, and zebrafish models, and detail the immense contribution these models have made to our knowledge of human melanoma development, and to melanocyte biology. We also highlight the opportunities for cross-species comparative genomic studies of melanoma to identify the key molecular events that drive this complex disease. PMID:26354726

  3. Model Comparison of Bayesian Semiparametric and Parametric Structural Equation Models

    ERIC Educational Resources Information Center

    Song, Xin-Yuan; Xia, Ye-Mao; Pan, Jun-Hao; Lee, Sik-Yum

    2011-01-01

    Structural equation models have wide applications. One of the most important issues in analyzing structural equation models is model comparison. This article proposes a Bayesian model comparison statistic, namely the "L[subscript nu]"-measure for both semiparametric and parametric structural equation models. For illustration purposes, we consider…

  4. Comparison of experimental respiratory tularemia in three nonhuman primate species.

    PubMed

    Glynn, Audrey R; Alves, Derron A; Frick, Ondraya; Erwin-Cohen, Rebecca; Porter, Aimee; Norris, Sarah; Waag, David; Nalca, Aysegul

    2015-04-01

    Tularemia is a zoonotic disease caused by Francisella tularensis, which is transmitted to humans most commonly by contact with infected animals, tick bites, or inhalation of aerosolized bacteria. F. tularensis is highly infectious via the aerosol route; inhalation of as few as 10-50 organisms can cause pneumonic tularemia. Left untreated, the pneumonic form has more than >30% case-fatality rate but with early antibiotic intervention can be reduced to 3%. This study compared tularemia disease progression across three species of nonhuman primates [African green monkey (AGM), cynomolgus macaque (CM), and rhesus macaque (RM)] following aerosolized F. tularensis Schu S4 exposure. Groups of the animals exposed to various challenge doses were observed for clinical signs of infection and blood samples were analyzed to characterize the disease pathogenesis. Whereas the AGMs and CMs succumbed to disease following challenge doses of 40 and 32 colony forming units (CFU), respectively, the RM lethal dose was 276,667 CFU. Following all challenge doses that caused disease, the NHPs experienced weight loss, bacteremia, fever as early as 4 days post exposure, and tissue burden. Necrotizing-to-pyogranulomatous lesions were observed most commonly in the lung, lymph nodes, spleen, and bone marrow. Overall, the CM model consistently manifested pathological responses similar to those resulting from inhalation of F. tularensis in humans and thereby most closely emulates human tularemia disease. The RM model displayed a higher tolerance to infection and survived exposures of up to 15,593 CFU of aerosolized F. tularensis. PMID:25766142

  5. In Silico Modeling of Geobacter Species.

    SciTech Connect

    Lovley, Derek, R.

    2008-01-29

    This project employed a combination of in silico modeling and physiological studies to begin the construction of models that could predict the activity of Geobacter species under different environmental conditions. A major accomplishment of the project was the development of the first genome-based models of organisms known environmental relevance. This included the modeling of two Geobacter species and two species of Pelobacter. Construction of these models required increased sophistication in the annotation of the original draft genomes as well as collection of physiological data on growth yields, cell composition, and metabolic reactions. Biochemical studies were conducted to determine whether proposed enzymatic reactions were in fact expressed. During this process we developed an Automodel Pipeline process to accelerate future model development of other environmentally relevant organisms by using bioinformatics techniques to leverage predicted protein sequences and the Genomatica database containing a collection of well-curated metabolic models. The Automodel Pipeline was also used for iterative updating of the primary Geobacter model of G. sulfurreducens to expand metabolic functions or to add alternative pathways. Although each iteration of the model does not lead to another publication, it is an invaluable resource for hypothesis development and evaluation of experimental data. In order to develop a more accurate G. sulfurreducens model, a series of physiological studies that could be analyzed in the context of the model were carried out. For example, previous field trials of in situ uranium bioremediation demonstrated that Geobacter species face an excess of electron donor and a limitation of electron acceptor near the point of acetate injection into the groundwater. Therefore, a model-based analysis of electron acceptor limitation physiology was conducted and model predictions were compared with growth observed in chemostats. Iterative studies resulted in

  6. Disease insights through cross-species phenotype comparisons.

    PubMed

    Haendel, Melissa A; Vasilevsky, Nicole; Brush, Matthew; Hochheiser, Harry S; Jacobsen, Julius; Oellrich, Anika; Mungall, Christopher J; Washington, Nicole; Köhler, Sebastian; Lewis, Suzanna E; Robinson, Peter N; Smedley, Damian

    2015-10-01

    New sequencing technologies have ushered in a new era for diagnosis and discovery of new causative mutations for rare diseases. However, the sheer numbers of candidate variants that require interpretation in an exome or genomic analysis are still a challenging prospect. A powerful approach is the comparison of the patient's set of phenotypes (phenotypic profile) to known phenotypic profiles caused by mutations in orthologous genes associated with these variants. The most abundant source of relevant data for this task is available through the efforts of the Mouse Genome Informatics group and the International Mouse Phenotyping Consortium. In this review, we highlight the challenges in comparing human clinical phenotypes with mouse phenotypes and some of the solutions that have been developed by members of the Monarch Initiative. These tools allow the identification of mouse models for known disease-gene associations that may otherwise have been overlooked as well as candidate genes may be prioritized for novel associations. The culmination of these efforts is the Exomiser software package that allows clinical researchers to analyse patient exomes in the context of variant frequency and predicted pathogenicity as well the phenotypic similarity of the patient to any given candidate orthologous gene. PMID:26092691

  7. A comparison of auditory brainstem responses across diving bird species.

    PubMed

    Crowell, Sara E; Wells-Berlin, Alicia M; Carr, Catherine E; Olsen, Glenn H; Therrien, Ronald E; Yannuzzi, Sally E; Ketten, Darlene R

    2015-08-01

    There is little biological data available for diving birds because many live in hard-to-study, remote habitats. Only one species of diving bird, the black-footed penguin (Spheniscus demersus), has been studied in respect to auditory capabilities (Wever et al., Proc Natl Acad Sci USA 63:676-680, 1969). We, therefore, measured in-air auditory threshold in ten species of diving birds, using the auditory brainstem response (ABR). The average audiogram obtained for each species followed the U-shape typical of birds and many other animals. All species tested shared a common region of the greatest sensitivity, from 1000 to 3000 Hz, although audiograms differed significantly across species. Thresholds of all duck species tested were more similar to each other than to the two non-duck species tested. The red-throated loon (Gavia stellata) and northern gannet (Morus bassanus) exhibited the highest thresholds while the lowest thresholds belonged to the duck species, specifically the lesser scaup (Aythya affinis) and ruddy duck (Oxyura jamaicensis). Vocalization parameters were also measured for each species, and showed that with the exception of the common eider (Somateria mollisima), the peak frequency, i.e., frequency at the greatest intensity, of all species' vocalizations measured here fell between 1000 and 3000 Hz, matching the bandwidth of the most sensitive hearing range. PMID:26156644

  8. A comparison of auditory brainstem responses across diving bird species

    USGS Publications Warehouse

    Crowell, Sara E.; Berlin, Alicia; Carr, Catherine E; Olsen, Glenn H.; Therrien, Ronald E; Yannuzzi, Sally E; Ketten, Darlene R

    2015-01-01

    There is little biological data available for diving birds because many live in hard-to-study, remote habitats. Only one species of diving bird, the black-footed penguin (Spheniscus demersus), has been studied in respect to auditory capabilities (Wever et al., Proc Natl Acad Sci USA 63:676–680, 1969). We, therefore, measured in-air auditory threshold in ten species of diving birds, using the auditory brainstem response (ABR). The average audiogram obtained for each species followed the U-shape typical of birds and many other animals. All species tested shared a common region of the greatest sensitivity, from 1000 to 3000 Hz, although audiograms differed significantly across species. Thresholds of all duck species tested were more similar to each other than to the two non-duck species tested. The red-throated loon (Gavia stellata) and northern gannet (Morus bassanus) exhibited the highest thresholds while the lowest thresholds belonged to the duck species, specifically the lesser scaup (Aythya affinis) and ruddy duck (Oxyura jamaicensis). Vocalization parameters were also measured for each species, and showed that with the exception of the common eider (Somateria mollisima), the peak frequency, i.e., frequency at the greatest intensity, of all species' vocalizations measured here fell between 1000 and 3000 Hz, matching the bandwidth of the most sensitive hearing range.

  9. Model comparison of oxygen ion loss at Mars

    NASA Astrophysics Data System (ADS)

    Curry, S.; Liemohn, M. W.; Fang, X.; Ma, Y.; Najib, D.; Brain, D.

    2011-12-01

    We present results from a Mars pick-up ion transport model in order to study the relative role of kinetic processes in planetary ion escape, as part of the first community-wide plasma interaction model comparison. Mars does not have a strong, intrinsic dipole magnetic field and consequently the solar wind directly interacts with the dayside upper atmosphere causing particles to be stripped away from the atmosphere. Ions can be picked up and carried away through this interaction, contributing to non-thermal atmospheric escape. A robust effort involving many of the global Mars space environment models is underway, selecting identical initial and boundary conditions for direct model-model comparisons between the codes. A multi-fluid and multi-species MHD model from this comparison will be used as background electric and magnetic fields for the ions in our Mars pick-up ion transport model. By simulating billions of test particles through these background fields, a comprehensive picture of the velocity space distributions of the pick-up ions is generated. Previous model comparisons have focused on pressure conservation and plasma boundaries, but this study will focus on comparing spatial patterns of escape rates and velocity space distributions at specific locations for the kinetic versus Maxwellian approaches. From these comparisons, conclusions are made about the relative contribution of kinetic and fluid physical processes in controlling the distribution of planetary ions and atmospheric escape.

  10. A comparison of auditory brainstem responses across diving bird species

    PubMed Central

    Crowell, Sara E.; Wells-Berlin, Alicia M.; Carr, Catherine E.; Olsen, Glenn H.; Therrien, Ronald E.; Yannuzzi, Sally E.; Ketten, Darlene R.

    2015-01-01

    There is little biological data available for diving birds because many live in hard-to-study, remote habitats. Only one species of diving bird, the black-footed penguin (Spheniscus demersus), has been studied in respect to auditory capabilities (Wever et al. 1969). We therefore measured in-air auditory threshold in ten species of diving birds, using the auditory brainstem response (ABR). The average audiogram obtained for each species followed the U-shape typical of birds and many other animals. All species tested shared a common region of greatest sensitivity, from 1000 to 3000 Hz, although audiograms differed significantly across species. Thresholds of all duck species tested were more similar to each other than to the two non-duck species tested. The red-throated loon (Gavia stellata) and northern gannet (Morus bassanus) exhibited the highest thresholds while the lowest thresholds belonged to the duck species, specifically the lesser scaup (Aythya affinis) and ruddy duck (Oxyura jamaicensis). Vocalization parameters were also measured for each species, and showed that with the exception of the common eider (Somateria mollisima), the peak frequency, i.e. frequency at the greatest intensity, of all species’ vocalizations measured here fell between 1000 and 3000 Hz, matching the bandwidth of the most sensitive hearing range. PMID:26156644

  11. Multi-Species Thermal Lattice Boltzmann Models

    NASA Astrophysics Data System (ADS)

    Wah, Darren; Vahala, George; Vahala, Linda; Pavlo, Pavol; Carter, Jonathan

    1998-11-01

    Thermal Lattice Boltzmann models (TLBM) are ideal for simulating nonlinear macroscopic conservation systems because of their inherent parallelizeability (nearly all operations are purely local). The TLBM solves a linear BGK-like kinetic equation so that the standard nonlinear convective terms in the standard fluid codes are now replaced by a simple shift operator (linear advection) at the kinetic level. Here we extend our previous TLBM to handle a two-species system, utilizing the models of Morse (1964),Greene (1973) and Kotelnikov & Montgomery (1997). Each kinetic equation now has 2 BGK-like relaxation terms : the first is due to self-collisions and the other is due to different- species collisions. The relaxation rates used are appropriate for electron-ion collisions. Certain constraints can be imposed on the relaxed distribution functions so that the cross-species momentum and energy evolutions relax at the rate determined from the full nonlinear Boltzmann integral collision operator. Ionization and recombination processes will also be examined. Both hexagonal and octagonal lattices are studied.

  12. Juniperus extraction: a comparison of species and solvents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effectiveness of the three solvents, hexane, methanol and ethanol were compared for their ability to extract non-polar and polar materials from sawdust from three species of Juniperus (i.e., J. virginianna, J. occidentalis and J. ashei). These species studied represent the junipers with the grea...

  13. CISNET lung models: Comparison of model assumptions and model structures

    PubMed Central

    McMahon, Pamela M.; Hazelton, William; Kimmel, Marek; Clarke, Lauren

    2012-01-01

    Sophisticated modeling techniques can be powerful tools to help us understand the effects of cancer control interventions on population trends in cancer incidence and mortality. Readers of journal articles are however rarely supplied with modeling details. Six modeling groups collaborated as part of the National Cancer Institute’s Cancer Intervention and Surveillance Modeling Network (CISNET) to investigate the contribution of US tobacco control efforts towards reducing lung cancer deaths over the period 1975 to 2000. The models included in this monograph were developed independently and use distinct, complementary approaches towards modeling the natural history of lung cancer. The models used the same data for inputs and agreed on the design of the analysis and the outcome measures. This article highlights aspects of the models that are most relevant to similarities of or differences between the results. Structured comparisons can increase the transparency of these complex models. PMID:22882887

  14. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

    PubMed Central

    Nyerges, Ákos; Csörgő, Bálint; Nagy, István; Bálint, Balázs; Bihari, Péter; Lázár, Viktória; Apjok, Gábor; Umenhoffer, Kinga; Bogos, Balázs; Pósfai, György; Pál, Csaba

    2016-01-01

    Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species. PMID:26884157

  15. A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species.

    PubMed

    Nyerges, Ákos; Csörgő, Bálint; Nagy, István; Bálint, Balázs; Bihari, Péter; Lázár, Viktória; Apjok, Gábor; Umenhoffer, Kinga; Bogos, Balázs; Pósfai, György; Pál, Csaba

    2016-03-01

    Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species. PMID:26884157

  16. Whistle comparison of four delphinid species in Southeastern Brazil.

    PubMed

    Lima, Isabela M S; Andrade, Luciana G; Bittencourt, Lis; Bisi, Tatiana L; Flach, Leonardo; Lailson-Brito, José; Azevedo, Alexandre F

    2016-05-01

    The present study evaluates variations in frequency and duration parameters of whistles of four dolphin species (Sotalia guianensis, Steno bredanensis, Stenella frontalis, and Tursiops truncatus), recorded in the Rio de Janeiro State Coast, Southeastern Brazil. A total of 487 whistles were analyzed. Acoustic parameters of the whistles were classified to species by discriminant function analysis. Overall classification score was 72.5%, with the highest classification score obtained for whistles of S. bredanensis and the lowest obtained for S. frontalis. Most differences were among S. bredanensis and S. guianensis, species that did not have their repertoires compared in other studies. PMID:27250196

  17. Comparison of produced water toxicity to Arctic and temperate species.

    PubMed

    Camus, L; Brooks, S; Geraudie, P; Hjorth, M; Nahrgang, J; Olsen, G H; Smit, M G D

    2015-03-01

    Produced water is the main discharge stream from oil and gas production. For offshore activities this water is usually discharged to the marine environment. Produced water contains traces of hydrocarbons such as polycyclic aromatic hydrocarbons as well as alkylphenols, which are relatively resistant to biodegradation and have been reported to cause adverse effects to marine organisms in laboratory studies. For management of produced water, risk-based tools have been developed using toxicity data for mainly non-Arctic species. Reliable risk assessment approaches for Arctic environments are requested to manage potential impacts of produced water associated with increased oil and gas activities in Arctic regions. In order to assess the applicability of existing risk tools for Arctic areas, basic knowledge on the sensitivity of Arctic species has to be developed. In the present study, acute and chronic toxicity of artificial produced water for 6 Arctic and 6 temperate species was experimentally tested and evaluated. The hazardous concentrations affecting 5% and 50% of the species were calculated from species sensitivity distribution curves. Hazardous concentrations were compared to elucidate whether temperate toxicity data used in risk assessment are sufficiently representative for Arctic species. From the study it can be concluded that hazardous concentration derived from individual species' toxicity data of temperate and Arctic species are comparable. However, the manner in which Arctic and non-Arctic populations and communities respond to exposure levels above established thresholds remains to be investigated. Hence, responses at higher levels of biological organization should be studied to reveal potential differences in sensitivities to produced water between Arctic and non-Arctic ecosystems. PMID:25521339

  18. Biomechanical comparison of menisci from different species and artificial constructs

    PubMed Central

    2013-01-01

    Background Loss of meniscal tissue is correlated with early osteoarthritis but few data exist regarding detailed biomechanical properties (e.g. viscoelastic behavior) of menisci in different species commonly used as animal models. The purpose of the current study was to biomechanically characterize bovine, ovine, and porcine menisci (each n = 6, midpart of the medial meniscus) and compare their properties to that of normal and degenerated human menisci (n = 6) and two commercially available artificial scaffolds (each n = 3). Methods Samples were tested in a cyclic, minimally constraint compression–relaxation test with a universal testing machine allowing the characterization of the viscoelastic properties including stiffness, residual force and relative sample compression. T-tests were used to compare the biomechanical parameters of all samples. Significance level was set at p < 0.05. Results Throughout cyclic testing stiffness, residual force and relative sample compression increased significantly (p < 0.05) in all tested meniscus samples. From the tested animal meniscus samples the ovine menisci showed the highest biomechanical similarity to human menisci in terms of stiffness (human: 8.54 N/mm ± 1.87, cycle 1; ovine: 11.24 N/mm ± 2.36, cycle 1, p = 0.0528), residual force (human: 2.99 N ± 0.63, cycle 1 vs. ovine 3.24 N ± 0.13, cycle 1, p = 0.364) and relative sample compression (human 19.92% ± 0.63, cycle 1 vs. 18.72% ± 1.84 in ovine samples at cycle 1, p = 0.162). The artificial constructs -as hypothesized- revealed statistically significant inferior biomechanical properties. Conclusions For future research the use of ovine meniscus would be desirable showing the highest biomechanical similarities to human meniscus tissue. The significantly different biomechanical properties of the artificial scaffolds highlight the necessity of cellular ingrowth and formation of extracellular matrix to gain

  19. Comparison of two strategies for detection of reactive oxygen species

    NASA Astrophysics Data System (ADS)

    Gao, Weidong; Zhou, Yuanshu; Gu, Yueqing

    2014-09-01

    Photodynamic therapy (PDT) is a clinically approved treatment that was applied to oncology , dermatology, and ophthalmology. Reactive oxygen species (ROS) play a important role in the efficacy of PDT. Online monitoring of reactive oxygen species is the key to understand effect of PDT treatment. We used Fluorescence probes DPBF and luminescent probe luminal to measure the ROS in cells. And we revaluate the relationship between the amount of light and cell survival. There is strongly correlated between the amount of light and cell kill.

  20. Molecular Systematic Comparison of North American Lygus Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Lygus is widely distributed in North America and Eurasia. The tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), is one of the most serious pest species within this genus. This pest has over 300 known host plants. We employed various molecular markers to investigate both inter- a...

  1. A comparison of facial expression properties in five hylobatid species.

    PubMed

    Scheider, Linda; Liebal, Katja; Oña, Leonardo; Burrows, Anne; Waller, Bridget

    2014-07-01

    Little is known about facial communication of lesser apes (family Hylobatidae) and how their facial expressions (and use of) relate to social organization. We investigated facial expressions (defined as combinations of facial movements) in social interactions of mated pairs in five different hylobatid species belonging to three different genera using a recently developed objective coding system, the Facial Action Coding System for hylobatid species (GibbonFACS). We described three important properties of their facial expressions and compared them between genera. First, we compared the rate of facial expressions, which was defined as the number of facial expressions per units of time. Second, we compared their repertoire size, defined as the number of different types of facial expressions used, independent of their frequency. Third, we compared the diversity of expression, defined as the repertoire weighted by the rate of use for each type of facial expression. We observed a higher rate and diversity of facial expression, but no larger repertoire, in Symphalangus (siamangs) compared to Hylobates and Nomascus species. In line with previous research, these results suggest siamangs differ from other hylobatids in certain aspects of their social behavior. To investigate whether differences in facial expressions are linked to hylobatid socio-ecology, we used a Phylogenetic General Least Square (PGLS) regression analysis to correlate those properties with two social factors: group-size and level of monogamy. No relationship between the properties of facial expressions and these socio-ecological factors was found. One explanation could be that facial expressions in hylobatid species are subject to phylogenetic inertia and do not differ sufficiently between species to reveal correlations with factors such as group size and monogamy level. PMID:24395677

  2. Inter-comparison of subglacial hydrological models

    NASA Astrophysics Data System (ADS)

    de Fleurian, Basile; Werder, Mauro

    2016-04-01

    The recent emergence of a number of subglacial hydrological models allows us to obtain theoretical insights on basal processes; for instance on the coupling between water pressure and the sliding of glaciers. In ice-flow models, it is relatively clear what the simulated physics ought to be. Conversely, the physical processes incorporated into subglacial hydrology models are diverse as it is yet unclear which ones are of relevance for a particular setting. An inter-comparison of hydrology models will therefore need a somewhat different approach to the one used in the many ice-flow model inter-comparisons (EISMINT, ISMIP, etc.). Here, we present a set of experiments that will allow the comparison of the behavior of different hydrology models. The design of the benchmark aims at allowing the participation of a wide range of models based on different physical approaches. We aim at evaluating the models with a focus on the effective pressure which has the most impact on the dynamics of glaciers. The aim of this inter-comparison is to provide modellers with the necessary data to make an informed decision on which subglacial hydrology model to use for a particular study.

  3. Comparison of Cas9 activators in multiple species.

    PubMed

    Chavez, Alejandro; Tuttle, Marcelle; Pruitt, Benjamin W; Ewen-Campen, Ben; Chari, Raj; Ter-Ovanesyan, Dmitry; Haque, Sabina J; Cecchi, Ryan J; Kowal, Emma J K; Buchthal, Joanna; Housden, Benjamin E; Perrimon, Norbert; Collins, James J; Church, George

    2016-07-01

    Several programmable transcription factors exist based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain unexplored. Here, we compare Cas9 activator systems and examine their ability to induce robust gene expression in several human, mouse, and fly cell lines. We also explore the potential for improved activation through the combination of the most potent activator systems, and we assess the role of cooperativity in maximizing gene expression. PMID:27214048

  4. Seminal plasma components in camelids and comparisons with other species.

    PubMed

    Kershaw-Young, C M; Maxwell, W M C

    2012-08-01

    Camelid semen is characterized by a highly viscous, low-volume ejaculate with a low concentration of spermatozoa that exhibit low progressive motility. The viscous seminal plasma is currently the major impediment to the development of assisted reproductive technologies (ARTs) in camelids. To advance ARTs such as sperm cryopreservation and artificial insemination in camelids, it is necessary to identify the cause of the viscosity and gain an understanding of the role of seminal plasma components on sperm function and fertility. Numerous compounds and proteins have been identified as mediators of sperm function and predictors of fertility in other livestock species, and understanding the importance of specific proteins has progressed the success of ARTs in these species. Current knowledge on the components of camelid seminal plasma is outlined, together with the implications of these components for the development of ARTs in camelids. The cause of semen viscosity, as well as proteins that are present in camelid seminal plasma, is described for the first time. Seminal plasma components are compared with those of other species to hypothesize their role in sperm function and fertility. PMID:22827394

  5. Effects of sample survey design on the accuracy of classification tree models in species distribution models

    USGS Publications Warehouse

    Edwards, T.C., Jr.; Cutler, D.R.; Zimmermann, N.E.; Geiser, L.; Moisen, G.G.

    2006-01-01

    We evaluated the effects of probabilistic (hereafter DESIGN) and non-probabilistic (PURPOSIVE) sample surveys on resultant classification tree models for predicting the presence of four lichen species in the Pacific Northwest, USA. Models derived from both survey forms were assessed using an independent data set (EVALUATION). Measures of accuracy as gauged by resubstitution rates were similar for each lichen species irrespective of the underlying sample survey form. Cross-validation estimates of prediction accuracies were lower than resubstitution accuracies for all species and both design types, and in all cases were closer to the true prediction accuracies based on the EVALUATION data set. We argue that greater emphasis should be placed on calculating and reporting cross-validation accuracy rates rather than simple resubstitution accuracy rates. Evaluation of the DESIGN and PURPOSIVE tree models on the EVALUATION data set shows significantly lower prediction accuracy for the PURPOSIVE tree models relative to the DESIGN models, indicating that non-probabilistic sample surveys may generate models with limited predictive capability. These differences were consistent across all four lichen species, with 11 of the 12 possible species and sample survey type comparisons having significantly lower accuracy rates. Some differences in accuracy were as large as 50%. The classification tree structures also differed considerably both among and within the modelled species, depending on the sample survey form. Overlap in the predictor variables selected by the DESIGN and PURPOSIVE tree models ranged from only 20% to 38%, indicating the classification trees fit the two evaluated survey forms on different sets of predictor variables. The magnitude of these differences in predictor variables throws doubt on ecological interpretation derived from prediction models based on non-probabilistic sample surveys. ?? 2006 Elsevier B.V. All rights reserved.

  6. Chromosome comparison of 17 species / sub-species of African Goliathini (Coleoptera, Scarabaeidae, Cetoniinae)

    PubMed Central

    Dutrillaux, Anne-Marie; Dutrillaux, Bernard

    2016-01-01

    Abstract The mitotic karyotypes of 17 species of African Goliathini (Cetoniinae) are described using various chromosome banding techniques. All but one are composed of 20 chromosomes, mostly metacentric, forming a karyotype assumed to be close to that of the Polyphaga ancestor. The most derived karyotypes are those of Goliathus goliatus Drury, 1770, with eight pairs of acrocentrics and Chlorocana africana Drury, 1773, with only14 chromosomes. In species of the genera Cyprolais Burmeister, 1842, Megalorhina Westwood, 1847, Stephanocrates Kolbe, 1894 and Stephanorrhina Burmeister, 1842, large additions of variable heterochromatin are observed on both some particular autosomes and the X chromosome. Species of the genera Eudicella White, 1839 and Dicronorrhina Burmeister, 1842 share the same sub-metacentric X. Although each species possesses its own karyotype, it remains impossible to propose robust phylogenetic relationships on the basis of chromosome data only. PMID:27551348

  7. COMPARISON BETWEEN FOUR USUAL METHODS OF IDENTIFICATION OF Candida SPECIES

    PubMed Central

    SOUZA, Margarida Neves; ORTIZ, Stéfanie Otowicz; MELLO, Marcelo Martins; OLIVEIRA, Flávio de Mattos; SEVERO, Luiz Carlos; GOEBEL, Cristine Souza

    2015-01-01

    SUMMARY Infection by Candidaspp. is associated with high mortality rates, especially when treatment is not appropriate and/or not immediate. Therefore, it is necessary to correctly identify the genus and species of Candida. The aim of this study was to compare the identification of 89 samples of Candida spp. by the manual methods germ tube test, auxanogram and chromogenic medium in relation to the ID 32C automated method. The concordances between the methods in ascending order, measured by the Kappa index were: ID 32C with CHROMagar Candida(κ = 0.38), ID 32C with auxanogram (κ = 0.59) and ID 32C with germ tube (κ = 0.9). One of the species identified in this study was C. tropicalis,which demonstrated a sensitivity of 46.2%, a specificity of 95.2%, PPV of 80%, NPV of 81.1%, and an accuracy of 80.9% in tests performed with CHROMagar Candida;and a sensitivity of 76.9%, a specificity of 96.8%, PPV of 90.9%, NPV of 91%, and an accuracy of 91% in the auxanogram tests. Therefore, it is necessary to know the advantages and limitations of methods to choose the best combination between them for a fast and correct identification of Candidaspecies. PMID:26422150

  8. Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species

    PubMed Central

    Beltrao, Pedro; Trinidad, Jonathan C.; Fiedler, Dorothea; Roguev, Assen; Lim, Wendell A.; Shokat, Kevan M.; Burlingame, Alma L.; Krogan, Nevan J.

    2009-01-01

    The extent by which different cellular components generate phenotypic diversity is an ongoing debate in evolutionary biology that is yet to be addressed by quantitative comparative studies. We conducted an in vivo mass-spectrometry study of the phosphoproteomes of three yeast species (Saccharomyces cerevisiae, Candida albicans, and Schizosaccharomyces pombe) in order to quantify the evolutionary rate of change of phosphorylation. We estimate that kinase–substrate interactions change, at most, two orders of magnitude more slowly than transcription factor (TF)–promoter interactions. Our computational analysis linking kinases to putative substrates recapitulates known phosphoregulation events and provides putative evolutionary histories for the kinase regulation of protein complexes across 11 yeast species. To validate these trends, we used the E-MAP approach to analyze over 2,000 quantitative genetic interactions in S. cerevisiae and Sc. pombe, which demonstrated that protein kinases, and to a greater extent TFs, show lower than average conservation of genetic interactions. We propose therefore that protein kinases are an important source of phenotypic diversity. PMID:19547744

  9. Comparison of Frictional Heating Models

    SciTech Connect

    Davies, Nicholas R; Blau, Peter Julian

    2013-10-01

    The purpose of this work was to compare the predicted temperature rises using four well-known models for frictional heating under a few selected conditions in which similar variable inputs are provided to each model. Classic papers by Archard, Kuhlmann-Wilsdorf, Lim and Ashby, and Rabinowicz have been examined, and a spreadsheet (Excel ) was developed to facilitate the calculations. This report may be used in conjunction with that spreadsheet. It explains the background, assumptions, and rationale used for the calculations. Calculated flash temperatures for selected material combinations, under a range of applied loads and sliding speeds, are tabulated. The materials include AISI 52100 bearing steel, CDA 932 bronze, NBD 200 silicon nitride, Ti-6Al-4V alloy, and carbon-graphite material. Due to the assumptions made by the different models, and the direct way in which certain assumed quantities, like heat sink distances or asperity dimensions, enter into the calculations, frictional hearing results may differ significantly; however, they can be similar in certain cases in light of certain assumptions that are shared between the models.

  10. Independent Learning Models: A Comparison.

    ERIC Educational Resources Information Center

    Wickett, R. E. Y.

    Five models of independent learning are suitable for use in adult education programs. The common factor is a facilitator who works in some way with the student in the learning process. They display different characteristics, including the extent of independence in relation to content and/or process. Nondirective tutorial instruction and learning…

  11. Predicting fish species distribution in estuaries: Influence of species' ecology in model accuracy

    NASA Astrophysics Data System (ADS)

    França, Susana; Cabral, Henrique N.

    2016-10-01

    Current threats to biodiversity, combined with limited data availability, have made for species distribution models (SDMs) to be increasingly used due to their ability to predict species' potential distribution, by relating species occurrence with environmental estimates. Often used in ecology, conservation biology and environmental management, SDMs have been informing conservation strategies, and thus it is becoming crucial to understand how trustworthy their predictions are. Uncertainty in model predictions is expected, but knowing the origin of prediction errors may help reducing it. Indeed, uncertainty may be related not only with data quality and the modelling algorithm used, but also with species ecological characteristics. To investigate whether the performance of SDM's may vary with species' ecological characteristics, distribution models for 21 fish species occurring in estuaries from the Portuguese coast were examined. These models were built at two distinct spatial resolutions and seven environmental explanatory variables were used as predictors. SDMs' accuracy was assessed with the area under the curve (AUC) of receiver operating characteristics (ROC) plots, sensitivity and specificity. Relationships between each measure of accuracy and species ecological characteristics were then examined. SDMs of the fish species presented small differences between the considered scales, and predictors as latitude, temperature and salinity were often selected at both scales. Measures of model accuracy presented differences between species and scales, but generally higher accuracy was obtained at smaller spatial scales. Among the ecological traits tested, species feeding mode and estuarine use functional groups were the most influential on the performance of distribution models. Habitat tolerance (number of habitat types frequented), species abundance, body size and spawning period also showed some effect. This analyses will contribute to distinguish, based on species

  12. A double species model for study of relaxation of impure Ni 3Al grain boundaries

    NASA Astrophysics Data System (ADS)

    Zheng, Li-Ping; Ma, Yu-Gang; Han, Jia-Guang; Li, D. X.; Zhang, Xiu-Rong

    2004-04-01

    Based on the Monte Carlo simulation conjoined with the embedded atom method (EAM) potentials, the double species model is established to study relaxation of impure Ni 3Al grain boundaries. The present double species model suggests that the impure atoms are not only segregating species but also inducing species. The present model also suggests that study of combination of the positive (the impure atoms induce Ni atoms to substitute into Al sites) and the negative (the impure atoms substitute into Ni sites) bulk effects of impure atoms is available, in order to understand dependence of the cohesion of the impure Ni 3Al grain boundary (or the Ni enrichment at the impure Ni 3Al grain boundary) on the bulk concentration of impure atoms. The double species model is clarified in comparison between the Ni 3AlB and the Ni 3AlMg systems.

  13. Differential estrogen receptor binding of estrogenic substances: a species comparison.

    PubMed

    Matthews, J; Celius, T; Halgren, R; Zacharewski, T

    2000-11-15

    The study investigated the ability of 34 natural and synthetic chemicals to compete with [3H]17beta-estradiol (E2) for binding to bacterially expressed glutathione-S-transferase (GST)-estrogen receptors (ER) fusion proteins from five different species. Fusion proteins consisted of the ER D, E and F domains of human alpha (GST-hERalphadef), mouse alpha (GST-mERalphadef), chicken (GST-cERdef), green anole (GST-aERdef) and rainbow trout ERs (GST-rtERdef). All five fusion proteins displayed high affinity for E2 with dissociation constants (K(d)) ranging from 0.3 to 0.9 nM. Although, the fusion proteins exhibited similar binding preferences and binding affinities for many of the chemicals, several differences were observed. For example, alpha-zearalenol bound with greater affinity to GST-rtERdef than E2, which was in contrast to other GST-ERdef fusion proteins examined. Coumestrol, genistein and naringenin bound with higher affinity to the GST-aERdef, than to the other GST-ERdef fusion proteins. Many of the industrial chemicals examined preferentially bound to GST-rtERdef. Bisphenol A, 4-t-octylphenol and o,p' DDT bound with approximately a ten-fold greater affinity to GST-rtERdef than to other GST-ERdefs. Methoxychlor, p,p'-DDT, o,p'-DDE, p,p'-DDE, alpha-endosulfan and dieldrin weakly bound to the ERs from the human, mouse, chicken and green anole. In contrast, these compounds completely displaced [3H]E2 from GST-rtERdef. These results demonstrate that ERs from different species exhibit differential ligand preferences and relative binding affinities for estrogenic compounds and that these differences may be due to the variability in the amino acid sequence within their respective ER ligand binding domains. PMID:11162928

  14. Comparison of the volatile oil composition of three Atalantia species.

    PubMed

    Das, Arun K; Swamy, P S

    2013-05-01

    The members of the genus Atalantia belonging to the family Rutaceae have many uses in traditional medicine. The aim of the present study was to investigate and compare the chemical composition of essential oils of three species of Atalantia namely Atalantia monophylla (Roxb.) DC., Atalantia racemosa Wight. and Atalantia wightii Tanaka. The extract percentage of the obtained essential oil was found to be 0.2, 0.17 and 0.31% in A. monophylla, A. racemosa and A. wightii respectively. The major compounds identified were alpha-Asarone (28.82%), Sabinene (13.19%), Eugenol methyl ether (12.71%), 1,2-Dimethoxy-4-(2-methoxyethenyl)benzene (11.63%) and beta-Pinene (5.3%) in the essential oil of A. monophylla. In A. racemosa, T-Cadinol (11.08%), Caryophyllene oxide (9.78%), beta-Caryophyllene (9.20%), Spathulenol (7.21%), beta-Phellandrene (5.67%) and Decanal (4.01%) and in A. wightii beta-Caryophyllene (16.37%), D-Limnonene (12.15%), Decanal (10.49%), beta-Myrcene (7.67%), Tetradecanal (6.99%), Caryophyllene oxide (6.29%) and Hexadecylene oxide (5.87%) were the main constituents. Sesquiterpenes were the major class of compounds in A. racemosa and A. wightii, while in A. monophylla the essential oil was predominated by ether compounds. The results showed that GC/MS analysis of essential oils is a significant step in the bio-chemical profiling and bio-prospecting of Atalantia species. PMID:24617143

  15. Addressing potential local adaptation in species distribution models: implications for conservation under climate change.

    PubMed

    Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C; Hellmann, Jessica J

    2016-06-01

    Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate Max-Ent models, one considering the species as a single population and two of disjunct populations. Principal component analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species vs. population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered. PMID:27509755

  16. Addressing potential local adaptation in species distribution models: implications for conservation under climate change

    USGS Publications Warehouse

    Hällfors, Maria Helena; Liao, Jishan; Dzurisin, Jason D. K.; Grundel, Ralph; Hyvärinen, Marko; Towle, Kevin; Wu, Grace C.; Hellmann, Jessica J.

    2016-01-01

    Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat a species as a single entity, although populations of many species differ due to local adaptation or other genetic differentiation. Not taking local adaptation into account, may lead to incorrect range prediction and therefore misplaced conservation efforts. A constraint is that we often do not know the degree to which populations are locally adapted, however. Lacking experimental evidence, we still can evaluate niche differentiation within a species' range to promote better conservation decisions. We explore possible conservation implications of making type I or type II errors in this context. For each of two species, we construct three separate MaxEnt models, one considering the species as a single population and two of disjunct populations. PCA analyses and response curves indicate different climate characteristics in the current environments of the populations. Model projections into future climates indicate minimal overlap between areas predicted to be climatically suitable by the whole species versus population-based models. We present a workflow for addressing uncertainty surrounding local adaptation in SDM application and illustrate the value of conducting population-based models to compare with whole-species models. These comparisons might result in more cautious management actions when alternative range outcomes are considered.

  17. Nyala and Bushbuck I: A Competing Species Model.

    ERIC Educational Resources Information Center

    Fay, Temple H.; Greeff, Johanna C.

    1999-01-01

    Introduces a model of differential equations for students--a very real overpopulation problem is occurring in the Ndumu Game Reserve in KwaZulu-Natal, South Africa, where one species of antelope, the Nyala, is crowding out another species, the Bushbuck. Constructs a competing species model to mathematically describe what is occurring in Ndumu.…

  18. [A comparison of the superficial argentophilic structures of miracidia from 12 species of the genus Schistosoma].

    PubMed

    Albaret, J L

    1984-01-01

    Observation of miracidia of twelve species of Schistosoma shows the fundamental epidermal cell pattern is: 6, 9, 4, 3. Comparison of superficial argentophilic organites permits us: --to divide these species into three inequal groups: mansoni group: Schistosoma mansoni, S. rodhaini. haematobium group: S. haematobium, S. bovis, S. indicum , S. intercalatum, S. margrebowiei , S. mattheei, S. nasale and S. spindale . japonicum group: S. japonicum, S. incognitum . --to emphasize the relatively narrow specificity between members of each group and the snail-hosts. --to position the above species of Schistosoma within the Schistosomatoidea . Furthermore this character gives us some idea of the degree of evolution of species of Schistosoma. PMID:6721370

  19. Applications of species distribution modeling to paleobiology

    NASA Astrophysics Data System (ADS)

    Svenning, Jens-Christian; Fløjgaard, Camilla; Marske, Katharine A.; Nógues-Bravo, David; Normand, Signe

    2011-10-01

    Species distribution modeling (SDM: statistical and/or mechanistic approaches to the assessment of range determinants and prediction of species occurrence) offers new possibilities for estimating and studying past organism distributions. SDM complements fossil and genetic evidence by providing (i) quantitative and potentially high-resolution predictions of the past organism distributions, (ii) statistically formulated, testable ecological hypotheses regarding past distributions and communities, and (iii) statistical assessment of range determinants. In this article, we provide an overview of applications of SDM to paleobiology, outlining the methodology, reviewing SDM-based studies to paleobiology or at the interface of paleo- and neobiology, discussing assumptions and uncertainties as well as how to handle them, and providing a synthesis and outlook. Key methodological issues for SDM applications to paleobiology include predictor variables (types and properties; special emphasis is given to paleoclimate), model validation (particularly important given the emphasis on cross-temporal predictions in paleobiological applications), and the integration of SDM and genetics approaches. Over the last few years the number of studies using SDM to address paleobiology-related questions has increased considerably. While some of these studies only use SDM (23%), most combine them with genetically inferred patterns (49%), paleoecological records (22%), or both (6%). A large number of SDM-based studies have addressed the role of Pleistocene glacial refugia in biogeography and evolution, especially in Europe, but also in many other regions. SDM-based approaches are also beginning to contribute to a suite of other research questions, such as historical constraints on current distributions and diversity patterns, the end-Pleistocene megafaunal extinctions, past community assembly, human paleobiogeography, Holocene paleoecology, and even deep-time biogeography (notably, providing

  20. Sustainability in single-species population models.

    PubMed

    Quinn, Terrance J; Collie, Jeremy S

    2005-01-29

    In this paper, we review the concept of sustainability with regard to a single-species, age-structured fish population with density dependence at some stage of its life history. We trace the development of the view of sustainability through four periods. The classical view of sustainability, prevalent in the 1970s and earlier, developed from deterministic production models, in which equilibrium abundance or biomass is derived as a function of fishing mortality. When there is no fishing mortality, the population equilibrates about its carrying capacity. We show that carrying capacity is the result of reproductive and mortality processes and is not a fixed constant unless these processes are constant. There is usually a fishing mortality, F(MSY), which results in MSY, and a higher value, F(ext), for which the population is eventually driven to extinction. For each F between 0 and F(ext), there is a corresponding sustainable population. From this viewpoint, the primary tool for achieving sustainability is the control of fishing mortality. The neoclassical view of sustainability, developed in the 1980s, involved population models with depensation and stochasticity. This view point is in accord with the perception that a population at a low level is susceptible to collapse or to a lack of rebuilding regardless of fishing. Sustainability occurs in a more restricted range from that in the classical view and includes an abundance threshold. A variety of studies has suggested that fishing mortality should not let a population drop below a threshold at 10-20% of carrying capacity. The modern view of sustainability in the 1990s moves further in the direction of precaution. The fishing mortality limit is the former target of F(MSY) (or some proxy), and the target fishing mortality is set lower. This viewpoint further reduces the range of permissible fishing mortalities and resultant desired population sizes. The objective has shifted from optimizing long-term catch to

  1. Do stacked species distribution models reflect altitudinal diversity patterns?

    PubMed

    Mateo, Rubén G; Felicísimo, Ángel M; Pottier, Julien; Guisan, Antoine; Muñoz, Jesús

    2012-01-01

    The objective of this study was to evaluate the performance of stacked species distribution models in predicting the alpha and gamma species diversity patterns of two important plant clades along elevation in the Andes. We modelled the distribution of the species in the Anthurium genus (53 species) and the Bromeliaceae family (89 species) using six modelling techniques. We combined all of the predictions for the same species in ensemble models based on two different criteria: the average of the rescaled predictions by all techniques and the average of the best techniques. The rescaled predictions were then reclassified into binary predictions (presence/absence). By stacking either the original predictions or binary predictions for both ensemble procedures, we obtained four different species richness models per taxa. The gamma and alpha diversity per elevation band (500 m) was also computed. To evaluate the prediction abilities for the four predictions of species richness and gamma diversity, the models were compared with the real data along an elevation gradient that was independently compiled by specialists. Finally, we also tested whether our richness models performed better than a null model of altitudinal changes of diversity based on the literature. Stacking of the ensemble prediction of the individual species models generated richness models that proved to be well correlated with the observed alpha diversity richness patterns along elevation and with the gamma diversity derived from the literature. Overall, these models tend to overpredict species richness. The use of the ensemble predictions from the species models built with different techniques seems very promising for modelling of species assemblages. Stacking of the binary models reduced the over-prediction, although more research is needed. The randomisation test proved to be a promising method for testing the performance of the stacked models, but other implementations may still be developed. PMID

  2. Hydraulic fracture model comparison study: Complete results

    SciTech Connect

    Warpinski, N.R.; Abou-Sayed, I.S.; Moschovidis, Z.; Parker, C.

    1993-02-01

    Large quantities of natural gas exist in low permeability reservoirs throughout the US. Characteristics of these reservoirs, however, make production difficult and often economic and stimulation is required. Because of the diversity of application, hydraulic fracture design models must be able to account for widely varying rock properties, reservoir properties, in situ stresses, fracturing fluids, and proppant loads. As a result, fracture simulation has emerged as a highly complex endeavor that must be able to describe many different physical processes. The objective of this study was to develop a comparative study of hydraulic-fracture simulators in order to provide stimulation engineers with the necessary information to make rational decisions on the type of models most suited for their needs. This report compares the fracture modeling results of twelve different simulators, some of them run in different modes for eight separate design cases. Comparisons of length, width, height, net pressure, maximum width at the wellbore, average width at the wellbore, and average width in the fracture have been made, both for the final geometry and as a function of time. For the models in this study, differences in fracture length, height and width are often greater than a factor of two. In addition, several comparisons of the same model with different options show a large variability in model output depending upon the options chosen. Two comparisons were made of the same model run by different companies; in both cases the agreement was good. 41 refs., 54 figs., 83 tabs.

  3. Competition in the chemostat: A stochastic multi-species model and its asymptotic behavior.

    PubMed

    Xu, Chaoqun; Yuan, Sanling

    2016-10-01

    In this paper, a stochastic chemostat model in which n-species compete for a single growth-limiting substrate is considered. We first prove that the stochastic model has an unique global positive solution by using the comparison theorem for stochastic differential equations. Then we show that when the noise intensities are small, the competition outcome in the chemostat is completely determined by the species' stochastic break-even concentrations: the species with the lowest stochastic break-even concentration survives and all other species will go to extinction in the chemostat. In other words, the competitive exclusion principle holds for stochastic competition chemostat model when the noise intensities are small. Moreover, we find that noise may change the destiny of the species. Numerical simulations illustrate the obtained results. PMID:27474206

  4. Comparison and Characterization of Immunoglobulin G Subclasses among Primate Species

    PubMed Central

    Shearer, Michael H.; Dark, Robyn D.; Chodosh, James; Kennedy, Ronald C.

    1999-01-01

    Little information is available on the immunoglobulin G (IgG) subclasses expressed in the sera of nonhuman primate species. To address this issue, we compared the IgG subclasses found in humans (IgG1, IgG2, IgG3, and IgG4) to those of nonhuman primates, such as baboons and macaques. Cross-reactive antihuman IgG subtype-specific reagents were identified and used to analyze purified IgG from sera by solid-phase enzyme-linked immunosorbent assay. Protein A-purified human IgG obtained from sera was composed of IgG1, IgG2, IgG3, and IgG4, whereas baboon and macaque IgG was composed of IgG1, IgG2, and IgG4. Protein G-purified human IgG was composed of IgG1, IgG2, IgG3, and IgG4, whereas baboon and macaque IgG was composed of IgG1, IgG2, and IgG4. To test the possibility that baboon and macaque IgG3 is actually present, but is outcompeted for binding to proteins A and G by the other more abundant IgG subclasses, we repurified the IgG from sera that did not bind either protein A or protein G. We found a baboon IgG3 population in the sera that did not bind protein A, but bound protein G. No IgG3 subtype was detectable in macaque sera. These data suggest that baboon sera, like human sera, contain four IgG subtypes, whereas macaque sera exhibit only three of the human subclass analogs. In addition, the IgG subtype-specific reagents were shown to be useful in determining the IgG subclass distribution following vaccination of baboons with hepatitis B surface antigen. PMID:10548592

  5. Eleven-Species Thermochemical Model Of Air

    NASA Technical Reports Server (NTRS)

    Thompson, Richard A.; Lee, Kam-Pui; Gupta, Roop N.

    1992-01-01

    SPECIES program computes thermodynamic and transport properties and equilibrium constants. Uses least-squares polynomial curve fits of most accurate data available to provide requested values more quickly than table-lookup methods. Subroutines computing transport coefficients and collision cross sections include additional code to correct for any electron pressure when working with ionic species. Species represented: diatomic nitrogen, diatomic oxygen, atomic nitrogen, atomic oxygen, nitric oxide, ionized nitric oxide, free electron, ionized atomic nitrogen, ionized atomic oxygen, ionized diatomic nitrogen, and ionized diatomic oxygen. Written in FORTRAN 77.

  6. A comparison of crop and non-crop plants as sensitive indicator species for regulatory testing.

    PubMed

    McKelvey, Robert A; Wright, John P; Honegger, Joy L

    2002-12-01

    The effectiveness of regulatory non-target plant testing using crop species to predict the phytotoxicicity of herbicides to non-crop species was evaluated for eleven herbicides. These herbicides were representative of eight chemical classes and six modes of action. Data for non-crop plants from pre-emergence and post-emergence efficacy screening studies were compared with those for the most sensitive crop species defined by regulatory tests conducted to meet US EPA requirements. Testing under pre-emergence conditions for ten compounds indicated that for five of the compounds (K-815910, trifluralin, pyridyloxy A, pyridyloxy B and cyanazine), the most sensitive crop species was more sensitive than all the non-crop species evaluated. For metsulfuron-methyl, chlorimuron-ethyl, hexazinone and bromacil, only one of the non-crop species evaluated was more sensitive than the most sensitive crop species from regulatory tests. Data for the tenth compound, chloroacetamide, showed that four of 32 non-crop species tested in efficacy screens had at least one rate at which greater visual effects were observed than were observed for the most sensitive crop response in a regulatory test. The results of post-emergence exposure comparisons for five of the compounds (pyridyloxy A, cloransulam-methyl, chlorimuron-ethyl, cyanazine and hexazinone) indicated that the most sensitive crop species were more sensitive than all the non-crop species evaluated. Data for pyridyloxy B, metsulfuron-methyl and bromacil indicated that only one of the non-crop species evaluated was more sensitive than the most sensitive crop species. For trifluralin, three of the eight non-crop species were more sensitive than the most sensitive crop species. Data for K-815910 indicated that four of the fourteen non-crop species tested were marginally more sensitive than the most sensitive crop, but were within the same range of sensitivity. These results indicate that the current regulatory test batteries and methods

  7. Global attractivity of an almost periodic N-species nonlinear ecological competitive model

    NASA Astrophysics Data System (ADS)

    Xia, Yonghui; Han, Maoan; Huang, Zhenkun

    2008-01-01

    By using comparison theorem and constructing suitable Lyapunov functional, we study the following almost periodic nonlinear N-species competitive Lotka-Volterra model: A set of sufficient conditions is obtained for the existence and global attractivity of a unique positive almost periodic solution of the above model. As applications, some special competition models are studied again, our new results improve and generalize former results. Examples and their simulations show the feasibility of our main results.

  8. Model Comparison for Electron Thermal Transport

    NASA Astrophysics Data System (ADS)

    Moses, Gregory; Chenhall, Jeffrey; Cao, Duc; Delettrez, Jacques

    2015-11-01

    Four electron thermal transport models are compared for their ability to accurately and efficiently model non-local behavior in ICF simulations. Goncharov's transport model has accurately predicted shock timing in implosion simulations but is computationally slow and limited to 1D. The iSNB (implicit Schurtz Nicolai Busquet electron thermal transport method of Cao et al. uses multigroup diffusion to speed up the calculation. Chenhall has expanded upon the iSNB diffusion model to a higher order simplified P3 approximation and a Monte Carlo transport model, to bridge the gap between the iSNB and Goncharov models while maintaining computational efficiency. Comparisons of the above models for several test problems will be presented. This work was supported by Sandia National Laboratory - Albuquerque and the University of Rochester Laboratory for Laser Energetics.

  9. A Comparison of the Recruitment Success of Introduced and Native Species Under Natural Conditions

    PubMed Central

    Flores-Moreno, Habacuc; Moles, Angela T.

    2013-01-01

    It is commonly accepted that introduced species have recruitment advantages over native species. However, this idea has not been widely tested, and those studies that have compared survival of introduced and native species have produced mixed results. We compiled data from the literature on survival through germination (seed to seedling survival), early seedling survival (survival through one week from seedling emergence) and survival to adulthood (survival from germination to first reproduction) under natural conditions for 285 native and 63 introduced species. Contrary to expectations, we found that introduced and native species do not significantly differ in survival through germination, early seedling survival, or survival from germination to first reproduction. These comparisons remained non-significant after accounting for seed mass, longevity and when including a random effect for site. Results remained consistent after excluding naturalized species from the introduced species data set, after performing phylogenetic independent contrasts, and after accounting for the effect of life form (woody/non-woody). Although introduced species sometimes do have advantages over native species (for example, through enemy release, or greater phenotypic plasticity), our findings suggest that the overall advantage conferred by these factors is either counterbalanced by advantages of native species (such as superior adaptation to local conditions) or is simply too small to be detected at a broad scale. PMID:23951326

  10. [Caucasian cryptic species of rodents as models for studying the problem of species and speciation].

    PubMed

    Baskevich, M I; Potapov, S G; Mironova, T A

    2015-01-01

    The problem of species and speciation is considered using as a model the cryptic species of rodents inhabiting the Caucasus, the mountain chain with prominent altitude environmental gradient and insular pattern of mountain habitats. These circumstances open additional possibilities for the choice of species conception (biological or phylogenetic), exploration of ancestry pathways (sympatric or allopatric speciation) of model cryptic species groups, and testing the 'refuge' hypothesis. As model species, sibling-species Sicista from the group 'caucasica' (a group of unstriped birch mice) and representatives of the vole subspecies Terricola (Microtus, Arvicolinae) were used. Based on the new data on karyology, nucleotide sequences of mitochondrial gene cytb, multivariate statistical analysis of odontologic traits, and biogeography of sibling-species Sicista from the group 'caucasica' and voles from subspecies Terricola (Microtus, Arvicolinae), their evolutionary history is reconstructed and applicable species concepts are examined. For the present sibling-species Sicista from the group 'caucasica' the allopatric dispersion is typical, which agrees with the hypothesis of speciation in refuges. The sympatry of Terricola sibling-species in the Caucasus is considered as being secondary, and their phenotypic likeness--as an adaptation to similar environmental conditions. Affirmed coexistence of sibling-species Microtus (Terricola) majori and Microtus (Terricola) daghestanicus in the Caucasus (without their hybridization) supports the biological conception of species. The existence of Sicista allospecies from the group of Caucasian unstriped birch mice is best conformed to the phylogenetic conception. However, the high level of chromosomal differences between sibling-species and, in particular, between extreme variants of common evolutionary line (Sicista kazbegica, Sicista kluchorica) does not contradict the biological conception of species. PMID:26353399

  11. Evolution of species from Darwin theory: A simple model

    NASA Astrophysics Data System (ADS)

    Moret, M. A.; Pereira, H. B. B.; Monteiro, S. L.; Galeão, A. C.

    2012-04-01

    Evolution of species is a complex phenomenon. Some theoretical models take into account evolution of species, like the Bak-Sneppen model that obtain punctuated equilibrium from self-organized criticality and the Penna model for biological aging that consists in a bit-string model subjected to aging, reproduction and death. In this work we propose a simple model to study different scenarios used to simulate the evolution of species. This model is based on Darwin's ideas of evolution. The present findings show that punctuated equilibria and stasis seem to be obtained directly from the mutation, selection of parents and the genetic crossover, and are very close to the fossil data analysis.

  12. Middle Atmosphere Program. Handbook for MAP. Volume 31: Reference models of trace species for the COSPAR international reference atmosphere

    NASA Technical Reports Server (NTRS)

    Keating, G. M. (Editor)

    1989-01-01

    A set of preliminary reference atmosphere models of significant trace species which play important roles in controlling the chemistry, radiation budget, and circulation patterns of the atmosphere were produced. These models of trace species distributions are considered to be reference models rather than standard models; thus, it was not crucial that they be correct in an absolute sense. These reference models can serve as a means of comparison between individual observations, as a first guess in inversion algorithms, and as an approximate representation of observations for comparison to theoretical calculations.

  13. Model Comparison of Nonlinear Structural Equation Models with Fixed Covariates.

    ERIC Educational Resources Information Center

    Lee, Sik-Yum; Song, Xin-Yuan

    2003-01-01

    Proposed a new nonlinear structural equation model with fixed covariates to deal with some complicated substantive theory and developed a Bayesian path sampling procedure for model comparison. Illustrated the approach with an illustrative example using data from an international study. (SLD)

  14. Richards-like two species population dynamics model.

    PubMed

    Ribeiro, Fabiano; Cabella, Brenno Caetano Troca; Martinez, Alexandre Souto

    2014-12-01

    The two-species population dynamics model is the simplest paradigm of inter- and intra-species interaction. Here, we present a generalized Lotka-Volterra model with intraspecific competition, which retrieves as particular cases, some well-known models. The generalization parameter is related to the species habitat dimensionality and their interaction range. Contrary to standard models, the species coupling parameters are general, not restricted to non-negative values. Therefore, they may represent different ecological regimes, which are derived from the asymptotic solution stability analysis and are represented in a phase diagram. In this diagram, we have identified a forbidden region in the mutualism regime, and a survival/extinction transition with dependence on initial conditions for the competition regime. Also, we shed light on two types of predation and competition: weak, if there are species coexistence, or strong, if at least one species is extinguished. PMID:25112794

  15. Species diversity and predation strategies in a multiple species predator-prey model

    NASA Astrophysics Data System (ADS)

    Mullan, Rory; Glass, David H.; McCartney, Mark

    2015-08-01

    A single predator, single prey ecological model, in which the behaviour of the populations relies upon two control parameters has been expanded to allow for multiple predators and prey to occupy the ecosystem. The diversity of the ecosystem that develops as the model runs is analysed by assessing how many predator or prey species survive. Predation strategies that dictate how the predators distribute their efforts across the prey are introduced in this multiple species model. The paper analyses various predation strategies and highlights their effect on the survival of the predators and prey species.

  16. Infusing considerations of trophic dependencies into species distribution modelling.

    PubMed

    Trainor, Anne M; Schmitz, Oswald J

    2014-12-01

    Community ecology involves studying the interdependence of species with each other and their environment to predict their geographical distribution and abundance. Modern species distribution analyses characterise species-environment dependency well, but offer only crude approximations of species interdependency. Typically, the dependency between focal species and other species is characterised using other species' point occurrences as spatial covariates to constrain the focal species' predicted range. This implicitly assumes that the strength of interdependency is homogeneous across space, which is not generally supported by analyses of species interactions. This discrepancy has an important bearing on the accuracy of inferences about habitat suitability for species. We introduce a framework that integrates principles from consumer-resource analyses, resource selection theory and species distribution modelling to enhance quantitative prediction of species geographical distributions. We show how to apply the framework using a case study of lynx and snowshoe hare interactions with each other and their environment. The analysis shows how the framework offers a spatially refined understanding of species distribution that is sensitive to nuances in biophysical attributes of the environment that determine the location and strength of species interactions. PMID:25250672

  17. Marginal Likelihood Estimate Comparisons to Obtain Optimal Species Delimitations in Silene sect. Cryptoneurae (Caryophyllaceae)

    PubMed Central

    Aydin, Zeynep; Marcussen, Thomas; Ertekin, Alaattin Selcuk; Oxelman, Bengt

    2014-01-01

    Coalescent-based inference of phylogenetic relationships among species takes into account gene tree incongruence due to incomplete lineage sorting, but for such methods to make sense species have to be correctly delimited. Because alternative assignments of individuals to species result in different parametric models, model selection methods can be applied to optimise model of species classification. In a Bayesian framework, Bayes factors (BF), based on marginal likelihood estimates, can be used to test a range of possible classifications for the group under study. Here, we explore BF and the Akaike Information Criterion (AIC) to discriminate between different species classifications in the flowering plant lineage Silene sect. Cryptoneurae (Caryophyllaceae). We estimated marginal likelihoods for different species classification models via the Path Sampling (PS), Stepping Stone sampling (SS), and Harmonic Mean Estimator (HME) methods implemented in BEAST. To select among alternative species classification models a posterior simulation-based analog of the AIC through Markov chain Monte Carlo analysis (AICM) was also performed. The results are compared to outcomes from the software BP&P. Our results agree with another recent study that marginal likelihood estimates from PS and SS methods are useful for comparing different species classifications, and strongly support the recognition of the newly described species S. ertekinii. PMID:25216034

  18. Modeling Emergent Macrophyte Distributions: Including Sub-dominant Species

    EPA Science Inventory

    Mixed stands of emergent vegetation are often present following drawdowns but models of wetland plant distributions fail to include subdominant species when predicting distributions. Three variations of a spatial plant distribution cellular automaton model were developed to explo...

  19. Comparisons of Air Radiation Model with Shock Tube Measurements

    NASA Technical Reports Server (NTRS)

    Bose, Deepak; McCorkle, Evan; Bogdanoff, David W.; Allen, Gary A., Jr.

    2009-01-01

    This paper presents an assessment of the predictive capability of shock layer radiation model appropriate for NASA s Orion Crew Exploration Vehicle lunar return entry. A detailed set of spectrally resolved radiation intensity comparisons are made with recently conducted tests in the Electric Arc Shock Tube (EAST) facility at NASA Ames Research Center. The spectral range spanned from vacuum ultraviolet wavelength of 115 nm to infrared wavelength of 1400 nm. The analysis is done for 9.5-10.5 km/s shock passing through room temperature synthetic air at 0.2, 0.3 and 0.7 Torr. The comparisons between model and measurements show discrepancies in the level of background continuum radiation and intensities of atomic lines. Impurities in the EAST facility in the form of carbon bearing species are also modeled to estimate the level of contaminants and their impact on the comparisons. The discrepancies, although large is some cases, exhibit order and consistency. A set of tests and analyses improvements are proposed as forward work plan in order to confirm or reject various proposed reasons for the observed discrepancies.

  20. Projecting future expansion of invasive species: comparing and improving methodologies for species distribution modeling.

    PubMed

    Mainali, Kumar P; Warren, Dan L; Dhileepan, Kunjithapatham; McConnachie, Andrew; Strathie, Lorraine; Hassan, Gul; Karki, Debendra; Shrestha, Bharat B; Parmesan, Camille

    2015-12-01

    Modeling the distributions of species, especially of invasive species in non-native ranges, involves multiple challenges. Here, we developed some novel approaches to species distribution modeling aimed at reducing the influences of such challenges and improving the realism of projections. We estimated species-environment relationships for Parthenium hysterophorus L. (Asteraceae) with four modeling methods run with multiple scenarios of (i) sources of occurrences and geographically isolated background ranges for absences, (ii) approaches to drawing background (absence) points, and (iii) alternate sets of predictor variables. We further tested various quantitative metrics of model evaluation against biological insight. Model projections were very sensitive to the choice of training dataset. Model accuracy was much improved using a global dataset for model training, rather than restricting data input to the species' native range. AUC score was a poor metric for model evaluation and, if used alone, was not a useful criterion for assessing model performance. Projections away from the sampled space (i.e., into areas of potential future invasion) were very different depending on the modeling methods used, raising questions about the reliability of ensemble projections. Generalized linear models gave very unrealistic projections far away from the training region. Models that efficiently fit the dominant pattern, but exclude highly local patterns in the dataset and capture interactions as they appear in data (e.g., boosted regression trees), improved generalization of the models. Biological knowledge of the species and its distribution was important in refining choices about the best set of projections. A post hoc test conducted on a new Parthenium dataset from Nepal validated excellent predictive performance of our 'best' model. We showed that vast stretches of currently uninvaded geographic areas on multiple continents harbor highly suitable habitats for parthenium

  1. Inter-species variation in yolk steroid levels and a cowbird-host comparison

    USGS Publications Warehouse

    Hahn, D.C.; Hatfield, J.S.; Abdelnabi, M.A.; Wu, J.M.; Igl, L.D.; Ottinger, M.A.

    2005-01-01

    We examined variability in yolk hormone levels among songbird species and the role of yolk steroids as a mechanism for enhanced exploitation of hosts by the parasitic brown-headed cowbird Molothrus ater. Within-clutch variation in yolk steroids has been found in several avian species in single species studies, but few comparisons have been made among species. We found a large range of differences in yolk testosterone among the seven passerine species examined, with significant differences between those at the high end (song sparrow Melospiza melodia, red-winged blackbird Agelaius phoeniceus, and house sparrow, Passer domesticus) and those at the low end (eastern phoebe Sayornis phoebe, and house finch Carpodacus mexicanus). We also found that the testosterone level in cowbird eggs was intermediate in relation to host species levels and was significantly lower than that in three common cowbird hosts (song sparrow, red-winged blackbird, and house sparrow), but not significantly different from three others. Geographical comparisons of yolk testosterone levels in all cowbird subspecies and populations from several regions showed no significant differences, though a trend that deserves further exploration was the pattern of lowest level in the ancestral population of cowbirds in the central prairies and of highest level in the northwestern population where range invasion occurred approximately 40 years ago. The levels of 17 beta-estradiol were similar in the seven songbird species examined, which is consistent with current hypotheses that this hormone plays a role in embryonic sexual differentiation. Further investigation is needed to determine whether the large differences observed among species in absolute level of yolk testosterone are the relevant focal point or whether target tissue sensitivity differences mediate the effects of this yolk steroid, particularly between parasitic and non-parasitic species.

  2. Inter-species variation in yolk steroid levels and a cowbird-host comparison

    USGS Publications Warehouse

    Hahn, D.C.; Hatfield, J.S.; Abdelnabi, M.; Wu, J.; Igl, L.D.; Ottinger, M.A.

    2005-01-01

    We examined variability in yolk hormone levels among songbird species and the role of yolk steroids as a mechanism for enhanced exploitation of hosts by the parasitic Brown-headed Cowbird Molothrus ater. Within-clutch variation in yolk steroids has been found in several avian species in single species studies, but few comparisons have been made among species. We found a large range of differences in yolk testosterone among the seven passerine species examined, with significant differences between those at the high end (Song Sparrow Melospiza melodia , Red-winged Blackbird Agelaius phoeniceus, and House Sparrow, Passer domesticus ) and those at the low end (Eastern Phoebe Sayornis phoebe, and House Finch Carpodacus mexicanus ). We also found that the testosterone level in cowbird eggs was intermediate in relation to host species levels and was significantly lower than that in three common cowbird hosts (Song Sparrow, Red-winged Blackbird, and House Sparrow), but not significantly different from three others. Geographical comparisons of yolk testosterone levels in all cowbird subspecies and populations from several regions showed no significant differences, though a trend that deserves further exploration was the pattern of lowest level in the ancestral population of cowbirds in the central prairies and of highest level in the northwestern population where range invasion occurred approximately 40 years ago. The levels of 17 betaestradiol were similar in the seven songbird species examined, which is consistent with current hypotheses that this hormone plays a role in embryonic sexual differentiation. Further investigation is needed to determine whether the large differences observed among species in absolute level of yolk testosterone are the relevant focal point or whether target tissue sensitivity differences mediate the effects of this yolk steroid, particularly between parasitic and non-parasitic species.

  3. GCSS Idealized Cirrus Model Comparison Project

    NASA Technical Reports Server (NTRS)

    Starr, David OC.; Benedetti, Angela; Boehm, Matt; Brown, Philip R. A.; Gierens, Klaus; Girard, Eric; Giraud, Vincent; Jakob, Christian; Jensen, Eric; Khvorostyanov, Vitaly; Einaudi, Franco (Technical Monitor)

    2000-01-01

    The GCSS Working Group on Cirrus Cloud Systems (WG2) is conducting a systematic comparison and evaluation of cirrus cloud models. This fundamental activity seeks to support the improvement of models used for climate simulation and numerical weather prediction through assessment and improvement of the "process" models underlying parametric treatments of cirrus cloud processes in large-scale models. The WG2 Idealized Cirrus Model Comparison Project is an initial comparison of cirrus cloud simulations by a variety of cloud models for a series of idealized situations with relatively simple initial conditions and forcing. The models (16) represent the state-of-the-art and include 3-dimensional large eddy simulation (LES) models, two-dimensional cloud resolving models (CRMs), and single column model (SCM) versions of GCMs. The model microphysical components are similarly varied, ranging from single-moment bulk (relative humidity) schemes to fully size-resolved (bin) treatments where ice crystal growth is explicitly calculated. Radiative processes are included in the physics package of each model. The baseline simulations include "warm" and "cold" cirrus cases where cloud top initially occurs at about -47C and -66C, respectively. All simulations are for nighttime conditions (no solar radiation) where the cloud is generated in an ice supersaturated layer, about 1 km in depth, with an ice pseudoadiabatic thermal stratification (neutral). Continuing cloud formation is forced via an imposed diabatic cooling representing a 3 cm/s uplift over a 4-hour time span followed by a 2-hour dissipation stage with no cooling. Variations of these baseline cases include no-radiation and stable-thermal-stratification cases. Preliminary results indicated the great importance of ice crystal fallout in determining even the gross cloud characteristics, such as average vertically-integrated ice water path (IWP). Significant inter-model differences were found. Ice water fall speed is directly

  4. Modeling Considerations for Using Expression Data from Multiple Species

    PubMed Central

    Siewert, Elizabeth; Kechris, Katerina J.

    2016-01-01

    Although genome-wide expression data sets from multiple species are now more commonly generated, there have been few studies on how to best integrate this type of correlated data into models. Starting with a single-species, linear regression model that predicts transcription factor binding sites as a case study, we investigated how best to take into account the correlated expression data when extending this model to multiple species. Using a multivariate regression model, the phylogenetic relationships among the species were accounted for in two ways: 1) a repeated-measures model, where the error term is constrained, and 2) a Bayesian hierarchical model, where the prior distributions of the regression coefficients are constrained. We show that both multiple-species models improve predictive performance over the single-species model. When compared with each other, the repeated-measures model out-performed the Bayesian model. We suggest a possible explanation for the better performance of the model with the constrained error term. PMID:23703923

  5. Integrating species distribution models (SDMs) and phylogeography for two species of Alpine Primula

    PubMed Central

    Schorr, G; Holstein, N; Pearman, P B; Guisan, A; Kadereit, J W

    2012-01-01

    The major intention of the present study was to investigate whether an approach combining the use of niche-based palaeodistribution modeling and phylo-geography would support or modify hypotheses about the Quaternary distributional history derived from phylogeographic methods alone. Our study system comprised two closely related species of Alpine Primula. We used species distribution models based on the extant distribution of the species and last glacial maximum (LGM) climate models to predict the distribution of the two species during the LGM. Phylogeographic data were generated using amplified fragment length polymorphisms (AFLPs). In Primula hirsuta, models of past distribution and phylogeographic data are partly congruent and support the hypothesis of widespread nunatak survival in the Central Alps. Species distribution models (SDMs) allowed us to differentiate between alpine regions that harbor potential nunatak areas and regions that have been colonized from other areas. SDMs revealed that diversity is a good indicator for nunataks, while rarity is a good indicator for peripheral relict populations that were not source for the recolonization of the inner Alps. In P. daonensis, palaeo-distribution models and phylogeographic data are incongruent. Besides the uncertainty inherent to this type of modeling approach (e.g., relatively coarse 1-km grain size), disagreement of models and data may partly be caused by shifts of ecological niche in both species. Nevertheless, we demonstrate that the combination of palaeo-distribution modeling with phylogeographical approaches provides a more differentiated picture of the distributional history of species and partly supports (P. hirsuta) and partly modifies (P. daonensis and P. hirsuta) hypotheses of Quaternary distributional history. Some of the refugial area indicated by palaeodistribution models could not have been identified with phylogeographic data. PMID:22833799

  6. Integrating species distribution models (SDMs) and phylogeography for two species of Alpine Primula.

    PubMed

    Schorr, G; Holstein, N; Pearman, P B; Guisan, A; Kadereit, J W

    2012-06-01

    The major intention of the present study was to investigate whether an approach combining the use of niche-based palaeodistribution modeling and phylo-geography would support or modify hypotheses about the Quaternary distributional history derived from phylogeographic methods alone. Our study system comprised two closely related species of Alpine Primula. We used species distribution models based on the extant distribution of the species and last glacial maximum (LGM) climate models to predict the distribution of the two species during the LGM. Phylogeographic data were generated using amplified fragment length polymorphisms (AFLPs). In Primula hirsuta, models of past distribution and phylogeographic data are partly congruent and support the hypothesis of widespread nunatak survival in the Central Alps. Species distribution models (SDMs) allowed us to differentiate between alpine regions that harbor potential nunatak areas and regions that have been colonized from other areas. SDMs revealed that diversity is a good indicator for nunataks, while rarity is a good indicator for peripheral relict populations that were not source for the recolonization of the inner Alps. In P. daonensis, palaeo-distribution models and phylogeographic data are incongruent. Besides the uncertainty inherent to this type of modeling approach (e.g., relatively coarse 1-km grain size), disagreement of models and data may partly be caused by shifts of ecological niche in both species. Nevertheless, we demonstrate that the combination of palaeo-distribution modeling with phylogeographical approaches provides a more differentiated picture of the distributional history of species and partly supports (P. hirsuta) and partly modifies (P. daonensis and P. hirsuta) hypotheses of Quaternary distributional history. Some of the refugial area indicated by palaeodistribution models could not have been identified with phylogeographic data. PMID:22833799

  7. Using spatiotemporal species distribution models to identify temporally evolving hotspots of species co-occurrence.

    PubMed

    Ward, Eric J; Jannot, Jason E; Lee, Yong-Woo; Ono, Kotaro; Shelton, Andrew O; Thorson, James T

    2015-12-01

    Identifying spatiotemporal hotspots is important for understanding basic ecological processes, but is particularly important for species at risk. A number of terrestrial and aquatic species are indirectly affected by anthropogenic impacts, simply because they tend to be associated with species that are targeted for removals. Using newly developed statistical models that allow for the inclusion of time-varying spatial effects, we examine how the co-occurrence of a targeted and nontargeted species can be modeled as a function of environmental covariates (temperature, depth) and interannual variability. The nontarget species in our case study (eulachon) is listed under the U.S. Endangered Species Act, and is encountered by fisheries off the U.S. West Coast that target pink shrimp. Results from our spatiotemporal model indicated that eulachon bycatch risk decreases with depth and has a convex relationship with sea surface temperature. Additionally, we found that over the 2007-2012 period, there was support for an increase in eulachon density from both a fishery data set (+40%) and a fishery-independent data set (+55%). Eulachon bycatch has increased in recent years, but the agreement between these two data sets implies that increases in bycatch are not due to an increase in incidental targeting of eulachon by fishing vessels, but because of an increasing population size of eulachon. Based on our results, the application of spatiotemporal models to species that are of conservation concern appears promising in identifying the spatial distribution of environmental and anthropogenic risks to the population. PMID:26910949

  8. Cirrus Parcel Model Comparison Project. Phase 1

    NASA Technical Reports Server (NTRS)

    Lin, Ruei-Fong; Starr, David O'C.; DeMott, Paul J.; Cotton, Richard; Jensen, Eric; Sassen, Kenneth

    2000-01-01

    The Cirrus Parcel Model Comparison (CPMC) is a project of the GEWEX Cloud System Study Working Group on Cirrus Cloud Systems (GCSS WG2). The primary goal of this project is to identify cirrus model sensitivities to the state of our knowledge of nucleation and microphysics. Furthermore, the common ground of the findings may provide guidelines for models with simpler cirrus microphysics modules. We focus on the nucleation regimes of the warm (parcel starting at -40 C and 340 hPa) and cold (-60 C and 170 hPa) cases studied in the GCSS WG2 Idealized Cirrus Model Comparison Project. Nucleation and ice crystal growth were forced through an externally imposed rate of lift and consequent adiabatic cooling. The background haze particles are assumed to be lognormally-distributed H2SO4 particles. Only the homogeneous nucleation mode is allowed to form ice crystals in the HN-ONLY runs; all nucleation modes are switched on in the ALL-MODE runs. Participants were asked to run the HN-lambda-fixed runs by setting lambda = 2 (lambda is further discussed in section 2) or tailoring the nucleation rate calculation in agreement with lambda = 2 (exp 1). The depth of parcel lift (800 m) was set to assure that parcels underwent complete transition through the nucleation regime to a stage of approximate equilibrium between ice mass growth and vapor supplied by the specified updrafts.

  9. Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons

    NASA Technical Reports Server (NTRS)

    Armstrong, T. W.; Colborn, B. L.

    2000-01-01

    The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP, LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir Space Station. This report gives the details of the model-data comparisons-summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a combination report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian-trapped radiation models.

  10. Trapped Radiation Model Uncertainties: Model-Data and Model-Model Comparisons

    NASA Technical Reports Server (NTRS)

    Armstrong, T. W.; Colborn, B. L.

    2000-01-01

    The standard AP8 and AE8 models for predicting trapped proton and electron environments have been compared with several sets of flight data to evaluate model uncertainties. Model comparisons are made with flux and dose measurements made on various U.S. low-Earth orbit satellites (APEX, CRRES, DMSP. LDEF, NOAA) and Space Shuttle flights, on Russian satellites (Photon-8, Cosmos-1887, Cosmos-2044), and on the Russian Mir space station. This report gives the details of the model-data comparisons -- summary results in terms of empirical model uncertainty factors that can be applied for spacecraft design applications are given in a companion report. The results of model-model comparisons are also presented from standard AP8 and AE8 model predictions compared with the European Space Agency versions of AP8 and AE8 and with Russian trapped radiation models.

  11. SPECIES - EVALUATING THERMODYNAMIC PROPERTIES, TRANSPORT PROPERTIES & EQUILIBRIUM CONSTANTS OF AN 11-SPECIES AIR MODEL

    NASA Technical Reports Server (NTRS)

    Thompson, R. A.

    1994-01-01

    Accurate numerical prediction of high-temperature, chemically reacting flowfields requires a knowledge of the physical properties and reaction kinetics for the species involved in the reacting gas mixture. Assuming an 11-species air model at temperatures below 30,000 degrees Kelvin, SPECIES (Computer Codes for the Evaluation of Thermodynamic Properties, Transport Properties, and Equilibrium Constants of an 11-Species Air Model) computes values for the species thermodynamic and transport properties, diffusion coefficients and collision cross sections for any combination of the eleven species, and reaction rates for the twenty reactions normally occurring. The species represented in the model are diatomic nitrogen, diatomic oxygen, atomic nitrogen, atomic oxygen, nitric oxide, ionized nitric oxide, the free electron, ionized atomic nitrogen, ionized atomic oxygen, ionized diatomic nitrogen, and ionized diatomic oxygen. Sixteen subroutines compute the following properties for both a single species, interaction pair, or reaction, and an array of all species, pairs, or reactions: species specific heat and static enthalpy, species viscosity, species frozen thermal conductivity, diffusion coefficient, collision cross section (OMEGA 1,1), collision cross section (OMEGA 2,2), collision cross section ratio, and equilibrium constant. The program uses least squares polynomial curve-fits of the most accurate data believed available to provide the requested values more quickly than is possible with table look-up methods. The subroutines for computing transport coefficients and collision cross sections use additional code to correct for any electron pressure when working with ionic species. SPECIES was developed on a SUN 3/280 computer running the SunOS 3.5 operating system. It is written in standard FORTRAN 77 for use on any machine, and requires roughly 92K memory. The standard distribution medium for SPECIES is a 5.25 inch 360K MS-DOS format diskette. The contents of the

  12. Legume Diversity Patterns in West Central Africa: Influence of Species Biology on Distribution Models

    PubMed Central

    de la Estrella, Manuel; Mateo, Rubén G.; Wieringa, Jan J.; Mackinder, Barbara; Muñoz, Jesús

    2012-01-01

    Objectives Species Distribution Models (SDMs) are used to produce predictions of potential Leguminosae diversity in West Central Africa. Those predictions are evaluated subsequently using expert opinion. The established methodology of combining all SDMs is refined to assess species diversity within five defined vegetation types. Potential species diversity is thus predicted for each vegetation type respectively. The primary aim of the new methodology is to define, in more detail, areas of species richness for conservation planning. Methodology Using Maxent, SDMs based on a suite of 14 environmental predictors were generated for 185 West Central African Leguminosae species, each categorised according to one of five vegetation types: Afromontane, coastal, non-flooded forest, open formations, or riverine forest. The relative contribution of each environmental variable was compared between different vegetation types using a nonparametric Kruskal-Wallis analysis followed by a post-hoc Kruskal-Wallis Paired Comparison contrast. Legume species diversity patterns were explored initially using the typical method of stacking all SDMs. Subsequently, five different ensemble models were generated by partitioning SDMs according to vegetation category. Ecological modelers worked with legume specialists to improve data integrity and integrate expert opinion in the interpretation of individual species models and potential species richness predictions for different vegetation types. Results/Conclusions Of the 14 environmental predictors used, five showed no difference in their relative contribution to the different vegetation models. Of the nine discriminating variables, the majority were related to temperature variation. The set of variables that played a major role in the Afromontane species diversity model differed significantly from the sets of variables of greatest relative important in other vegetation categories. The traditional approach of stacking all SDMs indicated overall

  13. Comparison of Photovoltaic Models in the System Advisor Model: Preprint

    SciTech Connect

    Blair, N. J.; Dobos, A. P.; Gilman, P.

    2013-08-01

    The System Advisor Model (SAM) is free software developed by the National Renewable Energy Laboratory (NREL) for predicting the performance of renewable energy systems and analyzing the financial feasibility of residential, commercial, and utility-scale grid-connected projects. SAM offers several options for predicting the performance of photovoltaic (PV) systems. The model requires that the analyst choose from three PV system models, and depending on that choice, possibly choose from three module and two inverter component models. To obtain meaningful results from SAM, the analyst must be aware of the differences between the model options and their applicability to different modeling scenarios. This paper presents an overview the different PV model options and presents a comparison of results for a 200-kW system using different model options.

  14. The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species.

    PubMed

    Rougier, Thibaud; Lassalle, Géraldine; Drouineau, Hilaire; Dumoulin, Nicolas; Faure, Thierry; Deffuant, Guillaume; Rochard, Eric; Lambert, Patrick

    2015-01-01

    Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold

  15. The Combined Use of Correlative and Mechanistic Species Distribution Models Benefits Low Conservation Status Species

    PubMed Central

    Rougier, Thibaud; Lassalle, Géraldine; Drouineau, Hilaire; Dumoulin, Nicolas; Faure, Thierry; Deffuant, Guillaume; Rochard, Eric; Lambert, Patrick

    2015-01-01

    Species can respond to climate change by tracking appropriate environmental conditions in space, resulting in a range shift. Species Distribution Models (SDMs) can help forecast such range shift responses. For few species, both correlative and mechanistic SDMs were built, but allis shad (Alosa alosa), an endangered anadromous fish species, is one of them. The main purpose of this study was to provide a framework for joint analyses of correlative and mechanistic SDMs projections in order to strengthen conservation measures for species of conservation concern. Guidelines for joint representation and subsequent interpretation of models outputs were defined and applied. The present joint analysis was based on the novel mechanistic model GR3D (Global Repositioning Dynamics of Diadromous fish Distribution) which was parameterized on allis shad and then used to predict its future distribution along the European Atlantic coast under different climate change scenarios (RCP 4.5 and RCP 8.5). We then used a correlative SDM for this species to forecast its distribution across the same geographic area and under the same climate change scenarios. First, projections from correlative and mechanistic models provided congruent trends in probability of habitat suitability and population dynamics. This agreement was preferentially interpreted as referring to the species vulnerability to climate change. Climate change could not be accordingly listed as a major threat for allis shad. The congruence in predicted range limits between SDMs projections was the next point of interest. The difference, when noticed, required to deepen our understanding of the niche modelled by each approach. In this respect, the relative position of the northern range limit between the two methods strongly suggested here that a key biological process related to intraspecific variability was potentially lacking in the mechanistic SDM. Based on our knowledge, we hypothesized that local adaptations to cold

  16. Solar Sail GN and C Model Comparisons

    NASA Technical Reports Server (NTRS)

    Heaton, Andrew F.

    2004-01-01

    The Solar Sail Propulsion project is engaged in an ambitious program to raise the Technology Readiness Level of solar sails and prepare for a validation flight via a series of hardware ground demonstrations and development of a number of high fidelity simulations and models. Guidance, navigation, and control of solar sails is a key part of this effort. The large flexible structure and optical nature of solar sails create a considerable challenge for attitude control, thrust modeling, and navigation. In this paper, we present an overview and comparison of two recently delivered prototype solar sail guidance, navigation, and control software tools currently funded by the Solar Sail Propulsion project. The results of some key test cases are presented. Where possible, we also make comparisons to other software tools. We discuss the implications of the results of these comparative studies to the future direction and scope of development efforts for guidance, navigation and control software for solar sails, including the relationship to hardware test efforts such as the Thrust Vector Control Authority Demonstration.

  17. INVASIVE SPECIES: PREDICTING GEOGRAPHIC DISTRIBUTIONS USING ECOLOGICAL NICHE MODELING

    EPA Science Inventory

    Present approaches to species invasions are reactive in nature. This scenario results in management that perpetually lags behind the most recent invasion and makes control much more difficult. In contrast, spatially explicit ecological niche modeling provides an effective solut...

  18. Dynamic species distribution models from categorical survey data.

    PubMed

    Mieszkowska, Nova; Milligan, Gregg; Burrows, Michael T; Freckleton, Rob; Spencer, Matthew

    2013-11-01

    1. Species distribution models are static models for the distribution of a species, based on Hutchinson's niche concept. They make probabilistic predictions about the distribution of a species, but do not have a temporal interpretation. In contrast, density-structured models based on categorical abundance data make it possible to incorporate population dynamics into species distribution modelling. 2. Using dynamic species distribution models, temporal aspects of a species' distribution can be investigated, including the predictability of future abundance categories and the expected persistence times of local populations, and how these may respond to environmental or anthropogenic drivers. 3. We built density-structured models for two intertidal marine invertebrates, the Lusitanian trochid gastropods Phorcus lineatus and Gibbula umbilicalis, based on 9 years of field data from around the United Kingdom. Abundances were recorded on a categorical scale, and stochastic models for year-to-year changes in abundance category were constructed with winter mean sea surface temperature (SST) and wave fetch (a measure of the exposure of a shore) as explanatory variables. 4. Both species were more likely to be present at sites with high SST, but differed in their responses to wave fetch. Phorcus lineatus had more predictable future abundance and longer expected persistence times than G. umbilicalis. This is consistent with the longer lifespan of P. lineatus. 5. Where data from multiple time points are available, dynamic species distribution models of the kind described here have many applications in population and conservation biology. These include allowing for changes over time when combining historical and contemporary data, and predicting how climate change might alter future abundance conditional on current distributions. PMID:23889003

  19. Models comparison for JET polarimeter data

    SciTech Connect

    Mazzotta, C.; Orsitto, F. P.; Giovannozzi, E.; Boboc, A.; Tudisco, O.; Zabeo, L.; Brombin, M.; Murari, A.

    2008-03-12

    A complete comparison between the theory and the measurements in polarimetry was done by using the Far Infrared Polarimeter at JET. More than 300 shots were analyzed, including a wide spectrum of JET scenarios in all critical conditions for polarimetry: high density, high and very low fields, high temperatures.This work is aimed at the demonstration of the robustness of the theoretical models for the JET polarimeter measurements in the perspective of using these models for ITER like plasma scenarios . In this context, an assessment was performed on how the line-integrated plasma density along the central vertical chord of FIR polarimeter could be evaluated using the Cotton-Mouton effect and its possible concrete use to correct fringe jumps of the interferometer.The models considered are: i) the rigorous numerical solution of the Stokes propagation equations, using dielectric tensor evaluated from JET equilibrium and Thomson scattering [1,2]; ii) two types of approximated solutions [2,3] and iii) the Guenther empirical model [4] that considers the mutual effect between Cotton-Mouton and Faraday rotation angle. The model calculations have been compared with polarimeter measurements for the Cotton-Mouton phase shift.The agreement with theory is satisfactory within the limits of experimental errors [3].

  20. Modeling Transformations of Neurodevelopmental Sequences across Mammalian Species

    PubMed Central

    Workman, Alan D.; Charvet, Christine J.; Clancy, Barbara; Darlington, Richard B.

    2013-01-01

    A general model of neural development is derived to fit 18 mammalian species, including humans, macaques, several rodent species, and six metatherian (marsupial) mammals. The goal of this work is to describe heterochronic changes in brain evolution within its basic developmental allometry, and provide an empirical basis to recognize equivalent maturational states across animals. The empirical data generating the model comprises 271 developmental events, including measures of initial neurogenesis, axon extension, establishment, and refinement of connectivity, as well as later events such as myelin formation, growth of brain volume, and early behavioral milestones, to the third year of human postnatal life. The progress of neural events across species is sufficiently predictable that a single model can be used to predict the timing of all events in all species, with a correlation of modeled values to empirical data of 0.9929. Each species' rate of progress through the event scale, described by a regression equation predicting duration of development in days, is highly correlated with adult brain size. Neural heterochrony can be seen in selective delay of retinogenesis in the cat, associated with greater numbers of rods in its retina, and delay of corticogenesis in all species but rodents and the rabbit, associated with relatively larger cortices in species with delay. Unexpectedly, precocial mammals (those unusually mature at birth) delay the onset of first neurogenesis but then progress rapidly through remaining developmental events. PMID:23616543

  1. Modeling transformations of neurodevelopmental sequences across mammalian species.

    PubMed

    Workman, Alan D; Charvet, Christine J; Clancy, Barbara; Darlington, Richard B; Finlay, Barbara L

    2013-04-24

    A general model of neural development is derived to fit 18 mammalian species, including humans, macaques, several rodent species, and six metatherian (marsupial) mammals. The goal of this work is to describe heterochronic changes in brain evolution within its basic developmental allometry, and provide an empirical basis to recognize equivalent maturational states across animals. The empirical data generating the model comprises 271 developmental events, including measures of initial neurogenesis, axon extension, establishment, and refinement of connectivity, as well as later events such as myelin formation, growth of brain volume, and early behavioral milestones, to the third year of human postnatal life. The progress of neural events across species is sufficiently predictable that a single model can be used to predict the timing of all events in all species, with a correlation of modeled values to empirical data of 0.9929. Each species' rate of progress through the event scale, described by a regression equation predicting duration of development in days, is highly correlated with adult brain size. Neural heterochrony can be seen in selective delay of retinogenesis in the cat, associated with greater numbers of rods in its retina, and delay of corticogenesis in all species but rodents and the rabbit, associated with relatively larger cortices in species with delay. Unexpectedly, precocial mammals (those unusually mature at birth) delay the onset of first neurogenesis but then progress rapidly through remaining developmental events. PMID:23616543

  2. An analytically tractable model for community ecology with many species

    NASA Astrophysics Data System (ADS)

    Dickens, Benjamin; Fisher, Charles; Mehta, Pankaj; Pankaj Mehta Biophysics Theory Group Team

    A fundamental problem in community ecology is to understand how ecological processes such as selection, drift, and immigration yield observed patterns in species composition and diversity. Here, we present an analytically tractable, presence-absence (PA) model for community assembly and use it to ask how ecological traits such as the strength of competition, diversity in competition, and stochasticity affect species composition in a community. In our PA model, we treat species as stochastic binary variables that can either be present or absent in a community: species can immigrate into the community from a regional species pool and can go extinct due to competition and stochasticity. Despite its simplicity, the PA model reproduces the qualitative features of more complicated models of community assembly. In agreement with recent work on large, competitive Lotka-Volterra systems, the PA model exhibits distinct ecological behaviors organized around a special (``critical'') point corresponding to Hubbell's neutral theory of biodiversity. Our results suggest that the concepts of ``phases'' and phase diagrams can provide a powerful framework for thinking about community ecology and that the PA model captures the essential ecological dynamics of community assembly. Pm was supported by a Simons Investigator in the Mathematical Modeling of Living Systems and a Sloan Research Fellowship.

  3. Improved intra-species collision models for PIC simulations

    SciTech Connect

    Jones, M.E.; Lemons, D.S.; Winske, D.

    1998-07-01

    In recent years, the authors have investigated methods to improve the effectiveness of modeling collisional processes in particle-in-cell codes. Through the use of generalized collision models, plasma dynamics can be followed both in the regime of nearly collisionless plasmas as well as in the hydrodynamic limit of collisional plasmas. They have developed a collision-field method to treat both the case of collisions between unlike plasma species (inter-species collisions), through the use of a deterministic, grid-based force, and between particles of the same species (intra-species collisions), through the use of a Langevin equation. While the approach used for inter-species collisions is noise-free in that the collision experienced by a particle does not require any random numbers, such random numbers are used for intra-species collisions. This gives rise to a stochastic cooling effect inherent in the Langevin approach. In this paper, the authors concentrate on intra-species collisions and describe how the accuracy of the model can be improved by appropriate corrections to velocity and spatial moments.

  4. Mapping, Monitoring and Modeling Submersed Aquatic Vegetation Species and Communities

    NASA Astrophysics Data System (ADS)

    Hartis, Brett Michael

    Aquatic macrophyte communities are critically important habitat species in aquatic systems worldwide. None are more important than those found beneath the water's surface, commonly referred to as submersed aquatic vegetation (SAV). Although vital to such systems, many native submersed plants have shown near irreversible declines in recent decades as water quality impairment, habitat destruction, and encroachment by invasive species have increased. In the past, aquatic plant science has emphasized the restoration and protection of native species and the management of invasive species. Comparatively little emphasis has been directed toward adequately mapping and monitoring these resources to track their viability over time. Modeling the potential intrusion of certain invasive plant species has also been given little attention, likely because aquatic systems in general can be difficult to assess. In recent years, scientists and resource managers alike have begun paying more attention to mapping SAV communities and to address the spread of invasive species across various regions. This research attempts to provide new, cutting-edge techniques to improve SAV mapping and monitoring efforts in coastal regions, at both community and individual species levels, while also providing insights about the establishment potential of Hydrilla verticillata, a noxious, highly invasive submersed plant. Technological advances in satellite remote sensing, interpolation and spatial analysis in geographic information systems, and state-of-the-art climate envelope modeling techniques were used to further assess the dynamic nature of SAV on various scales. This work contributes to the growing science of mapping, monitoring, and modeling of SAV

  5. Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions

    USGS Publications Warehouse

    Royle, J. Andrew; Chandler, Richard B.; Yackulic, Charles; Nichols, James D.

    2012-01-01

    1. Understanding the factors affecting species occurrence is a pre-eminent focus of applied ecological research. However, direct information about species occurrence is lacking for many species. Instead, researchers sometimes have to rely on so-called presence-only data (i.e. when no direct information about absences is available), which often results from opportunistic, unstructured sampling. MAXENT is a widely used software program designed to model and map species distribution using presence-only data. 2. We provide a critical review of MAXENT as applied to species distribution modelling and discuss how it can lead to inferential errors. A chief concern is that MAXENT produces a number of poorly defined indices that are not directly related to the actual parameter of interest – the probability of occurrence (ψ). This focus on an index was motivated by the belief that it is not possible to estimate ψ from presence-only data; however, we demonstrate that ψ is identifiable using conventional likelihood methods under the assumptions of random sampling and constant probability of species detection. 3. The model is implemented in a convenient r package which we use to apply the model to simulated data and data from the North American Breeding Bird Survey. We demonstrate that MAXENT produces extreme under-predictions when compared to estimates produced by logistic regression which uses the full (presence/absence) data set. We note that MAXENT predictions are extremely sensitive to specification of the background prevalence, which is not objectively estimated using the MAXENT method. 4. As with MAXENT, formal model-based inference requires a random sample of presence locations. Many presence-only data sets, such as those based on museum records and herbarium collections, may not satisfy this assumption. However, when sampling is random, we believe that inference should be based on formal methods that facilitate inference about interpretable ecological quantities

  6. Population distribution models: species distributions are better modeled using biologically relevant data partitions

    PubMed Central

    2011-01-01

    Background Predicting the geographic distribution of widespread species through modeling is problematic for several reasons including high rates of omission errors. One potential source of error for modeling widespread species is that subspecies and/or races of species are frequently pooled for analyses, which may mask biologically relevant spatial variation within the distribution of a single widespread species. We contrast a presence-only maximum entropy model for the widely distributed oldfield mouse (Peromyscus polionotus) that includes all available presence locations for this species, with two composite maximum entropy models. The composite models either subdivided the total species distribution into four geographic quadrants or by fifteen subspecies to capture spatially relevant variation in P. polionotus distributions. Results Despite high Area Under the ROC Curve (AUC) values for all models, the composite species distribution model of P. polionotus generated from individual subspecies models represented the known distribution of the species much better than did the models produced by partitioning data into geographic quadrants or modeling the whole species as a single unit. Conclusions Because the AUC values failed to describe the differences in the predictability of the three modeling strategies, we suggest using omission curves in addition to AUC values to assess model performance. Dividing the data of a widespread species into biologically relevant partitions greatly increased the performance of our distribution model; therefore, this approach may prove to be quite practical and informative for a wide range of modeling applications. PMID:21929792

  7. Quantifying the dispersal potential of seagrass vegetative fragments: A comparison of multiple subtropical species

    NASA Astrophysics Data System (ADS)

    Weatherall, E. J.; Jackson, E. L.; Hendry, R. A.; Campbell, M. L.

    2016-02-01

    Seagrass meadows are threatened by anthropogenic and natural disturbances on both a local and global scale. Understanding the potential for seagrasses to disperse, connecting populations separated by unsuitable habitat is important to assess the resilience of regional populations. This study investigated the relative dispersal potential of vegetative fragments of seagrass from five subtropical species (Zostera muelleri, Halodule uninervis, Halophila ovalis, Halophila spinulosa, Halophila decipiens). Five questions were examined: 1) do vegetative fragments of different species settle at different velocities; 2) does a species morphometric variables influence settling velocities; 3) is a species settling velocity related to the species local distribution; 4) does temperature stress affect settling velocity; and 5) what is the composition and potential viability of seagrass fragments floating in the bay. A proportional distribution index for each species was determined using data from a habitat prediction model. It was found that H. spinulosa settled significantly faster than the remaining species and Z. muelleri settled the slowest. Variables influencing settling velocity included rhizome length, weight and surface area. In both Z. muelleri and H. ovalis settling velocities were significantly greater at higher temperatures (although there was no significant difference between approximately 5 and 10 °C above ambient temperature). H. uninervis was not significantly influenced by temperature. There was a significant negative correlation between species settling velocities and their distribution.

  8. Using habitat suitability models to target invasive plant species surveys

    USGS Publications Warehouse

    Crall, Alycia W.; Jarnevich, Catherine S.; Panke, Brendon; Young, Nick; Renz, Mark; Morisette, Jeffrey

    2013-01-01

    Managers need new tools for detecting the movement and spread of nonnative, invasive species. Habitat suitability models are a popular tool for mapping the potential distribution of current invaders, but the ability of these models to prioritize monitoring efforts has not been tested in the field. We tested the utility of an iterative sampling design (i.e., models based on field observations used to guide subsequent field data collection to improve the model), hypothesizing that model performance would increase when new data were gathered from targeted sampling using criteria based on the initial model results. We also tested the ability of habitat suitability models to predict the spread of invasive species, hypothesizing that models would accurately predict occurrences in the field, and that the use of targeted sampling would detect more species with less sampling effort than a nontargeted approach. We tested these hypotheses on two species at the state scale (Centaurea stoebe and Pastinaca sativa) in Wisconsin (USA), and one genus at the regional scale (Tamarix) in the western United States. These initial data were merged with environmental data at 30-m2 resolution for Wisconsin and 1-km2 resolution for the western United States to produce our first iteration models. We stratified these initial models to target field sampling and compared our models and success at detecting our species of interest to other surveys being conducted during the same field season (i.e., nontargeted sampling). Although more data did not always improve our models based on correct classification rate (CCR), sensitivity, specificity, kappa, or area under the curve (AUC), our models generated from targeted sampling data always performed better than models generated from nontargeted data. For Wisconsin species, the model described actual locations in the field fairly well (kappa = 0.51, 0.19, P 2) = 47.42, P < 0.01). From these findings, we conclude that habitat suitability models can be

  9. A Rapid Approach to Modeling Species-Habitat Relationships

    NASA Technical Reports Server (NTRS)

    Carter, Geoffrey M.; Breinger, David R.; Stolen, Eric D.

    2005-01-01

    A growing number of species require conservation or management efforts. Success of these activities requires knowledge of the species' occurrence pattern. Species-habitat models developed from GIS data sources are commonly used to predict species occurrence but commonly used data sources are often developed for purposes other than predicting species occurrence and are of inappropriate scale and the techniques used to extract predictor variables are often time consuming and cannot be repeated easily and thus cannot efficiently reflect changing conditions. We used digital orthophotographs and a grid cell classification scheme to develop an efficient technique to extract predictor variables. We combined our classification scheme with a priori hypothesis development using expert knowledge and a previously published habitat suitability index and used an objective model selection procedure to choose candidate models. We were able to classify a large area (57,000 ha) in a fraction of the time that would be required to map vegetation and were able to test models at varying scales using a windowing process. Interpretation of the selected models confirmed existing knowledge of factors important to Florida scrub-jay habitat occupancy. The potential uses and advantages of using a grid cell classification scheme in conjunction with expert knowledge or an habitat suitability index (HSI) and an objective model selection procedure are discussed.

  10. Analytically tractable model for community ecology with many species.

    PubMed

    Dickens, Benjamin; Fisher, Charles K; Mehta, Pankaj

    2016-08-01

    A fundamental problem in community ecology is understanding how ecological processes such as selection, drift, and immigration give rise to observed patterns in species composition and diversity. Here, we analyze a recently introduced, analytically tractable, presence-absence (PA) model for community assembly, and we use it to ask how ecological traits such as the strength of competition, the amount of diversity, and demographic and environmental stochasticity affect species composition in a community. In the PA model, species are treated as stochastic binary variables that can either be present or absent in a community: species can immigrate into the community from a regional species pool and can go extinct due to competition and stochasticity. Building upon previous work, we show that, despite its simplicity, the PA model reproduces the qualitative features of more complicated models of community assembly. In agreement with recent studies of large, competitive Lotka-Volterra systems, the PA model exhibits distinct ecological behaviors organized around a special ("critical") point corresponding to Hubbell's neutral theory of biodiversity. These results suggest that the concepts of ecological "phases" and phase diagrams can provide a powerful framework for thinking about community ecology, and that the PA model captures the essential ecological dynamics of community assembly. PMID:27627348

  11. An exactly solvable coarse-grained model for species diversity

    NASA Astrophysics Data System (ADS)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

    We present novel analytical results concerning ecosystem species diversity that stem from a proposed coarse-grained neutral model based on birth-death processes. The relevance of the problem lies in the urgency for understanding and synthesizing both theoretical results from ecological neutral theory and empirical evidence on species diversity preservation. The neutral model of biodiversity deals with ecosystems at the same trophic level, where per capita vital rates are assumed to be species independent. Closed-form analytical solutions for the neutral theory are obtained within a coarse-grained model, where the only input is the species persistence time distribution. Our results pertain to: the probability distribution function of the number of species in the ecosystem, both in transient and in stationary states; the n-point connected time correlation function; and the survival probability, defined as the distribution of time spans to local extinction for a species randomly sampled from the community. Analytical predictions are also tested on empirical data from an estuarine fish ecosystem. We find that emerging properties of the ecosystem are very robust and do not depend on specific details of the model, with implications for biodiversity and conservation biology.

  12. Minipig and beagle animal model genomes aid species selection in pharmaceutical discovery and development

    SciTech Connect

    Vamathevan, Jessica J.; Hall, Matthew D.; Hasan, Samiul; Woollard, Peter M.; Xu, Meng; Yang, Yulan; Li, Xin; Wang, Xiaoli; Kenny, Steve; Brown, James R.; Huxley-Jones, Julie; Lyon, Jon; Haselden, John; Min, Jiumeng; Sanseau, Philippe

    2013-07-15

    Improving drug attrition remains a challenge in pharmaceutical discovery and development. A major cause of early attrition is the demonstration of safety signals which can negate any therapeutic index previously established. Safety attrition needs to be put in context of clinical translation (i.e. human relevance) and is negatively impacted by differences between animal models and human. In order to minimize such an impact, an earlier assessment of pharmacological target homology across animal model species will enhance understanding of the context of animal safety signals and aid species selection during later regulatory toxicology studies. Here we sequenced the genomes of the Sus scrofa Göttingen minipig and the Canis familiaris beagle, two widely used animal species in regulatory safety studies. Comparative analyses of these new genomes with other key model organisms, namely mouse, rat, cynomolgus macaque, rhesus macaque, two related breeds (S. scrofa Duroc and C. familiaris boxer) and human reveal considerable variation in gene content. Key genes in toxicology and metabolism studies, such as the UGT2 family, CYP2D6, and SLCO1A2, displayed unique duplication patterns. Comparisons of 317 known human drug targets revealed surprising variation such as species-specific positive selection, duplication and higher occurrences of pseudogenized targets in beagle (41 genes) relative to minipig (19 genes). These data will facilitate the more effective use of animals in biomedical research. - Highlights: • Genomes of the minipig and beagle dog, two species used in pharmaceutical studies. • First systematic comparative genome analysis of human and six experimental animals. • Key drug toxicology genes display unique duplication patterns across species. • Comparison of 317 drug targets show species-specific evolutionary patterns.

  13. Benchmarking novel approaches for modelling species range dynamics.

    PubMed

    Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

    2016-08-01

    Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches

  14. Modeling symbiosis by interactions through species carrying capacities

    NASA Astrophysics Data System (ADS)

    Yukalov, V. I.; Yukalova, E. P.; Sornette, D.

    2012-08-01

    We introduce a mathematical model of symbiosis between different species by taking into account the influence of each species on the carrying capacities of the others. The modeled entities can pertain to biological and ecological societies or to social, economic and financial societies. Our model includes three basic types: symbiosis with direct mutual interactions, symbiosis with asymmetric interactions, and symbiosis without direct interactions. In all cases, we provide a complete classification of all admissible dynamical regimes. The proposed model of symbiosis turned out to be very rich, as it exhibits four qualitatively different regimes: convergence to stationary states, unbounded exponential growth, finite-time singularity, and finite-time death or extinction of species.

  15. Current themes and recent advances in modelling species occurrences

    PubMed Central

    2009-01-01

    Recent years have seen a huge expansion in the range of methods and approaches that are being used to predict species occurrences. This expansion has been accompanied by many improvements in statistical methods, including more accurate ways of comparing models, better null models, methods to cope with autocorrelation, and greater awareness of the importance of scale and prevalence. However, the field still suffers from problems with incorporating temporal variation, overfitted models and poor out-of-sample prediction, confusion between explanation and prediction, simplistic assumptions, and a focus on pattern over process. The greatest advances in recent years have come from integrative studies that have linked species occurrence models with other themes and topics in ecology, such as island biogeography, climate change, disease geography, and invasive species. PMID:20948597

  16. MODEL FOR COMPARISON OF ANIMAL AND HUMAN ALVEOLAR DOSE AND TOXIC EFFECT OF INHALED OZONE

    EPA Science Inventory

    Present models for predicting human pulmonary toxicity of ozone from the toxic effects observed in animals rely on dosimetric measurements of ozone mass balance, and species comparisons of tissue protective mechanisms against ozone. The goal of the present study was to identify a...

  17. Hindlimb muscle architecture in non-human great apes and a comparison of methods for analysing inter-species variation.

    PubMed

    Myatt, Julia P; Crompton, Robin H; Thorpe, Susannah K S

    2011-08-01

    By relating an animal's morphology to its functional role and the behaviours performed, we can further develop our understanding of the selective factors and constraints acting on the adaptations of great apes. Comparison of muscle architecture between different ape species, however, is difficult because only small sample sizes are ever available. Further, such samples are often comprised of different age-sex classes, so studies have to rely on scaling techniques to remove body mass differences. However, the reliability of such scaling techniques has been questioned. As datasets increase in size, more reliable statistical analysis may eventually become possible. Here we employ geometric and allometric scaling techniques, and ancovas (a form of general linear model, GLM) to highlight and explore the different methods available for comparing functional morphology in the non-human great apes. Our results underline the importance of regressing data against a suitable body size variable to ascertain the relationship (geometric or allometric) and of choosing appropriate exponents by which to scale data. ancova models, while likely to be more robust than scaling for species comparisons when sample sizes are high, suffer from reduced power when sample sizes are low. Therefore, until sample sizes are radically increased it is preferable to include scaling analyses along with ancovas in data exploration. Overall, the results obtained from the different methods show little significant variation, whether in muscle belly mass, fascicle length or physiological cross-sectional area between the different species. This may reflect relatively close evolutionary relationships of the non-human great apes; a universal influence on morphology of generalised orthograde locomotor behaviours or, quite likely, both. PMID:21507000

  18. Centrifuge Rotor Models: A Comparison of the Euler-Lagrange and the Bond Graph Modeling Approach

    NASA Technical Reports Server (NTRS)

    Granda, Jose J.; Ramakrishnan, Jayant; Nguyen, Louis H.

    2006-01-01

    A viewgraph presentation on centrifuge rotor models with a comparison using Euler-Lagrange and bond graph methods is shown. The topics include: 1) Objectives; 2) MOdeling Approach Comparisons; 3) Model Structures; and 4) Application.

  19. Item Response Modeling of Paired Comparison and Ranking Data

    ERIC Educational Resources Information Center

    Maydeu-Olivares, Alberto; Brown, Anna

    2010-01-01

    The comparative format used in ranking and paired comparisons tasks can significantly reduce the impact of uniform response biases typically associated with rating scales. Thurstone's (1927, 1931) model provides a powerful framework for modeling comparative data such as paired comparisons and rankings. Although Thurstonian models are generally…

  20. Comparison of two freshwater turtle species as monitors of environmental contamination

    SciTech Connect

    Meyers-Schoene, L. ); Walton, B.T. )

    1990-04-01

    Two species of turtles that occupy different ecological niches were compared for their usefulness as monitors of contamination in freshwater ecosystems. Trachemys scripta (Agassiz) and Chelydra serpentina (Linnaeus) were selected for comparison based on species abundance and differences in food habits and sediment contact. A review of the literature on contaminants in turtles and results of preliminary surveys conducted at the field sites, which are included in this study, were used to direct and focus this research project. White Oak Lake, a settling basin for low-level radioactive and nonradioactive contaminants, and Bearden Creek Embayment, an uncontaminated reference site upriver, were used as study sites in the investigation of turtles as indicators of chemical contamination. Turtles were analyzed for concentrations of strontium-90, cesium-137, cobalt 60, and mercury in specific target tissues, and for single-stranded DNA breaks, a non-specific indicator of possible exposure to genotoxic agents in the environment. 133 refs., 2 figs., 15 tabs.

  1. GCSS Cirrus Parcel Model Comparison Project

    NASA Technical Reports Server (NTRS)

    Lin, Ruei-Fong; Starr, David OC.; DeMott, Paul J.; Cotton, Richard; Jensen, Eric; Sassen, Kenneth; Einaudi, Franco (Technical Monitor)

    2000-01-01

    The Cirrus Parcel Model Comparison Project, a project of GCSS Working Group on Cirrus Cloud Systems (WG2), involves the systematic comparison of current models of ice crystal nucleation and growth for specified, typical, cirrus cloud environments. The goal of this project is to document and understand the factors resulting in significant inter-model differences. The intent is to foment research leading to model improvement and validation. In Phase 1 of the project reported here, simulated cirrus cloud microphysical properties are compared for situations of "warm" (-40 C) and "cold" (-60 C) cirrus subject to updrafts of 4, 20 and 100 cm/s, respectively. Five models participated. These models employ explicit microphysical schemes wherein the size distribution of each class of particles (aerosols and ice crystals) is resolved into bins. Simulations are made including both homogeneous and heterogeneous ice nucleation mechanisms. A single initial aerosol population of sulfuric acid particles is prescribed for all simulations. To isolate the treatment of the homogeneous freezing (of haze drops) nucleation process, the heterogeneous nucleation mechanism is disabled for a second parallel set of simulations. Qualitative agreement is found for the homogeneous-nucleation-only simulations, e.g., the number density of nucleated ice crystals increases with the strength of the prescribed updraft. However, non-negligible quantitative differences are found. Detailed analysis reveals that the homogeneous nucleation formulation, aerosol size, ice crystal growth rate (particularly the deposition coefficient), and water vapor uptake rate are critical components that lead to differences in predicted microphysics. Systematic bias exists between results based on a modified classical theory approach and models using an effective freezing temperature approach to the treatment of nucleation. Each approach is constrained by critical freezing data from laboratory studies, but each includes

  2. Modelling survival: exposure pattern, species sensitivity and uncertainty

    NASA Astrophysics Data System (ADS)

    Ashauer, Roman; Albert, Carlo; Augustine, Starrlight; Cedergreen, Nina; Charles, Sandrine; Ducrot, Virginie; Focks, Andreas; Gabsi, Faten; Gergs, André; Goussen, Benoit; Jager, Tjalling; Kramer, Nynke I.; Nyman, Anna-Maija; Poulsen, Veronique; Reichenberger, Stefan; Schäfer, Ralf B.; van den Brink, Paul J.; Veltman, Karin; Vogel, Sören; Zimmer, Elke I.; Preuss, Thomas G.

    2016-07-01

    The General Unified Threshold model for Survival (GUTS) integrates previously published toxicokinetic-toxicodynamic models and estimates survival with explicitly defined assumptions. Importantly, GUTS accounts for time-variable exposure to the stressor. We performed three studies to test the ability of GUTS to predict survival of aquatic organisms across different pesticide exposure patterns, time scales and species. Firstly, using synthetic data, we identified experimental data requirements which allow for the estimation of all parameters of the GUTS proper model. Secondly, we assessed how well GUTS, calibrated with short-term survival data of Gammarus pulex exposed to four pesticides, can forecast effects of longer-term pulsed exposures. Thirdly, we tested the ability of GUTS to estimate 14-day median effect concentrations of malathion for a range of species and use these estimates to build species sensitivity distributions for different exposure patterns. We find that GUTS adequately predicts survival across exposure patterns that vary over time. When toxicity is assessed for time-variable concentrations species may differ in their responses depending on the exposure profile. This can result in different species sensitivity rankings and safe levels. The interplay of exposure pattern and species sensitivity deserves systematic investigation in order to better understand how organisms respond to stress, including humans.

  3. Modelling survival: exposure pattern, species sensitivity and uncertainty.

    PubMed

    Ashauer, Roman; Albert, Carlo; Augustine, Starrlight; Cedergreen, Nina; Charles, Sandrine; Ducrot, Virginie; Focks, Andreas; Gabsi, Faten; Gergs, André; Goussen, Benoit; Jager, Tjalling; Kramer, Nynke I; Nyman, Anna-Maija; Poulsen, Veronique; Reichenberger, Stefan; Schäfer, Ralf B; Van den Brink, Paul J; Veltman, Karin; Vogel, Sören; Zimmer, Elke I; Preuss, Thomas G

    2016-01-01

    The General Unified Threshold model for Survival (GUTS) integrates previously published toxicokinetic-toxicodynamic models and estimates survival with explicitly defined assumptions. Importantly, GUTS accounts for time-variable exposure to the stressor. We performed three studies to test the ability of GUTS to predict survival of aquatic organisms across different pesticide exposure patterns, time scales and species. Firstly, using synthetic data, we identified experimental data requirements which allow for the estimation of all parameters of the GUTS proper model. Secondly, we assessed how well GUTS, calibrated with short-term survival data of Gammarus pulex exposed to four pesticides, can forecast effects of longer-term pulsed exposures. Thirdly, we tested the ability of GUTS to estimate 14-day median effect concentrations of malathion for a range of species and use these estimates to build species sensitivity distributions for different exposure patterns. We find that GUTS adequately predicts survival across exposure patterns that vary over time. When toxicity is assessed for time-variable concentrations species may differ in their responses depending on the exposure profile. This can result in different species sensitivity rankings and safe levels. The interplay of exposure pattern and species sensitivity deserves systematic investigation in order to better understand how organisms respond to stress, including humans. PMID:27381500

  4. Modelling survival: exposure pattern, species sensitivity and uncertainty

    PubMed Central

    Ashauer, Roman; Albert, Carlo; Augustine, Starrlight; Cedergreen, Nina; Charles, Sandrine; Ducrot, Virginie; Focks, Andreas; Gabsi, Faten; Gergs, André; Goussen, Benoit; Jager, Tjalling; Kramer, Nynke I.; Nyman, Anna-Maija; Poulsen, Veronique; Reichenberger, Stefan; Schäfer, Ralf B.; Van den Brink, Paul J.; Veltman, Karin; Vogel, Sören; Zimmer, Elke I.; Preuss, Thomas G.

    2016-01-01

    The General Unified Threshold model for Survival (GUTS) integrates previously published toxicokinetic-toxicodynamic models and estimates survival with explicitly defined assumptions. Importantly, GUTS accounts for time-variable exposure to the stressor. We performed three studies to test the ability of GUTS to predict survival of aquatic organisms across different pesticide exposure patterns, time scales and species. Firstly, using synthetic data, we identified experimental data requirements which allow for the estimation of all parameters of the GUTS proper model. Secondly, we assessed how well GUTS, calibrated with short-term survival data of Gammarus pulex exposed to four pesticides, can forecast effects of longer-term pulsed exposures. Thirdly, we tested the ability of GUTS to estimate 14-day median effect concentrations of malathion for a range of species and use these estimates to build species sensitivity distributions for different exposure patterns. We find that GUTS adequately predicts survival across exposure patterns that vary over time. When toxicity is assessed for time-variable concentrations species may differ in their responses depending on the exposure profile. This can result in different species sensitivity rankings and safe levels. The interplay of exposure pattern and species sensitivity deserves systematic investigation in order to better understand how organisms respond to stress, including humans. PMID:27381500

  5. An ion species model for positive ion sources: I. Description of the model

    NASA Astrophysics Data System (ADS)

    Surrey, E.; Holmes, A. J. T.

    2015-02-01

    A one-dimensional model of the magnetic multipole volume plasma source has been developed for use in intense ion/neutral atom beam injectors. The model uses plasma transport coefficients for particle and energy flow to create a detailed description of the plasma parameters along an axis parallel to that of the extracted beam. Primarily constructed for applications to neutral beam injection systems on fusion devices, the model concentrates on the hydrogenic isotopes but can be extended to any gas by substitution of the relevant masses, cross-sections and rate coefficients. The model considers the flow of fast ionizing electrons that create the ratios of the three hydrogenic isotope ion species, H+, H2+ , H3+ (and similarly for deuterium and tritium) as they flow towards the beam extraction electrode, together with the production of negative hydrogenic ions through volume processes. The use of detailed energy balance in the discharge allows the determination of the fraction of the gas density that is in an atomic state and also the gas temperature as well as the electron temperatures and plasma potential. Comparisons are made between the results of the model and experimental measurements in deuterium from a number of different filament driven sources used on beam heating facilities.

  6. Mixture models for gene expression experiments with two species

    PubMed Central

    2014-01-01

    Cross-species research in drug development is novel and challenging. A bivariate mixture model utilizing information across two species was proposed to solve the fundamental problem of identifying differentially expressed genes in microarray experiments in order to potentially improve the understanding of translation between preclinical and clinical studies for drug development. The proposed approach models the joint distribution of treatment effects estimated from independent linear models. The mixture model posits up to nine components, four of which include groups in which genes are differentially expressed in both species. A comprehensive simulation to evaluate the model performance and one application on a real world data set, a mouse and human type II diabetes experiment, suggest that the proposed model, though highly structured, can handle various configurations of differential gene expression and is practically useful on identifying differentially expressed genes, especially when the magnitude of differential expression due to different treatment intervention is weak. In the mouse and human application, the proposed mixture model was able to eliminate unimportant genes and identify a list of genes that were differentially expressed in both species and could be potential gene targets for drug development. PMID:25085578

  7. Comparison of isoenzymes of some species of the subgenus schizotrypanum from bats by isoelectrofocusing.

    PubMed

    Ebert, F

    1983-06-01

    Culture forms of bat-trypanosomes of the species T. dionisii, T. vespertilionis and T.c. marinkellei were compared isoenzymatically by isoelectrofocusing. The enzymes tested were: nonspecific esterase (NSE, E.C.3.1.1.), phosphoglucomutase (PGM, E.C. 2.7.5.1), glucose-6-phosphate dehydrogenase (G-6-PD, E.C. 1.1.1.49), glucosephosphate isomerase (GPI, E.C. 5.3.1.9), malate dehydrogenase (MDH, E.C. 1.1.1.37), alcohol dehydrogenase (NADP+) (ADH, E.C. 1.1.1.2). Their enzyme types were related to those of T. cruzi. The comparison of enzyme patterns of the six enzymes has shown that each species was characterized by species-specific enzyme profiles. Among the stocks of the European species, T. dionisii, and T. vespertilionis, variations of the enzyme patterns of PGM, G-6-PD and GPI suggesting that the final status of this subspecies is probably not yet established. In relation to T. cruzi it has been found that T. dionisii showed identical enzyme profiles with group II of T. cruzi. For T. vespertilionis no enzyme types identical with T. cruzi were detectable. T.c. marinkellei showed only identical enzyme patterns to T. cruzi-group I by the enzymes NSE and GPI. PMID:6224326

  8. Mitochondrial Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

    PubMed Central

    Asaf, Sajjad; Khan, Abdul Latif; Khan, Abdur Rahim; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad Aaqil; Shahzad, Raheem; Seo, Chang-Woo; Shin, Jae-Ho; Lee, In-Jung

    2016-01-01

    Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O. rufipogon. Comparison with other related species revealed that most of the genes with known function are conserved among the Poaceae members. Similarly, O. minuta mt genome shared 24 protein-coding genes, 15 tRNA genes and 1 ribosomal RNA gene with other rice species (indica and japonica). The evolutionary relationship and phylogenetic analysis revealed that O. minuta is more closely related to O. rufipogon than to any other related species. Such studies are essential to understand the evolutionary divergence among species and analyze common gene pools to combat risks in the current scenario of a changing environment. PMID:27045847

  9. Marine and estuarine porewater toxicity testing -- species and end point comparisons

    SciTech Connect

    Carr, R.S.; Chapman, D.C.; Biedenbach, J.M.; Robertson, L.

    1994-12-31

    As part of their continuing development and evaluation of the porewater toxicity test approach for assessing the quality of marine and estuarine sediments, a variety of studies involving species and endpoint comparisons as well as validation studies have recently been conducted. The results from numerous extensive sediment quality assessment surveys have demonstrated that porewater toxicity tests are considerably more sensitive than the standard solid-phase tests and invariably exhibit a higher degree of concordance with sediment quality assessment guidelines than the standard tests. Species that have been evaluated for use in testing marine and estuarine pore water include a life-cycle test with the polychaete Dinophilus gyrociliatus, survival and hatching success with embryo-larval stages of red drum Sciaaenops ocellatus, survival of nauplii stages of the harpacticoid copepod Longipedia sp., and three different assays (fertilization, embryological development, and cytogenetic) with the sea urchin Arbacia punctulata. The different species and end points have been compared using sediment pore water from a variety of contaminated sites. Although the results of tests with the different species and end points were often comparable, in general, the sea urchin embryological development assay appears to be the most sensitive porewater test evaluated thus far in their laboratory.

  10. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

    PubMed Central

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-01-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

  11. Engineering Large Animal Species to Model Human Diseases.

    PubMed

    Rogers, Christopher S

    2016-01-01

    Animal models are an important resource for studying human diseases. Genetically engineered mice are the most commonly used species and have made significant contributions to our understanding of basic biology, disease mechanisms, and drug development. However, they often fail to recreate important aspects of human diseases and thus can have limited utility as translational research tools. Developing disease models in species more similar to humans may provide a better setting in which to study disease pathogenesis and test new treatments. This unit provides an overview of the history of genetically engineered large animals and the techniques that have made their development possible. Factors to consider when planning a large animal model, including choice of species, type of modification and methodology, characterization, production methods, and regulatory compliance, are also covered. © 2016 by John Wiley & Sons, Inc. PMID:27367161

  12. Habitat Suitability Index Models: Wildlife Species Richness in Shelterbelts

    USGS Publications Warehouse

    Schroeder, Richard L.

    1986-01-01

    A review and synthesis of existing information were used to develop a Habitat Suitability Index (HSI) model for evaluating potential species richness in shelterbelts. The model consolidates habitat use information into a framework appropriate for field application, and is scaled to produce an index between 0.0 (unsuitable habitat) to 1.0 (optimum habitat). HSI models are designed to be used with Habitat Evaluation Procedures previously developed by the U.S. Fish and Wildlife Service.

  13. Multispecies diffusion models: A study of uranyl species diffusion

    NASA Astrophysics Data System (ADS)

    Liu, Chongxuan; Shang, Jianying; Zachara, John M.

    2011-12-01

    Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found that a diffusion model with a single, common diffusion coefficient for all species was sufficient to describe multispecies U(VI) diffusion under a steady state condition of major chemical composition, but not under transient chemical conditions. Simulations revealed that for multispecies U(VI) diffusion under transient chemical conditions, a fully coupled diffusion model could be well approximated by a component-based diffusion model when the diffusion coefficient for each chemical component was properly selected. The component-based diffusion model considers the difference in diffusion coefficients between chemical components, but not between the species within each chemical component. This treatment significantly enhanced computational efficiency at the expense of minor charge conservation. The charge balance in the component-based diffusion model can be enforced, if necessary, by adding a secondary migration term resulting from model simplification. The effect of ion activity coefficient gradients on multispecies diffusion is also discussed. The diffusion models were applied to describe U(VI) diffusive mass transfer in intragranular domains in two sediments collected from U.S. Department of Energy's Hanford 300A

  14. Wildlife species richness in shelterbelts: test of a habitat model

    USGS Publications Warehouse

    Schroeder, Richard L.; Cable, Ted T.; Haire, Sandra L.

    1992-01-01

    Shelterbelts are human-made habitats consisting of rows of shrubs and trees planted either in fields or on the windward side of farmstead dwellings. Shelterbelts provide wooded habitat for a large variety of birds and other wildlife. A model to predict wildlife species richness in shelterbelts (Schroeder 1986) was published as part of the U.S. Fish and Wildlife Service Habitat Suitability Index (HSI) model series (Schamberger et al. 1982). HSI models have been used extensively by wildlife managers and land use planners to assess habitat quality. Several HSI models have become the focus of a test program that includes analysis of field data for corroboration, refutation, or modification of model hypotheses. Previous tests of HSI models focused either on single species (e.g., Cook and Irwin 1985, Morton et al. 1989, Schroeder 1990) or examined portions of HSI models, such as the relationship between cavity abundance and tree diameter (Allen and Corn 1990). The shelterbelt model, however, assesses habitat value at the community level. The effects of habitat characteristics, area, and perimeter on diversity and abundance of bird and mammal species in shelterbelts were first studied by Yahner (1983a, b). Johnson and Beck (1988) confirmed the importance of shelterbelts to wildlife and identified area, perimeter, and diversity and complexity of vegetation as key measurements of habitat quality. The shelterbelt model incorporates both specific habitat variables and larger scale parameters, such as area and configuration, to predict wildlife species richness. This shift in perspective comes at a time of increasing interest in conservation and planning beyond the species levels (e.g., Graul and Miller 1984, Hutto et al. 1987, Schroeder 1987: 26). We report results of a 3-year study of spatial and vegetative parameters and their relationship to breeding bird species richness (BSR) in 34 Kansas shelterbelts. Our objectives were to test the hypothesis presented in the original

  15. Poised to prosper? A cross-system comparison of climate change effects on native and non-native species performance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Climate change and biological invasions are primary threats to global biodiversity that may operate synergistically in the future. To date, the hypothesis that climate change will favor non-native species has been examined though local comparisons of single or few species. We took a meta-analytical ...

  16. Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.

    PubMed

    Kim, Jaebum; Cunningham, Ryan; James, Brian; Wyder, Stefan; Gibson, Joshua D; Niehuis, Oliver; Zdobnov, Evgeny M; Robertson, Hugh M; Robinson, Gene E; Werren, John H; Sinha, Saurabh

    2010-01-01

    We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif-function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations. PMID:20126523

  17. Comparison between the effect of Lawsonia inermis and flubendazole on Strongyloides species using scanning electron microscopy.

    PubMed

    Ismail, Khadiga Ahmed; Ibrahim, Ayman Nabil; Ahmed, Mona Abdel-Fattah; Hetta, Mona Hafez

    2016-06-01

    Strongyloides species is a helminth of worldwide distribution primarily in tropical and subtropical regions. It is the only soil-transmitted helminth with the ability for autoinfection so; it may lead to severe systemic manifestations especially in immunosuppressed patients. Chemotherapy is currently considered the best therapeutic option for strongyloidiasis but some drugs are expensive and others have side effects as nausea, diarrhea and headache. Strongyloides larva is resistant to most chemical agents so, search for plant extracts may provide other effective but less expensive treatment. Lawsonia inermis Linn, popularly known as Henna, has been proven to have antihelminthic, antibacterial and antifungal properties. The current study was carried out to evaluate the efficacy of Lawsonia inermis on Strongyloides spp. In vitro using scanning electron microscopy. Fifty Strongyloides species. larvae and free living females were incubated with different concentrations of Lawsonia (1, 10, 100 mg/ml), for different incubation periods (24, 48, 72 and 96 h) in comparison to the same concentrations of flubendazole at the same different time points. The results showed that Lawsonia inermis in a concentration of 10 mg/ml incubated with Strongyloides spp. female for 24 h affected the parasite cuticular surface in the form of transverse and longitudinal fissures and transverse depression in comparison to no cuticular change with flubendazole (100 mg/ml). This suggests that Lawsonia inermis may be a promising phytotherapeutic agent for strongyloidiasis. PMID:27413314

  18. Modeling phytoplankton community in reservoirs. A comparison between taxonomic and functional groups-based models.

    PubMed

    Di Maggio, Jimena; Fernández, Carolina; Parodi, Elisa R; Diaz, M Soledad; Estrada, Vanina

    2016-01-01

    In this paper we address the formulation of two mechanistic water quality models that differ in the way the phytoplankton community is described. We carry out parameter estimation subject to differential-algebraic constraints and validation for each model and comparison between models performance. The first approach aggregates phytoplankton species based on their phylogenetic characteristics (Taxonomic group model) and the second one, on their morpho-functional properties following Reynolds' classification (Functional group model). The latter approach takes into account tolerance and sensitivity to environmental conditions. The constrained parameter estimation problems are formulated within an equation oriented framework, with a maximum likelihood objective function. The study site is Paso de las Piedras Reservoir (Argentina), which supplies water for consumption for 450,000 population. Numerical results show that phytoplankton morpho-functional groups more closely represent each species growth requirements within the group. Each model performance is quantitatively assessed by three diagnostic measures. Parameter estimation results for seasonal dynamics of the phytoplankton community and main biogeochemical variables for a one-year time horizon are presented and compared for both models, showing the functional group model enhanced performance. Finally, we explore increasing nutrient loading scenarios and predict their effect on phytoplankton dynamics throughout a one-year time horizon. PMID:26406877

  19. GIS-based niche modeling for mapping species' habitats

    USGS Publications Warehouse

    Rotenberry, J.T.; Preston, K.L.; Knick, S.

    2006-01-01

    Ecological a??niche modelinga?? using presence-only locality data and large-scale environmental variables provides a powerful tool for identifying and mapping suitable habitat for species over large spatial extents. We describe a niche modeling approach that identifies a minimum (rather than an optimum) set of basic habitat requirements for a species, based on the assumption that constant environmental relationships in a species' distribution (i.e., variables that maintain a consistent value where the species occurs) are most likely to be associated with limiting factors. Environmental variables that take on a wide range of values where a species occurs are less informative because they do not limit a species' distribution, at least over the range of variation sampled. This approach is operationalized by partitioning Mahalanobis D2 (standardized difference between values of a set of environmental variables for any point and mean values for those same variables calculated from all points at which a species was detected) into independent components. The smallest of these components represents the linear combination of variables with minimum variance; increasingly larger components represent larger variances and are increasingly less limiting. We illustrate this approach using the California Gnatcatcher (Polioptila californica Brewster) and provide SAS code to implement it.

  20. Modeling of Alkane Oxidation Using Constituents and Species

    NASA Technical Reports Server (NTRS)

    Bellan, Jasette; Harstad, Kenneth G.

    2010-01-01

    It is currently not possible to perform simulations of turbulent reactive flows due in particular to complex chemistry, which may contain thousands of reactions and hundreds of species. This complex chemistry results in additional differential equations, making the numerical solution of the equation set computationally prohibitive. Reducing the chemical kinetics mathematical description is one of several important goals in turbulent reactive flow modeling. A chemical kinetics reduction model is proposed for alkane oxidation in air that is based on a parallel methodology to that used in turbulence modeling in the context of the Large Eddy Simulation. The objective of kinetic modeling is to predict the heat release and temperature evolution. This kinetic mechanism is valid over a pressure range from atmospheric to 60 bar, temperatures from 600 K to 2,500 K, and equivalence ratios from 0.125 to 8. This range encompasses diesel, HCCI, and gas-turbine engines, including cold ignition. A computationally efficient kinetic reduction has been proposed for alkanes that has been illustrated for n-heptane using the LLNL heptane mechanism. This model is consistent with turbulence modeling in that scales were first categorized into either those modeled or those computed as progress variables. Species were identified as being either light or heavy. The heavy species were decomposed into defined 13 constituents, and their total molar density was shown to evolve in a quasi-steady manner. The light species behave either in a quasi-steady or unsteady manner. The modeled scales are the total constituent molar density, Nc, and the molar density of the quasi-steady light species. The progress variables are the total constituent molar density rate evolution and the molar densities of the unsteady light species. The unsteady equations for the light species contain contributions of the type gain/loss rates from the heavy species that are modeled consistent with the developed mathematical

  1. Modelling Favourability for Invasive Species Encroachment to Identify Areas of Native Species Vulnerability

    PubMed Central

    Báez, José C.; Ferri-Yáñez, Francisco; Bellido, Jesús J.

    2014-01-01

    We assessed the vulnerability of the native Mediterranean pond turtle to encroachment by the invasive red-eared slider in southern Spain. We first obtained an ecogeographical favourability model for the Mediterranean pond turtle. We then modelled the presence/absence of the red-eared slider in the Mediterranean pond turtle range and obtained an encroachment favourability model. We also obtained a favourability model for the red-eared slider using the ecogeographical favourability for the Mediterranean pond turtle as a predictor. When favourability for the Mediterranean pond turtle was high, favourability for the red-eared slider was low, suggesting that in these areas the Mediterranean pond turtle may resist encroachment by the red-eared slider. We also calculated favourability overlap between the two species, which is their simultaneous favourability. Grids with low overlap had higher favourability values for the Mediterranean pond turtle and, consequently, were of lesser conservation concern. A few grids had high values for both species, being potentially suitable for coexistence. Grids with intermediate overlap had similar intermediate favourability values for both species and were therefore areas where the Mediterranean pond turtle was more vulnerable to encroachment by the red-eared slider. We mapped the favourability overlap to provide a map of vulnerability of the Mediterranean pond turtle to encroachment by the red-eared slider. PMID:24719577

  2. Modelling favourability for invasive species encroachment to identify areas of native species vulnerability.

    PubMed

    Romero, David; Báez, José C; Ferri-Yáñez, Francisco; Bellido, Jesús J; Real, Raimundo

    2014-01-01

    We assessed the vulnerability of the native Mediterranean pond turtle to encroachment by the invasive red-eared slider in southern Spain. We first obtained an ecogeographical favourability model for the Mediterranean pond turtle. We then modelled the presence/absence of the red-eared slider in the Mediterranean pond turtle range and obtained an encroachment favourability model. We also obtained a favourability model for the red-eared slider using the ecogeographical favourability for the Mediterranean pond turtle as a predictor. When favourability for the Mediterranean pond turtle was high, favourability for the red-eared slider was low, suggesting that in these areas the Mediterranean pond turtle may resist encroachment by the red-eared slider. We also calculated favourability overlap between the two species, which is their simultaneous favourability. Grids with low overlap had higher favourability values for the Mediterranean pond turtle and, consequently, were of lesser conservation concern. A few grids had high values for both species, being potentially suitable for coexistence. Grids with intermediate overlap had similar intermediate favourability values for both species and were therefore areas where the Mediterranean pond turtle was more vulnerable to encroachment by the red-eared slider. We mapped the favourability overlap to provide a map of vulnerability of the Mediterranean pond turtle to encroachment by the red-eared slider. PMID:24719577

  3. Beyond the zebrafish: diverse fish species for modeling human disease

    PubMed Central

    Schartl, Manfred

    2014-01-01

    ABSTRACT In recent years, zebrafish, and to a lesser extent medaka, have become widely used small animal models for human diseases. These organisms have convincingly demonstrated the usefulness of fish for improving our understanding of the molecular and cellular mechanisms leading to pathological conditions, and for the development of new diagnostic and therapeutic tools. Despite the usefulness of zebrafish and medaka in the investigation of a wide spectrum of traits, there is evidence to suggest that other fish species could be better suited for more targeted questions. With the emergence of new, improved sequencing technologies that enable genomic resources to be generated with increasing efficiency and speed, the potential of non-mainstream fish species as disease models can now be explored. A key feature of these fish species is that the pathological condition that they model is often related to specific evolutionary adaptations. By exploring these adaptations, new disease-causing and disease-modifier genes might be identified; thus, diverse fish species could be exploited to better understand the complexity of disease processes. In addition, non-mainstream fish models could allow us to study the impact of environmental factors, as well as genetic variation, on complex disease phenotypes. This Review will discuss the opportunities that such fish models offer for current and future biomedical research. PMID:24271780

  4. Distribution models and species discovery: the story of a new Solanum species from the Peruvian Andes

    PubMed Central

    Särkinen, Tiina; Gonzáles, Paúl; Knapp, Sandra

    2013-01-01

    Abstract A new species of Solanum sect. Solanum from Peru is described here. Solanum pseudoamericanum Särkinen, Gonzáles & S.Knapp sp. nov. is a member of the Morelloid clade of Solanum, and is characterized by the combination of mostly forked inflorescences, flowers with small stamens 2.5 mm long including the filament, and strongly exerted styles with capitate stigmas. The species was first thought to be restricted to the seasonally dry tropical forests of southern Peru along the dry valleys of Río Pampas and Río Apurímac. Results from species distribution modelling (SDM) analysis with climatic predictors identified further potential suitable habitat areas in northern and central Peru. These areas were visited during field work in 2013. A total of 17 new populations across the predicted distribution were discovered using the model-based sampling method, and five further collections were identified amongst herbarium loans. Although still endemic to Peru, Solanum pseudoamericanum is now known from across northern, central and southern Peru. Our study demonstrates the usefulness of SDM for predicting new occurrences of rare plants, especially in the Andes where collection densities are still low in many areas and where many new species remain to be discovered. PMID:24399901

  5. Orion Landing Simulation Eight Soil Model Comparison

    NASA Technical Reports Server (NTRS)

    Mark, Stephen D.

    2009-01-01

    LS-DYNA finite element simulations of a rigid Orion Crew Module (CM) were used to investigate the CM impact behavior on eight different soil models. Ten different landing conditions, characterized by the combination of CM vertical and horizontal velocity, hang angle, and roll angle were simulated on the eight different soils. The CM center of gravity accelerations, pitch angle, kinetic energy, and soil contact forces were the outputs of interest. The simulation results are presented, with comparisons of the CM behavior on the different soils. The soils analyzed in this study can be roughly categorized as soft, medium, or hard, according to the CM accelerations that occur when landing on them. The soft group is comprised of the Carson Sink Wet soil and the Kennedy Space Center (KSC) Low Density Dry Sand. The medium group includes Carson Sink Dry, the KSC High Density In-Situ Moisture Sand and High Density Flooded Sand, and Cuddeback B. The hard soils are Cuddeback A and the Gantry Unwashed Sand. The softer soils were found to produce lower peak accelerations, have more stable pitch behavior, and to be less sensitive to the landing conditions. This investigation found that the Cuddeback A soil produced the highest peak accelerations and worst stability conditions, and that the best landing performance was achieved on the KSC Low Density Dry Sand.

  6. Comparison of Two Freshwater Turtle Species as Monitors of Environmental Contamination

    SciTech Connect

    Meyers-Schone, L.

    1990-01-01

    Two species of turtles that occupy different ecological niches were compared for their usefulness as monitors of contamination in freshwater ecosystems. Trachemvs scrinta (Agassiz) (yellow-bellied slider) and Chelvdra sernentina (Linnaeus) (common snapping turtle) were selected for comparison based on species abundance and differences in food habits and sediment contact. A review of the literature on contaminants in turtles and results of preliminary surveys conducted at the field sites, which are included in this study, were used to direct and focus this research project. White Oak Lake, a settling basin for low-level radioactive and nonradioactive contaminants, and Bearden Creek Embayment, an uncontaminated reference site upriver, were used as study sites in the investigation of turtles as indicators of chemical contamination. Turtles were analyzed for concentrations of strontium-go, cesium-137, cobalt 60, and mercury in specific target tissues, and for single-stranded DNA breaks, a non-specific indicator of possible exposure to genotoxic agents in the environment. Significantly higher concentrations of {sup 90}Sr, {sup 137}Cs, {sup 60}Co, and mercury were detected in turtles from White Oak Lake than in turtles from the reference site. In addition, turtles from White Oak Lake contained a significantly greater amount of DNA damage than those from the reference site. Although this suggests greater exposure of White Oak Lake turtles to genotoxic agents, further studies are needed to establish the cause of the enhanced amount of single-stranded breaks. Interspecific comparisons of the turtles from White Oak Lake indicated that diet may play a significant role in the exposure of turtles to certain contaminants. No difference was detected between the concentrations of {sup 90}Sr, {sup 137}Cs, {sup 60}Co between the two species.

  7. Challenges and perspectives for species distribution modelling in the neotropics

    PubMed Central

    Kamino, Luciana H. Y.; Stehmann, João Renato; Amaral, Silvana; De Marco, Paulo; Rangel, Thiago F.; de Siqueira, Marinez F.; De Giovanni, Renato; Hortal, Joaquín

    2012-01-01

    The workshop ‘Species distribution models: applications, challenges and perspectives’ held at Belo Horizonte (Brazil), 29–30 August 2011, aimed to review the state-of-the-art in species distribution modelling (SDM) in the neotropical realm. It brought together researchers in ecology, evolution, biogeography and conservation, with different backgrounds and research interests. The application of SDM in the megadiverse neotropics—where data on species occurrences are scarce—presents several challenges, involving acknowledging the limitations imposed by data quality, including surveys as an integral part of SDM studies, and designing the analyses in accordance with the question investigated. Specific solutions were discussed, and a code of good practice in SDM studies and related field surveys was drafted. PMID:22031720

  8. Respiratory and cuticular water loss in insects with continuous gas exchange: comparison across five ant species.

    PubMed

    Schilman, Pablo E; Lighton, John R B; Holway, David A

    2005-12-01

    Respiratory water loss (RWL) in insects showing continuous emission of CO(2) is poorly studied because few methodologies can measure it. Comparisons of RWL between insects showing continuous and discontinuous gas exchange cycles (DGC) are therefore difficult. We used two recently developed methodologies (the hyperoxic switch and correlation between water-loss and CO(2) emission rates) to compare cuticular permeabilities and rates of RWL in five species of ants, the Argentine ant (Linepithema humile) and four common native ant competitors. Our results showed that RWL in groups of ants with moderate levels of activity and continuous gas exchange were similar across the two measurement methods, and were similar to published values on insects showing the DGC. Furthermore, ants exposed to anoxia increased their total water loss rates by 50-150%. These results suggest that spiracular control under continuous gas exchange can be as effective as the DGC in reducing RWL. Finally, the mesic-adapted Argentine ant showed significantly higher rates of water loss and cuticular permeability compared to four ant species native to dry environments. Physiological limitations may therefore be responsible for restricting the distribution of this invasive species in seasonally dry environments. PMID:16154585

  9. Comparison of pathogenicity of Alternaria pellucida and Curvularia lunata on weed Echinochloa species.

    PubMed

    Reza, Mohammad; Motlagh, Safari

    2015-07-01

    Echinochloa spp. are the most important weeds in rice fields. In this research Curvularia lunata and Alternaria pellucida were isolated from these weeds and their pathogenicity effects were compared on these weeds and five rice cultivars in a completely random design with three replications in greenhouse conditions. Fungi were inoculated on weeds and rice cultivars, using spore suspension consisting of 10' spore ml(-1) of distilled water. Results indicated significant effect of Curvularia lunata and Alternaria pellucida on Echinochloa oryzicola and E. crus-galli. In the present study, effect of C. lunata on fresh weight, dry weight and height of Echinochloa species based on variance analysis table, a significant reaction was observed for height and fresh weight, but for dry weight reaction was not significant. The effect of A. pellucida on fresh weight, dry weight and height of Echinochloa species based on variance analysis table, a significant reaction was observed for all the three traits. Also, rice cultivars did not show any significant reaction to C. lunata and A. pellucida. The results showed that in comparison between effect of Curvularia lunata and Alternaria pellucida on Echinochloa spp., disease rating caused by A. pellucida on E. oryzicola and E. crusalli was more than disease rating caused by C. lunata and these species of weed were more susceptible to A. pellucida. However, A. alternata can be considered as a better promising bioherbicide to control Echinochloa spp. PMID:26364476

  10. Modeling the Emergence of Three Arable Bedstraw (Galium) Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seedling emergence was modelled for three arable species of bedstraw (Galium), which may coexist in winter cereal fields, using multi-year field data from Spain. The relationships between cumulative emergence and both growing degree days (GDD) and hydrothermal time (HTT) in soil were analyzed as sig...

  11. Multiple-species analysis of point count data: A more parsimonious modelling framework

    USGS Publications Warehouse

    Alldredge, M.W.; Pollock, K.H.; Simons, T.R.; Shriner, S.A.

    2007-01-01

    1. Although population surveys often provide information on multiple species, these data are rarely analysed within a multiple-species framework despite the potential for more efficient estimation of population parameters. 2. We have developed a multiple-species modelling framework that uses similarities in capture/detection processes among species to model multiple species data more parsimoniously. We present examples of this approach applied to distance, time of detection and multiple observer sampling for avian point count data. 3. Models that included species as a covariate and individual species effects were generally selected as the best models for distance sampling, but group models without species effects performed best for the time of detection and multiple observer methods. Population estimates were more precise for no-species-effect models than for species-effect models, demonstrating the benefits of exploiting species' similarities when modelling multiple species data. Partial species-effect models and additive models were also useful because they modelled similarities among species while allowing for species differences. 4. Synthesis and applications. We recommend the adoption of multiple-species modelling because of its potential for improved population estimates. This framework will be particularly beneficial for modelling count data from rare species because information on the detection process can be 'borrowed' from more common species. The multiple-species modelling framework presented here is applicable to a wide range of sampling techniques and taxa. ?? 2007 The Authors.

  12. Development of Solar Drying Model for Selected Cambodian Fish Species

    PubMed Central

    Hubackova, Anna; Kucerova, Iva; Chrun, Rithy; Chaloupkova, Petra; Banout, Jan

    2014-01-01

    A solar drying was investigated as one of perspective techniques for fish processing in Cambodia. The solar drying was compared to conventional drying in electric oven. Five typical Cambodian fish species were selected for this study. Mean solar drying temperature and drying air relative humidity were 55.6°C and 19.9%, respectively. The overall solar dryer efficiency was 12.37%, which is typical for natural convection solar dryers. An average evaporative capacity of solar dryer was 0.049 kg·h−1. Based on coefficient of determination (R2), chi-square (χ2) test, and root-mean-square error (RMSE), the most suitable models describing natural convection solar drying kinetics were Logarithmic model, Diffusion approximate model, and Two-term model for climbing perch and Nile tilapia, swamp eel and walking catfish and Channa fish, respectively. In case of electric oven drying, the Modified Page 1 model shows the best results for all investigated fish species except Channa fish where the two-term model is the best one. Sensory evaluation shows that most preferable fish is climbing perch, followed by Nile tilapia and walking catfish. This study brings new knowledge about drying kinetics of fresh water fish species in Cambodia and confirms the solar drying as acceptable technology for fish processing. PMID:25250381

  13. Development of solar drying model for selected Cambodian fish species.

    PubMed

    Hubackova, Anna; Kucerova, Iva; Chrun, Rithy; Chaloupkova, Petra; Banout, Jan

    2014-01-01

    A solar drying was investigated as one of perspective techniques for fish processing in Cambodia. The solar drying was compared to conventional drying in electric oven. Five typical Cambodian fish species were selected for this study. Mean solar drying temperature and drying air relative humidity were 55.6 °C and 19.9%, respectively. The overall solar dryer efficiency was 12.37%, which is typical for natural convection solar dryers. An average evaporative capacity of solar dryer was 0.049 kg · h(-1). Based on coefficient of determination (R(2)), chi-square (χ(2)) test, and root-mean-square error (RMSE), the most suitable models describing natural convection solar drying kinetics were Logarithmic model, Diffusion approximate model, and Two-term model for climbing perch and Nile tilapia, swamp eel and walking catfish and Channa fish, respectively. In case of electric oven drying, the Modified Page 1 model shows the best results for all investigated fish species except Channa fish where the two-term model is the best one. Sensory evaluation shows that most preferable fish is climbing perch, followed by Nile tilapia and walking catfish. This study brings new knowledge about drying kinetics of fresh water fish species in Cambodia and confirms the solar drying as acceptable technology for fish processing. PMID:25250381

  14. Comparison of Ablation Predictions for Carbonaceous Materials Using CEA and JANAF-Based Species Thermodynamics

    NASA Technical Reports Server (NTRS)

    Milos, Frank S.

    2011-01-01

    In most previous work at NASA Ames Research Center, ablation predictions for carbonaceous materials were obtained using a species thermodynamics database developed by Aerotherm Corporation. This database is derived mostly from the JANAF thermochemical tables. However, the CEA thermodynamics database, also used by NASA, is considered more up to date. In this work, the FIAT code was modified to use CEA-based curve fits for species thermodynamics, then analyses using both the JANAF and CEA thermodynamics were performed for carbon and carbon phenolic materials over a range of test conditions. The ablation predictions are comparable at lower heat fluxes where the dominant mechanism is carbon oxidation. However, the predictions begin to diverge in the sublimation regime, with the CEA model predicting lower recession. The disagreement is more significant for carbon phenolic than for carbon, and this difference is attributed to hydrocarbon species that may contribute to the ablation rate.

  15. Comparison of Turbulent Thermal Diffusivity and Scalar Variance Models

    NASA Technical Reports Server (NTRS)

    Yoder, Dennis A.

    2016-01-01

    This paper will include a detailed comparison of heat transfer models that rely upon the thermal diffusivity. The goals are to inform users of the development history of the various models and the resulting differences in model formulations, as well as to evaluate the models on a variety of validation cases so that users might better understand which models are more broadly applicable.

  16. Benchmarking novel approaches for modelling species range dynamics

    PubMed Central

    Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H.; Moore, Kara A.; Zimmermann, Niklaus E.

    2016-01-01

    Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species’ range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species’ response to climate change but also emphasise several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches

  17. Demographic modeling of selected fish species with RAMAS

    SciTech Connect

    Saila, S.; Martin, B.; Ferson, S.; Ginzburg, L.; Millstein, J. )

    1991-03-01

    The microcomputer program RAMAS 3 developed for EPRI, has been used to model the intrinsic natural variability of seven important fish species: cod, Atlantic herring, yellowtail flounder, haddock, striped bass, American shad and white perch. Demographic data used to construct age-based population models included information on spawning biology, longevity, sex ratio and (age-specific) mortality and fecundity. These data were collected from published and unpublished sources. The natural risks of extinction and of falling below threshold population abundances (quasi-extinction) are derived for each of the seven fish species based on measured and estimated values for their demographic parameters. The analysis of these species provides evidence that including density-dependent compensation in the demographic model typically lowers the expected chance of extinction. This is because if density dependence generally acts as a restoring force it seems reasonable to conclude that models which include density dependence would exhibit less fluctuation than models without compensation since density-dependent populations experience a pull towards equilibrium. Since extinction probabilities are determined by the size of the fluctuation of population abundance, models without density dependence will show higher risks of extinction, given identical circumstances. Thus, models without compensation can be used as conservative estimators of risk, that is, if a compensation-free model yields acceptable extinction risk, adding compensation will not increase this risk. Since it is usually difficult to estimate the parameters needed for a model with compensation, such conservative estimates of the risks of extinction based on a model without compensation are very useful in the methodology of impact assessment. 103 refs., 19 figs., 10 tabs.

  18. The predictive skill of species distribution models for plankton in a changing climate.

    PubMed

    Brun, Philipp; Kiørboe, Thomas; Licandro, Priscilla; Payne, Mark R

    2016-09-01

    Statistical species distribution models (SDMs) are increasingly used to project spatial relocations of marine taxa under future climate change scenarios. However, tests of their predictive skill in the real-world are rare. Here, we use data from the Continuous Plankton Recorder program, one of the longest running and most extensive marine biological monitoring programs, to investigate the reliability of predicted plankton distributions. We apply three commonly used SDMs to 20 representative plankton species, including copepods, diatoms, and dinoflagellates, all found in the North Atlantic and adjacent seas. We fit the models to decadal subsets of the full (1958-2012) dataset, and then use them to predict both forward and backward in time, comparing the model predictions against the corresponding observations. The probability of correctly predicting presence was low, peaking at 0.5 for copepods, and model skill typically did not outperform a null model assuming distributions to be constant in time. The predicted prevalence increasingly differed from the observed prevalence for predictions with more distance in time from their training dataset. More detailed investigations based on four focal species revealed that strong spatial variations in skill exist, with the least skill at the edges of the distributions, where prevalence is lowest. Furthermore, the scores of traditional single-value model performance metrics were contrasting and some implied overoptimistic conclusions about model skill. Plankton may be particularly challenging to model, due to its short life span and the dispersive effects of constant water movements on all spatial scales, however there are few other studies against which to compare these results. We conclude that rigorous model validation, including comparison against null models, is essential to assess the robustness of projections of marine planktonic species under climate change. PMID:27040720

  19. HABITAT DISTRIBUTION MODELS FOR 37 VERTEBRATE SPECIES ADDRESSED BY THE MULTI-SPECIES HABITAT CONSERVATION PLAN OF CLARK COUNTY, NEVADA

    EPA Science Inventory

    Thirty-seven species identified in the Clark County Multi-Species Habitat Conservation Plan were

    previously modeled through the Southwest Regional Gap Analysis Project. Existing SWReGAP habitat

    models and modeling databases were used to facilitate the revision of mo...

  20. Effect of species rarity on the accuracy of species distribution models for reptiles and amphibians in southern California

    USGS Publications Warehouse

    Franklin, J.; Wejnert, K.E.; Hathaway, S.A.; Rochester, C.J.; Fisher, R.N.

    2009-01-01

    Aim: Several studies have found that more accurate predictive models of species' occurrences can be developed for rarer species; however, one recent study found the relationship between range size and model performance to be an artefact of sample prevalence, that is, the proportion of presence versus absence observations in the data used to train the model. We examined the effect of model type, species rarity class, species' survey frequency, detectability and manipulated sample prevalence on the accuracy of distribution models developed for 30 reptile and amphibian species. Location: Coastal southern California, USA. Methods: Classification trees, generalized additive models and generalized linear models were developed using species presence and absence data from 420 locations. Model performance was measured using sensitivity, specificity and the area under the curve (AUC) of the receiver-operating characteristic (ROC) plot based on twofold cross-validation, or on bootstrapping. Predictors included climate, terrain, soil and vegetation variables. Species were assigned to rarity classes by experts. The data were sampled to generate subsets with varying ratios of presences and absences to test for the effect of sample prevalence. Join count statistics were used to characterize spatial dependence in the prediction errors. Results: Species in classes with higher rarity were more accurately predicted than common species, and this effect was independent of sample prevalence. Although positive spatial autocorrelation remained in the prediction errors, it was weaker than was observed in the species occurrence data. The differences in accuracy among model types were slight. Main conclusions: Using a variety of modelling methods, more accurate species distribution models were developed for rarer than for more common species. This was presumably because it is difficult to discriminate suitable from unsuitable habitat for habitat generalists, and not as an artefact of the

  1. Species distribution models of tropical deep-sea snappers.

    PubMed

    Gomez, Céline; Williams, Ashley J; Nicol, Simon J; Mellin, Camille; Loeun, Kim L; Bradshaw, Corey J A

    2015-01-01

    Deep-sea fisheries provide an important source of protein to Pacific Island countries and territories that are highly dependent on fish for food security. However, spatial management of these deep-sea habitats is hindered by insufficient data. We developed species distribution models using spatially limited presence data for the main harvested species in the Western Central Pacific Ocean. We used bathymetric and water temperature data to develop presence-only species distribution models for the commercially exploited deep-sea snappers Etelis Cuvier 1828, Pristipomoides Valenciennes 1830, and Aphareus Cuvier 1830. We evaluated the performance of four different algorithms (CTA, GLM, MARS, and MAXENT) within the BIOMOD framework to obtain an ensemble of predicted distributions. We projected these predictions across the Western Central Pacific Ocean to produce maps of potential deep-sea snapper distributions in 32 countries and territories. Depth was consistently the best predictor of presence for all species groups across all models. Bathymetric slope was consistently the poorest predictor. Temperature at depth was a good predictor of presence for GLM only. Model precision was highest for MAXENT and CTA. There were strong regional patterns in predicted distribution of suitable habitat, with the largest areas of suitable habitat (> 35% of the Exclusive Economic Zone) predicted in seven South Pacific countries and territories (Fiji, Matthew & Hunter, Nauru, New Caledonia, Tonga, Vanuatu and Wallis & Futuna). Predicted habitat also varied among species, with the proportion of predicted habitat highest for Aphareus and lowest for Etelis. Despite data paucity, the relationship between deep-sea snapper presence and their environments was sufficiently strong to predict their distribution across a large area of the Pacific Ocean. Our results therefore provide a strong baseline for designing monitoring programs that balance resource exploitation and conservation planning, and

  2. CARBON-CHAIN SPECIES IN WARM-UP MODELS

    SciTech Connect

    Hassel, George E.; Harada, Nanase; Herbst, Eric

    2011-12-20

    In previous warm-up chemical models of the low-mass star-forming region L1527, we investigated the evolution of carbon-chain unsaturated hydrocarbon species when the envelope temperature is slightly elevated to T Almost-Equal-To 30 K. These models demonstrated that enhanced abundances of such species can be explained by gas-phase ion-molecule chemistry following the partial sublimation of methane from grain surfaces. We also concluded that the abundances of hydrocarbon radicals such as the C{sub n}H family should be further enhanced as the temperatures increase to higher values, but this conclusion stood in contrast with the lack of unambiguous detection of these species toward hot core and corino sources. Meanwhile, observational surveys have identified C{sub 2}H, C{sub 4}H, CH{sub 3}CCH, and CH{sub 3}OH toward hot corinos (especially IRAS 16293-2422) as well as toward L1527, with lower abundances for the carbon-chain radicals and higher abundances for the other two species toward the hot corinos. In addition, the Herschel Space Telescope has detected the bare linear chain C{sub 3} in 50 K material surrounding young high-mass stellar objects. To understand these new results, we revisit previous warm-up models with an augmented gas-grain network that incorporated reactions from a gas-phase network that was constructed for use with increased temperature up to 800 K. Some of the newly adopted reactions between carbon-chain species and abundant H{sub 2} possess chemical activation energy barriers. The revised model results now better reproduce the observed abundances of unsaturated carbon chains under hot corino (100 K) conditions and make predictions for the abundances of bare carbon chains in the 50 K regions observed by the Herschel HIFI detector.

  3. Species Distribution Models of Tropical Deep-Sea Snappers

    PubMed Central

    Gomez, Céline; Williams, Ashley J.; Nicol, Simon J.; Mellin, Camille; Loeun, Kim L.; Bradshaw, Corey J. A.

    2015-01-01

    Deep-sea fisheries provide an important source of protein to Pacific Island countries and territories that are highly dependent on fish for food security. However, spatial management of these deep-sea habitats is hindered by insufficient data. We developed species distribution models using spatially limited presence data for the main harvested species in the Western Central Pacific Ocean. We used bathymetric and water temperature data to develop presence-only species distribution models for the commercially exploited deep-sea snappers Etelis Cuvier 1828, Pristipomoides Valenciennes 1830, and Aphareus Cuvier 1830. We evaluated the performance of four different algorithms (CTA, GLM, MARS, and MAXENT) within the BIOMOD framework to obtain an ensemble of predicted distributions. We projected these predictions across the Western Central Pacific Ocean to produce maps of potential deep-sea snapper distributions in 32 countries and territories. Depth was consistently the best predictor of presence for all species groups across all models. Bathymetric slope was consistently the poorest predictor. Temperature at depth was a good predictor of presence for GLM only. Model precision was highest for MAXENT and CTA. There were strong regional patterns in predicted distribution of suitable habitat, with the largest areas of suitable habitat (> 35% of the Exclusive Economic Zone) predicted in seven South Pacific countries and territories (Fiji, Matthew & Hunter, Nauru, New Caledonia, Tonga, Vanuatu and Wallis & Futuna). Predicted habitat also varied among species, with the proportion of predicted habitat highest for Aphareus and lowest for Etelis. Despite data paucity, the relationship between deep-sea snapper presence and their environments was sufficiently strong to predict their distribution across a large area of the Pacific Ocean. Our results therefore provide a strong baseline for designing monitoring programs that balance resource exploitation and conservation planning, and

  4. Establishing endangered species recovery criteria using predictive simulation modeling

    USGS Publications Warehouse

    McGowan, Conor P.; Catlin, Daniel H.; Shaffer, Terry L.; Gratto-Trevor, Cheri L.; Aron, Carol

    2014-01-01

    Listing a species under the Endangered Species Act (ESA) and developing a recovery plan requires U.S. Fish and Wildlife Service to establish specific and measurable criteria for delisting. Generally, species are listed because they face (or are perceived to face) elevated risk of extinction due to issues such as habitat loss, invasive species, or other factors. Recovery plans identify recovery criteria that reduce extinction risk to an acceptable level. It logically follows that the recovery criteria, the defined conditions for removing a species from ESA protections, need to be closely related to extinction risk. Extinction probability is a population parameter estimated with a model that uses current demographic information to project the population into the future over a number of replicates, calculating the proportion of replicated populations that go extinct. We simulated extinction probabilities of piping plovers in the Great Plains and estimated the relationship between extinction probability and various demographic parameters. We tested the fit of regression models linking initial abundance, productivity, or population growth rate to extinction risk, and then, using the regression parameter estimates, determined the conditions required to reduce extinction probability to some pre-defined acceptable threshold. Binomial regression models with mean population growth rate and the natural log of initial abundance were the best predictors of extinction probability 50 years into the future. For example, based on our regression models, an initial abundance of approximately 2400 females with an expected mean population growth rate of 1.0 will limit extinction risk for piping plovers in the Great Plains to less than 0.048. Our method provides a straightforward way of developing specific and measurable recovery criteria linked directly to the core issue of extinction risk. Published by Elsevier Ltd.

  5. Saprolegnia bulbosa sp. nov. isolated from an Argentine stream: taxonomy and comparison with related species.

    PubMed

    Steciow, Mónica Mirta; Paul, Alan; Bala, Kanak

    2007-03-01

    Saprolegnia bulbosa sp. nov. was isolated from floating and decaying twigs and leaves in El Gato stream, Partido de La Plata, Buenos Aires Province, Argentina. The distinctive characteristics of S. bulbosa are the product of smooth oogonia and predominantly contorted monoclinous, androgynous and diclinous antheridia. The oogonial stalks are usually bent, curved or once coiled; oospores are subcentric, (1) 2-15 (45) per oogonium and are variable in size. Taxonomical description of this new species, its comparison with related oomycetes of the genus and the nucleotide sequences of the internal transcribed region (spacers ITS1, ITS2 and the gene 5.8S) of its rRNA gene are given here. PMID:17328749

  6. Methods-comparison measurements during the Carbonaceous-Species Methods Comparison Study, Glendora, California, August 1986: tunable-diode laser absorption spectrometer measurements of HCHO, H/sub 2/O/sub 2/ and HNO/sub 3/. Final report

    SciTech Connect

    Mackay, G.I.; Schiff, H.I.

    1987-10-21

    As part of the Carbonaceous-Species Methods Comparison Study at Citrus College, Glendora CA, on August 11-21, 1986, Unisearch Associates participated in methods evaluation studies for formaldehyde (HCHO), hydrogen peroxide (H/sub 2/O/sub 2/) and nitric acid (HNO/sub 3/). These three species play important roles in photochemistry of urban and rural air, and their measurements provide sensitive tests for current acid deposition and urban smog models. Two tunable diode laser absorption spectrometers (TDLAS) were used in the methods evaluation study.

  7. Traveling Pulses for a Two-Species Chemotaxis Model.

    PubMed

    Emako, Casimir; Gayrard, Charlène; Buguin, Axel; Neves de Almeida, Luís; Vauchelet, Nicolas

    2016-04-01

    Mathematical models have been widely used to describe the collective movement of bacteria by chemotaxis. In particular, bacterial concentration waves traveling in a narrow channel have been experimentally observed and can be precisely described thanks to a mathematical model at the macroscopic scale. Such model was derived in [1] using a kinetic model based on an accurate description of the mesoscopic run-and-tumble process. We extend this approach to study the behavior of the interaction between two populations of E. Coli. Separately, each population travels with its own speed in the channel. When put together, a synchronization of the speed of the traveling pulses can be observed. We show that this synchronization depends on the fraction of the fast population. Our approach is based on mathematical analysis of a macroscopic model of partial differential equations. Numerical simulations in comparison with experimental observations show qualitative agreement. PMID:27071058

  8. Traveling Pulses for a Two-Species Chemotaxis Model

    PubMed Central

    Emako, Casimir; Gayrard, Charlène; Buguin, Axel; Neves de Almeida, Luís; Vauchelet, Nicolas

    2016-01-01

    Mathematical models have been widely used to describe the collective movement of bacteria by chemotaxis. In particular, bacterial concentration waves traveling in a narrow channel have been experimentally observed and can be precisely described thanks to a mathematical model at the macroscopic scale. Such model was derived in [1] using a kinetic model based on an accurate description of the mesoscopic run-and-tumble process. We extend this approach to study the behavior of the interaction between two populations of E. Coli. Separately, each population travels with its own speed in the channel. When put together, a synchronization of the speed of the traveling pulses can be observed. We show that this synchronization depends on the fraction of the fast population. Our approach is based on mathematical analysis of a macroscopic model of partial differential equations. Numerical simulations in comparison with experimental observations show qualitative agreement. PMID:27071058

  9. Comparing population recovery after insecticide exposure for four aquatic invertebrate species using models of different complexity.

    PubMed

    Baveco, J M Hans; Norman, Steve; Roessink, Ivo; Galic, Nika; Van den Brink, Paul J

    2014-07-01

    Population models, in particular individual-based models (IBMs), are becoming increasingly important in chemical risk assessment. They can be used to assess recovery of spatially structured populations after chemical exposure that varies in time and space. The authors used an IBM coupled to a toxicokinetic-toxicodynamic model, the threshold damage model (TDM), to assess recovery times for 4 aquatic organisms, after insecticide application, in a nonseasonal environment and in 3 spatial settings (pond, stream, and ditch). The species had different life histories (e.g., voltinism, reproductive capacity, mobility). Exposure was derived from a pesticide fate model, following standard European Union scenarios. The results of the IBM-TDM were compared with results from simpler models: one in which exposure was linked to effects by means of concentration-effect relationships (IBM-CE) and one in which the IBM was replaced by a nonspatial, logistic growth model (logistic). For the first, exposure was based on peak concentrations only; for the second, exposure was spatially averaged as well. By using comparisons between models of different complexity and species with different life histories, the authors obtained an understanding of the role spatial processes play in recovery and the conditions under which the full time-varying exposure needs to be considered. The logistic model, which is amenable to an analytic approach, provided additional insights into the sensitivity of recovery times to density dependence and spatial dimensions. PMID:24733666

  10. One-dimensional turbulence modeling of a turbulent counterflow flame with comparison to DNS

    SciTech Connect

    Jozefik, Zoltan; Kerstein, Alan R.; Schmidt, Heiko; Lyra, Sgouria; Kolla, Hemanth; Chen, Jackie H.

    2015-06-01

    The one-dimensional turbulence (ODT) model is applied to a reactant-to-product counterflow configuration and results are compared with DNS data. The model employed herein solves conservation equations for momentum, energy, and species on a one dimensional (1D) domain corresponding to the line spanning the domain between nozzle orifice centers. The effects of turbulent mixing are modeled via a stochastic process, while the Kolmogorov and reactive length and time scales are explicitly resolved and a detailed chemical kinetic mechanism is used. Comparisons between model and DNS results for spatial mean and root-meansquare (RMS) velocity, temperature, and major and minor species profiles are shown. The ODT approach shows qualitatively and quantitatively reasonable agreement with the DNS data. Scatter plots and statistics conditioned on temperature are also compared for heat release rate and all species. ODT is able to capture the range of results depicted by DNS. However, conditional statistics show signs of underignition.

  11. Comparison of ACCENT 2000 Shuttle Plume Data with SIMPLE Model Predictions

    NASA Astrophysics Data System (ADS)

    Swaminathan, P. K.; Taylor, J. C.; Ross, M. N.; Zittel, P. F.; Lloyd, S. A.

    2001-12-01

    The JHU/APL Stratospheric IMpact of PLume Effluents (SIMPLE)model was employed to analyze the trace species in situ composition data collected during the ACCENT 2000 intercepts of the space shuttle Space Transportation Launch System (STS) rocket plume as a function of time and radial location within the cold plume. The SIMPLE model is initialized using predictions for species depositions calculated using an afterburning model based on standard TDK/SPP nozzle and SPF plume flowfield codes with an expanded chemical kinetic scheme. The time dependent ambient stratospheric chemistry is fully coupled to the plume species evolution whose transport is based on empirically derived diffusion. Model/data comparisons are encouraging through capturing observed local ozone recovery times as well as overall morphology of chlorine chemistry.

  12. A new species of the genus Castoponera (Araneae, Corinnidae) from Sarawak, Borneo, with comparison to a related species

    PubMed Central

    Yamasaki, Takeshi; Hashimoto, Yoshiaki; Endo, Tomoji; Hyodo, Fujio; Itioka, Takao

    2016-01-01

    Abstract A new species of the genus Castoponera Deeleman-Reinhold, 2001, Castoponera christae sp. n., is described here. The species is closely related to Castoponera lecythus Deeleman-Reinhold, 2001, but can be distinguished by the structures of the male palp and the female genitalia. PMID:27408573

  13. 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.

  14. Competing species system as a qualitative model of radiation therapy

    NASA Astrophysics Data System (ADS)

    Wendykier, Jacek; Bieniasiewicz, Marcin; Lipowski, Adam; Pawlak, Andrzej

    2016-07-01

    To examine complex features of tumor dynamics we analyze a competing-species lattice model that takes into account the competition for nutrients or space as well as interaction with therapeutic factors such as drugs or radiation. Our model might be interpreted as a certain prey-predator system having three trophic layers: (i) the basal species that might be interpreted as nutrients; (ii) normal and tumor cells that consume nutrients, and (iii) therapeutic factors that might kill either nutrient, normal or tumor cells. Using a wide spectrum of parameters we examined survival of our species and tried to identify the corresponding dynamical regimes. It was found that the radiotherapy influences mainly the limit of starvation i.e. the value of an update probability where the tumor cells go extinct as a result of insufficient nutrient supply and competition with normal cells. The other limiting value of this probability, corresponding to the coexistence of the normal and tumor cells in abundance of nutrients, is almost not affected by radiotherapy. We have also found the coexistence of all species on the phase diagrams.

  15. Understanding defect distributions in polythiophenes via comparison of regioregular and regiorandom species

    SciTech Connect

    Muntasir, Tanvir E-mail: sumitc@iastate.edu; Chaudhary, Sumit E-mail: sumitc@iastate.edu

    2015-11-28

    Organic photovoltaics (OPVs) are regarded as promising for solar-electric conversion with steadily improving power conversion efficiencies. For further progress, it is crucial to understand and mitigate defect states (traps) residing in the band-gap of OPV materials. In this work, using capacitance measurements, we analyzed two major bands in the density of states (DOS) energy spectra of defects in poly(3-hexylthiophene) (P3HT); regio-regular and regio-random species of P3HT were compared to elucidate the role of morphological disorder. To accurately interpret the obtained DOS profile, trap emission prefactors and activation energy were extracted from temperature dependent capacitance-frequency measurements, while doping, Fermi energy, built-in voltage, and energy levels of the defects were extracted from capacitance-voltage measurements. We identified that the lower energy band—misinterpreted in literature as a defect distribution—stems from free carrier response. The higher energy defect distribution band for regio-random P3HT was an order of magnitude higher than region-regular P3HT, thus stemming from morphological disorder. Impedance spectroscopy was also employed for further comparison of the two P3HT species.

  16. Comparison of Different EO Sensors for Mapping Tree Species- A Case Study in Southwest Germany

    NASA Astrophysics Data System (ADS)

    Enβle, Fabian; Kattenborn, Teja; Koch, Barbara

    2014-11-01

    The variety of different remote sensing sensors and thus the types of data specifications which are available is increasing continuously. Especially the differences in geometric, radiometric and temporal resolutions of different platforms affect their ability for the mapping of forests. These differences hinder the comparability and application of uniform methods of different remotely sensed data across the same region of interest. The quality and quantity of retrieved forest parameters is directly dependent on the data source, and therefore the objective of this project is to analyse the relationship between the data source and its derived parameters. A comparison of different optical EO-data (e.g. spatial resolution and spectral resolution of specific bands) will help to define the optimum data sets to produce a reproducible method to provide additional inputs to the Dragon cooperative project, specifically to method development for woody biomass estimation and biodiversity assessment services. This poster presents the first results on tree species mapping in a mixed temperate forest by satellite imagery taken from four different sensors. Tree species addressed in this pilot study are: Scots pine (Pinus sylvestris), sessile oak (Quercus petraea) and red oak (Quercus rubra). The spatial resolution varies from 2m to 30m and the spectral resolutions range from 8bands up to 155bands.

  17. The neocortex of cetaceans: cytoarchitecture and comparison with other aquatic and terrestrial species.

    PubMed

    Butti, Camilla; Raghanti, Mary Ann; Sherwood, Chet C; Hof, Patrick R

    2011-04-01

    The evolutionary process of readaptation to the aquatic environment was accompanied by extreme anatomical and physiological changes in the brain. This review discusses cortical specializations in the three major lineages of marine mammals in comparison to related terrestrial and semiaquatic species. Different groups of marine mammals adopted a wide range of strategies to cope with the challenges of aquatic living. Cetaceans and hippopotamids possess a completely agranular neocortex in contrast to phocids and sirenians; vertical modules are observed in deep layers V and VI in manatees, cetaceans, phocids, and hippopotamids, but in different cortical areas; and clustering in layer II appears in the insular cortex of hippopotamids, phocids, and cetaceans. Finally, von Economo neurons are present in cetaceans, hippopotamids, sirenians, and some phocids, with specific, yet different, cortical distributions. The interpretation of the evolutionary and functional significance of such specializations, and their relationships with the degrees of adaptation to the aquatic environment and phylogeny, remain difficult to trace, at least until comprehensive data, including representative species from all of the major mammalian families, become available. PMID:21534992

  18. Understanding defect distributions in polythiophenes via comparison of regioregular and regiorandom species

    NASA Astrophysics Data System (ADS)

    Muntasir, Tanvir; Chaudhary, Sumit

    2015-11-01

    Organic photovoltaics (OPVs) are regarded as promising for solar-electric conversion with steadily improving power conversion efficiencies. For further progress, it is crucial to understand and mitigate defect states (traps) residing in the band-gap of OPV materials. In this work, using capacitance measurements, we analyzed two major bands in the density of states (DOS) energy spectra of defects in poly(3-hexylthiophene) (P3HT); regio-regular and regio-random species of P3HT were compared to elucidate the role of morphological disorder. To accurately interpret the obtained DOS profile, trap emission prefactors and activation energy were extracted from temperature dependent capacitance-frequency measurements, while doping, Fermi energy, built-in voltage, and energy levels of the defects were extracted from capacitance-voltage measurements. We identified that the lower energy band—misinterpreted in literature as a defect distribution—stems from free carrier response. The higher energy defect distribution band for regio-random P3HT was an order of magnitude higher than region-regular P3HT, thus stemming from morphological disorder. Impedance spectroscopy was also employed for further comparison of the two P3HT species.

  19. Comparison of antioxidant and antiproliferation activities of polysaccharides from eight species of medicinal mushrooms.

    PubMed

    Chen, Peiying; Yong, Yangyang; Gu, Yifan; Wang, Zeliang; Zhang, Shizhu; Lu, Ling

    2015-01-01

    Polysaccharides from mushrooms including Pleurotus eryngii, P. ostreatus, P. nebrodensis, Lentinus edodes, Hypsizygus marmoreus, Flammulina velutipes, Ganoderma lucidum, and Hericium erinaceus were isolated by water extraction and alcohol precipitation. Our results suggest that all tested polysaccharides have the significant antioxidant capacities of scavenging free radicals (1,1-diphenyl-2-picrylhydrazyl and hydroxyl radicals). Among them, the H. erinaceus polysaccharide exhibits the highest 1,1-diphenyl-2-picrylhydrazyl radical-scavenging activity, whereas the L. edodes polysaccharide shows the strongest scavenging ability for hydroxyl radicals. Furthermore, using the MCF-7 breast cancer cell line and HeLa cells, all 8 selected polysaccharides are able to inhibit the proliferation of tumor cells, but the strength of inhibition varied depending on the mushroom species and the concentration used. Notably, G. lucidum polysaccharide shows the highest inhibition activity on MCF-7 cells. By comparison, H. erinaceus polysaccharide has the strongest inhibitory effect on HeLa cells. Moreover, high-performance liquid chromatography with a carbohydrate analysis column showed significant differences in polysaccharide components among these mushrooms. Thus our data suggest that the different species of mushrooms have the variable functions because of their own specific polysaccharide components. The 8 mushroom polysaccharides have the potential to be used as valuable functional food additives or sources of therapeutic agents for antioxidant and cancer treatments, especially polysaccharides from H. erinaceus, L. edodes, and G. lucidum. PMID:25954912

  20. Comparison of sterols and fatty acids in two species of Ganoderma

    PubMed Central

    2012-01-01

    Background Two species of Ganoderma, G. sinense and G. lucidum, are used as Lingzhi in China. Howerver, the content of triterpenoids and polysaccharides, main actives compounds, are significant different, though the extracts of both G. lucidum and G. sinense have antitumoral proliferation effect. It is suspected that other compounds contribute to their antitumoral activity. Sterols and fatty acids have obvious bioactivity. Therefore, determination and comparison of sterols and fatty acids is helpful to elucidate the active components of Lingzhi. Results Ergosterol, a specific component of fungal cell membrane, was rich in G. lucidum and G. sinense. But its content in G. lucidum (median content 705.0 μg·g-1, range 189.1-1453.3 μg·g-1, n = 19) was much higher than that in G. sinense (median content 80.1 μg·g-1, range 16.0-409.8 μg·g-1, n = 13). Hierarchical clustering analysis based on the content of ergosterol showed that 32 tested samples of Ganoderma were grouped into two main clusters, G. lucidum and G. sinense. Hierarchical clustering analysis based on the contents of ten fatty acids showed that two species of Ganoderma had no significant difference though two groups were also obtained. The similarity of two species of Ganoderma in fatty acids may be related to their antitumoral proliferation effect. Conclusions The content of ergosterol is much higher in G. lucidum than in G. sinense. Palmitic acid, linoleic acid, oleic acid, stearic acid are main fatty acids in Ganoderma and their content had no significant difference between G. lucidum and G. sinense, which may contribute to their antitumoral proliferation effect. PMID:22293530

  1. Leaf respiratory acclimation to climate: comparisons among boreal and temperate tree species along a latitudinal transect.

    PubMed

    Dillaway, Dylan N; Kruger, Eric L

    2011-10-01

    In common gardens along an ∼900 km latitudinal transect through Wisconsin and Illinois, U.S.A., tree species typical of boreal and temperate forests were compared with respect to the nature and magnitude of leaf respiratory acclimation to contrasting climates. The boreal representatives were trembling aspen (Populus tremuloides Michx.) and paper birch (Betula papyrifera Marsh.), while the temperate species were eastern cottonwood (Populus deltoides Bartr ex. Marsh var. deltoides) and sweetgum (Liquidambar styraciflua L.). Assessments were conducted on seedlings grown from seed sources collected near southern and northern range boundaries, respectively. Nighttime rates of leaf dark respiration (R(d)) at common temperatures, as well as R(d)'s short-term temperature sensitivity (energy of activation, E(o)), were assessed for all species and gardens twice during a growing season. Little evidence of R(d) thermal acclimation was observed, despite a 12 °C range in average air temperature across gardens. Instead, R(d) variation at warm temperatures was linked most closely with prior leaf photosynthetic performance, while R(d) variation at cooler temperatures was most strongly related to leaf nitrogen concentration. Moreover, E(o) differences across species and gardens appeared to stem from the somewhat independent limitations on warm versus cool R(d). Based on this construct, an empirical model relying on R(d) estimates from leaf photosynthesis and nitrogen concentration explained 55% of the observed E(o) variation. PMID:21990024

  2. Regional climate model downscaling may improve the prediction of alien plant species distributions

    NASA Astrophysics Data System (ADS)

    Liu, Shuyan; Liang, Xin-Zhong; Gao, Wei; Stohlgren, Thomas J.

    2014-12-01

    Distributions of invasive species are commonly predicted with species distribution models that build upon the statistical relationships between observed species presence data and climate data. We used field observations, climate station data, and Maximum Entropy species distribution models for 13 invasive plant species in the United States, and then compared the models with inputs from a General Circulation Model (hereafter GCM-based models) and a downscaled Regional Climate Model (hereafter, RCM-based models).We also compared species distributions based on either GCM-based or RCM-based models for the present (1990-1999) to the future (2046-2055). RCM-based species distribution models replicated observed distributions remarkably better than GCM-based models for all invasive species under the current climate. This was shown for the presence locations of the species, and by using four common statistical metrics to compare modeled distributions. For two widespread invasive taxa ( Bromus tectorum or cheatgrass, and Tamarix spp. or tamarisk), GCM-based models failed miserably to reproduce observed species distributions. In contrast, RCM-based species distribution models closely matched observations. Future species distributions may be significantly affected by using GCM-based inputs. Because invasive plants species often show high resilience and low rates of local extinction, RCM-based species distribution models may perform better than GCM-based species distribution models for planning containment programs for invasive species.

  3. Complete mitochondrial genome of Military Macaw (Ara militaris): its comparison with mitogenomes of two other Ara species.

    PubMed

    Dawid Urantowka, Adam

    2016-09-01

    The Military Macaw is one of the eight species of the genus Ara. The genus is one of six genera, which form morphologically diverse group termed as Macaws. Parrots of this group differ in body size on demand of the genus and species. Six of Ara species are classified as large Macaws. Based on morphological similarities and differences, these species can be segregated into three pairs according to their plumage coloration. Representative mitochondrial genomes were sequenced only for A. glaucogularis (blue and yellow coloration) and A. macao (predominantly red/scarlet). Ara militaris is one of two predominantly green species and full mitochondrial genome of considered species was sequenced in this study. It's comparison with A. glaucogularis and A. macao mitogenomes revealed higher degree of identity between militaris and macao sequences than between militaris and glaucogularis mtDNAs. Ara militaris mitogenome will be indispensable to refine the phylogenetic relationships within Macaw group. PMID:25703844

  4. On species sampling sequences induced by residual allocation models.

    PubMed

    Rodríguez, Abel; Quintana, Fernando A

    2015-02-01

    We discuss fully Bayesian inference in a class of species sampling models that are induced by residual allocation (sometimes called stick-breaking) priors on almost surely discrete random measures. This class provides a generalization of the well-known Ewens sampling formula that allows for additional flexibility while retaining computational tractability. In particular, the procedure is used to derive the exchangeable predictive probability functions associated with the generalized Dirichlet process of Hjort (2000) and the probit stick-breaking prior of Chung and Dunson (2009) and Rodriguez and Dunson (2011). The procedure is illustrated with applications to genetics and nonparametric mixture modeling. PMID:25477705

  5. On species sampling sequences induced by residual allocation models

    PubMed Central

    Rodríguez, Abel; Quintana, Fernando A.

    2014-01-01

    We discuss fully Bayesian inference in a class of species sampling models that are induced by residual allocation (sometimes called stick-breaking) priors on almost surely discrete random measures. This class provides a generalization of the well-known Ewens sampling formula that allows for additional flexibility while retaining computational tractability. In particular, the procedure is used to derive the exchangeable predictive probability functions associated with the generalized Dirichlet process of Hjort (2000) and the probit stick-breaking prior of Chung and Dunson (2009) and Rodriguez and Dunson (2011). The procedure is illustrated with applications to genetics and nonparametric mixture modeling. PMID:25477705

  6. ClusCo: clustering and comparison of protein models

    PubMed Central

    2013-01-01

    Background The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main reason for the development of Clusco software was to create a high-throughput tool for all-versus-all comparison, because calculating similarity matrix is the one of the bottlenecks in the protein modeling pipeline. Results Clusco is fast and easy-to-use software for high-throughput comparison of protein models with different similarity measures (cRMSD, dRMSD, GDT_TS, TM-Score, MaxSub, Contact Map Overlap) and clustering of the comparison results with standard methods: K-means Clustering or Hierarchical Agglomerative Clustering. Conclusions The application was highly optimized and written in C/C++, including the code for parallel execution on CPU and GPU, which resulted in a significant speedup over similar clustering and scoring computation programs. PMID:23433004

  7. Dynamic models for problems of species occurrence with multiple states

    USGS Publications Warehouse

    MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

    2009-01-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture?recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics.

  8. Modeling species occurrence dynamics with multiple states and imperfect detection

    USGS Publications Warehouse

    MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

    2009-01-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture-recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics. ?? 2009 by the Ecological Society of America.

  9. Species distribution modelling for conservation of an endangered endemic orchid

    PubMed Central

    Wang, Hsiao-Hsuan; Wonkka, Carissa L.; Treglia, Michael L.; Grant, William E.; Smeins, Fred E.; Rogers, William E.

    2015-01-01

    Concerns regarding the long-term viability of threatened and endangered plant species are increasingly warranted given the potential impacts of climate change and habitat fragmentation on unstable and isolated populations. Orchidaceae is the largest and most diverse family of flowering plants, but it is currently facing unprecedented risks of extinction. Despite substantial conservation emphasis on rare orchids, populations continue to decline. Spiranthes parksii (Navasota ladies' tresses) is a federally and state-listed endangered terrestrial orchid endemic to central Texas. Hence, we aimed to identify potential factors influencing the distribution of the species, quantify the relative importance of each factor and determine suitable habitat for future surveys and targeted conservation efforts. We analysed several geo-referenced variables describing climatic conditions and landscape features to identify potential factors influencing the likelihood of occurrence of S. parksii using boosted regression trees. Our model classified 97 % of the cells correctly with regard to species presence and absence, and indicated that probability of existence was correlated with climatic conditions and landscape features. The most influential variables were mean annual precipitation, mean elevation, mean annual minimum temperature and mean annual maximum temperature. The most likely suitable range for S. parksii was the eastern portions of Leon and Madison Counties, the southern portion of Brazos County, a portion of northern Grimes County and along the borders between Burleson and Washington Counties. Our model can assist in the development of an integrated conservation strategy through: (i) focussing future survey and research efforts on areas with a high likelihood of occurrence, (ii) aiding in selection of areas for conservation and restoration and (iii) framing future research questions including those necessary for predicting responses to climate change. Our model could also

  10. Comparison between observed and calculated distributions of trace species in the middle atmosphere

    NASA Technical Reports Server (NTRS)

    Brasseur, G.; Derudder, A.

    1989-01-01

    The purpose is to identify major discrepancies between empirical models and theoretical models and to stress the need for additional observations in the atmosphere and for further laboratory work, since these differences suggest either problems associated with observation techniques or errors in chemical kinetics data (or the existence of unknown processes which appear to play an important role). The model used for this investigation extends from the earth's surface to the lower thermosphere. It includes the important chemical and photochemical processes related to the oxygen, hydrogen, carbon, nitrogen and chlorine families. The chemical code is coupled with a radiative scheme which provides the heating rate due to absorption of solar radiation by ozone and the cooling rate due to the emission and absorption of terrestrial radiation by CO2, H2O and O3. The vertical transport of the species is expressed by an eddy diffusion parameterization.

  11. THE NORTH AMERICAN MERCURY MODEL INTER-COMPARISON STUDY (NAMMIS)

    EPA Science Inventory

    This paper describes the North American Mercury Model Inter-comparison Study (NAMMIS). The NAMMIS is an effort to apply atmospheric Hg models in a tightly constrained testing environment with a focus on North America. With each model using the same input data sets for initial co...

  12. Ares 1X Hybrid Modeling with Comparisons to Flight Data

    NASA Technical Reports Server (NTRS)

    Niedermaier, Dan; Kaouk, Mo

    2010-01-01

    This slide presentation reviews the Ares 1X test flight and compares the resultant flight data with the results of modeled data from siumulations of the flight. It includes: (1) Ares 1X Flight Summary, (2) Ares 1X Data Summary (3) Model Descriptions (4) Model Comparisons to Flight Data in three areas: (a) Liftoff, (b) Transonic and (c) Roll Control Firings (RCS) Firings.

  13. The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling

    PubMed Central

    Wisz, Mary Susanne; Pottier, Julien; Kissling, W Daniel; Pellissier, Loïc; Lenoir, Jonathan; Damgaard, Christian F; Dormann, Carsten F; Forchhammer, Mads C; Grytnes, John-Arvid; Guisan, Antoine; Heikkinen, Risto K; Høye, Toke T; Kühn, Ingolf; Luoto, Miska; Maiorano, Luigi; Nilsson, Marie-Charlotte; Normand, Signe; Öckinger, Erik; Schmidt, Niels M; Termansen, Mette; Timmermann, Allan; Wardle, David A; Aastrup, Peter; Svenning, Jens-Christian

    2013-01-01

    Predicting which species will occur together in the future, and where, remains one of the greatest challenges in ecology, and requires a sound understanding of how the abiotic and biotic environments interact with dispersal processes and history across scales. Biotic interactions and their dynamics influence species' relationships to climate, and this also has important implications for predicting future distributions of species. It is already well accepted that biotic interactions shape species' spatial distributions at local spatial extents, but the role of these interactions beyond local extents (e.g. 10 km2 to global extents) are usually dismissed as unimportant. In this review we consolidate evidence for how biotic interactions shape species distributions beyond local extents and review methods for integrating biotic interactions into species distribution modelling tools. Drawing upon evidence from contemporary and palaeoecological studies of individual species ranges, functional groups, and species richness patterns, we show that biotic interactions have clearly left their mark on species distributions and realised assemblages of species across all spatial extents. We demonstrate this with examples from within and across trophic groups. A range of species distribution modelling tools is available to quantify species environmental relationships and predict species occurrence, such as: (i) integrating pairwise dependencies, (ii) using integrative predictors, and (iii) hybridising species distribution models (SDMs) with dynamic models. These methods have typically only been applied to interacting pairs of species at a single time, require a priori ecological knowledge about which species interact, and due to data paucity must assume that biotic interactions are constant in space and time. To better inform the future development of these models across spatial scales, we call for accelerated collection of spatially and temporally explicit species data. Ideally

  14. Description and comparison of two economically important fish species mitogenomes: Prochilodus argenteus and Prochilodus costatus (Characiformes, Prochilodontidae).

    PubMed

    Chagas, Aline Torres de Azevedo; Carmo, Anderson Oliveira; Costa, Maísa Aparecida; Resende, Leonardo Cardoso; Brandão Dias, Pedro Ferreira Pinto; Martins, Ana Paula Vimieiro; Kalapothakis, Evanguedes

    2016-07-01

    Prochilodus spp. are important Brazilian freshwater migratory fishes with substantial economic and ecological importance. Prochilodus argenteus and Prochilodus costatus are morphologically similar and a molecular species delimitation is impaired due to high degree of sequence identity among the available genetic markers. Here, the complete mitochondrial genome of P. argenteus and P. costatus and their comparison to the mitogenome of P. lineatus are described. The three species displayed a similar mtDNA annotation. A phylogenetic analysis was performed with other Characiformes species. The genus Prochilodus was recovered as a monophyletic group, as well as the family Prochilodontidae, both with high bootstrap probability. PMID:26171874

  15. Modelling Canopy Photosynthesis for Two Grassland Competing Species

    NASA Astrophysics Data System (ADS)

    Silva, Brenner; Bendix, Jorg

    2011-01-01

    A modelling approach have been used to investigate two competing species in grassland areas in the Southern Andes of Ecuador. In this approach a land surface model framework has been used, which includes evaluation of the radiation transfer, the biochemistry of photosynthesis and the plant rooting systems. For a proper parameterization of new average individuals, field and laboratory measurements have been undertaken, in which two photosynthetic pathways are considered, the C3 bracken fern and the C4 Setaria pasture grass. In addition shade acclimation is considered by duplicating measurements on shade and sunlit leaves. As a result, canopy net assimilation and potential primary productivity could be simulated for these two competing species in a very good agreement with measurements and literature data. It is shown that the exotic pasture grass is still competitive, despite contrary field observations. Most of land surface models has the same implementation being investigated here, which makes insights of a detailed one-dimensional approach valuable and easy extendable to a spatial explicit model.

  16. A comparison of the toxinological characteristics of two Cassiopea and Aurelia species.

    PubMed

    Radwan, F F; Burnett, J W; Bloom, D A; Coliano, T; Eldefrawi, M E; Erderly, H; Aurelian, L; Torres, M; Heimer-de la Cotera, E P

    2001-01-01

    A comparison of the toxinological properties of nematocyst venoms from Old and New World Cassiopea and Aurelia species was undertaken. The cnidom of venomous Cassiopea andromeda (Ca) and Aurelia (Aa(RS)) from the Red Sea was identical to that of nonvenomous Bahamian Cassiopea xamancha (Cx) and Chesapeake Bay Aurelia aurita (Aa(CB)), respectively. A clean nematocyst preparation of Ca and both Aurelias could be obtained but algal particles could not be separated completely from the Cx nematocysts. Further purification of all four nematocyst preparations showed significant differences in the action of their protein. Only the Cassiopea had coexisting dermonecrotic and vasopermeability producing properties and Ca's hemolytic activity was associated with mouse lethality. The protein, hemolysin and phospholipase gel filtration eluant curves of Ca venom were similar. Venomous Aa(RS) actively stung lips and contained more potent mouse lethal, demonecrotic, vasopermeability plus hemolytic factors than Aa(CB). Cross reactivity of convalescent human serum obtained from patients stung by Ca and venomous Cx collected in Central America occurred. This was also observed between sera of bathers stung by Aa(RS) and stinging Aurelia which appeared in Florida during the recent El Niño year. IgG was stimulated by several nematocyst proteins since many venom subfractions tested positive at high titers against convalescent sera. T-cell proliferation of mice primed with either Aurelia venom was positive against the homologous preparation with cross reactivity to the heterologous venom. Crude venoms of both Red Sea jellyfish metabolically stimulated cultured human hepatocytes more than their New World counterparts. This data shows that considerable similarities and differences exist in the venoms of these Old and New World Cassiopea and Aurelia medusae with the Eastern species being more potent. PMID:10978742

  17. Comparison of tryptophan biosynthetic operon regulation in different Gram-positive bacterial species.

    PubMed

    Gutiérrez-Preciado, Ana; Yanofsky, Charles; Merino, Enrique

    2007-09-01

    The tryptophan biosynthetic operon has been widely used as a model system for studying transcription regulation. In Bacillus subtilis, the trp operon is primarily regulated by a tryptophan-activated RNA-binding protein, TRAP. Here we show that in many other Gram-positive species the trp operon is regulated differently, by tRNA(Trp) sensing by the RNA-based T-box mechanism, with T-boxes arranged in tandem. Our analyses reveal an apparent relationship between trp operon organization and the specific regulatory mechanism(s) used. PMID:17555843

  18. A cross-modal, cross-species comparison of connectivity measures in the primate brain.

    PubMed

    Reid, Andrew T; Lewis, John; Bezgin, Gleb; Khundrakpam, Budhachandra; Eickhoff, Simon B; McIntosh, Anthony R; Bellec, Pierre; Evans, Alan C

    2016-01-15

    In systems neuroscience, the term "connectivity" has been defined in numerous ways, according to the particular empirical modality from which it is derived. Due to large differences in the phenomena measured by these modalities, the assumptions necessary to make inferences about axonal connections, and the limitations accompanying each, brain connectivity remains an elusive concept. Despite this, only a handful of studies have directly compared connectivity as inferred from multiple modalities, and there remains much ambiguity over what the term is actually referring to as a biological construct. Here, we perform a direct comparison based on the high-resolution and high-contrast Enhanced Nathan Klein Institute (NKI) Rockland Sample neuroimaging data set, and the CoCoMac database of tract tracing studies. We compare four types of commonly-used primate connectivity analyses: tract tracing experiments, compiled in CoCoMac; group-wise correlation of cortical thickness; tractographic networks computed from diffusion-weighted MRI (DWI); and correlational networks obtained from resting-state BOLD (fMRI). We find generally poor correspondence between all four modalities, in terms of correlated edge weights, binarized comparisons of thresholded networks, and clustering patterns. fMRI and DWI had the best agreement, followed by DWI and CoCoMac, while other comparisons showed striking divergence. Networks had the best correspondence for local ipsilateral and homotopic contralateral connections, and the worst correspondence for long-range and heterotopic contralateral connections. k-Means clustering highlighted the lowest cross-modal and cross-species consensus in lateral and medial temporal lobes, anterior cingulate, and the temporoparietal junction. Comparing the NKI results to those of the lower resolution/contrast International Consortium for Brain Imaging (ICBM) dataset, we find that the relative pattern of intermodal relationships is preserved, but the correspondence

  19. Equations for water-triolein partition coefficients for neutral species; comparison with other water-solvent partitions, and environmental and toxicological processes.

    PubMed

    Abraham, Michael H; Acree, William E

    2016-07-01

    Linear free energy relationships, LFERs, have been constructed for water-triolein partition coefficients for neutral species. It is shown that separate equations are required for wet and dry triolein. From a comparison of the equation coefficients for water-wet triolein with those for 52 other water-solvent systems it is shown that there is little correspondence between triolein and any of the 52 other solvents - only the water-isopropyl myristate system is close to the water-wet triolen system. A comparison of equation coefficients for the water-wet triolein system with LFER coefficients of 16 environmentally important processes shows that wet triolein is not a suitable model for any of the processes, although a number of other water-solvent systems are possible models for some of the environmental processes. A comparison of LFER coefficients with those of 17 aqueous toxicological processes reveals that most of the water-solvent systems, including water-wet triolein, will be poor models for any of the toxicological systems, but the water-lower alcohol systems show promise as models for a number of the toxicological systems. Our method of comparison of coefficients for LFERs that have exactly the same independent variables can be extended to various other types of system. PMID:27038899

  20. Performance of Candida ID, a New Chromogenic Medium for Presumptive Identification of Candida Species, in Comparison to CHROMagar Candida

    PubMed Central

    Willinger, Birgit; Hillowoth, Cornelia; Selitsch, Brigitte; Manafi, Mammad

    2001-01-01

    Candida ID agar allows identification of Candida albicans and differentiation of other Candida species. In comparison with CHROMagar Candida, we evaluated the performance of this medium directly from 596 clinical specimens. In particular, detection of C. albicans after 24 h of incubation was easier on Candida ID (sensitivity, 96.8%) than on CHROMagar (sensitivity, 49.6%). PMID:11574621

  1. A comparison of regional and national values for recovering threatened and endangered marine species in the United States.

    PubMed

    Wallmo, Kristy; Lew, Daniel K

    2016-09-01

    It is generally acknowledged that willingness-to-pay (WTP) estimates for environmental goods exhibit some degree of spatial variation. In a policy context, spatial variation in threatened and endangered species values is important to understand, as the benefit stream from policies affecting threatened and endangered species may vary locally, regionally, or among certain population segments. In this paper we present WTP estimates for eight different threatened and endangered marine species estimated from a stated preference choice experiment. WTP is estimated at two different spatial scales: (a) a random sample of over 5000 U.S. households and (b) geographically embedded samples (relative to the U.S. household sample) of nine U.S. Census regions. We conduct region-to-region and region-to-nation statistical comparisons to determine whether species values differ among regions and between each region and the entire U.S. Our results show limited spatial variation between national values and values estimated from regionally embedded samples, and differences are only found for three of the eight species. More variation exists between regions, and for all species there is a significant difference in at least one region-to-region comparison. Given that policy analyses involving threatened and endangered marine species can often be regional in scope (e.g., ecosystem management) or may disparately affect different regions, our results should be of high interest to the marine management community. PMID:27160027

  2. Sequence similarity and functional comparisons of pheromone receptor orthologs in two closely related Helicoverpa species.

    PubMed

    Jiang, Xiao-Jing; Guo, Hao; Di, Chang; Yu, Shanlin; Zhu, Ligui; Huang, Ling-Qiao; Wang, Chen-Zhu

    2014-05-01

    The olfactory system of moth species in subfamily Heliothinae is an attractive model to study the evolution of the pheromone reception because they show distinct differentiation in sex pheromone components or ratios that activate pheromone receptors (PRs). However, functional assessment of PRs in closely related species remains largely untried. Here we present a special cloning strategy to isolate full-length cDNAs encoding candidate odorant receptors (ORs) from Helicoverpa armigera (Harm) and Helicoverpa assulta (Hass) on the basis of Heliothis virescens ORs, and investigate the functional properties of PRs to determine how the evolution of moth PRs contribute to intraspecific mating choice and speciation extension. We cloned 11 OR orthologs from H. armigera and 10 from H. assulta. We functionally characterized the responses of PRs of both species to seven pheromone compounds using the heterologous expression system of Xenopus ooctyes. HassOR13 was found to be highly tuned to the sex pheromone component Z11-16:Ald, and unexpectedly, both HarmOR14b and HassOR16 were specific for Z9-14:Ald. However, HarmOR6 and HassOR6 showed much higher specificity to Z9-16:OH than to Z9-16:Ald or Z9-14:Ald. HarmOR11, HarmOR14a, HassOR11 and HassOR14b failed to respond to the tested chemicals. Based on our results and previous research, we can show that some PR orthologs from H. armigera, H. assulta and H. virescens such as OR13s have similar ligand selectivity, but others have different ligand specificity. The combined PR function and sex pheromone component analysis suggests that the evolution of PRs can meet species-specific demands. PMID:24632377

  3. Modeling metapopulation dynamics for single species of seabirds

    USGS Publications Warehouse

    Buckley, P.A.; Downer, R.

    1992-01-01

    Seabirds share many characteristics setting them apart from other birds. Importantly, they breed more or less obligatorily in local clusters of colonies that can move regularly from site to site, and they routinely exchange breeders. The properties of such metapopulations have only recently begun to be examined, often with models that are occupancy-based (using only colony presence or absence data) and deterministic (using single, empirically determined values for each of several population biology parameters). Some recent models are now frequency-based (using actual population sizes at each site), as well as stochastic (randomly varying critical parameters between biologically realistic limits), yielding better estimates of the behavior of future populations. Using two such models designed to quantify relative risks of population changes under different future scenarios (RAMAS/stage and RAMAS/space), we have examined probable future populations dynamics for three hypothetical seabirds -- an albatross, a cormorant, and a tern. With real parameters and ranges of values we alternatively modelled each species with and without density dependence, as well as with their numbers in a single, large colony, or in many smaller ones, distributed evenly or lognormally. We produced a series of species-typical lines for different population risks over the 50 years we simulated. We call these curves Instantaneous Threat Assessments (ITAs), and their shapes mirror the varying life history characteristics of our three species. We also demonstrated (by a process known as sensitivity analysis) that the most important parameters determining future population fates of all three species were correlation of mean growth rate among colonies; dispersal rate of present and future breeders; subadult survivorship; and the number of subpopulations (=colonies) - in roughly that descending order of importance. In addition, density dependence was found to markedly alter ITA line shape and position

  4. ESTIMATION OF CHEMICAL TOXICITY TO WILDLIFE SPECIES USING INTERSPECIES CORRELATION MODELS

    EPA Science Inventory

    Ecological risks to wildlife are typically assessed using toxicity data for relataively few species and with limited understanding of differences in species sensitivity to contaminants. Empirical interspecies correlation models were derived from LD50 values for 49 wildlife speci...

  5. Occupancy modeling and estimation of the holiday darter species complex within the Etowah River system

    USGS Publications Warehouse

    Anderson, Gregory B.; Freeman, Mary C.; Hagler, Megan M.; Freeman, Byron J.

    2012-01-01

    Documenting the status of rare fishes is a crucial step in effectively managing populations and implementing regulatory mechanisms of protection. In recent years, site occupancy has become an increasingly popular metric for assessing populations, but species distribution models that do not account for imperfect detection can underestimate the proportion of sites occupied and the strength of the relationship with a hypothesized covariate. However, valid detection requires temporal or spatial replication, which is often not feasible due to logistical or budget constraints. In this study, we used a method that allowed for spatial replication during a single visit to evaluate the current status of the holiday darter species complex, Etheostoma sp. cf. E. brevirostrum, within the Etowah River system. Moreover, the modeling approach used in this study facilitated comparisons of factors influencing stream occupancy as well as species detection within sites. The results suggest that there is less habitat available for the Etowah holiday darter form (Etheostoma sp. cf. E. brevirostrum B) than for the Amicalola holiday darter form (Etheostoma sp. cf. E. brevirostrum A). Additionally, occupancy models suggest that even small decreases in forest cover within these headwater systems adversely affect holiday darter populations.

  6. Confirmatory Measurement Model Comparisons Using Latent Means.

    ERIC Educational Resources Information Center

    Millsap, Roger E.; Everson, Howard

    1991-01-01

    Use of confirmatory factor analysis (CFA) with nonzero latent means in testing six different measurement models from classical test theory is discussed. Implications of the six models for observed mean and covariance structures are described, and three examples of the use of CFA in testing the models are presented. (SLD)

  7. Hidden diversity in the Andes: comparison of species delimitation methods in montane marsupials.

    PubMed

    Giarla, Thomas C; Voss, Robert S; Jansa, Sharon A

    2014-01-01

    Cryptic genetic diversity is a significant challenge for systematists faced with ever-increasing amounts of DNA sequence data. Computationally intensive coalescent-based analyses involving multiple unlinked loci are the only currently viable methods by which to assess the extent to which phenotypically similar populations (or metapopulations) are genetically distinct lineages. Although coalescent-based approaches have been tested extensively via simulations, few empirical studies have examined the impact of prior assumptions and dataset size on the ability to assess genetic isolation (evolutionary independence) using molecular data alone. Here, we consider the efficacy of two coalescent-based approaches (BPP and SpeDeSTEM) for testing the evolutionary independence of cryptic mtDNA haplogroups within three morphologically diagnosable species of Andean mouse opossums (Thylamys pallidior, T. sponsorius, and T. venustus). Fourteen anonymous nuclear loci, one X-linked nuclear intron, and one mitochondrial gene were analyzed for multiple individuals within each haplogroup of interest. We inferred individual gene trees for each locus and considered all of the nuclear loci jointly in a species-tree analysis. Using only the nuclear loci, we performed "species validation" tests for the cryptic mitochondrial lineages in SpeDeSTEM and BPP. For BPP, we also tested a wide range of prior assumptions, assessed performance of the rjMCMC algorithm, and examined how many loci were necessary to confidently delimit lineages. Results from BPP provided strong support for two independent evolutionary lineages each within T. pallidior, T. sponsorius, and T. venustus, whereas SpeDeSTEM results did not support splitting out mtDNA haplogroups as distinct evolutionary units. For most tests, BPP was robust to prior assumptions, although priors were shown to have an effect on both the strength of lineage recognition among T. venustus haplotypes and on the efficiency of the rjMCMC algorithm

  8. Prediction of Desiccation Sensitivity in Seeds of Woody Species: A Probabilistic Model Based on Two Seed Traits and 104 Species

    PubMed Central

    DAWS, M. I.; GARWOOD, N. C.; PRITCHARD, H. W.

    2006-01-01

    • Background and Aims Seed desiccation sensitivity limits the ex situ conservation of up to 47 % of plant species, dependent on habitat. Whilst desirable, empirically determining desiccation tolerance levels in seeds of all species is unrealistic. A probabilistic model for the rapid identification of woody species at high risk of displaying seed desiccation sensitivity is presented. • Methods The model was developed using binary logistic regression on seed trait data [seed mass, moisture content, seed coat ratio (SCR) and rainfall in the month of seed dispersal] for 104 species from 37 families from a semi-deciduous tropical forest in Panamá. • Key Results For the Panamanian species, only seed mass and SCR were significantly related to the response to desiccation, with the desiccation-sensitive seeds being large and having a relatively low SCR (i.e. thin ‘seed’ coats). Application of this model to a further 38 species, of known seed storage behaviour, from two additional continents and differing vegetation types (dryland Africa and temperate Europe) correctly predicted the response to desiccation in all cases, and resolved conflicting published data for two species (Acer pseudoplatanus and Azadirachta indica). • Conclusions This model may have application as a decision-making tool in the handling of species of unknown seed storage behaviour in species from three disparate habitats. PMID:16464874

  9. Comparison of Recognized Pestivirus Species with Two New Putative Species Represented by the Strains Pronghorn and Bungowannah

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aim: Currently four species of pestiviruses are recognized by the International Committee on Viral Taxonomy (ICTV). They are bovine viral diarrhea virus genotype 1 (BVDV1), bovine viral diarrhea virus genotype 2 (BVDV2), border disease virus (BDV) and classical swine fever virus (CSFV). A tentati...

  10. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

    NASA Technical Reports Server (NTRS)

    Haney, P. J.; Badger, J. H.; Buldak, G. L.; Reich, C. I.; Woese, C. R.; Olsen, G. J.

    1999-01-01

    The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs from mesophilic Methanococcus species. Although the growth temperatures of the mesophiles are about 50 degrees C below that of M. jannaschii, their genomic G+C contents are nearly identical. The properties most correlated with the proteins of the thermophile include higher residue volume, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and fewer uncharged polar residues (Ser, Thr, Asn, and Gln). These are recurring themes, with all trends applying to 83-92% of the proteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature change are the same relatively conservative changes observed in all proteins, but in the case of the mesophile/thermophile comparison there is a directional bias. We identify 26 specific pairs of amino acids with a statistically significant (P < 0.01) preferred direction of replacement.

  11. Comparison of nonerythroid alpha-spectrin genes reveals strict homology among diverse species.

    PubMed Central

    Leto, T L; Fortugno-Erikson, D; Barton, D; Yang-Feng, T L; Francke, U; Harris, A S; Morrow, J S; Marchesi, V T; Benz, E J

    1988-01-01

    The spectrins are a family of widely distributed filamentous proteins. In association with actin, spectrins form a supporting and organizing scaffold for cell membranes. Using antibodies specific for human brain alpha-spectrin (alpha-fodrin), we have cloned a rat brain alpha-spectrin cDNA from an expression library. Several closely related human clones were also isolated by hybridization. Comparison of sequences of these and other overlapping nonerythroid and erythroid alpha-spectrin genes demonstrated that the nonerythroid genes are strictly conserved across species, while the mammalian erythroid genes have diverged rapidly. Peptide sequences deduced from these cDNAs revealed that the nonerythroid alpha-spectrin chain, like the erythroid spectrin, is composed of multiple 106-amino-acid repeating units, with the characteristic invariant tryptophan as well as other charged and hydrophobic residues in conserved locations. However, the carboxy-terminal sequence varies markedly from this internal repeat pattern and may represent a specialized functional site. The nonerythroid alpha-spectrin gene was mapped to human chromosome 9, in contrast to the erythroid alpha-spectrin gene, which has previously been assigned to a locus on chromosome 1. Images PMID:3336352

  12. Reference gene selection for cross-species and cross-ploidy level comparisons in Chrysanthemum spp.

    PubMed Central

    Wang, Haibin; Chen, Sumei; Jiang, Jiafu; Zhang, Fei; Chen, Fadi

    2015-01-01

    The establishment of a (set of) stably expressed reference gene(s) is required to normalize transcription data. Polyploidy is very common in the plant kingdom, but it is not necessarily the case that a reference gene which works well at the diploid level will also work well at the polyploid level. Here, ten candidate reference genes are compared in the context of gene transcription in the genus Chrysanthemum. The robustness of some, but not all, of these was shown to be high across ploidy levels. MTP (metalloprotease) and ACTIN (actin) were the most stable in diploid and tetraploid C. nankingense, while PSAA (photosynthesis-related plastid gene representing photosystem I) and EF-1α (elongation factor-1α) were the most stable in tetraploid and hexaploid C. zawadskii. EF-1α and PGK (phosphoglycerate kinase) was the best combination for the complete set of four taxa. These results suggest that when making cross-species comparison of transcript abundance involving different ploidy levels, care needs to be taken in the selection of reference gene(s). PMID:25627791

  13. Turbulent Chemical Interaction Models in NCC: Comparison

    NASA Technical Reports Server (NTRS)

    Norris, Andrew T.; Liu, Nan-Suey

    2006-01-01

    The performance of a scalar PDF hydrogen-air combustion model in predicting a complex reacting flow is evaluated. In addition the results are compared to those obtained by running the same case with the so-called laminar chemistry model and also a new model based on the concept of mapping partially stirred reactor data onto perfectly stirred reactor data. The results show that the scalar PDF model produces significantly different results from the other two models, and at a significantly higher computational cost.

  14. Refining Pathways: A Model Comparison Approach

    PubMed Central

    Moffa, Giusi; Erdmann, Gerrit; Voloshanenko, Oksana; Hundsrucker, Christian; Sadeh, Mohammad J.; Boutros, Michael; Spang, Rainer

    2016-01-01

    Cellular signalling pathways consolidate multiple molecular interactions into working models of signal propagation, amplification, and modulation. They are described and visualized as networks. Adjusting network topologies to experimental data is a key goal of systems biology. While network reconstruction algorithms like nested effects models are well established tools of computational biology, their data requirements can be prohibitive for their practical use. In this paper we suggest focussing on well defined aspects of a pathway and develop the computational tools to do so. We adapt the framework of nested effect models to focus on a specific aspect of activated Wnt signalling in HCT116 colon cancer cells: Does the activation of Wnt target genes depend on the secretion of Wnt ligands or do mutations in the signalling molecule β-catenin make this activation independent from them? We framed this question into two competing classes of models: Models that depend on Wnt ligands secretion versus those that do not. The model classes translate into restrictions of the pathways in the network topology. Wnt dependent models are more flexible than Wnt independent models. Bayes factors are the standard Bayesian tool to compare different models fairly on the data evidence. In our analysis, the Bayes factors depend on the number of potential Wnt signalling target genes included in the models. Stability analysis with respect to this number showed that the data strongly favours Wnt ligands dependent models for all realistic numbers of target genes. PMID:27248690

  15. A comparison of needle bending models.

    PubMed

    Dehghan, Ehsan; Goksel, Orcun; Salcudean, Septimiu E

    2006-01-01

    Modeling the deflection of flexible needles is an essential part of needle insertion simulation and path planning. In this paper, three models are compared in terms of accuracy in simulating the bending of a prostate brachytherapy needle. The first two utilize the finite element method, one using geometric non-linearity and triangular plane elements, the other using non-linear beam elements. The third model uses angular springs to model cantilever deflection. The simulations are compared with the experimental bent needle configurations. The models are assessed in terms of geometric conformity using independently identified and pre-identified model parameters. The results show that the angular spring model, which is also the simplest, simulates the needle more accurately than the others. PMID:17354904

  16. A comparison of viscoelastic damping models

    NASA Technical Reports Server (NTRS)

    Slater, Joseph C.; Belvin, W. Keith; Inman, Daniel J.

    1993-01-01

    Modern finite element methods (FEM's) enable the precise modeling of mass and stiffness properties in what were in the past overwhelmingly large and complex structures. These models allow the accurate determination of natural frequencies and mode shapes. However, adequate methods for modeling highly damped and high frequency dependent structures did not exist until recently. The most commonly used method, Modal Strain Energy, does not correctly predict complex mode shapes since it is based on the assumption that the mode shapes of a structure are real. Recently, many techniques have been developed which allow the modeling of frequency dependent damping properties of materials in a finite element compatible form. Two of these methods, the Golla-Hughes-McTavish method and the Lesieutre-Mingori method, model the frequency dependent effects by adding coordinates to the existing system thus maintaining the linearity of the model. The third model, proposed by Bagley and Torvik, is based on the Fractional Calculus method and requires fewer empirical parameters to model the frequency dependence at the expense of linearity of the governing equations. This work examines the Modal Strain Energy, Golla-Hughes-McTavish and Bagley and Torvik models and compares them to determine the plausibility of using them for modeling viscoelastic damping in large structures.

  17. Telehomecare: a comparison of three Canadian models.

    PubMed

    Young, Nancy L; Barden, Wendy; Lefort, Sandra; Nijssen-Jordan, Cheri; Daniels, Carolyn; Booth, Marilyn; Dick, Paul T

    2004-01-01

    The delivery of health care is often segmented into sectors. In Canada, hospital care has traditionally been distinct from community care, and thus the transition of patients across sectors has been challenging. This paper focuses on the systematic development of an integrated model of care for children, for the purpose of smoothing the transition from hospital to home. The new service model uses emerging telecommunications technology to link hospital care providers to patients at home and is termed "telehomecare" (THC). Independent models of THC were developed for three sites across Canada through semistructured interviews and focus groups. Participants included health care providers and administrators from the hospital and community, and patient families. The resulting models were compared using content analysis to determine whether there was a core model of THC that was generalisable across Canada. A core model of THC was identified that includes the use of videoconferencing to enable the integration of hospital- and community-based care to support patients during the initial stages of the transition to home. Each site also articulated unique characteristics in their service model that were related to the nature of their health care delivery system and patient population. This paper describes the core model of transitional care, presents a synopsis of each of the three models, and compares the models. THC provides opportunities to address limitations in the current system and to improve upon equity of access to quality care for children making the transition from hospital to home. PMID:15104915

  18. Traffic flow forecasting: Comparison of modeling approaches

    SciTech Connect

    Smith, B.L.; Demetsky, M.J.

    1997-08-01

    The capability to forecast traffic volume in an operational setting has been identified as a critical need for intelligent transportation systems (ITS). In particular, traffic volume forecasts will support proactive, dynamic traffic control. However, previous attempts to develop traffic volume forecasting models have met with limited success. This research effort focused on developing traffic volume forecasting models for two sites on Northern Virginia`s Capital Beltway. Four models were developed and tested for the freeway traffic flow forecasting problem, which is defined as estimating traffic flow 15 min into the future. They were the historical average, time-series, neural network, and nonparametric regression models. The nonparametric regression model significantly outperformed the other models. A Wilcoxon signed-rank test revealed that the nonparametric regression model experienced significantly lower errors than the other models. In addition, the nonparametric regression model was easy to implement, and proved to be portable, performing well at two distinct sites. Based on its success, research is ongoing to refine the nonparametric regression model and to extend it to produce multiple interval forecasts.

  19. Comparison of statistical and theoretical habitat models for conservation planning: the benefit of ensemble prediction

    USGS Publications Warehouse

    Jones-Farrand, D. Todd; Fearer, Todd M.; Thogmartin, Wayne E.; Thompson, Frank R., III; Nelson, Mark D.; Tirpak, John M.

    2011-01-01

    Selection of a modeling approach is an important step in the conservation planning process, but little guidance is available. We compared two statistical and three theoretical habitat modeling approaches representing those currently being used for avian conservation planning at landscape and regional scales: hierarchical spatial count (HSC), classification and regression tree (CRT), habitat suitability index (HSI), forest structure database (FS), and habitat association database (HA). We focused our comparison on models for five priority forest-breeding species in the Central Hardwoods Bird Conservation Region: Acadian Flycatcher, Cerulean Warbler, Prairie Warbler, Red-headed Woodpecker, and Worm-eating Warbler. Lacking complete knowledge on the distribution and abundance of each species with which we could illuminate differences between approaches and provide strong grounds for recommending one approach over another, we used two approaches to compare models: rank correlations among model outputs and comparison of spatial correspondence. In general, rank correlations were significantly positive among models for each species, indicating general agreement among the models. Worm-eating Warblers had the highest pairwise correlations, all of which were significant (P , 0.05). Red-headed Woodpeckers had the lowest agreement among models, suggesting greater uncertainty in the relative conservation value of areas within the region. We assessed model uncertainty by mapping the spatial congruence in priorities (i.e., top ranks) resulting from each model for each species and calculating the coefficient of variation across model ranks for each location. This allowed identification of areas more likely to be good targets of conservation effort for a species, those areas that were least likely, and those in between where uncertainty is higher and thus conservation action incorporates more risk. Based on our results, models developed independently for the same purpose

  20. nIFTy cosmology: comparison of galaxy formation models

    NASA Astrophysics Data System (ADS)

    Knebe, Alexander; Pearce, Frazer R.; Thomas, Peter A.; Benson, Andrew; Blaizot, Jeremy; Bower, Richard; Carretero, Jorge; Castander, Francisco J.; Cattaneo, Andrea; Cora, Sofia A.; Croton, Darren J.; Cui, Weiguang; Cunnama, Daniel; De Lucia, Gabriella; Devriendt, Julien E.; Elahi, Pascal J.; Font, Andreea; Fontanot, Fabio; Garcia-Bellido, Juan; Gargiulo, Ignacio D.; Gonzalez-Perez, Violeta; Helly, John; Henriques, Bruno; Hirschmann, Michaela; Lee, Jaehyun; Mamon, Gary A.; Monaco, Pierluigi; Onions, Julian; Padilla, Nelson D.; Power, Chris; Pujol, Arnau; Skibba, Ramin A.; Somerville, Rachel S.; Srisawat, Chaichalit; Vega-Martínez, Cristian A.; Yi, Sukyoung K.

    2015-08-01

    We present a comparison of 14 galaxy formation models: 12 different semi-analytical models and 2 halo occupation distribution models for galaxy formation based upon the same cosmological simulation and merger tree information derived from it. The participating codes have proven to be very successful in their own right but they have all been calibrated independently using various observational data sets, stellar models, and merger trees. In this paper, we apply them without recalibration and this leads to a wide variety of predictions for the stellar mass function, specific star formation rates, stellar-to-halo mass ratios, and the abundance of orphan galaxies. The scatter is much larger than seen in previous comparison studies primarily because the codes have been used outside of their native environment within which they are well tested and calibrated. The purpose of the `nIFTy comparison of galaxy formation models' is to bring together as many different galaxy formation modellers as possible and to investigate a common approach to model calibration. This paper provides a unified description for all participating models and presents the initial, uncalibrated comparison as a baseline for our future studies where we will develop a common calibration framework and address the extent to which that reduces the scatter in the model predictions seen here.

  1. Augmenting aquatic species sensitivity distributions with interspecies toxicity estimation models

    EPA Science Inventory

    Species sensitivity distributions (SSD) are cumulative distribution functions of species toxicity values. The SSD approach is increasingly being used in ecological risk assessment, but is often limited by available toxicity data necessary for diverse species representation. In ...

  2. Comparison of global and regional ionospheric models

    NASA Astrophysics Data System (ADS)

    Ranner, H.-P.; Krauss, S.; Stangl, G.

    2012-04-01

    Modelling of the Earth's ionosphere means the description of the variability of the vertical TEC (Total Electron Content) in dependence of geographic latitude and longitude, height, diurnal and seasonal variation as well as solar activity. Within the project GIOMO (next Generation near real-time IOnospheric MOdels) the objectives are the identification and consolidation of improved ionospheric modelling technologies. The global models Klobuchar (GPS) and NeQuick (currently in use by EGNOS, in future used by Galileo) are compared to the IGS (International GNSS Service) Final GIM (Global Ionospheric Map). Additionally a RIM (Regional Ionospheric Map) for Europe provided by CODE (Center for Orbit Determination in Europe) is investigated. Furthermore the OLG (Observatorium Lustbühel Graz) regional models are calculated for two test beds with different latitudes and extensions (Western Austria and the Aegean region). There are three different approaches, two RIMs are based on spherical harmonics calculated either from code or phase measurements and one RIM is based on a Taylor series expansion around a central point estimated from zero-difference observations. The benefits of regional models are the local flexibility using a dense network of GNSS stations. Near real-time parameters are provided within ten minutes after every clock hour. All models have been compared according to their general behavior, the ability to react upon extreme solar events and the robustness of estimation. A ranking of the different models showed a preference for the RIMs while the global models should be used within a fall-back strategy.

  3. Radiation Belt Modeling for Spacecraft Design: Model Comparisons for Common Orbits

    NASA Technical Reports Server (NTRS)

    Lauenstein, J.-M.; Barth, J. L.

    2005-01-01

    We present the current status of radiation belt modeling, providing model details and comparisons with AP-8 and AE-8 for commonly used orbits. Improved modeling of the particle environment enables smarter space system design.

  4. Multi-Scale Multi-Species Modeling for Plasma Devices

    NASA Astrophysics Data System (ADS)

    Araki, Samuel Jun

    This dissertation describes three computational models developed to simulate important aspects of low-temperature plasma devices, most notably ring-cusp ion discharges and thrusters. The main findings of this dissertation are related to (1) the mechanisms of cusp confinement for micro-scale plasmas, (2) the implementation and merits of magnetic field aligned meshes, and (3) an improved method for describing heavy species interactions. The Single Cusp (SC) model focuses on the near-cusp region of the discharge chamber to investigate the near surface cusp confinement of a micro-scale plasma. The model employs the multi-species iterative Monte Carlo method and uses various advanced methods such as electric field calculation and particle weighting algorithm that are compatible with a non-uniform mesh in cylindrical coordinates. Three different plasma conditions are simulated with the SC model, including an electron plasma, a sparse plasma, and a weakly ionized plasma. It is found that the scaling of plasma loss to the cusp for a sparse plasma can be similar to that for a weakly ionized plasma, while the loss mechanism is significantly different; the primary electrons strongly influence the loss structure of the sparse plasma. The model is also used, along with experimental results, to describe the importance of the local magnetic field on the primary electron loss behavior at the cusp. Many components of the 2D/3D hybrid fluid/particle model (DC-ION) are improved from the original version. The DC-ION code looks at the macroscopic structure of the discharge plasma and can be used to address the design and optimization challenges of miniature to micro discharges on the order of 3 cm to 1 cm in diameter. Among the work done for DC-ION, detailed steps for the magnetic field aligned (MFA) mesh are provided. Solving the plasma diffusion equation in the ring-cusp configuration, the benefit of the MFA mesh has been fully investigated by comparing the solution with a uniform

  5. Climate Impact of Transportation A Model Comparison

    SciTech Connect

    Girod, Bastien; Van Vuuren, Detlef; Grahn, Maria; Kitous, Alban; Kim, Son H.; Kyle, G. Page

    2013-06-01

    Transportation contributes to a significant and rising share of global energy use and GHG emissions. Therefore modeling future travel demand, its fuel use, and resulting CO2 emission is highly relevant for climate change mitigation. In this study we compare the baseline projections for global service demand (passenger-kilometers, ton-kilometers), fuel use, and CO2 emissions of five different global transport models using harmonized input assumptions on income and population. For four models we also evaluate the impact of a carbon tax. All models project a steep increase in service demand over the century. Technology is important for limiting energy consumption and CO2 emissions, but quite radical changes in the technology mix are required to stabilize or reverse the trend. While all models project liquid fossil fuels dominating up to 2050, they differ regarding the use of alternative fuels (natural gas, hydrogen, biofuels, and electricity), because of different fuel price projections. The carbon tax of US$200/tCO2 in 2050 stabilizes or reverses global emission growth in all models. Besides common findings many differences in the model assumptions and projections indicate room for improvement in modeling and empirical description of the transport system.

  6. Reactive oxygen species and energy machinery: an integrated dynamic model.

    PubMed

    Korla, Kalyani

    2016-08-01

    The role of several important reactive oxygen species (ROS) on the Krebs cycle, the electron transport chain (ETC) and the two important shuttles has been modelled. Major part of the ROS is produced during oxygen reduction in the ETC, which has been kinetically simulated, and the changes in the final concentrations of several important metabolites were found. The simulation is based on chemical kinetics equation, and the associated set of differential equations was solved by the ordinary differential equation package in Octave. The validity of the model is checked by comparing the experimental results available in the literature with the simulations when a part of the ETC is blocked (80%) in the script. The present approach is versatile and flexible and has potential applications in various simulations. It is easy to study the change in concentrations of various metabolites when a particular enzyme or pathway is blocked (say by a drug). The Octave script is presented in the text. PMID:26309069

  7. Comparison of Mediated Effects: A Correlation Structure Modeling Approach

    ERIC Educational Resources Information Center

    Raykov, Tenko; Brennan, Mark; Reinhardt, Joann P.; Horowitz, Amy

    2008-01-01

    A correlation structure modeling method for comparison of mediated effects is outlined. The procedure permits point and interval estimation of differences in mediator effects, and is useful with models postulating 1 or more predictor, intervening, or response variables that may also be latent constructs. The approach allows scale-free evaluation…

  8. A Distribution-Free Test for Model Comparisons.

    ERIC Educational Resources Information Center

    Keats, John B.; Brewer, James K.

    This paper presents an index of goodness-of-fit for comparing m models over n trials. The index allows for differentiated weighting of the trials as to their importance in the comparison of the models. Several possible weighting schemes are suggested and the conditions on the weights which assure asymptotic normality of the index distribution are…

  9. Delay driven spatiotemporal chaos in single species population dynamics models.

    PubMed

    Jankovic, Masha; Petrovskii, Sergei; Banerjee, Malay

    2016-08-01

    Questions surrounding the prevalence of complex population dynamics form one of the central themes in ecology. Limit cycles and spatiotemporal chaos are examples that have been widely recognised theoretically, although their importance and applicability to natural populations remains debatable. The ecological processes underlying such dynamics are thought to be numerous, though there seems to be consent as to delayed density dependence being one of the main driving forces. Indeed, time delay is a common feature of many ecological systems and can significantly influence population dynamics. In general, time delays may arise from inter- and intra-specific trophic interactions or population structure, however in the context of single species populations they are linked to more intrinsic biological phenomena such as gestation or resource regeneration. In this paper, we consider theoretically the spatiotemporal dynamics of a single species population using two different mathematical formulations. Firstly, we revisit the diffusive logistic equation in which the per capita growth is a function of some specified delayed argument. We then modify the model by incorporating a spatial convolution which results in a biologically more viable integro-differential model. Using the combination of analytical and numerical techniques, we investigate the effect of time delay on pattern formation. In particular, we show that for sufficiently large values of time delay the system's dynamics are indicative to spatiotemporal chaos. The chaotic dynamics arising in the wake of a travelling population front can be preceded by either a plateau corresponding to dynamical stabilisation of the unstable equilibrium or by periodic oscillations. PMID:27154920

  10. Marmosets as model species in neuroscience and evolutionary anthropology.

    PubMed

    Burkart, Judith M; Finkenwirth, Christa

    2015-04-01

    Marmosets are increasingly used as model species by both neuroscientists and evolutionary anthropologists, but with a different rationale for doing so. Whereas neuroscientists stress that marmosets share many cognitive traits with humans due to common descent, anthropologists stress those traits shared with marmosets - and callitrichid monkeys in general - due to convergent evolution, as a consequence of the cooperative breeding system that characterizes both humans and callitrichids. Similarities in socio-cognitive abilities due to convergence, rather than homology, raise the question whether these similarities also extend to the proximate regulatory mechanisms, which is particularly relevant for neuroscientific investigations. In this review, we first provide an overview of the convergent adaptations to cooperative breeding at the psychological and cognitive level in primates, which bear important implications for our understanding of human cognitive evolution. In the second part, we zoom in on two of these convergent adaptations, proactive prosociality and social learning, and compare their proximate regulation in marmosets and humans with regard to oxytocin and cognitive top down regulation. Our analysis suggests considerable similarity in these regulatory mechanisms presumably because the convergent traits emerged due to small motivational changes that define how pre-existing cognitive mechanisms are quantitatively combined. This finding reconciles the prima facie contradictory rationale for using marmosets as high priority model species in neuroscience and anthropology. PMID:25242577

  11. Adaptive invasive species distribution models: A framework for modeling incipient invasions

    USGS Publications Warehouse

    Uden, Daniel R.; Allen, Craig R.; Angeler, David G.; Corral, Lucia; Fricke, Kent A.

    2015-01-01

    The utilization of species distribution model(s) (SDM) for approximating, explaining, and predicting changes in species’ geographic locations is increasingly promoted for proactive ecological management. Although frameworks for modeling non-invasive species distributions are relatively well developed, their counterparts for invasive species—which may not be at equilibrium within recipient environments and often exhibit rapid transformations—are lacking. Additionally, adaptive ecological management strategies address the causes and effects of biological invasions and other complex issues in social-ecological systems. We conducted a review of biological invasions, species distribution models, and adaptive practices in ecological management, and developed a framework for adaptive, niche-based, invasive species distribution model (iSDM) development and utilization. This iterative, 10-step framework promotes consistency and transparency in iSDM development, allows for changes in invasive drivers and filters, integrates mechanistic and correlative modeling techniques, balances the avoidance of type 1 and type 2 errors in predictions, encourages the linking of monitoring and management actions, and facilitates incremental improvements in models and management across space, time, and institutional boundaries. These improvements are useful for advancing coordinated invasive species modeling, management and monitoring from local scales to the regional, continental and global scales at which biological invasions occur and harm native ecosystems and economies, as well as for anticipating and responding to biological invasions under continuing global change.

  12. The Predictive Performance and Stability of Six Species Distribution Models

    PubMed Central

    Huang, Min-Yi; Fan, Wei-Yi; Wang, Zhi-Gao

    2014-01-01

    Background Predicting species’ potential geographical range by species distribution models (SDMs) is central to understand their ecological requirements. However, the effects of using different modeling techniques need further investigation. In order to improve the prediction effect, we need to assess the predictive performance and stability of different SDMs. Methodology We collected the distribution data of five common tree species (Pinus massoniana, Betula platyphylla, Quercus wutaishanica, Quercus mongolica and Quercus variabilis) and simulated their potential distribution area using 13 environmental variables and six widely used SDMs: BIOCLIM, DOMAIN, MAHAL, RF, MAXENT, and SVM. Each model run was repeated 100 times (trials). We compared the predictive performance by testing the consistency between observations and simulated distributions and assessed the stability by the standard deviation, coefficient of variation, and the 99% confidence interval of Kappa and AUC values. Results The mean values of AUC and Kappa from MAHAL, RF, MAXENT, and SVM trials were similar and significantly higher than those from BIOCLIM and DOMAIN trials (p<0.05), while the associated standard deviations and coefficients of variation were larger for BIOCLIM and DOMAIN trials (p<0.05), and the 99% confidence intervals for AUC and Kappa values were narrower for MAHAL, RF, MAXENT, and SVM. Compared to BIOCLIM and DOMAIN, other SDMs (MAHAL, RF, MAXENT, and SVM) had higher prediction accuracy, smaller confidence intervals, and were more stable and less affected by the random variable (randomly selected pseudo-absence points). Conclusions According to the prediction performance and stability of SDMs, we can divide these six SDMs into two categories: a high performance and stability group including MAHAL, RF, MAXENT, and SVM, and a low performance and stability group consisting of BIOCLIM, and DOMAIN. We highlight that choosing appropriate SDMs to address a specific problem is an important

  13. A virtual species set for robust and reproducible species distribution modelling tests

    PubMed Central

    Garzon-Lopez, Carol X.; Bastin, Lucy; Foody, Giles M.; Rocchini, Duccio

    2016-01-01

    Predicting species potential and future distribution has become a relevant tool in biodiversity monitoring and conservation. In this data article we present the suitability map of a virtual species generated based on two bioclimatic variables, and a dataset containing more than 700,000 random observations at the extent of Europe. The dataset includes spatial attributes such as: distance to roads, protected areas, country codes, and the habitat suitability of two spatially clustered species (grassland and forest species) and a wide-spread species. PMID:27014734

  14. A virtual species set for robust and reproducible species distribution modelling tests.

    PubMed

    Garzon-Lopez, Carol X; Bastin, Lucy; Foody, Giles M; Rocchini, Duccio

    2016-06-01

    Predicting species potential and future distribution has become a relevant tool in biodiversity monitoring and conservation. In this data article we present the suitability map of a virtual species generated based on two bioclimatic variables, and a dataset containing more than 700,000 random observations at the extent of Europe. The dataset includes spatial attributes such as: distance to roads, protected areas, country codes, and the habitat suitability of two spatially clustered species (grassland and forest species) and a wide-spread species. PMID:27014734

  15. Numerical comparison of strong Langmuir turbulence models

    NASA Technical Reports Server (NTRS)

    Shen, Mei-Mei; Nicholson, D. R.

    1987-01-01

    Two models of Langmuir turbulence, the nonlinear Schroedinger equation and the Zakharov equations, are solved numerically for an initial value problem in which the electric field evolves from an almost flat initial condition via the modulational instability and finally saturates into a set of solitons. The two models agree well with each other only when the initial dimensionless electric field has an amplitude less than unity. An analytic soliton gas model consisting of equal-amplitude, randomly spaced, zero-speed solitons is remarkably good at reproducing the time-averaged Fourier spectra in both cases.

  16. Integrative modelling reveals mechanisms linking productivity and plant species richness

    NASA Astrophysics Data System (ADS)

    Grace, James B.; Anderson, T. Michael; Seabloom, Eric W.; Borer, Elizabeth T.; Adler, Peter B.; Harpole, W. Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M.; Pärtel, Meelis; Bakker, Jonathan D.; Buckley, Yvonne M.; Crawley, Michael J.; Damschen, Ellen I.; Davies, Kendi F.; Fay, Philip A.; Firn, Jennifer; Gruner, Daniel S.; Hector, Andy; Knops, Johannes M. H.; MacDougall, Andrew S.; Melbourne, Brett A.; Morgan, John W.; Orrock, John L.; Prober, Suzanne M.; Smith, Melinda D.

    2016-01-01

    How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems.

  17. Integrative modelling reveals mechanisms linking productivity and plant species richness.

    PubMed

    Grace, James B; Anderson, T Michael; Seabloom, Eric W; Borer, Elizabeth T; Adler, Peter B; Harpole, W Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M; Pärtel, Meelis; Bakker, Jonathan D; Buckley, Yvonne M; Crawley, Michael J; Damschen, Ellen I; Davies, Kendi F; Fay, Philip A; Firn, Jennifer; Gruner, Daniel S; Hector, Andy; Knops, Johannes M H; MacDougall, Andrew S; Melbourne, Brett A; Morgan, John W; Orrock, John L; Prober, Suzanne M; Smith, Melinda D

    2016-01-21

    How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a single model and using data from 1,126 grassland plots spanning five continents, we detect the clear signals of numerous underlying mechanisms linking productivity and richness. We find that an integrative model has substantially higher explanatory power than traditional bivariate analyses. In addition, the specific results unveil several surprising findings that conflict with classical models. These include the isolation of a strong and consistent enhancement of productivity by richness, an effect in striking contrast with superficial data patterns. Also revealed is a consistent importance of competition across the full range of productivity values, in direct conflict with some (but not all) proposed models. The promotion of local richness by macroecological gradients in climatic favourability, generally seen as a competing hypothesis, is also found to be important in our analysis. The results demonstrate that an integrative modelling approach leads to a major advance in our ability to discern the underlying processes operating in ecological systems. PMID:26760203

  18. A comparison of the copper sensitivity of six invertebrate species in ambient salt water of varying dissolved organic matter concentrations.

    PubMed

    Arnold, W Ray; Cotsifas, Jeffrey S; Ogle, R Scott; Depalma, Sarah G S; Smith, D Scott

    2010-02-01

    The copper sensitivity of four saltwater invertebrates (the mussel Mytilus galloprovincialis, the oyster Crassostrea virginica, the sand dollar Dendraster excentricus, and the sea urchin Strongylocentrotus purpuratus) was determined experimentally using chronic-estimator embryo-larval test procedures. The effect of sample dissolved organic matter (DOM) content on Cu bioavailability was determined for these species using commonly prescribed test procedures. Comparisons were made among these test results and test results reported previously for two other invertebrate species: the mussel Mytilus edulis and the copepod Eurytemora affinis. All six species exhibited a direct and significant relationship between the sample dissolved organic carbon (DOC; a surrogate measure of DOM) and either the dissolved Cu median lethal concentration (LC50) values or median effect concentration (EC50) values. This relationship is significant even when the DOM has different quality as evidenced by molecular fluorescence spectroscopy. Once normalized for the effects of DOM, the Cu sensitivity of these species from least to most sensitive were E. affinis < D. excitricus < C. virginica approximately S. purpuratus approximately M. edulis approximately M. galloprovincialis. This ranking of species sensitivity differs from the saltwater species sensitivity distribution proposed in 2003 by the U.S. Environmental Protection Agency. These results support the need to account for factors that modify Cu bioavailability in future saltwater Cu criteria development efforts. More specifically, Cu saltwater species sensitivity distribution data will need to be normalized by factors affecting Cu bioavailability to assure that accurate and protective criteria are subsequently developed for saltwater species and their uses. PMID:20821449

  19. Do species distribution models predict species richness in urban and natural green spaces? A case study using amphibians

    EPA Science Inventory

    Urban green spaces are potentially important to biodiversity conservation because they represent habitat islands in a mosaic of development, and could harbor high biodiversity or provide connectivity to nearby habitat. Presence only species distribution models (SDMs) represent a ...

  20. An optimized TOPS+ comparison method for enhanced TOPS models

    PubMed Central

    2010-01-01

    Background Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+. Results We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method. Conclusions Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90% accuracy for SCOP alpha+beta; a 6% increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98% accuracy. Software Availability The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/. PMID:20236520

  1. Quantile-Quantile Plots:. AN Approach for the Inter-Species Comparison of Promoter Architecture in Eukaryotes

    NASA Astrophysics Data System (ADS)

    Feldmeier, Kaspar; Kilian, Joachim; Harter, Klaus; Wanke, Dierk; Berendzen, Kenneth W.

    2011-01-01

    Regulatory non-coding DNA is important to drive gene transcription and thereby influence mRNA and consequently protein abundance. Therefore, biologists and bioinformation scientists aim to extract meaningful information from these sequence regions, in particular upstream regulation regions called promoters, and conclude on regulatory sequence function. While some approaches have been successful for single genes or a single genome, it is an open question whether information on promoter function can readily be transferred between different species. Thus, it is useful for biologists to know more about the general structure and composition of promoters including the occurrence of cisregulatory DNA-elements (CREs) to be able to compare promoter architecture between organisms. To approach this task, we utilized the fully sequenced genomes of the plant model organisms: mouse-ear cress (Arabidopsis thaliana), western balsam poplar (Populus trichocarpa), Sorghum bicolor and rice (Oryza sativa). For the interspecies comparison we made use of quantile-quantile (QQ)-plots of the variances of hexanucleotides or known functional CREs of core-promoter regions. Here, we suggest that the differences in promoter architecture correlate with the sizes of the intergenic space, i.e. regions, in which the promoters are located. In contrast, analysis of CREs is hampered by the general lack of well characterized transcription factor-CRE-relationships.

  2. Quantity quotient reporting. Comparison of various models.

    PubMed

    Haeckel, Rainer; Wosniok, Werner; Postma, Theo

    2015-11-01

    Quantity quotient (QQ) reporting has been proposed by several authors to improve or support the present situation of presenting quantitative laboratory results. This proposal is based on a concept (symmetrical model) known from the intelligence quotient, which was developed to make intelligence tests comparable. In laboratory medicine, however, most measurands follow a non-symmetrical (skewed) distribution, leading to a compression of the QQ values at the lower end of the reference interval. This effect can be avoided by several alternatives. Three models considering non-symmetrical distributions are compared with the symmetrical model in the present study. The corresponding algorithms can be easily handled on the Excel platform. Graphical presentation of the QQ allows a quick overview of test results if they occur in a large number. PMID:26536582

  3. Comparison of pelvic muscle architecture between humans and commonly used laboratory species

    PubMed Central

    Alperin, Marianna; Tuttle, Lori J.; Conner, Blair R.; Dixon, Danielle M.; Mathewson, Margie A.; Ward, Samuel R.

    2014-01-01

    Introduction and hypothesis Pelvic floor muscles (PFM) are deleteriously affected by vaginal birth, which contributes to the development of pelvic floor disorders. To mechanistically link these events, experiments using animal models are required, as access to human PFM tissue is challenging. In choosing an animal model, a comparative study of PFM design is necessary, since gross anatomy alone is insufficient to guide the selection. Methods Human PFM architecture was measured using micromechanical dissection and then compared with mouse (n=10), rat (n=10), and rabbit (n=10) using the Architectural Difference Index (ADI) (parameterizing a combined measure of sarcomere length-to-optimal-sarcomere ratio, fiber-to-muscle-length ratio, and fraction of total PFM mass and physiological cross-sectional area (PCSA) contributed by each muscle). Coccygeus (C), iliocaudalis (IC), and pubocaudalis (PC) were harvested and subjected to architectural measurements. Parameters within species were compared using repeated measures analysis of variance (ANOVA) with post hoc Tukey's tests. The scaling relationships of PFM across species were quantified using least-squares regression of log-10-transformed variables. Results Based on the ADI, rat was found to be the most similar to humans (ADI = 2.5), followed by mouse (ADI = 3.3). When animals' body mass was regressed against muscle mass, muscle length, fiber length, and PCSA scaling coefficients showed a negative allometric relationship or smaller increase than predicted by geometric scaling. Conclusion In terms of muscle design among commonly used laboratory animals, rat best approximates the human PFM, followed by mouse. Negative allometric scaling of PFM architectural parameters is likely due to the multifaceted function of these muscles. PMID:24915840

  4. The Distribution and Abundance of Bird Species: Towards a Satellite, Data Driven Avian Energetics and Species Richness Model

    NASA Technical Reports Server (NTRS)

    Smith, James A.

    2003-01-01

    This paper addresses the fundamental question of why birds occur where and when they do, i.e., what are the causative factors that determine the spatio-temporal distributions, abundance, or richness of bird species? In this paper we outline the first steps toward building a satellite, data-driven model of avian energetics and species richness based on individual bird physiology, morphology, and interaction with the spatio-temporal habitat. To evaluate our model, we will use the North American Breeding Bird Survey and Christmas Bird Count data for species richness, wintering and breeding range. Long term and current satellite data series include AVHRR, Landsat, and MODIS.

  5. Dealing with Noisy Absences to Optimize Species Distribution Models: An Iterative Ensemble Modelling Approach

    PubMed Central

    Lauzeral, Christine; Grenouillet, Gaël; Brosse, Sébastien

    2012-01-01

    Species distribution models (SDMs) are widespread in ecology and conservation biology, but their accuracy can be lowered by non-environmental (noisy) absences that are common in species occurrence data. Here we propose an iterative ensemble modelling (IEM) method to deal with noisy absences and hence improve the predictive reliability of ensemble modelling of species distributions. In the IEM approach, outputs of a classical ensemble model (EM) were used to update the raw occurrence data. The revised data was then used as input for a new EM run. This process was iterated until the predictions stabilized. The outputs of the iterative method were compared to those of the classical EM using virtual species. The IEM process tended to converge rapidly. It increased the consensus between predictions provided by the different methods as well as between those provided by different learning data sets. Comparing IEM and EM showed that for high levels of non-environmental absences, iterations significantly increased prediction reliability measured by the Kappa and TSS indices, as well as the percentage of well-predicted sites. Compared to EM, IEM also reduced biases in estimates of species prevalence. Compared to the classical EM method, IEM improves the reliability of species predictions. It particularly deals with noisy absences that are replaced in the data matrices by simulated presences during the iterative modelling process. IEM thus constitutes a promising way to increase the accuracy of EM predictions of difficult-to-detect species, as well as of species that are not in equilibrium with their environment. PMID:23166691

  6. Ozone Budgets from a Global Chemistry/Transport Model and Comparison to Observations from POLARIS

    NASA Technical Reports Server (NTRS)

    Kawa, S. Randolph; Newman, P. A.; Douglass, A. R.; Weaver, C. J.; Gao, R.-S.; Salawitch, R. J.; Johnson, D. G.; Jucks, K. W.

    1998-01-01

    The objective of the Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) field mission was to obtain data to better characterize the summertime seasonal decrease of ozone at mid to high latitudes. The decrease in ozone occurs mainly in the lower stratosphere and is expected to result from in situ chemical destruction. Instrumented balloons and aircraft were used in POLARIS, along with satellites, to measure ozone and chemical species which are involved with stratospheric ozone chemistry. In order to close the seasonal ozone budget, however, ozone transport must also be estimated. Comparison to a global chemistry and transport model (CTM) of the stratosphere indicates how well the summertime ozone loss processes are simulated and thus how well we can predict the ozone response to changing amounts of chemical source gases. Moreover, the model gives insight into the possible relative magnitude of transport contributions to the seasonal ozone decline. Initial comparison to the Goddard CTM, which uses transport winds and temperatures from meteorological data assimilation, shows a high ozone bias in the model and an attenuated summertime ozone loss cycle. Comparison of the model chemical partitioning and ozone catalytic loss rates to those derived from measurements shows fairly close agreement both at ER-2 altitudes (20 km) and higher. This suggests that the model transport is too active in resupplying ozone to the high latitude region, although chemistry failings cannot be completely ruled out. Comparison of ozone and related species will be shown along with a full diagnosis of the model ozone budget and its possible sources of error.

  7. Ozone Budgets from a Global Chemistry/ Transport Model and Comparison to Observations from POLARIS

    NASA Technical Reports Server (NTRS)

    Kawa, S. Randy

    1999-01-01

    The objective of the Photochemistry of Ozone Loss in the Arctic Region in Summer (POLARIS) field mission was to obtain data to better characterize the summertime seasonal decrease of ozone at mid to high latitudes. The decrease in ozone occurs mainly in the lower stratosphere and is expected to result from in situ chemical destruction. Instrumented balloons and aircraft were used in POLARIS, along with satellites, to measure ozone and chemical species which are involved with stratospheric ozone chemistry. In order to close the seasonal ozone budget, however, ozone transport must also be estimated. Comparison to a global chemistry and transport model (CTM) of the stratosphere indicates how well the summertime ozone loss processes are simulated and thus how well we can predict the ozone response to changing amounts of chemical source gases. Moreover, the model gives insight into the possible relative magnitude of transport contributions to the seasonal ozone decline. Initial comparison to the Goddard CTM, which uses transport winds and temperatures from meteorological data assimilation, shows a high ozone bias in the model and an attenuated summertime ozone loss cycle. Comparison of the model chemical partitioning, and ozone catalytic loss rates to those derived from measurements shows fairly close agreement both at ER-2 altitudes (20 km) and higher. This suggests that the model transport is too active in resupplying ozone to the high latitude region, although chemistry failings cannot be completely ruled out. Comparison of ozone and related species will be shown along with a full diagnosis of the model ozone budget and its possible sources of error.

  8. A model for improving endangered species recovery programs

    NASA Astrophysics Data System (ADS)

    Miller, Brian; Reading, Richard; Conway, Courtney; Jackson, Jerome A.; Hutchins, Michael; Snyder, Noel; Forrest, Steve; Frazier, Jack; Derrickson, Scott

    1994-09-01

    This paper discusses common organizational problems that cause inadequate planning and implementation processes of endangered species recovery across biologically dissimilar species. If these problems occur, even proven biological conservation techniques are jeopardized. We propose a solution that requires accountability in all phases of the restoration process and is based on cooperative input among government agencies, nongovernmental conservation organizations, and the academic community. The first step is formation of a task-oriented recovery team that integrates the best expertise into the planning process. This interdisciplinary team should be composed of people whose skills directly address issues critical for recovery. Once goals and procedures are established, the responsible agency (for example, in the United States, the US Fish and Wildlife Service) could divest some or all of its obligation for implementing the plan, yet still maintain oversight by holding implementing entities contractually accountable. Regular, periodic outside review and public documentation of the recovery team, lead agency, and the accomplishments of implementing bodies would permit evaluation necessary to improve performance. Increased cooperation among agency and nongovernmental organizations provided by this model promises a more efficient use of limited resources toward the conservation of biodiversity.

  9. Mapping National Plant Biodiversity Patterns in South Korea with the MARS Species Distribution Model.

    PubMed

    Choe, Hyeyeong; Thorne, James H; Seo, Changwan

    2016-01-01

    Accurate information on the distribution of existing species is crucial to assess regional biodiversity. However, data inventories are insufficient in many areas. We examine the ability of Multivariate Adaptive Regression Splines (MARS) multi-response species distribution model to overcome species' data limitations and portray plant species distribution patterns for 199 South Korean plant species. The study models species with two or more observations, examines their contribution to national patterns of species richness, provides a sensitivity analysis of different range threshold cutoff approaches for modeling species' ranges, and presents considerations for species modeling at fine spatial resolution. We ran MARS models for each species and tested four threshold methods to transform occurrence probabilities into presence or absence range maps. Modeled occurrence probabilities were extracted at each species' presence points, and the mean, median, and one standard deviation (SD) calculated to define data-driven thresholds. A maximum sum of sensitivity and specificity threshold was also calculated, and the range maps from the four cutoffs were tested using independent plant survey data. The single SD values were the best threshold tested for minimizing omission errors and limiting species ranges to areas where the associated occurrence data were correctly classed. Eight individual species range maps for rare plant species were identified that are potentially affected by resampling predictor variables to fine spatial scales. We portray spatial patterns of high species richness by assessing the combined range maps from three classes of species: all species, endangered and endemic species, and range-size rarity of all species, which could be used in conservation planning for South Korea. The MARS model is promising for addressing the common problem of few species occurrence records. However, projected species ranges are highly dependent on the threshold and scale

  10. Modeling of the Martian exosphere and first comparisons to IUVS/MAVEN observations

    NASA Astrophysics Data System (ADS)

    Chaufray, Jean-Yves; Forget, Francois; Modolo, M. Ronan; Leblanc, Francois; Lopez-Valverde, Miguel; Clarke, John; Chaffin, Michael; Schneider, Nick; Yelle, Roger; Gonzalez-Galindo, Francisco; Jakosky, Bruce; Deighan, Justin; Esteban-Hernandez, Rosa

    2016-07-01

    Understanding the formation of the Martian exosphere is crucial to understand the escape processes of the Martian atmosphere. To understand this formation, our team has developed and coupled several 3D models able to simulate the Martian atmosphere from the surface to the exosphere and its interaction with the solar wind. These models have been used to study Jeans escape for light species (H, H2), and non-thermal escape (photochemical, sputtering induced escape and ion escape) for heavier species, especially O. In this presentation, I will describe some recent updates of the upper atmosphere modeling and simulations focusing on the neutral atomic hydrogen and oxygen at present time and their extrapolation to past EUV solar flux. I will also present the first comparisons of our simulations with the exospheric emissions measured by the Imaging Ultraviolet Spectrograph (IUVS) aboard the MAVEN spacecraft during its first year and discuss the differences.

  11. LDEF data: Comparisons with existing models

    NASA Technical Reports Server (NTRS)

    Coombs, Cassandra R.; Watts, Alan J.; Wagner, John D.; Atkinson, Dale R.

    1993-01-01

    The relationship between the observed cratering impact damage on the Long Duration Exposure Facility (LDEF) versus the existing models for both the natural environment of micrometeoroids and the man-made debris was investigated. Experimental data was provided by several LDEF Principal Investigators, Meteoroid and Debris Special Investigation Group (M&D SIG) members, and by the Kennedy Space Center Analysis Team (KSC A-Team) members. These data were collected from various aluminum materials around the LDEF satellite. A PC (personal computer) computer program, SPENV, was written which incorporates the existing models of the Low Earth Orbit (LEO) environment. This program calculates the expected number of impacts per unit area as functions of altitude, orbital inclination, time in orbit, and direction of the spacecraft surface relative to the velocity vector, for both micrometeoroids and man-made debris. Since both particle models are couched in terms of impact fluxes versus impactor particle size, and much of the LDEF data is in the form of crater production rates, scaling laws have been used to relate the two. Also many hydrodynamic impact computer simulations were conducted, using CTH, of various impact events, that identified certain modes of response, including simple metallic target cratering, perforations and delamination effects of coatings.

  12. LDEF data: Comparisons with existing models

    NASA Astrophysics Data System (ADS)

    Coombs, Cassandra R.; Watts, Alan J.; Wagner, John D.; Atkinson, Dale R.

    1993-04-01

    The relationship between the observed cratering impact damage on the Long Duration Exposure Facility (LDEF) versus the existing models for both the natural environment of micrometeoroids and the man-made debris was investigated. Experimental data was provided by several LDEF Principal Investigators, Meteoroid and Debris Special Investigation Group (M&D SIG) members, and by the Kennedy Space Center Analysis Team (KSC A-Team) members. These data were collected from various aluminum materials around the LDEF satellite. A PC (personal computer) computer program, SPENV, was written which incorporates the existing models of the Low Earth Orbit (LEO) environment. This program calculates the expected number of impacts per unit area as functions of altitude, orbital inclination, time in orbit, and direction of the spacecraft surface relative to the velocity vector, for both micrometeoroids and man-made debris. Since both particle models are couched in terms of impact fluxes versus impactor particle size, and much of the LDEF data is in the form of crater production rates, scaling laws have been used to relate the two. Also many hydrodynamic impact computer simulations were conducted, using CTH, of various impact events, that identified certain modes of response, including simple metallic target cratering, perforations and delamination effects of coatings.

  13. MicroShield/ISOCS gamma modeling comparison.

    SciTech Connect

    Sansone, Kenneth R

    2013-08-01

    Quantitative radiological analysis attempts to determine the quantity of activity or concentration of specific radionuclide(s) in a sample. Based upon the certified standards that are used to calibrate gamma spectral detectors, geometric similarities between sample shape and the calibration standards determine if the analysis results developed are qualitative or quantitative. A sample analyzed that does not mimic a calibrated sample geometry must be reported as a non-standard geometry and thus the results are considered qualitative and not quantitative. MicroShieldR or ISOCSR calibration software can be used to model non-standard geometric sample shapes in an effort to obtain a quantitative analytical result. MicroShieldR and Canberra's ISOCSR software contain several geometry templates that can provide accurate quantitative modeling for a variety of sample configurations. Included in the software are computational algorithms that are used to develop and calculate energy efficiency values for the modeled sample geometry which can then be used with conventional analysis methodology to calculate the result. The response of the analytical method and the sensitivity of the mechanical and electronic equipment to the radionuclide of interest must be calibrated, or standardized, using a calibrated radiological source that contains a known and certified amount of activity.

  14. Squares of different sizes: effect of geographical projection on model parameter estimates in species distribution modeling.

    PubMed

    Budic, Lara; Didenko, Gregor; Dormann, Carsten F

    2016-01-01

    In species distribution analyses, environmental predictors and distribution data for large spatial extents are often available in long-lat format, such as degree raster grids. Long-lat projections suffer from unequal cell sizes, as a degree of longitude decreases in length from approximately 110 km at the equator to 0 km at the poles. Here we investigate whether long-lat and equal-area projections yield similar model parameter estimates, or result in a consistent bias. We analyzed the environmental effects on the distribution of 12 ungulate species with a northern distribution, as models for these species should display the strongest effect of projectional distortion. Additionally we choose four species with entirely continental distributions to investigate the effect of incomplete cell coverage at the coast. We expected that including model weights proportional to the actual cell area should compensate for the observed bias in model coefficients, and similarly that using land coverage of a cell should decrease bias in species with coastal distribution. As anticipated, model coefficients were different between long-lat and equal-area projections. Having progressively smaller and a higher number of cells with increasing latitude influenced the importance of parameters in models, increased the sample size for the northernmost parts of species ranges, and reduced the subcell variability of those areas. However, this bias could be largely removed by weighting long-lat cells by the area they cover, and marginally by correcting for land coverage. Overall we found little effect of using long-lat rather than equal-area projections in our analysis. The fitted relationship between environmental parameters and occurrence probability differed only very little between the two projection types. We still recommend using equal-area projections to avoid possible bias. More importantly, our results suggest that the cell area and the proportion of a cell covered by land should be

  15. New Metrics for Comparison of Taxonomies Reveal Striking Discrepancies among Species Delimitation Methods in Madascincus Lizards

    PubMed Central

    Miralles, Aurélien; Vences, Miguel

    2013-01-01

    Delimiting and describing species is fundamental to numerous biological disciplines such as evolution, macroecology, and conservation. Delimiting species as independent evolutionary lineages may and often does yield different outcomes depending on the species criteria applied, but methods should be chosen that minimize the inference of objectively erroneous species limits. Several protocols exploit single-gene or multi-gene coalescence statistics, assignment tests or other rationales related to nuclear DNA (nDNA) allele sharing to automatically delimit species. We apply seven different species delimitation protocols to a taxonomically confusing group of Malagasy lizards (Madascincus), and compare the resulting taxonomies with two newly developed metrics: the Taxonomic index of congruence Ctax which quantifies the congruence between two taxonomies, and the Relative taxonomic resolving power index Rtax which quantifies the potential of an approach to capture a high number of species boundaries. The protocols differed in the total number of species proposed, between 9 and 34, and were also highly incongruent in placing species boundaries. The Generalized Mixed Yule-Coalescent approach captured the highest number of potential species boundaries but many of these were clearly contradicted by extensive nDNA admixture between sympatric mitochondrial DNA (mtDNA) haplotype lineages. Delimiting species as phenotypically diagnosable mtDNA clades failed to detect two cryptic species that are unambiguous due to a lack of nDNA gene flow despite sympatry. We also consider the high number of species boundaries and their placement by multi-gene Bayesian species delimitation as poorly reliable whereas the Bayesian assignment test approach provided a species delimitation highly congruent with integrative taxonomic practice. The present study illustrates the trade-off in taxonomy between reliability (favored by conservative approaches) and resolving power (favored by inflationist

  16. Transport and photochemical modeling. Studies of atmospheric species

    NASA Technical Reports Server (NTRS)

    Natarajan, M.

    1987-01-01

    A program of research studies related to the photochemistry, radiative transfer, and dynamics of the stratosphere is described. Investigations were conducted in two broad areas: (1) studies of the stratospheric processes and their response to external perturbations, and (2) analysis of satellite measurements in conjunction with theoretical models. Contemporary one dimensional photochemical, radiative-convective model was used to assess the impact of perturbations such as solar flux variability, increases in atmospheric carbon dioxide, chlorofluoromethanes and other greenhouse gases. Data from satellite experiments such as LIMS and SBUV, were used along with theoretical models to develop a climatology of trace species in the stratosphere. The consistency of contemporary ozone photochemistry was examined in the light of LIMS data. Research work also includes analysis of stratospheric nitrogen dioxide distributions from different satellite experiments, investigation of the wintertime latitudinal gradients in NO2, estimation of the stratospheric odd nitrogen level and its variability, and studies related to the changes in ozone in the Antarctic, and mid latitude Southern Hemisphere.

  17. Transport and photochemical modeling. Studies of atmospheric species

    SciTech Connect

    Natarajan, M.

    1987-03-01

    A program of research studies related to the photochemistry, radiative transfer, and dynamics of the stratosphere is described. Investigations were conducted in two broad areas: (1) studies of the stratospheric processes and their response to external perturbations, and (2) analysis of satellite measurements in conjunction with theoretical models. Contemporary one dimensional photochemical, radiative-convective model was used to assess the impact of perturbations such as solar flux variability, increases in atmospheric carbon dioxide, chlorofluoromethanes and other greenhouse gases. Data from satellite experiments such as LIMS and SBUV, were used along with theoretical models to develop a climatology of trace species in the stratosphere. The consistency of contemporary ozone photochemistry was examined in the light of LIMS data. Research work also includes analysis of stratospheric nitrogen dioxide distributions from different satellite experiments, investigation of the wintertime latitudinal gradients in NO/sub 2/, estimation of the stratospheric odd nitrogen level and its variability, and studies related to the changes in ozone in the Antarctic, and midlatitude Southern Hemisphere.

  18. Information-theoretic model comparison unifies saliency metrics

    PubMed Central

    Kümmerer, Matthias; Wallis, Thomas S. A.; Bethge, Matthias

    2015-01-01

    Learning the properties of an image associated with human gaze placement is important both for understanding how biological systems explore the environment and for computer vision applications. There is a large literature on quantitative eye movement models that seeks to predict fixations from images (sometimes termed “saliency” prediction). A major problem known to the field is that existing model comparison metrics give inconsistent results, causing confusion. We argue that the primary reason for these inconsistencies is because different metrics and models use different definitions of what a “saliency map” entails. For example, some metrics expect a model to account for image-independent central fixation bias whereas others will penalize a model that does. Here we bring saliency evaluation into the domain of information by framing fixation prediction models probabilistically and calculating information gain. We jointly optimize the scale, the center bias, and spatial blurring of all models within this framework. Evaluating existing metrics on these rephrased models produces almost perfect agreement in model rankings across the metrics. Model performance is separated from center bias and spatial blurring, avoiding the confounding of these factors in model comparison. We additionally provide a method to show where and how models fail to capture information in the fixations on the pixel level. These methods are readily extended to spatiotemporal models of fixation scanpaths, and we provide a software package to facilitate their use. PMID:26655340

  19. Comparison and Analysis of Geometric Correction Models of Spaceborne SAR

    PubMed Central

    Jiang, Weihao; Yu, Anxi; Dong, Zhen; Wang, Qingsong

    2016-01-01

    Following the development of synthetic aperture radar (SAR), SAR images have become increasingly common. Many researchers have conducted large studies on geolocation models, but little work has been conducted on the available models for the geometric correction of SAR images of different terrain. To address the terrain issue, four different models were compared and are described in this paper: a rigorous range-doppler (RD) model, a rational polynomial coefficients (RPC) model, a revised polynomial (PM) model and an elevation derivation (EDM) model. The results of comparisons of the geolocation capabilities of the models show that a proper model for a SAR image of a specific terrain can be determined. A solution table was obtained to recommend a suitable model for users. Three TerraSAR-X images, two ALOS-PALSAR images and one Envisat-ASAR image were used for the experiment, including flat terrain and mountain terrain SAR images as well as two large area images. Geolocation accuracies of the models for different terrain SAR images were computed and analyzed. The comparisons of the models show that the RD model was accurate but was the least efficient; therefore, it is not the ideal model for real-time implementations. The RPC model is sufficiently accurate and efficient for the geometric correction of SAR images of flat terrain, whose precision is below 0.001 pixels. The EDM model is suitable for the geolocation of SAR images of mountainous terrain, and its precision can reach 0.007 pixels. Although the PM model does not produce results as precise as the other models, its efficiency is excellent and its potential should not be underestimated. With respect to the geometric correction of SAR images over large areas, the EDM model has higher accuracy under one pixel, whereas the RPC model consumes one third of the time of the EDM model. PMID:27347973

  20. Comparison and Analysis of Geometric Correction Models of Spaceborne SAR.

    PubMed

    Jiang, Weihao; Yu, Anxi; Dong, Zhen; Wang, Qingsong

    2016-01-01

    Following the development of synthetic aperture radar (SAR), SAR images have become increasingly common. Many researchers have conducted large studies on geolocation models, but little work has been conducted on the available models for the geometric correction of SAR images of different terrain. To address the terrain issue, four different models were compared and are described in this paper: a rigorous range-doppler (RD) model, a rational polynomial coefficients (RPC) model, a revised polynomial (PM) model and an elevation derivation (EDM) model. The results of comparisons of the geolocation capabilities of the models show that a proper model for a SAR image of a specific terrain can be determined. A solution table was obtained to recommend a suitable model for users. Three TerraSAR-X images, two ALOS-PALSAR images and one Envisat-ASAR image were used for the experiment, including flat terrain and mountain terrain SAR images as well as two large area images. Geolocation accuracies of the models for different terrain SAR images were computed and analyzed. The comparisons of the models show that the RD model was accurate but was the least efficient; therefore, it is not the ideal model for real-time implementations. The RPC model is sufficiently accurate and efficient for the geometric correction of SAR images of flat terrain, whose precision is below 0.001 pixels. The EDM model is suitable for the geolocation of SAR images of mountainous terrain, and its precision can reach 0.007 pixels. Although the PM model does not produce results as precise as the other models, its efficiency is excellent and its potential should not be underestimated. With respect to the geometric correction of SAR images over large areas, the EDM model has higher accuracy under one pixel, whereas the RPC model consumes one third of the time of the EDM model. PMID:27347973

  1. Systematic comparison of model polymer nanocomposite mechanics.

    PubMed

    Xiao, Senbo; Peter, Christine; Kremer, Kurt

    2016-01-01

    Polymer nanocomposites render a range of outstanding materials from natural products such as silk, sea shells and bones, to synthesized nanoclay or carbon nanotube reinforced polymer systems. In contrast to the fast expanding interest in this type of material, the fundamental mechanisms of their mixing, phase behavior and reinforcement, especially for higher nanoparticle content as relevant for bio-inorganic composites, are still not fully understood. Although polymer nanocomposites exhibit diverse morphologies, qualitatively their mechanical properties are believed to be governed by a few parameters, namely their internal polymer network topology, nanoparticle volume fraction, particle surface properties and so on. Relating material mechanics to such elementary parameters is the purpose of this work. By taking a coarse-grained molecular modeling approach, we study an range of different polymer nanocomposites. We vary polymer nanoparticle connectivity, surface geometry and volume fraction to systematically study rheological/mechanical properties. Our models cover different materials, and reproduce key characteristics of real nanocomposites, such as phase separation, mechanical reinforcement. The results shed light on establishing elementary structure, property and function relationship of polymer nanocomposites. PMID:27623170

  2. Further Development of the PCRTM Model and RT Model Inter Comparison

    NASA Technical Reports Server (NTRS)

    Yang, Qiguang; Liu, Xu; Wu, Wan; Kizer, Susan

    2015-01-01

    New results for the development of the PCRTM model will be presented. The new results were used for IASI retrieval validation inter comparison and better results were obtained compare to other fast radiative transfer models.

  3. A critical comparison of two-equation turbulence models

    NASA Technical Reports Server (NTRS)

    Lang, N. J.; Shih, T. H.

    1991-01-01

    Several two-equation models were proposed and tested against benchmark flows by various researchers. For each study, different numerical methods or codes were used to obtain the results which were reported to be an improvement over other models. However, these comparisons may be overshadowed by the different numerical schemes used to obtain the results. With this in mind, several existing two-equation turbulence models, including k-epsilon, k-tau, k-omega, and q-omega models, are implemented into a common flow solver code for near wall turbulent flows. The quality of each model is based on several criteria, including robustness and accuracy of predicting the turbulent quantities.

  4. Selection bias in species distribution models: An econometric approach on forest trees based on structural modeling

    NASA Astrophysics Data System (ADS)

    Martin-StPaul, N. K.; Ay, J. S.; Guillemot, J.; Doyen, L.; Leadley, P.

    2014-12-01

    Species distribution models (SDMs) are widely used to study and predict the outcome of global changes on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of applications on forest trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8km). We also compared the outputs of the SSDM with outputs of a classical SDM (i.e. Biomod ensemble modelling) in terms of bioclimatic response curves and potential distributions under current climate and climate change scenarios. The shapes of the bioclimatic response curves and the modelled species distribution maps differed markedly between SSDM and classical SDMs, with contrasted patterns according to species and spatial resolutions. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents

  5. Comparison of observed and modeled longwave radiances

    NASA Technical Reports Server (NTRS)

    Stone, Kenneth; Coakley, J. A., Jr.

    1990-01-01

    Calculated LW radiances based on NMC profiles of temperature and humidities for the month of July 1985 are obtained using standard procedures for performing radiative transfer calculations, and are within 3 percent (against a standard deviation of 4 percent) for global daytime land comparsions and within 1 percent (against a standard deviation of 1.5 percent) for a case study located over North America. The calculated values over the global data set show a slight trend with the surface temperature, and since there is no obvious trend with the column amount of water vapor, it is argued that the trend with temperature is evidence that absorption by other components (i.e., CO2O3 and other trace gases not included in these calculations) in the model could be improved.

  6. A Comparison of Combustor-Noise Models

    NASA Technical Reports Server (NTRS)

    Hultgren, Lennart S.

    2012-01-01

    The present status of combustor-noise prediction in the NASA Aircraft Noise Prediction Program (ANOPP)1 for current-generation (N) turbofan engines is summarized. Several semi-empirical models for turbofan combustor noise are discussed, including best methods for near-term updates to ANOPP. An alternate turbine-transmission factor2 will appear as a user selectable option in the combustor-noise module GECOR in the next release. The three-spectrum model proposed by Stone et al.3 for GE turbofan-engine combustor noise is discussed and compared with ANOPP predictions for several relevant cases. Based on the results presented herein and in their report,3 it is recommended that the application of this fully empirical combustor-noise prediction method be limited to situations involving only General-Electric turbofan engines. Long-term needs and challenges for the N+1 through N+3 time frame are discussed. Because the impact of other propulsion-noise sources continues to be reduced due to turbofan design trends, advances in noise-mitigation techniques, and expected aircraft configuration changes, the relative importance of core noise is expected to greatly increase in the future. The noise-source structure in the combustor, including the indirect one, and the effects of the propagation path through the engine and exhaust nozzle need to be better understood. In particular, the acoustic consequences of the expected trends toward smaller, highly efficient gas-generator cores and low-emission fuel-flexible combustors need to be fully investigated since future designs are quite likely to fall outside of the parameter space of existing (semi-empirical) prediction tools.

  7. Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences.

    PubMed

    Laakmann, S; Gerdts, G; Erler, R; Knebelsberger, T; Martínez Arbizu, P; Raupach, M J

    2013-09-01

    Calanoid copepods play an important role in the pelagic ecosystem making them subject to various taxonomic and ecological studies, as well as indicators for detecting changes in the marine habitat. For all these investigations, valid identification, mainly of sibling and cryptic species as well as early life history stages, represents a central issue. In this study, we compare species identification methods for pelagic calanoid copepod species from the North Sea and adjacent regions in a total of 333 specimens. Morphologically identified specimens were analysed on the basis of nucleotide sequences (i.e. partial mitochondrial cytochrome c oxidase subunit I (COI) and complete 18S rDNA) and on proteome fingerprints using the technology of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). On all three molecular approaches, all specimens were classified to species level indicated by low intraspecific and high interspecific variability. Sequence divergences in both markers revealed a second Pseudocalanus species for the southern North Sea identified as Pseudocalanus moultoni by COI sequence comparisons to GenBank. Proteome fingerprints were valid for species clusters irrespective of high intraspecific variability, including significant differences between early developmental stages and adults. There was no effect of sampling region or time; thus, trophic effect, when analysing the whole organisms, was observed in species-specific protein mass spectra, underlining the power of this tool in the application on metazoan species identification. Because of less sample preparation steps, we recommend proteomic fingerprinting using the MALDI-TOF MS as an alternative or supplementary approach for rapid, cost-effective species identification. PMID:23848968

  8. Multiple Comparisons in Genetic Association Studies: A Hierarchical Modeling Approach

    PubMed Central

    Yi, Nengjun; Xu, Shizhong; Lou, Xiang-Yang; Mallick, Himel

    2016-01-01

    Multiple comparisons or multiple testing has been viewed as a thorny issue in genetic association studies aiming to detect disease-associated genetic variants from a large number of genotyped variants. We alleviate the problem of multiple comparisons by proposing a hierarchical modeling approach that is fundamentally different from the existing methods. The proposed hierarchical models simultaneously fit as many variables as possible and shrink unimportant effects towards zero. Thus, the hierarchical models yield more efficient estimates of parameters than the traditional methods that analyze genetic variants separately, and also coherently address the multiple comparisons problem due to largely reducing the effective number of genetic effects and the number of statistically ‘significant’ effects. We develop a method for computing the effective number of genetic effects in hierarchical generalized linear models, and propose a new adjustment for multiple comparisons, the hierarchical Bonferroni correction, based on the effective number of genetic effects. Our approach not only increases the power to detect disease-associated variants but also controls the Type I error. We illustrate and evaluate our method with real and simulated data sets from genetic association studies. The method has been implemented in our freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/). PMID:24259248

  9. LED luminaire longevity strategy models comparison

    NASA Astrophysics Data System (ADS)

    Lemieux, Hugo; Thibault, Simon; Martel, Alain A.

    2010-08-01

    As energy efficiency becomes more and more important, light-emitting diodes (LEDs) are a promising alternative to traditional lighting. Indeed, the energy efficiency of LEDs is still improving as their luminosity is modulated by current. Moreover, for applications such as exterior lamp posts, their small size, directionality, colors and high frequency response allow to combine them and provide design possibilities which are impossible with any other light source. However, as any lamp, LEDs have a lumen depreciation which is a function of both current and temperature. Thus, to take advantage of the full characteristics of LEDs, LED luminaire longevity strategies must be carefully studied and planned, especially since the IES and CIE guidelines state clearly that the luminaire must maintain the rated recommended light level until the end of the system's operating life. The recommended approach for LED luminaire specification is therefore to use the end-of-life light level when evaluating the luminaire. Different power supply strategies have been simulated to determine which one maximizes energy saving and lifetime. With these results, it appears that active control can save at least 25% in energy, but the best strategy cannot be determined because of uncertainties in luminosity degradation models.

  10. Statistical comparison of the AGDISP model with deposit data

    NASA Astrophysics Data System (ADS)

    Duan, Baozhong; Yendol, William G.; Mierzejewski, Karl

    An aerial spray Agricultural Dispersal (AGDISP) model was tested against quantitative field data. The microbial pesticide Bacillus thuringiensis (Bt) was sprayed as fine spray from a helicopted over a flat site in various meteorological conditions. Droplet deposition on evenly spaced Kromekote cards, 0.15 m above the ground, was measured with image analysis equipment. Six complete data sets out of the 12 trials were selected for data comparison. A set of statistical parameters suggested by the American Meteorological Society and other authors was applied for comparisons of the model prediction with the ground deposit data. The results indicated that AGDISP tended to overpredict the average volume deposition by a factor of two. The sensitivity test of the AGDISP model to the input wind direction showed that the model may not be sensitive to variations in wind direction within 10 degrees relative to aircraft flight path.

  11. Comparison of compounds of three Rubus species and their antioxidant activity.

    PubMed

    Caidan, Rezeng; Cairang, Limao; Pengcuo, Jiumei; Tong, Li

    2015-12-01

    Rubus amabilis, Rubus niveus Thunb., and Rubus sachalinensis are three Rubus species that are alternatively found in Manubzhithang, a Tibetan medicine, in different areas of China. The current study analyzed HPLC/UV chromatograms and it compared compounds of these three Rubus species in contrast to reference substances such as 2,6-dimethoxy-4-hydroxyphenol-1-O-β-D-glucopyranoside, procyanidin B4, and isovitexin-7-O-glucoside. The three Rubus species produced similar peaks in chromatograms. The antioxidant activity of the three Rubus species was determined using an assay for DPPH free radical scavenging activity. Results indicated that the three Rubus species extracts had almost the same level of free radical scavenging activity. Thus, findings indicated the rationality of substituting these species for one another as an ingredient in Manubzhithang. PMID:26781923

  12. Network analysis and cross species comparison of protein-protein interaction networks of human, mouse and rat cytochrome P450 proteins that degrade xenobiotics.

    PubMed

    Karthikeyan, Bagavathy Shanmugam; Akbarsha, Mohammad Abdulkader; Parthasarathy, Subbiah

    2016-06-21

    Cytochrome P450 (CYP) enzymes that degrade xenobiotics play a critical role in the metabolism and biotransformation of drugs and xenobiotics in humans as well as experimental animal models such as mouse and rat. These proteins function as a network collectively as well as independently. Though there are several reports on the organization, regulation and functionality of various CYP enzymes at the molecular level, the understanding of organization and functionality of these proteins at the holistic level remain unclear. The objective of this study is to understand the organization and functionality of xenobiotic degrading CYP enzymes of human, mouse and rat using network theory approaches and to study species differences that exist among them at the holistic level. For our analysis, a protein-protein interaction (PPI) network for CYP enzymes of human, mouse and rat was constructed using the STRING database. Topology, centrality, modularity and robustness analyses were performed for our predicted CYP PPI networks that were then validated by comparison with randomly generated network models. Network centrality analyses of CYP PPI networks reveal the central/hub proteins in the network. Modular analysis of the CYP PPI networks of human, mouse and rat resulted in functional clusters. These clusters were subjected to ontology and pathway enrichment analysis. The analyses show that the cluster of the human CYP PPI network is enriched with pathways principally related to xenobiotic/drug metabolism. Endo-xenobiotic crosstalk dominated in mouse and rat CYP PPI networks, and they were highly enriched with endogenous metabolic and signaling pathways. Thus, cross-species comparisons and analyses of human, mouse and rat CYP PPI networks gave insights about species differences that existed at the holistic level. More investigations from both reductionist and holistic perspectives can help understand CYP metabolism and species extrapolation in a much better way. PMID:27194593

  13. Prediction of human drug clearance from two species: a comparison of several allometric methods.

    PubMed

    Goteti, Kosalaram; Garner, C Edwin; Mahmood, Iftekhar

    2010-03-01

    The objective of the study was to assess the degree of accuracy in human drug clearance prediction from two species using four different allometric approaches: simple allometry (SA), multiexponential allometry (ME), rule of exponents (ROE), and fixed exponents (FE) as suggested by Tang et al. There were 45 compounds in this analysis and the two species used were either rat-dog or rat-monkey. In addition, > or = 3 species scaling was also performed to evaluate the comparative accuracy in the prediction of human drug clearance between two or more than two-species scaling. The results of the study indicated that the two-species scaling with different methods provided different degrees of accuracy in the prediction of clearance. Prediction by a particular method was also species dependent. For example, a given drug with rat-dog scaling provided a reasonably accurate prediction of clearance whereas with rat-monkey scaling the prediction of clearance was highly erratic or vice versa. The results of the study indicated that the two-species scaling can be useful for prediction purposes but the prediction of clearance from > or = 3 species was far more accurate than two-species scaling. PMID:19827101

  14. 3D shape decomposition and comparison for gallbladder modeling

    NASA Astrophysics Data System (ADS)

    Huang, Weimin; Zhou, Jiayin; Liu, Jiang; Zhang, Jing; Yang, Tao; Su, Yi; Law, Gim Han; Chui, Chee Kong; Chang, Stephen

    2011-03-01

    This paper presents an approach to gallbladder shape comparison by using 3D shape modeling and decomposition. The gallbladder models can be used for shape anomaly analysis and model comparison and selection in image guided robotic surgical training, especially for laparoscopic cholecystectomy simulation. The 3D shape of a gallbladder is first represented as a surface model, reconstructed from the contours segmented in CT data by a scheme of propagation based voxel learning and classification. To better extract the shape feature, the surface mesh is further down-sampled by a decimation filter and smoothed by a Taubin algorithm, followed by applying an advancing front algorithm to further enhance the regularity of the mesh. Multi-scale curvatures are then computed on the regularized mesh for the robust saliency landmark localization on the surface. The shape decomposition is proposed based on the saliency landmarks and the concavity, measured by the distance from the surface point to the convex hull. With a given tolerance the 3D shape can be decomposed and represented as 3D ellipsoids, which reveal the shape topology and anomaly of a gallbladder. The features based on the decomposed shape model are proposed for gallbladder shape comparison, which can be used for new model selection. We have collected 19 sets of abdominal CT scan data with gallbladders, some shown in normal shape and some in abnormal shapes. The experiments have shown that the decomposed shapes reveal important topology features.

  15. Comparison of Dst Forecast Models for Intense Geomagnetic Storms

    NASA Technical Reports Server (NTRS)

    Ji, Eun-Young; Moon, Y.-J.; Gopalswamy, N.; Lee, D.-H.

    2012-01-01

    We have compared six disturbance storm time (Dst) forecast models using 63 intense geomagnetic storms (Dst <=100 nT) that occurred from 1998 to 2006. For comparison, we estimated linear correlation coefficients and RMS errors between the observed Dst data and the predicted Dst during the geomagnetic storm period as well as the difference of the value of minimum Dst (Delta Dst(sub min)) and the difference in the absolute value of Dst minimum time (Delta t(sub Dst)) between the observed and the predicted. As a result, we found that the model by Temerin and Li gives the best prediction for all parameters when all 63 events are considered. The model gives the average values: the linear correlation coefficient of 0.94, the RMS error of 14.8 nT, the Delta Dst(sub min) of 7.7 nT, and the absolute value of Delta t(sub Dst) of 1.5 hour. For further comparison, we classified the storm events into two groups according to the magnitude of Dst. We found that the model of Temerin and Lee is better than the other models for the events having 100 <= Dst < 200 nT, and three recent models (the model of Wang et al., the model of Temerin and Li, and the model of Boynton et al.) are better than the other three models for the events having Dst <= 200 nT.

  16. Comparison of models for piping transmission loss estimations

    NASA Astrophysics Data System (ADS)

    Catron, Fred W.; Mann, J. Adin

    2005-09-01

    A frequency dependent model for the transmission loss of piping is important for accurate estimates of the external radiation from pipes and the vibration level of the pipe walls. A statistical energy analysis model is used to predict the transmission loss of piping. Key terms in the model are the modal density and the radiation efficiency of the piping wall. Several available models for each are compared in reference to measured data. In low frequency octave bands, the modal density is low. The model of the transmission loss in these octave bands is augmented with a mass law model in the low frequency regime where the number of modes is small. The different models and a comparison of the models will be presented.

  17. Leaf nitrate assimilation during leaf expansion period: comparison of temperate and boreal tree species

    NASA Astrophysics Data System (ADS)

    Koyama, L.; Tokuchi, N.; Kielland, K.

    2011-12-01

    We examined nitrate assimilation in several tree species to test the hypothesis that plant N acquisition is highest in early spring due to the N demands of leaf growth and the seasonal availability of soil N. Specifically, we advance the idea that trees acquire N most actively during the leaf expansion period, which serves to offset growth-dilution of foliar N. However, it has been observed that boreal species expand their leaves more rapidly than do temperate species, suggesting that they exhibit a different seasonal pattern of N acquisition than do temperate species. To examine these relationships we measured leaf nitrate reductase activity (NRA) as a proxy for nitrate assimilation, leaf expansion rates, and foliar N concentrations on three boreal tree species and three temperate tree species throughout their leaf expansion period. An evergreen species (Quercus glauca) and two deciduous species (Acer palmatum and Zelkova serrata) were investigated in temperate Japan, and three deciduous species Alnus crispa, Betula papyrifera and Populus tremuloides were chosen in a boreal forest in interior Alaska, US. The patterns of foliar N concentrations were very similar across all six species, but the mean leaf expansion period was shorter in the boreal species (about 25 days) than in temperate species (about 29 days). All temperate species showed clear peaks of leaf NRA in the middle of leaf expansion period, suggesting that leaves partly compensate for the N dilution during expansion via foliar nitrate assimilation, and that plant nitrate acquisition was effectively timed to coincide with soil N availability generally increased in early spring. By contrast, peak NRA in the boreal species were observed in different stage of leaf expansion, but as in the temperate species declined to very low levels after the leaves were fully expanded. Our results demonstrate that plant nitrate assimilation is concentrated during leaf expansion in spring and early summer, but declines to

  18. Mapping National Plant Biodiversity Patterns in South Korea with the MARS Species Distribution Model

    PubMed Central

    Choe, Hyeyeong; Thorne, James H.; Seo, Changwan

    2016-01-01

    Accurate information on the distribution of existing species is crucial to assess regional biodiversity. However, data inventories are insufficient in many areas. We examine the ability of Multivariate Adaptive Regression Splines (MARS) multi-response species distribution model to overcome species’ data limitations and portray plant species distribution patterns for 199 South Korean plant species. The study models species with two or more observations, examines their contribution to national patterns of species richness, provides a sensitivity analysis of different range threshold cutoff approaches for modeling species’ ranges, and presents considerations for species modeling at fine spatial resolution. We ran MARS models for each species and tested four threshold methods to transform occurrence probabilities into presence or absence range maps. Modeled occurrence probabilities were extracted at each species’ presence points, and the mean, median, and one standard deviation (SD) calculated to define data-driven thresholds. A maximum sum of sensitivity and specificity threshold was also calculated, and the range maps from the four cutoffs were tested using independent plant survey data. The single SD values were the best threshold tested for minimizing omission errors and limiting species ranges to areas where the associated occurrence data were correctly classed. Eight individual species range maps for rare plant species were identified that are potentially affected by resampling predictor variables to fine spatial scales. We portray spatial patterns of high species richness by assessing the combined range maps from three classes of species: all species, endangered and endemic species, and range-size rarity of all species, which could be used in conservation planning for South Korea. The MARS model is promising for addressing the common problem of few species occurrence records. However, projected species ranges are highly dependent on the threshold and scale

  19. CO2 exposure as translational cross-species experimental model for panic.

    PubMed

    Leibold, N K; van den Hove, D L A; Viechtbauer, W; Buchanan, G F; Goossens, L; Lange, I; Knuts, I; Lesch, K P; Steinbusch, H W M; Schruers, K R J

    2016-01-01

    The current diagnostic criteria of the Diagnostic and Statistical Manual of Mental Disorders are being challenged by the heterogeneity and the symptom overlap of psychiatric disorders. Therefore, a framework toward a more etiology-based classification has been initiated by the US National Institute of Mental Health, the research domain criteria project. The basic neurobiology of human psychiatric disorders is often studied in rodent models. However, the differences in outcome measurements hamper the translation of knowledge. Here, we aimed to present a translational panic model by using the same stimulus and by quantitatively comparing the same outcome measurements in rodents, healthy human subjects and panic disorder patients within one large project. We measured the behavioral-emotional and bodily response to CO2 exposure in all three samples, allowing for a reliable cross-species comparison. We show that CO2 exposure causes a robust fear response in terms of behavior in mice and panic symptom ratings in healthy volunteers and panic disorder patients. To improve comparability, we next assessed the respiratory and cardiovascular response to CO2, demonstrating corresponding respiratory and cardiovascular effects across both species. This project bridges the gap between basic and human research to improve the translation of knowledge between these disciplines. This will allow significant progress in unraveling the etiological basis of panic disorder and will be highly beneficial for refining the diagnostic categories as well as treatment strategies. PMID:27598969

  20. Arima model and exponential smoothing method: A comparison

    NASA Astrophysics Data System (ADS)

    Wan Ahmad, Wan Kamarul Ariffin; Ahmad, Sabri

    2013-04-01

    This study shows the comparison between Autoregressive Moving Average (ARIMA) model and Exponential Smoothing Method in making a prediction. The comparison is focused on the ability of both methods in making the forecasts with the different number of data sources and the different length of forecasting period. For this purpose, the data from The Price of Crude Palm Oil (RM/tonne), Exchange Rates of Ringgit Malaysia (RM) in comparison to Great Britain Pound (GBP) and also The Price of SMR 20 Rubber Type (cents/kg) with three different time series are used in the comparison process. Then, forecasting accuracy of each model is measured by examinethe prediction error that producedby using Mean Squared Error (MSE), Mean Absolute Percentage Error (MAPE), and Mean Absolute deviation (MAD). The study shows that the ARIMA model can produce a better prediction for the long-term forecasting with limited data sources, butcannot produce a better prediction for time series with a narrow range of one point to another as in the time series for Exchange Rates. On the contrary, Exponential Smoothing Method can produce a better forecasting for Exchange Rates that has a narrow range of one point to another for its time series, while itcannot produce a better prediction for a longer forecasting period.

  1. DIATOM INDICES OF STREAM ECOSYSTEM CONDITIONS: COMPARISON OF GENUS VS. SPECIES LEVEL IDENTIFICATIONS

    EPA Science Inventory

    Diatom assemblage data collected between 1993 and 1995 from 233 Mid-Appalachian streams were used to compare indices of biotic integrity based on genus vs. species level taxonomy. Thirty-seven genera and 197 species of diatoms were identified from these samples. Metrics included...

  2. Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae).

    PubMed

    Schwarzfeld, Marla D; Sperling, Felix A H

    2015-12-01

    DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC's) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89-121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus. PMID:26265257

  3. A description and morphometric comparison of eggs of species of the Anopheles gambiae complex.

    PubMed

    Lounibos, L P; Coetzee, M; Duzak, D; Nishimura, N; Linley, J R; Service, M W; Cornel, A J; Fontenille, D; Mukwaya, L G

    1999-06-01

    Eggs of the 6 named species of the Anopheles gambiae complex are described from scanning electron micrographs of specimens obtained from laboratory colonies or wild-caught females. Morphometric measurements of eggs from 5 sources of Anopheles arabiensis, 2 of Anopheles gambiae, one of Anopheles quadriannulatus, 2 of Anopheles bwambae, 2 of Anopheles merus, and one of Anopheles melas are compared, and relationships are analyzed by multivariate statistics. No morphologic characters were species-diagnostic, although tendencies of the saltwater species An. merus and An. melas to have wider decks and shorter floats were confirmed. Species and populations overlapped considerably in principal components and discriminant function analyses based on 10 attributes of eggs. Nevertheless, discriminant functions revealed similarities in eggs of species believed to be most closely related, namely, An. gambiae and An. arabiensis, An. merus and An. melas, and An. quadriannulatus and An. bwambae. PMID:10412112

  4. Identification of three morphologically indistinguishable Epicauta species (Coleoptera, Meloidae, Epicautini) through DNA barcodes and morphological comparisons.

    PubMed

    Liu, Shao-Pan; Pan, Zhao; Ren, Guo-Dong

    2016-01-01

    Three species that belong to the genus Epicauta (Coleopera: Meloidae), E. chinensis, E. dubia, and E. sibirica, appear morphologically indistinguishable. The present study aims to resolve the taxonomic status and the relationships among these three species. Identifying adult morphological characters among the three species were compared and illustrated and partial fragments of the mitochondrial gene (COI) for 77 samples, representing seven meloid species, were obtained and analyzed. Analyses of nucleotide composition, genetic distances and phylogenetics were performed. The results of the morphological studies and molecular analyses showed concordance, indicating that the three species are closely related and indistinguishable from one another. Consequently, two new synonyms are proposed: E. chinensis (Laporte, 1840) syn. n. = E. sibirica (Pallas, 1773) and E. dubia (Fabricius, 1781) syn. n. = E. sibirica (Pallas, 1773). PMID:27394741

  5. Comparison of climate model simulated and observed borehole temperature profiles

    NASA Astrophysics Data System (ADS)

    Gonzalez-Rouco, J. F.; Stevens, M. B.; Beltrami, H.; Goosse, H.; Rath, V.; Zorita, E.; Smerdon, J.

    2009-04-01

    Advances in understanding climate variability through the last millennium lean on simulation and reconstruction efforts. Progress in the integration of both approaches can potentially provide new means of assessing confidence on model projections of future climate change, of constraining the range of climate sensitivity and/or attributing past changes found in proxy evidence to external forcing. This work addresses specifically possible strategies for comparison of paleoclimate model simulations and the information recorded in borehole temperature profiles (BTPs). First efforts have allowed to design means of comparison of model simulated and observed BTPs in the context of the climate of the last millennium. This can be done by diffusing the simulated temperatures into the ground in order to produce synthetic BTPs that can be in turn assigned to collocated, real BTPs. Results suggest that there is sensitivity of borehole temperatures at large and regional scales to changes in external forcing over the last centuries. The comparison between borehole climate reconstructions and model simulations may also be subjected to non negligible uncertainties produced by the influence of past glacial and Holocene changes. While the thermal climate influence of the last deglaciation can be found well below 1000 m depth, such type of changes can potentially exert an influence on our understanding of subsurface climate in the top ca. 500 m. This issue is illustrated in control and externally forced climate simulations of the last millennium with the ECHO-G and LOVECLIM models, respectively.

  6. Bayesian Model Comparison for the Order Restricted RC Association Model

    ERIC Educational Resources Information Center

    Iliopoulos, G.; Kateri, M.; Ntzoufras, I.

    2009-01-01

    Association models constitute an attractive alternative to the usual log-linear models for modeling the dependence between classification variables. They impose special structure on the underlying association by assigning scores on the levels of each classification variable, which can be fixed or parametric. Under the general row-column (RC)…

  7. Model reduction for stochastic chemical systems with abundant species.

    PubMed

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems. PMID:26646867

  8. Model reduction for stochastic chemical systems with abundant species

    NASA Astrophysics Data System (ADS)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  9. Model reduction for stochastic chemical systems with abundant species

    SciTech Connect

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-07

    Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. We first identify the rate constant limits under which the concentrations of a given set of species will tend to infinity (the abundant species) while the concentrations of all other species remains constant (the non-abundant species). Subsequently, we prove that, in this limit, the fluctuations in the molecule numbers of non-abundant species are accurately described by a hybrid stochastic description consisting of a chemical master equation coupled to deterministic rate equations. This is a reduced description when compared to the conventional chemical master equation which describes the fluctuations in both abundant and non-abundant species. We show that the reduced master equation can be solved exactly for a number of biochemical networks involving gene expression and enzyme catalysis, whose conventional chemical master equation description is analytically impenetrable. We use the linear noise approximation to obtain approximate expressions for the difference between the variance of fluctuations in the non-abundant species as predicted by the hybrid approach and by the conventional chemical master equation. Furthermore, we show that surprisingly, irrespective of any separation in the mean molecule numbers of various species, the conventional and hybrid master equations exactly agree for a class of chemical systems.

  10. ESTIMATION OF AQUATIC SPECIES SENSITIVITY USING INTERSPECIES CORRELATION AND ACUTE TO CHRONIC TOXICITY MODELS

    EPA Science Inventory

    Abstract for presentation

    Estimation of aquatic species sensitivity using interspecies correlation and acute to chronic toxicity models

    Determining species sensitivity of aquatic organisms to contaminants is a critical component of criteria development and ecolog...

  11. Comparison of Transmission Line Methods for Surface Acoustic Wave Modeling

    NASA Technical Reports Server (NTRS)

    Wilson, William; Atkinson, Gary

    2009-01-01

    Surface Acoustic Wave (SAW) technology is low cost, rugged, lightweight, extremely low power and can be used to develop passive wireless sensors. For these reasons, NASA is investigating the use of SAW technology for Integrated Vehicle Health Monitoring (IVHM) of aerospace structures. To facilitate rapid prototyping of passive SAW sensors for aerospace applications, SAW models have been developed. This paper reports on the comparison of three methods of modeling SAWs. The three models are the Impulse Response Method (a first order model), and two second order matrix methods; the conventional matrix approach, and a modified matrix approach that is extended to include internal finger reflections. The second order models are based upon matrices that were originally developed for analyzing microwave circuits using transmission line theory. Results from the models are presented with measured data from devices. Keywords: Surface Acoustic Wave, SAW, transmission line models, Impulse Response Method.

  12. Integrating occupancy models and structural equation models to understand species occurrence

    PubMed Central

    Joseph, Maxwell B.; Preston, Daniel L.; Johnson, Pieter T. J.

    2016-01-01

    Understanding the drivers of species occurrence is a fundamental goal in basic and applied ecology. Occupancy models have emerged as a popular approach for inferring species occurrence because they account for problems associated with imperfect detection in field surveys. Current models, however, are limited because they assume covariates are independent (i.e., indirect effects do not occur). Here, we combined structural equation and occupancy models to investigate complex influences on species occurrence while accounting for imperfect detection. These two methods are inherently compatible because they both provide means to make inference on latent or unobserved quantities based on observed data. Our models evaluated the direct and indirect roles of cattle grazing, water chemistry, vegetation, nonnative fishes, and pond permanence on the occurrence of six pond-breeding amphibians, two of which are threatened: the California tiger salamander (Ambystoma californiense), and the California red-legged frog (Rana draytonii). While cattle had strong effects on pond vegetation and water chemistry, their overall effects on amphibian occurrence were small compared to the consistently negative effects of nonnative fish. Fish strongly reduced occurrence probabilities for four of five native amphibians, including both species of conservation concern. These results could help to identify drivers of amphibian declines and to prioritize strategies for amphibian conservation. More generally, this approach facilitates a more mechanistic representation of ideas about the causes of species distributions in space and time. As shown here, occupancy modeling and structural equation modeling are readily combined, and bring rich sets of techniques that may provide unique theoretical and applied insights into basic ecological questions. PMID:27197402

  13. Integrating occupancy models and structural equation models to understand species occurrence.

    PubMed

    Joseph, Maxwell B; Preston, Daniel L; Johnson, Pieter T J

    2016-03-01

    Understanding the drivers of species occrrece s a fundamenal goal in basic and applied ecology. Occupancy models have emerged as a popular approach for inferring species occurrence because they account for problems associated with imperfect detection in field surveys. Current models, however, are limited because they assume covariates are independent (i.e., indirect effects do not occur). Here, we combined structural equation and occupancy models to investigate complex influences on species occurrence while accounting for imperfect detection. These two methods are inherently compatible because they both provide means to make inference on latent or unobserved quantities based on observed data. Our models evaluated the direct and indirect roles of cattle grazing, water chemistry, vegetation, nonnative fishes, and pond permanence on the occurrence of six pond-breeding amphibians, two of which are threatened: the California tiger salamander (Ambysloma californiense) and the California red-legged frog (Rana draytonil). While cattle had strong effects on pond vegetation and water chemistry, their overall effects on amphibian occurrence were small compared to the consistently negative effects of nonnative fish. Fish strongly reduced occurrence probabilities for four of five native amphibians, including both species of conservation concern. These results could help to identify drivers of amphibian declines and to prioritize strategies for amphibian conservation. More generally, this approach facilitates a more mechanistic representation of ideas about the causes of species distributions in space and time. As shown here, occupancy modeling and structural equation modeling are readily combined, and bring rich sets of techniques that may provide unique theoretical and applied insights into basic ecological questions. PMID:27197402

  14. A Comparison of Approximation Modeling Techniques: Polynomial Versus Interpolating Models

    NASA Technical Reports Server (NTRS)

    Giunta, Anthony A.; Watson, Layne T.

    1998-01-01

    Two methods of creating approximation models are compared through the calculation of the modeling accuracy on test problems involving one, five, and ten independent variables. Here, the test problems are representative of the modeling challenges typically encountered in realistic engineering optimization problems. The first approximation model is a quadratic polynomial created using the method of least squares. This type of polynomial model has seen considerable use in recent engineering optimization studies due to its computational simplicity and ease of use. However, quadratic polynomial models may be of limited accuracy when the response data to be modeled have multiple local extrema. The second approximation model employs an interpolation scheme known as kriging developed in the fields of spatial statistics and geostatistics. This class of interpolating model has the flexibility to model response data with multiple local extrema. However, this flexibility is obtained at an increase in computational expense and a decrease in ease of use. The intent of this study is to provide an initial exploration of the accuracy and modeling capabilities of these two approximation methods.

  15. LUNG MODEL CASTING TECHNIQUES FOR INTERSPECIES MORPHOMETRIC COMPARISONS

    EPA Science Inventory

    Techniques have been developed for casting both solid and hollow lung models from lung specimens. These techniques have been used to make casts of rat, rabbit, baboon, and human lungs and may be used for other species. An air line at a positive pressure of 25 cm of water is conne...

  16. Comparison of four diagnostic methods for detection of Helicobacter species in laboratory mice.

    PubMed

    Mähler, M; Bedigian, H G; Burgett, B L; Bates, R J; Hogan, M E; Sundberg, J P

    1998-02-01

    Four species of Helicobacter--H. muridarum, "H. rappini," H. hepaticus, and H. bilis--have been identified in the gastrointestinal tract of rodents. The association of Helicobacter species with chronic gastrointestinal diseases in mice has raised concern about their impact on research results. In this study, different methods for detection of Helicobacter species in the mouse intestinal tract were compared: polymerase chain reaction (PCR) amplification of 16S rRNA gene sequences, bacterial culture, electron microscopy, and histologic examination (Steiner stain). The PCR method was more sensitive in detecting murine Helicobacter species than was culture, electron microscopy, or histologic examination. Of the cecal specimens identified as Helicobacter species-positive by PCR, approximately 60% were identified as positive by each of the other methods. An 87.5% concordance was obtained by PCR screening of DNA from fecal and cecal specimens. Differentiation among murine Helicobacter species by colony morphologic or histologic features was not possible. Scanning electron microscopy and histologic examination indicated greater numbers of helical microorganisms, specifically H. hepaticus, in the cecum than in the colon. These results indicate that the PCR assays used can be performed on feces as a noninvasive means for rapidly screening large numbers of colony mice for murine Helicobacter species. PMID:9517897

  17. Comparison of Genus and Species-Level Compilations of Metabolic Rate through Time

    NASA Astrophysics Data System (ADS)

    Sundararajan, D.; Heim, N. A.; Payne, J.

    2014-12-01

    Metabolism is the basis of fundamental principles of biology and sustains life through vital processes such as growth and reproduction. Brown et al. (2004) showed that metabolism is central to our understanding of patterns and dynamics at all levels of biological organization. Often, paleontologists use the holotypes of type species to represent genera in global analyses, but they rarely test how representative the type species are of the genus of a whole. Through my analyses, I compared genus and species-level compilations through time by comparing the mean metabolic rate of each genus to the metabolic rate of the type species to see if using this representative provided effective data when conducting genus-level analyses. To achieve these objectives, I used sizes collected from Catalogue of Ostracoda and Treatise on Invertebrate Paleontology. The range of the type species' metabolic rate varied, but there is no systematic bias towards higher or lower metabolic rates. Therefore, using type species in genus-level analyses is effective when looking for general trends, but the absolute values based on the holotype of type species have some bias to them and are not as accurate.

  18. The tangled nature model as an evolving quasi-species model

    NASA Astrophysics Data System (ADS)

    Avogadro di Collobiano, Simone; Christensen, Kim; Jeldtoft Jensen, Henrik

    2003-01-01

    We show that the tangled nature model can be interpreted as a general formulation of the quasi-species model by Eigen et al in a frequency-dependent fitness landscape. We present a detailed theoretical derivation of the mutation threshold, consistent with the simulation results, that provides a valuable insight into how the microscopic dynamics of the model determines the observed macroscopic phenomena published previously. The dynamics of the tangled nature model is defined on the microevolutionary time scale via reproduction, with heredity, variation and natural selection. Each organism reproduces at a rate that is linked to the individuals' genetic sequence and depends on the composition of the population in genotype space. Thus the microevolutionary dynamics of the fitness landscape is regulated by, and regulates, the evolution of the species by means of the mutual interactions. At low mutation rate, the macroevolutionary pattern mimics the fossil data: periods of stasis, where the population is concentrated in a network of coexisting species, are interrupted by bursts of activity. As the mutation rate increases, the duration and the frequency of bursts increase. Eventually, when the mutation rate reaches a certain threshold, the population is spread evenly throughout the genotype space showing that natural selection only leads to multiple distinct species if adaptation is allowed time to cause fixation.

  19. Comparison of the rotavirus nonstructural protein NSP1 (NS53) from different species by sequence analysis and northern blot hybridization.

    PubMed

    Dunn, S J; Cross, T L; Greenberg, H B

    1994-08-15

    The nucleotide sequence of gene 5 encoding the rotavirus nonstructural protein NSP1 (NS53) of 6 strains (EW, EHP, RRV, I321, OSU, and Gottfried) was determined and compared to 6 previously reported strains (SA11, UK, RF, Hu803, DS-1, and Wa). The 12 rotavirus strains were derived from a total of five separate species (murine, bovine, simian, porcine, and human). Gene sizes ranged from 1564 to 1611 nucleotides in length and the deduced protein sequences were found to be 486 to 495 amino acids in length. Comparisons of NSP1 amino acid sequences showed identities ranging from 36 to 92%. This diversity was most evident between strains from different species. Phylogenetic analysis revealed a clustering of NSP1 sequences according to species origin with the exception that the human and porcine strains were included in a single grouping. Northern blot hybridizations using additional rotavirus strains from the five species confirmed the grouping found by sequence analysis. The species specificity of NSP1 is consistent with the hypothesis that NSP1 plays a role in host range restriction. PMID:8030275

  20. LKB-Based Evaporation Duct Model Comparison with Buoy Data.

    NASA Astrophysics Data System (ADS)

    Babin, Steven M.; Dockery, G. Daniel

    2002-04-01

    A wave-riding catamaran with a mast-traveling sensor package (profiling buoy) was developed to make fine-scale atmospheric measurements within the first meter above the ocean surface. These measurements are used to generate time-averaged modified refractivity (M) profiles that are then compared with those determined from four evaporation duct models based on the surface layer theory of Liu, Katsaros, and Businger (LKB). Model inputs are derived from measurements from masts on the R/V Chessie and from a tethered sea surface temperature buoy. Because electromagnetic propagation is critically dependent on the M-profile slopes, different analytical techniques are employed to compare the curvature of the model profiles with that of the profiles measured by the profiling buoy. One comparison criterion was to use the rms M slope difference between the model and a curve fit to the buoy profile data. Another analytical technique was to use the rms M difference after mean M removal between the model and the buoy profiles. Using these criteria for comparison of these models with the data seems to indicate that the model-derived profiles may be missing some phenomena in the surface layer such as wave effects. Overall, however, the shapes of the measured M profiles showed log-linear characteristics near the surface. One interesting result is that each model was better at approximating the M-profile curvature for stable than for unstable conditions.

  1. Comparison of model predictions with LDEF satellite radiation measurements

    NASA Technical Reports Server (NTRS)

    Armstrong, T. W.; Colborn, B. L.; Harmon, B. A.; Parnell, T. A.; Watts, J. W., Jr.; Benton, E. V.

    1994-01-01

    Some early results are summarized from a program under way to utilize Long Duration Exposure Facility (LDEF) satellite data for evaluating and improving current models of the space radiation environment in low Earth orbit. Reported here are predictions and comparisons with some of the LDEF dose and induced radioactivity data, which are used to check the accuracy of current models describing the magnitude and directionality of the trapped proton environment. Preliminary findings are that the environment models underestimate both dose and activation from trapped protons by a factor of about two, and the observed anisotropy is higher than predicted.

  2. 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

  3. Neurobehavioral Integrity of Chimpanzee Newborns: Comparisons across groups and across species reveal gene-environment interaction effects

    PubMed Central

    Bard, Kim A.; Brent, Linda; Lester, Barry; Worobey, John; Suomi, Stephen J.

    2014-01-01

    The aims of this article are to describe the neurobehavioral integrity of chimpanzee newborns, to investigate how early experiences affect the neurobehavioral organization of chimpanzees, and to explore species differences by comparing chimpanzee newborns to a group of typically developing human newborns. Neurobehavioral integrity related to orientation, motor performance, arousal, and state regulation of 55 chimpanzee (raised in four different settings) and 42 human newborns was measured with the Neonatal Behavioral Assessment Scale (NBAS) a semi-structured 25-minute interactive assessment. Thirty-eight chimpanzees were tested every other day from birth, and analyses revealed significant developmental changes in 19 of 27 NBAS scores. The cross-group and cross-species comparisons were conducted at 2 and 30 days of age. Among the 4 chimpanzee groups, significant differences were found in 23 of 24 NBAS scores. Surprisingly, the cross-species comparisons revealed that the human group was distinct in only 1 of 25 NBAS scores (the human group had significantly less muscle tone than all the chimpanzee groups). The human group was indistinguishable from at least one of the chimpanzee groups in the remaining 24 of 25 NBAS scores. The results of this study support the conclusion that the interplay between genes and environment, rather than genes alone or environment alone, accounts for phenotypic expressions of newborn neurobehavioral integrity in hominids. PMID:25110465

  4. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.

    PubMed

    Wang, Yi; Coleman-Derr, Devin; Chen, Guoping; Gu, Yong Q

    2015-07-01

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters. OrthoVenn provides coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn. PMID:25964301

  5. Modeled Impacts of Anthropogenic Stressors on Listed Species in Southern California

    NASA Astrophysics Data System (ADS)

    Bell, M. D.; Hulton, H. L.; Allen, M. F.

    2013-12-01

    Based on data from the 2010 U.S. Census, Riverside County was the fastest growing county in California over the last decade. Urbanization has contributed to the disruption of the wildlands through fragmentation, changes in fire regimes, increased nitrogen deposition, and invasion of exotic plant species. These anthropogenic disturbances act independently and additively to disrupt environmental processes and community interactions even within protected wildlands. Here we incorporate these environmental stressors into Mahalanobis D2 species distribution models to measure the impact of multiple anthropogenic stressors on potential species distributions in Western Riverside County, with an emphasis on threatened species and species of concern. Species occurrence data from 1990 to 2010 of 6 rare and threatened species (2 bird, 2 mammal, and 2 plant) were used as inputs to develop a Habitat Suitability Index (HSI) for each species; potential species distributions were then modeled at a scale of a 250 m2 grid using terrain, climate, and vegetation community indices. We modeled the changing patterns of HSI across a landscape when anthropogenic stressors were added, individually and in combination. The changes in HSI of the rare and threatened species were compared to a common species from each group. Model outputs for endangered and threatened mammal and bird species show that there is a consistent decline in the HSI in cells with high nitrogen deposition and cells near urban development. The spatial shift in habitat suitability moved away from the environmental stressors, and there was also a reduction in area of patches modeled as high suitable habitat in all threatened species suggesting that the minimum habitat requirements for the species are reduced. There were not large changes in species distributions for the common species modeled. As rare species are often difficult to observe during surveys, monitoring the change of an easily measurable metric such a nitrogen

  6. Species comparisons of bronchoalveolar lavages from guinea pigs and rats exposed in vivo to diesel exhaust for one year

    SciTech Connect

    Chen, S.; Weller, M.A.; Barnhart, M.I.

    1982-01-01

    Male Hartly guinea pigs and Fischer rats 344 were exposed to diesel exhaust (DE) concentrations at 0, 250, and 1500 micrograms/m3 in short terms, as well as long term experiments up to one year. The effects of inhaled DE on these rodents were evaluated using bronchoalveolar lavage technique. Both the morphological and functional studies of free lung cells and the biochemical and immunologic studies of the supernatant lavage fluid provided the basis for a quantitative species comparison of the pulmonary responses of exposed guinea pigs and rats versus age matched controls. Following inhalation of 250 micrograms DE/m3, there were little or no significant changes in either species. In contrast, at higher DE concentration, leukocytic infiltration and elevation of specific proteins in lavage fluids were observed in both species. The findings occurred and persisted in both species. Some of the responses were species specific (e.g., the specific type of exudative leukocytes, appearance of reactive monocytes, and different amounts of free DE particles and debris in the lavage fluid). Other responses were similar in both species. Among them, the emergence and increase of lymphocytes was evidence of immunologic responses. Biochemical data from the supernatant fluid correlates with the changes in cellular population in the lavage. The responses appear to be dose and duration dependent. These data indicate that species differences occur. However, it is clear that the alveolar macrophage and granulocytic leukocytes continue to exert effective defense at the DE dose-durations studied. In general, rats appeared more resistant to DE exposure than guinea pigs.

  7. Feeding ecology and trophic comparisons of six shark species in a coastal ecosystem off southern Brazil.

    PubMed

    Bornatowski, H; Braga, R R; Abilhoa, V; Corrêa, M F M

    2014-08-01

    The diets of six shark species, Sphyrna lewini, Sphyrna zygaena, Carcharhinus obscurus, Carcharhinus limbatus, Rhizoprionodon lalandii and Galeocerdo cuvier, were investigated in a subtropical coastal ecosystem of southern Brazil. Stomach content data were obtained to assess foraging niche segregation and ontogenetic shifts in the diets of these sharks. Five of the shark species off the Paraná coast were ichthyophagous, with the exception of S. zygaena, which was teutophagous. With the exception of G. cuvier, which had a generalist diet, the other five species displayed specialization in their feeding. Ontogenetic shifts were observed in C. obscurus and S. lewini with large individuals consuming elasmobranchs. Owing to the diet overlap between C. obscurus and S. lewini, C. obscurus and C. limbatus and R. lalandii and C. limbatus, future studies on the spatial and temporal distributions of these species are needed to understand the extent of competitive interactions. PMID:24919949

  8. Comparison of immunodiffusion and enzyme linked immunosorbent assay for antibodies to four Aspergillus species.

    PubMed Central

    Froudist, J H; Harnett, G B; McAleer, R

    1989-01-01

    Antigenic extracts were prepared from Aspergillus fumigatus, A niger, A flavus and A terreus for use in enzyme linked immunosorbent assay (ELISA) and immunodiffusion (ID) tests for Aspergillus antibodies to determine whether the use of antigenic extracts from species other than A fumigatus increased the sensitivity of the ELISA. ELISA titres correlated well with positive ID tests. Patient titres by ELISA were significantly higher than control titres for all species. Patient titres to A niger were also significantly higher than titres to the other species. Total number of ID bands to A fumigatus correlated significantly with anti-A fumigatus ELISA titres. It is concluded that the use of antigenic extracts from species other than A fumigatus improves the sensitivity of the ELISA. PMID:2511230

  9. Comparison of visual and electronic evaluations of detached strawberry leaves inoculated with colletotrichum species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inoculation of detached strawberry leaves with Colletotrichum species may provide an accurate, rapid, non-destructive method of identifying anthracnose resistant germplasm. Two measures of anthracnose disease severity were compared on detached strawberry leaves inoculated with Colletotrichum fragar...

  10. Quantitative comparisons of numerical models of brittle deformation

    NASA Astrophysics Data System (ADS)

    Buiter, S.

    2009-04-01

    Numerical modelling of brittle deformation in the uppermost crust can be challenging owing to the requirement of an accurate pressure calculation, the ability to achieve post-yield deformation and localisation, and the choice of rheology (plasticity law). One way to approach these issues is to conduct model comparisons that can evaluate the effects of different implementations of brittle behaviour in crustal deformation models. We present a comparison of three brittle shortening experiments for fourteen different numerical codes, which use finite element, finite difference, boundary element and distinct element techniques. Our aim is to constrain and quantify the variability among models in order to improve our understanding of causes leading to differences between model results. Our first experiment of translation of a stable sand-like wedge serves as a reference that allows for testing against analytical solutions (e.g., taper angle, root-mean-square velocity and gravitational rate of work). The next two experiments investigate an unstable wedge in a sandbox-like setup which deforms by inward translation of a mobile wall. All models accommodate shortening by in-sequence formation of forward shear zones. We analyse the location, dip angle and spacing of thrusts in detail as previous comparisons have shown that these can be highly variable in numerical and analogue models of crustal shortening and extension. We find that an accurate implementation of boundary friction is important for our models. Our results are encouraging in the overall agreement in their dynamic evolution, but show at the same time the effort that is needed to understand shear zone evolution. GeoMod2008 Team: Markus Albertz, Michele Cooke, Susan Ellis, Taras Gerya, Luke Hodkinson, Kristin Hughes, Katrin Huhn, Boris Kaus, Walter Landry, Bertrand Maillot, Christophe Pascal, Anton Popov, Guido Schreurs, Christopher Beaumont, Tony Crook, Mario Del Castello and Yves Leroy

  11. Inter- and intraspecific comparisons of antiherbivore defenses in three species of rainforest understory shrubs.

    PubMed

    Fincher, R M; Dyer, L A; Dodson, C D; Richards, J L; Tobler, M A; Searcy, J; Mather, J E; Reid, A J; Rolig, J S; Pidcock, W

    2008-04-01

    Plants defend themselves against herbivores and pathogens with a suite of morphological, phenological, biochemical, and biotic defenses, each of which is presumably costly. The best studied are allocation costs that involve trade-offs in investment of resources to defense versus other plant functions. Decreases in growth or reproductive effort are the costs most often associated with antiherbivore defenses, but trade-offs among different defenses may also occur within a single plant species. We examined trade-offs among defenses in closely related tropical rain forest shrubs (Piper cenocladum, P. imperiale, and P. melanocladum) that possess different combinations of three types of defense: ant mutualists, secondary compounds, and leaf toughness. We also examined the effectiveness of different defenses and suites of defenses against the most abundant generalist and specialist Piper herbivores. For all species examined, leaf toughness was the most effective defense, with the toughest species, P. melanocladum, receiving the lowest incidence of total herbivory, and the least tough species, P. imperiale, receiving the highest incidence. Although variation in toughness within each species was substantial, there were no intraspecific relationships between toughness and herbivory. In other Piper studies, chemical and biotic defenses had strong intraspecific negative correlations with herbivory. A wide variety of defensive mechanisms was quantified in the three Piper species studied, ranging from low concentrations of chemical defenses in P. imperiale to a complex suite of defenses in P. cenocladum that includes ant mutualists, secondary metabolites, and moderate toughness. Ecological costs were evident for the array of defensive mechanisms within these Piper species, and the differences in defensive strategies among species may represent evolutionary trade-offs between costly defenses. PMID:18317843

  12. Comparison of small mammal species diversity near wastewater outfalls, natural streams, and dry canyons

    SciTech Connect

    Raymer, D.F.; Biggs, J.R.

    1994-03-01

    A wide range of plant and wildlife species utilizes water discharged from facilities at Los Alamos National Laboratory (LANL). The purpose of this study was to compare nocturnal small mammal communities at wet areas created by wastewater outfalls with communities in naturally created wet and dry areas. Thirteen locations within LANL boundaries were selected for small mammal mark-recapture trapping. Three of these locations lacked surface water sources and were classified as {open_quotes}dry,{close_quotes} while seven sites were associated with wastewater outfalls ({open_quotes}outfall{close_quotes} sites), and three were located near natural sources of surface water ({open_quotes}natural{close_quotes} sites). Data was collected on site type (dry, outfall or natural), location, species trapped, and the tag number of each individual captured. This data was used to calculate mean number of species, percent capture rate, and species diversity at each type of site. When data from each type of site was pooled, there were no significant differences in these variables between dry, outfall, and natural types. However, when data from individual sites was compared, tests revealed significant differences. All sites in natural areas were significantly higher than dry areas in daily mean number of species, percent capture rate, and species diversity. Most outfall sites were significantly higher than dry areas in all three variables tested. When volume of water from each outfall site was considered, these data indicated that the number of species, percent capture rate, and species diversity of nocturnal small mammals were directly related to the volume of water at a given outfall.

  13. Do laboratory species protect endangered species? Interspecies variation in responses to 17β-estradiol, a model endocrine active compound

    USGS Publications Warehouse

    Jorgenson, Zachary G.; Buhl, Kevin J.; Bartell, Stephen E.; Schoenfuss, Heiko L.

    2015-01-01

    Although the effects of estrogens on model laboratory species are well documented, their utility as surrogates for other species, including those listed as endangered, are less clear. Traditionally, conservation policies are evaluated based on model organism responses but are intended to protect all species in an environment. We tested the hypothesis that the endangered Rio Grande silvery minnow (Hybognathus amarus) is more vulnerable to endocrine disruption—as assessed through its larval predator-escape performance, survival, juvenile sex ratios, and whole-body vitellogenin concentration—than the commonly used toxicological model species fathead minnow (Pimephales promelas) and the bluegill sunfish (Lepomis macrochirus). Fish were exposed concurrently for 21 days to the model endocrine active compound (EAC) 17ß-estradiol (E2) at 10 ng E2/L and 30 ng E2/L in a flow-through system using reconstituted water that simulated the physicochemical conditions of the Middle Rio Grande in New Mexico, USA. No significant differences were observed between the fathead and silvery minnow in larval predator-escape response or juvenile sex ratio. Rio Grande silvery minnow survival decreased significantly at day 14 compared with the other two species; by day 21, both cyprinid species (silvery minnow and fathead minnow) exhibited a significant decrease in survival compared with bluegill sunfish, a member of the family Centrarchidae. Male Rio Grande silvery minnow showed a significant increase in whole-body vitellogenin concentration in the 10 ng/L treatment, whereas fathead minnow and bluegill sunfish showed no significant increases in vitellogenin concentrations across treatments. Our study showed response differences to estrogen exposures between the two cyprinid species and further divergence in responses between the families Cyprinidae and Centrarchidae. These results suggest that commonly used laboratory model organisms may be less sensitive to EACs than the endangered

  14. Do laboratory species protect endangered species? Interspecies variation in responses to 17β-estradiol, a model endocrine active compound.

    PubMed

    Jorgenson, Z G; Buhl, K; Bartell, S E; Schoenfuss, H L

    2015-01-01

    Although the effects of estrogens on model laboratory species are well documented, their utility as surrogates for other species, including those listed as endangered, are less clear. Traditionally, conservation policies are evaluated based on model organism responses but are intended to protect all species in an environment. We tested the hypothesis that the endangered Rio Grande silvery minnow (Hybognathus amarus) is more vulnerable to endocrine disruption-as assessed through its larval predator-escape performance, survival, juvenile sex ratios, and whole-body vitellogenin concentration-than the commonly used toxicological model species fathead minnow (Pimephales promelas) and the bluegill sunfish (Lepomis macrochirus). Fish were exposed concurrently for 21 days to the model endocrine active compound (EAC) 17ß-estradiol (E2) at 10 ng E2/L and 30 ng E2/L in a flow-through system using reconstituted water that simulated the physicochemical conditions of the Middle Rio Grande in New Mexico, USA. No significant differences were observed between the fathead and silvery minnow in larval predator-escape response or juvenile sex ratio. Rio Grande silvery minnow survival decreased significantly at day 14 compared with the other two species; by day 21, both cyprinid species (silvery minnow and fathead minnow) exhibited a significant decrease in survival compared with bluegill sunfish, a member of the family Centrarchidae. Male Rio Grande silvery minnow showed a significant increase in whole-body vitellogenin concentration in the 10 ng/L treatment, whereas fathead minnow and bluegill sunfish showed no significant increases in vitellogenin concentrations across treatments. Our study showed response differences to estrogen exposures between the two cyprinid species and further divergence in responses between the families Cyprinidae and Centrarchidae. These results suggest that commonly used laboratory model organisms may be less sensitive to EACs than the endangered Rio

  15. A Comparison of Surface Acoustic Wave Modeling Methods

    NASA Technical Reports Server (NTRS)

    Wilson, W. c.; Atkinson, G. M.

    2009-01-01

    Surface Acoustic Wave (SAW) technology is low cost, rugged, lightweight, extremely low power and can be used to develop passive wireless sensors. For these reasons, NASA is investigating the use of SAW technology for Integrated Vehicle Health Monitoring (IVHM) of aerospace structures. To facilitate rapid prototyping of passive SAW sensors for aerospace applications, SAW models have been developed. This paper reports on the comparison of three methods of modeling SAWs. The three models are the Impulse Response Method a first order model, and two second order matrix methods; the conventional matrix approach, and a modified matrix approach that is extended to include internal finger reflections. The second order models are based upon matrices that were originally developed for analyzing microwave circuits using transmission line theory. Results from the models are presented with measured data from devices.

  16. A generalized approach to the modeling of the species-area relationship.

    PubMed

    Conceição, Katiane Silva; Ulrich, Werner; Diniz, Carlos Alberto Ribeiro; Rodrigues, Francisco Aparecido; de Andrade, Marinho Gomes

    2014-01-01

    This paper proposes a statistical generalized species-area model (GSAM) to represent various patterns of species-area relationship (SAR), which is one of the fundamental patterns in ecology. The approach enables the generalization of many preliminary models, as power-curve model, which is commonly used to mathematically describe the SAR. The GSAM is applied to simulated data set of species diversity in areas of different sizes and a real-world data of insects of Hymenoptera order has been modeled. We show that the GSAM enables the identification of the best statistical model and estimates the number of species according to the area. PMID:25171161

  17. Comparison of basal and induced cytochromes P450 in 6 species of waterfowl

    USGS Publications Warehouse

    Melancon, M.J.; Rattner, B.A.; Hoffman, D.J.; Beeman, D.; Day, D.; Custer, T.

    1999-01-01

    Cytochrome P450-associated monooxygenase activities were measured in control and prototype inducer-treated mallard duck, black duck, wood duck, lesser scaup, Canada goose and mute swan. Ages of the birds ranged from pipping embryos (that were treated approximately 3 days before pipping) to adults. Three or more of the following hepatic microsomal monooxygenases were assayed in each species: Benzyloxyresorufin-O-dealkylase (BROD), Ethoxyresorufin-O-dealkylase (EROD), methoxyresorufin-O-dealkylase (MROD), and pentoxyresorufin-O-dealkylase (PROD). Baseline activities differed between species, but because of differences in ages, sources of the eggs or birds, and diets, these cannot be viewed as absolute differences. The cytochrome P450 inducers utilized were beta-naphthoflavone (BNF), 3-methylcholanthrene (3MC) and phenobarbital (PB). In general, there was little response to PB; only lesser scaup were induced to greater than three times control level and most species were well under this. Responses to BNF and 3MC occurred in each species studied, but differed in which of the monooxygenases was most induced (absolute values and ratios to control values) and in relative induction between species. BROD frequently had an induction ratio EROD. Overall, lesser scaup were the most responsive, canada geese the least responsive, and the other species intermediate in responsiveness to the cytochrome P450 inducers studied.

  18. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches

    PubMed Central

    Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. PMID:26644988

  19. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches.

    PubMed

    Wagner, Elena L E S; Roche, Dominique G; Binning, Sandra A; Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. PMID:26644988

  20. Analysing earthquake slip models with the spatial prediction comparison test

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    Earthquake rupture models inferred from inversions of geophysical and/or geodetic data exhibit remarkable variability due to uncertainties in modelling assumptions, the use of different inversion algorithms, or variations in data selection and data processing. A robust statistical comparison of different rupture models obtained for a single earthquake is needed to quantify the intra-event variability, both for benchmark exercises and for real earthquakes. The same approach may be useful to characterize (dis-)similarities in events that are typically grouped into a common class of events (e.g. moderate-size crustal strike-slip earthquakes or tsunamigenic large subduction earthquakes). For this purpose, we examine the performance of the spatial prediction comparison test (SPCT), a statistical test developed to compare spatial (random) fields by means of a chosen loss function that describes an error relation between a 2-D field (`model') and a reference model. We implement and calibrate the SPCT approach for a suite of synthetic 2-D slip distributions, generated as spatial random fields with various characteristics, and then apply the method to results of a benchmark inversion exercise with known solution. We find the SPCT to be sensitive to different spatial correlations lengths, and different heterogeneity levels of the slip distributions. The SPCT approach proves to be a simple and effective tool for ranking the slip models with respect to a reference model.

  1. A heterogeneity model comparison of highly resolved statistically anisotropic aquifers

    NASA Astrophysics Data System (ADS)

    Siirila-Woodburn, Erica R.; Maxwell, Reed M.

    2015-01-01

    Aquifer heterogeneity is known to affect solute characteristics such as spatial spreading, mixing, and residence time, and is often modeled geostatistically to address aquifer uncertainties. While parameter uncertainty is often considered, the model uncertainty of the heterogeneity structure is frequently ignored. In this high-resolution heterogeneity model comparison, we perform a stochastic analysis utilizing spatial moment and breakthrough curve (BTC) metrics on Gaussian (G), truncated Gaussian (TG), and non-Gaussian, or "facies" (F) heterogeneous domains. Three-dimensional plume behavior is rigorously assessed with meter (horizontal) and cm (vertical) scale discretization over a ten-kilometer aquifer. Model differences are quantified as a function of statistical anisotropy, ε, by varying the x-direction integral scale of hydraulic conductivity, K, from 15 to 960 (m). We demonstrate that the model is important only for certain metrics within a range of ε. For example, spreading is insensitive to the model selection at low ε, but not at high ε. In contrast, center of mass is sensitive to the model selection at low ε, and not at high ε. A conceptual model to explain these trends is proposed and validated with BTC metrics. Simulations show that G model effective K, and 1st and 2nd spatial moments are much greater than that of TG and F models. A comparison of G and TG models (which only differ in K-distribution tails) reveal drastically different behavior, exemplifying how accurate characterization of the K-distribution may be important in modeling efforts, especially in aquifers where extreme K values are often not measured, or inadvertently overlooked.

  2. Vertical transport by convective clouds: Comparisons of three modeling approaches

    NASA Technical Reports Server (NTRS)

    Pickering, Kenneth E.; Thompson, Anne M.; Tao, Wei-Kuo; Rood, Richard B.; Mcnamara, Donna P.; Molod, Andrea M.

    1995-01-01

    A preliminary comparison of the GEOS-1 (Goddard Earth Observing System) data assimilation system convective cloud mass fluxes with fluxes from a cloud-resolving model (the Goddard Cumulus Ensemble Model, GCE) is reported. A squall line case study (10-11 June 1985 Oklahoma PRESTORM episode) is the basis of the comparison. Regional (central U. S.) monthly total convective mass flux for June 1985 from GEOS-1 compares favorably with estimates from a statistical/dynamical approach using GCE simulations and satellite-derived cloud observations. The GEOS-1 convective mass fluxes produce reasonable estimates of monthly-averaged regional convective venting of CO from the boundary layer at least in an urban-influenced continental region, suggesting that they can be used in tracer transport simulations.

  3. Comparisons of fish species traits from small streams to large rivers

    USGS Publications Warehouse

    Goldstein, R.M.; Meador, M.R.

    2004-01-01

    To examine the relations between fish community function and stream size, we classified 429 lotic freshwater fish species based on multiple categories within six species traits: (1) substrate preference, (2) geomorphic preference, (3) trophic ecology, (4) locomotion morphology, (5) reproductive strategy, and (6) stream size preference. Stream size categories included small streams, small, medium, and large rivers, and no size preference. The frequencies of each species trait category were determined for each stream size category based on life history information from the literature. Cluster analysis revealed the presence of covarying groups of species trait categories. One cluster (RUN) included the traits of planktivore and herbivore feeding ecology, migratory reproductive behavior and broadcast spawning, preferences for main-channel habitats, and a lack of preferences for substrate type. The frequencies of classifications for the RUN cluster varied significantly across stream size categories (P = 0.009), being greater for large rivers than for small streams and rivers. Another cluster (RIFFLE) included the traits of invertivore feeding ecology, simple nester reproductive behavior, a preference for riffles, and a preference for bedrock, boulder, and cobble-rubble substrate. No significant differences in the frequency of classifications among stream size categories were detected for the RIFFLE cluster (P = 0.328). Our results suggest that fish community function is structured by large-scale differences in habitat and is different for large rivers than for small streams and rivers. Our findings support theoretical predictions of variation in species traits among stream reaches based on ecological frameworks such as landscape filters, habitat templates, and the river continuum concept. We believe that the species trait classifications presented here provide an opportunity for further examination of fish species' relations to physical, chemical, and biological factors

  4. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements

    NASA Technical Reports Server (NTRS)

    Danilin, Michael Y.; Rodriguez, Jose M.; Hu, Wen-Jie; Ko, Malcolm K. W.; Weisenstein, Debra K.; Kumer, John B.; Mergenthaler, John L.; Russel, James M., III; Koike, Makoto; Yue, Glenn K.

    1999-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include N2O, HNO3, and ClONO2 from the cryogenic limb array etalon spectrometer (CLAES), version 7 (v.7), and temperature, methane, ozone, H2O, HCl, NO and NO2 from the halogen occultation experiment (HALOE), version 18. The analysis is carried out for the UARS data obtained between January 1992 and September 1994 in the 100-to 1-mbar (approx. 17-47 km) altitude range and over 10 degrees latitude bins from 70 S to 70 N. The spatiotemporal evolution of aerosol surface area density (SAD) is adopted from analysis of the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD, and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOy) is obtained by three different methods: (1) as a sum of the UARS-measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NOy correlation, and (3) from the CH4-NOy correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated monthly averaged NOx/NOy ratios and the NO, NO2, and HNO3 profiles are compared with the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years, such as recovery of NOx after the eruption, their seasonal variability and vertical profiles. However, the model underestimates the NO2 content, particularly in the 30- to 7-mbar (approx.23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground-based measurements at 45 S and 45 N are also presented. Our analysis indicates that ground-based and HALOE v.18

  5. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements. Appendix F

    NASA Technical Reports Server (NTRS)

    Danilin, Michael Y.; Rodriguez, Jose M.; Hu, Wenjie; Ko, Malcolm K. W.; Weisenstein, Debra K.; Kumer, John B.; Mergenthaler, John L.; Russell, James M., III; Koike, Makoto; Yue, Glenn K.

    1999-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include N2O, HNO3, and ClONO2 from the cryogenic limb array etalon spectrometer (CLAES), version 7 (v.7), and temperature, methane, ozone, H2O, HCl, NO and NO2 from the halogen occultation experiment (HALOE), version 18. The analysis is carried out for the UARS data obtained between January 1992 and September 1994 in the 100- to 1-mbar (approx. 17-47 km) altitude range and over 10 deg latitude bins from 70 deg S to 70 deg N. The spatiotemporal evolution of aerosol surface area density (SAD) is adopted from analysis of the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD, and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOY) is obtained by three different methods: (1) as a sum of the UARS-measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NOY correlation; and (3) from the CH4-NOY correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated monthly averaged NO(x)/NO(y) ratios and the NO, NO2, and HNO3 profiles are compared with the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years, such as recovery of NO(x) after the eruption, their seasonal variability and vertical profiles. However, the model underestimates the NO2 content, particularly in the 30- to 7-mbar (approx. 23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground-based measurements at 45 deg S and 45 deg N are also presented. Our analysis indicates that ground

  6. Nitrogen species in the post-Pinatubo stratosphere: Model analysis utilizing UARS measurements

    NASA Astrophysics Data System (ADS)

    Danilin, Michael Y.; Rodriguez, Jose M.; Hu, Wenjie; Ko, Malcolm K. W.; Weisenstein, Debra K.; Kumer, John B.; Mergenthaler, John L.; Russell, James M.; Koike, Makoto; Yue, Glenn K.; Jones, Nicholas B.; Johnston, Paul V.

    1999-04-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include N2O, HNO3, and ClONO2 from the cryogenic limb array etalon spectrometer (CLAES), version 7 (v.7), and temperature, methane, ozone, H2O, HCl, NO and NO2 from the halogen occultation experiment (HALOE), version 18. The analysis is carried out for the UARS data obtained between January 1992 and September 1994 in the 100- to 1-mbar (˜17-47 km) altitude range and over 10° latitude bins from 70°S to 70°N. The spatiotemporal evolution of aerosol surface area density (SAD) is adopted from analysis of the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD, and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOy) is obtained by three different methods: (1) as a sum of the UARS-measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NOy correlation, and (3) from the CH4-NOy correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated monthly averaged NOx/NOy ratios and the NO, NO2, and HNO3 profiles are compared with the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years, such as recovery of NOx after the eruption, their seasonal variability and vertical profiles. However, the model underestimates the NO2 content, particularly in the 30- to 7-mbar (˜23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground-based measurements at 45°S and 45°N are also presented. Our analysis indicates that ground-based and HALOE v. 18 measurements of

  7. Investigation of the DSMC Approach for Ion/neutral Species in Modeling Low Pressure Plasma Reactor

    SciTech Connect

    Deng Hao; Li, Z.; Levin, D.; Gochberg, L.

    2011-05-20

    Low pressure plasma reactors are important tools for ionized metal physical vapor deposition (IMPVD), a semiconductor plasma processing technology that is increasingly being applied to deposit Cu seed layers on semiconductor surfaces of trenches and vias with the high aspect ratio (e.g., >5:1). A large fraction of ionized atoms produced by the IMPVD process leads to an anisotropic deposition flux towards the substrate, a feature which is critical for attaining a void-free and uniform fill. Modeling such devices is challenging due to their high plasma density, reactive environment, but low gas pressure. A modular code developed by the Computational Optical and Discharge Physics Group, the Hybrid Plasma Equipment Model (HPEM), has been successfully applied to the numerical investigations of IMPVD by modeling a hollow cathode magnetron (HCM) device. However, as the development of semiconductor devices progresses towards the lower pressure regime (e.g., <5 mTorr), the breakdown of the continuum assumption limits the application of the fluid model in HPEM and suggests the incorporation of the kinetic method, such as the direct simulation Monte Carlo (DSMC), in the plasma simulation.The DSMC method, which solves the Boltzmann equation of transport, has been successfully applied in modeling micro-fluidic flows in MEMS devices with low Reynolds numbers, a feature shared with the HCM. Modeling of the basic physical and chemical processes for ion/neutral species in plasma have been developed and implemented in DSMC, which include ion particle motion due to the Lorentz force, electron impact reactions, charge exchange reactions, and charge recombination at the surface. The heating of neutrals due to collisions with ions and the heating of ions due to the electrostatic field will be shown to be captured by the DSMC simulations. In this work, DSMC calculations were coupled with the modules from HPEM so that the plasma can be self-consistently solved. Differences in the Ar

  8. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements

    NASA Technical Reports Server (NTRS)

    Danilin, M. Y.; Rodriquez, J. M.; Hu, W.; Ko, M. K. W.; Weisenstein, D. K.; Mergenthaler, J. L.; Russell, J. M., III; Koike, M.; Yue, G. K.

    1998-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include: N2O, HNO3 and ClONO2 (Cryogen Limb Array Etalon Spectrometer (CLAES), version 7), temperature, methane, ozone, H2O, HCl, NO and NO2 (HALogen Occultation Experiment (HALOE), version 18). The analysis is carried out for the data from January 1992 to September 1994 in the 100-1 mbar (approx.17-47 km) altitude range and over 10 degree latitude bins from 70degS to 70degN. Temporal-spatial evolution of aerosol surface area density (SAD) is adopted according to the Stratospheric Aerosol and Gas Experiment (SAGE) 11 data. A diurnal steady-state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NO(y)) is obtained by three different methods: (1) as a sum of the UARS measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NO(y) correlation, and (3) from the CH4-NO(y) correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated NO(x)/NO(y) ratios and the NO, NO2, and HNO3 profiles are compared to the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years. However, the model underestimates the NO2 content, particularly, in the 30-7 mbar (approx. 23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground based measurements at 45degS and 45degN are also presented. Our analysis indicates that ground-based and HALOE v. 18 measurements of the NO2 vertical columns are consistent within the range of their uncertainties and are systematically higher (up to 50%) than the model

  9. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements

    NASA Technical Reports Server (NTRS)

    Danilin, M. Y.; Rodriguez, J. M.; Hu, W.; Ko, M. K. W.; Weisenstein, D. K.; Kumer, J. B.; Mergenthaler, J. L.; Russell, J. M., III; Koike, M.; Yue, G. K.

    1998-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include: N2O, HNO3 and ClONO2 (Cryogen Limb Array Etalon Spectrometer (CLAES), version 7), temperature, methane, ozone, H2O, HCI, NO and NO2 (HALogen Occultation Experiment (HALOE), version 18). The analysis is carried out for the data from January 1992 to September 1994 in the 100-1 mbar (approximately 17-47 km) altitude range and over 10 degree latitude bins from 70 deg S to 70 deg N. Temporal-spatial evolution of aerosol surface area density (SAD) is adopted according to the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady-state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOy) is obtained by three different methods: (1) as a sum of the UARS measured NO, NO2, HNO3, and CIONO2; (2) from the N2O-NOy correlation, (3) from the CH4-NOy correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated NOx/NOy ratios and the NO, NO2, and HNO3 profiles are compared to the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years. However, the model underestimates the NO2 content, particularly, in the 30-7 mbar (approximately 23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground based measurements at 45 deg S and 45 deg N are also presented. Our analysis indicates that ground-based and HALOE v.18 measurements of the NO2 vertical columns are consistent within the range of their uncertainties and are systematically higher (up to 50%) than the model

  10. Hysteresis and creep: Comparison between a power-law model and Kuhnen's model

    NASA Astrophysics Data System (ADS)

    Oliveri, Alberto; Stellino, Flavio; Parodi, Mauro; Storace, Marco

    2016-04-01

    In this paper we analyze some properties of a recently proposed model of hysteresis and creep (related to a circuit model, whose only nonlinear element is based on a power law) and compare it with the well-known Kuhnen's model. A first qualitative comparison relies on the analysis of the behavior of the elementary cell of each model. Their responses to step inputs (which allow to better evidence the creep effect) are analyzed and compared. Then, a quantitative comparison is proposed, based on the fitting performances of the two models on experimental data measured from a commercial piezoelectric actuator.

  11. One-dimensional turbulence modeling of a turbulent counterflow flame with comparison to DNS

    DOE PAGESBeta

    Jozefik, Zoltan; Kerstein, Alan R.; Schmidt, Heiko; Lyra, Sgouria; Kolla, Hemanth; Chen, Jackie H.

    2015-06-01

    The one-dimensional turbulence (ODT) model is applied to a reactant-to-product counterflow configuration and results are compared with DNS data. The model employed herein solves conservation equations for momentum, energy, and species on a one dimensional (1D) domain corresponding to the line spanning the domain between nozzle orifice centers. The effects of turbulent mixing are modeled via a stochastic process, while the Kolmogorov and reactive length and time scales are explicitly resolved and a detailed chemical kinetic mechanism is used. Comparisons between model and DNS results for spatial mean and root-meansquare (RMS) velocity, temperature, and major and minor species profiles aremore » shown. The ODT approach shows qualitatively and quantitatively reasonable agreement with the DNS data. Scatter plots and statistics conditioned on temperature are also compared for heat release rate and all species. ODT is able to capture the range of results depicted by DNS. However, conditional statistics show signs of underignition.« less

  12. A Statistical Comparison of PSC Model Simulations and POAM Observations

    NASA Technical Reports Server (NTRS)

    Strawa, A. W.; Drdla, K.; Fromm, M.; Bokarius, K.; Gore, Warren J. (Technical Monitor)

    2002-01-01

    A better knowledge of PSC composition and formation mechanisms is important to better understand and predict stratospheric ozone depletion. Several past studies have attempted to compare modeling results with satellite observations. These comparisons have concentrated on case studies. In this paper we adopt a statistical approach. POAM PSC observations from several Arctic winters are categorized into Type Ia and Ib PSCs using a technique based on Strawa et al. The discrimination technique has been modified to employ the wavelengths dependence of the extinction signal at all wavelengths rather than only at 603 and 10 18 nm. Winter-long simulations for the 1999-2000 Arctic winter have been made using the IMPACT model. These simulations have been constrained by aircraft observations made during the SOLVE/THESEO 2000 campaign. A complete set of winter-long simulations was run for several different microphysical and PSC formation scenarios. The simulations give us perfect knowledge of PSC type (Ia, Ib, or II), composition, especially condensed phase HNO3 which is important for denitrification, and condensed phase H2O. Comparisons are made between the simulation and observation of PSC extinction at 1018 rim versus wavelength dependence, winter-long percentages of Ia and Ib occurrence, and temporal and altitude trends of the PSCs. These comparisons allow us to comment on how realistic some modeling scenarios are.

  13. Dispersal kernel estimation: A comparison of empirical and modelled particle dispersion in a coastal marine system

    NASA Astrophysics Data System (ADS)

    Hrycik, Janelle M.; Chassé, Joël; Ruddick, Barry R.; Taggart, Christopher T.

    2013-11-01

    Early life-stage dispersal influences recruitment and is of significance in explaining the distribution and connectivity of marine species. Motivations for quantifying dispersal range from biodiversity conservation to the design of marine reserves and the mitigation of species invasions. Here we compare estimates of real particle dispersion in a coastal marine environment with similar estimates provided by hydrodynamic modelling. We do so by using a system of magnetically attractive particles (MAPs) and a magnetic-collector array that provides measures of Lagrangian dispersion based on the time-integration of MAPs dispersing through the array. MAPs released as a point source in a coastal marine location dispersed through the collector array over a 5-7 d period. A virtual release and observed (real-time) environmental conditions were used in a high-resolution three-dimensional hydrodynamic model to estimate the dispersal of virtual particles (VPs). The number of MAPs captured throughout the collector array and the number of VPs that passed through each corresponding model location were enumerated and compared. Although VP dispersal reflected several aspects of the observed MAP dispersal, the comparisons demonstrated model sensitivity to the small-scale (random-walk) particle diffusivity parameter (Kp). The one-dimensional dispersal kernel for the MAPs had an e-folding scale estimate in the range of 5.19-11.44 km, while those from the model simulations were comparable at 1.89-6.52 km, and also demonstrated sensitivity to Kp. Variations among comparisons are related to the value of Kp used in modelling and are postulated to be related to MAP losses from the water column and (or) shear dispersion acting on the MAPs; a process that is constrained in the model. Our demonstration indicates a promising new way of 1) quantitatively and empirically estimating the dispersal kernel in aquatic systems, and 2) quantitatively assessing and (or) improving regional hydrodynamic

  14. BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression

    PubMed Central

    Ogasawara, Osamu; Otsuji, Makiko; Watanabe, Kouji; Iizuka, Takayasu; Tamura, Takuro; Hishiki, Teruyoshi; Kawamoto, Shoko; Okubo, Kousaku

    2006-01-01

    BodyMap-Xs () is a database for cross-species gene expression comparison. It was created by the anatomical breakdown of 17 million animal expressed sequence tag (EST) records in DDBJ using a sorting program tailored for this purpose. In BodyMap-Xs, users are allowed to compare the expression patterns of orthologous and paralogous genes in a coherent manner. This will provide valuable insights for the evolutionary study of gene expression and identification of a responsive motif for a particular expression pattern. In addition, starting from a concise overview of the taxonomical and anatomical breakdown of all animal ESTs, users can navigate to obtain gene expression ranking of a particular tissue in a particular animal. This method may lead to the understanding of the similarities and differences between the homologous tissues across animal species. BodyMap-Xs will be automatically updated in synchronization with the major update in DDBJ, which occurs periodically. PMID:16381946

  15. Comparison of eye morphology and retinal topography in two species of New World vultures (Aves: Cathartidae).

    PubMed

    Lisney, Thomas J; Stecyk, Karyn; Kolominsky, Jeffrey; Graves, Gary R; Wylie, Douglas R; Iwaniuk, Andrew N

    2013-12-01

    Vultures are highly reliant on their sensory systems for the rapid detection and localization of carrion before other scavengers can exploit the resource. In this study, we compared eye morphology and retinal topography in two species of New World vultures (Cathartidae), turkey vultures (Cathartes aura), with a highly developed olfactory sense, and black vultures (Coragyps atratus), with a less developed sense of olfaction. We found that eye size relative to body mass was the same in both species, but that black vultures have larger corneas relative to eye size than turkey vultures. However, the overall retinal topography, the total number of cells in the retinal ganglion cell layer, peak and average cell densities, cell soma area frequency distributions, and the theoretical peak anatomical spatial resolving power were the same in both species. This suggests that the visual systems of these two species are similar and that vision plays an equally important role in the biology of both species, despite the apparently greater reliance on olfaction for finding carrion in turkey vultures. PMID:24249399

  16. Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species

    PubMed Central

    Asaf, Sajjad; Khan, Abdul L.; Khan, Abdur R.; Waqas, Muhammad; Kang, Sang-Mo; Khan, Muhammad A.; Lee, Seok-Min; Lee, In-Jung

    2016-01-01

    Nicotiana otophora is a wild parental species of Nicotiana tabacum, an interspecific hybrid of Nicotiana tomentosiformis and Nicotiana sylvestris. However, N. otophora is least understood as an alternative paternal donor. Here, we compared the fully assembled chloroplast (cp) genome of N. otophora and with those of closely related species. The analysis showed a cp genome size of 156,073 bp and exhibited a typical quadripartite structure, which contains a pair of inverted repeats separated by small and large single copies, containing 163 representative genes, with 165 microsatellites distributed unevenly throughout the genome. Comparative analysis of a gene with known function across Nicotiana species revealed 76 protein-coding sequences, 20 tRNA sequences, and 3 rRNA sequence shared between the cp genomes. The analysis revealed that N. otophora is a sister species to N. tomentosiformis within the Nicotiana genus, and Atropha belladonna and Datura stramonium are their closest relatives. These findings provide a valuable analysis of the complete N. otophora cp genome, which can identify species, elucidate taxonomy, and reconstruct the phylogeny of genus Nicotiana. PMID:27379132

  17. Plant pollinator interactions: comparison between an invasive and a native congeneric species

    NASA Astrophysics Data System (ADS)

    Vanparys, Valérie; Meerts, Pierre; Jacquemart, Anne-Laure

    2008-11-01

    Plant-pollinator interactions determine reproductive success for animal-pollinated species and, in the case of invasive plants, they are supposed to play an important role in invasive success. We compared the invasive Senecio inaequidens to its native congener S. jacobaea in terms of interactions with pollinators. Visitor guild, visitation rate, and seed set were compared over 3 years in three sites in Belgium. Floral display (capitula number and arrangement) and phenology were quantified, and visiting insects were individually censused, i.e. number of visited capitula and time per visited capitulum. As expected from capitula resemblance, visitor guilds of both species were very similar (proportional similarity = 0.94). Senecio inaequidens was visited by 33 species, versus 36 for S. jacobaea. For both species, main visitors were Diptera, especially Syrphidae, and Hymenoptera. Visitation rate averaged 0.13 visitor per capitulum per 10 min for S. inaequidens against 0.08 for S. jacobaea. However, insects visited more capitula per plant on S. jacobaea, due to high capitula density (886 m -2 versus 206 m -2 for S. inaequidens), which is likely to increase self-pollen deposition considerably. Seed set of S. jacobaea was lower than that of S. inaequidens. We suggest that floral display is the major factor explaining the differences in insect visitation and seed set between the two Senecio species.

  18. Comparison of species composition and richness of fish assemblages in altered and unaltered littoral habitats

    USGS Publications Warehouse

    Poe, T.P.; Hatcher, C.O.; Brown, C.L.; Schloesser, D.W.

    1986-01-01

    Species composition and richness of fish assemblages in altered and unaltered littoral habitats in Lake St. Clair, Michigan, differed between areas. A percid-cyprinid-cyprinodontid assemblage dominated in the unaltered area, Muscamoot Bay, which has a natural shoreline (with almost no alteration due to dredging or bulkheading), high water quality, and high species richness of aquatic macrophytes. A centrarchid assemblage dominated in the altered area, Belvidere Bay, which has a bulkheaded shoreline, many dredged areas, reduced water quality due to inputs of nutrients from a nearby river, and relatively low species richness of aquatic macrophytes. Habitat factors, species richness and abundance of aquatic macrophytes, had the most influence on fish community structure in both areas. The percid-cyprinid-cyprinodontid assemblage was significantly correlated with six species of macrophytes whereas the centrarchid assemblage was significantly correlated with only four. These patterns suggest that preference for diverse habitats was higher, and tolerance to habitat alteration lower, in percid-cyprinid-cyprinodontid assemblages than in centrarchid assemblages.

  19. Developmental and reproductive toxicity of dioxins and related compounds: cross-species comparisons.

    PubMed

    Peterson, R E; Theobald, H M; Kimmel, G L

    1993-01-01

    Developmental toxicity to TCDD-like congeners in fish, birds, and mammals, and reproductive toxicity in mammals are reviewed. In fish and bird species, the developmental lesions observed are species dependent, but any given species responds similarly to different TCDD-like congeners. Developmental toxicity in fish resembles "blue sac disease," whereas structural malformations can occur in at least one bird species. In mammals, developmental toxicity includes decreased growth, structural malformations, functional alterations, and prenatal mortality. At relatively low exposure levels, structural malformations are not common in mammalian species. In contrast, functional alterations are the most sensitive signs of developmental toxicity. These include effects on the male reproductive system and male reproductive behavior in rats, and neurobehavioral effects in monkeys. Human infants exposed during the Yusho and Yu-Cheng episodes, and monkeys and mice exposed perinatally to TCDD developed an ectodermal dysplasia syndrome that includes toxicity to the skin and teeth. Toxicity to the central nervous system in monkey and human infants is a potential part of the ectodermal dysplasia syndrome. Decreases in spermatogenesis and the ability to conceive and carry a pregnancy to term are the most sensitive signs of reproductive toxicity in male and female mammals, respectively. PMID:8260069

  20. Asymptotic Fitness Distribution in the Bak-Sneppen Model of Biological Evolution with Four Species

    NASA Astrophysics Data System (ADS)

    Schlemm, Eckhard

    2012-08-01

    We suggest a new method to compute the asymptotic fitness distribution in the Bak-Sneppen model of biological evolution. As applications we derive the full asymptotic distribution in the four-species model, and give an explicit linear recurrence relation for a set of coefficients determining the asymptotic distribution in the five-species model.

  1. The GEOS Chemistry Climate Model: Comparisons to Satellite Data

    NASA Technical Reports Server (NTRS)

    Stolarski, Richard S.; Douglass, Anne R.

    2008-01-01

    The Goddard Earth Observing System Chemistry Climate Model (GEOS CCM) has been developed by combining the atmospheric chemistry and transport modules developed over the years at Goddard and the GEOS general circulation model, also developed at Goddard. We will compare model simulations of ozone, and the minor constituents that affect ozone, for the period around 1980 with newly released revised data from the Limb Infrared Monitor of the Stratosphere (LIMS) instrument on Nimbus 4. We will also compare model simulations for the period of the early 2000s with the data from the Microwave Limb Sounder (MLS) and the High Resolution Dynamic Limb Sounder (HRDLS) on the Aura satellite. We will use these comparisons to examine the performance of the model for the present atmosphere and for the change that has occurred during the last 2 decades of ozone loss due to chlorine and bromine compounds released from chlorofluorocarbons and halons.

  2. Meridional Winds derived from ionosonde measurements: comparison of different models

    NASA Astrophysics Data System (ADS)

    Katamzi, Zama; Bosco Habarulema, John; Aruliah, Anasuya

    2016-07-01

    Thermospheric meridional winds are derived from ionospheric F2 region peak parameters (i.e. F2 maximum density, NmF2, and F2 peak height, hmF2) obtained using South African ionosonde for solar maximum (2001 and 2014) and solar minimum (2009). The study uses several different techniques and models to investigate the climatology behaviour of the winds in order to understand wind variability over South Africa. Detailed solar cycle, seasonal and diurnal trends will help establish how the winds influence ionospheric behaviour at this latitude. Comparisons of ionosonde derived neutral winds with empirical and numerical models such as the Coupled Middle Atmosphere Thermosphere Model (CMAT2) and Thermosphere-Ionosphere-Electrodynamics General Circulation Model (TIE-GCM) are important to understand the validity of theoretical and empirical models.

  3. The GEOS Chemistry Climate Model: Comparisons to Satellite Data

    NASA Astrophysics Data System (ADS)

    Stolarski, R. S.; Douglass, A. R.

    2008-05-01

    The Goddard Earth Observing System Chemistry Climate Model (GEOS CCM) has been developed by combining the atmospheric chemistry and transport modules developed over the years at Goddard and the GEOS general circulation model, also developed at Goddard. We will compare model simulations of ozone, and the minor constituents that affect ozone, for the period around 1980 with newly released revised data from the Limb Infrared Monitor of the Stratosphere (LIMS) instrument on Nimbus 4. We will also compare model simulations for the period of the early 2000s with the data from the Microwave Limb Sounder (MLS) and the High Resolution Dynamic Limb Sounder (HRDLS) on the Aura satellite. We will use these comparisons to examine the performance of the model for the present atmosphere and for the change that has occurred during the last 2 decades of ozone loss due to chlorine and bromine compounds released from chlorofluorocarbons and halons.

  4. Comparison of stream invertebrate response models for bioassessment metric

    USGS Publications Warehouse

    Waite, Ian R.; Kennen, Jonathan G.; May, Jason T.; Brown, Larry R.; Cuffney, Thomas F.; Jones, Kimberly A.; Orlando, James L.

    2012-01-01

    We aggregated invertebrate data from various sources to assemble data for modeling in two ecoregions in Oregon and one in California. Our goal was to compare the performance of models developed using multiple linear regression (MLR) techniques with models developed using three relatively new techniques: classification and regression trees (CART), random forest (RF), and boosted regression trees (BRT). We used tolerance of taxa based on richness (RICHTOL) and ratio of observed to expected taxa (O/E) as response variables and land use/land cover as explanatory variables. Responses were generally linear; therefore, there was little improvement to the MLR models when compared to models using CART and RF. In general, the four modeling techniques (MLR, CART, RF, and BRT) consistently selected the same primary explanatory variables for each region. However, results from the BRT models showed significant improvement over the MLR models for each region; increases in R2 from 0.09 to 0.20. The O/E metric that was derived from models specifically calibrated for Oregon consistently had lower R2 values than RICHTOL for the two regions tested. Modeled O/E R2 values were between 0.06 and 0.10 lower for each of the four modeling methods applied in the Willamette Valley and were between 0.19 and 0.36 points lower for the Blue Mountains. As a result, BRT models may indeed represent a good alternative to MLR for modeling species distribution relative to environmental variables.

  5. Comparison of two operational long-range transport air pollution forecast models

    NASA Astrophysics Data System (ADS)

    Brandt, J.; Geels, C.; Christensen, J. C.; Frohn, L. M.; Hansen, K. M.; Skjøth, C. A.; Hertel, O.

    2003-04-01

    An operational air pollution forecast system, THOR, covering scales from regional over urban background to urban street scales has been developed. The long-range transport model, The Danish Eulerian Operational Model (DEOM) is presently used in the system to calculate the long-range transported air pollution from European sources to the areas of interest. DEOM is an Eulerian model covering Europe and includes 35 chemical compounds. In order to carry out fast computations in operational mode, the model is applied with three vertical layers (bottom layer representing the mixing height, second layer representing the old advected mixing height from the day before and finally a reservoir top layer). In the last years, computer power has increased to a level where real 3-D calculations are possible for forecasting. Therefore a new comprehensive 3-D model, The Danish Eulerian Hemispheric Model (DEHM), including 62 chemical species and 18 vertical layers has been developed. Both models operate on the same polar stereographic projection with a 50 km x 50 km horizontal resolution and uses the same meteorological data from the Eta model as input. The models have been run for the year of 1999, and comparisons of model results with measurements from the European Monitoring and Evaluation Programme (EMEP) will be shown. The differences in the model characteristics will be described together with an intercomparison of the models, using different statistical tests.

  6. Polymerase chain reaction comparison of the gene for strictosidine synthase from ten Rauvolfia species.

    PubMed

    Bracher, D; Kutchan, T M

    1992-05-01

    The gene for strictosidine synthase, str1, has been analyzed by the polymerase chain reaction in ten species of Rauvolfia, the origins of which span the tropical belt: R. cambodiana (Indochina), R. canescens (India), R. chinensis (China), R. heterophylla (Central America), R. mannii (West Africa), R. nitida (West Indies), R. praecox (Brasil), R. serpentina (India), R. sumatrana (Indonesia) and R. verticillata (Indochina). Restriction endonuclease analysis of the gene fragments produced with genomic DNA from each of the ten species as template revealed that str1 is highly conserved in the Rauvolfia species investigated. These results suggest that there is a stringent selection pressure on the gene for this key enzyme of indole alkaloid biosynthesis. PMID:24202981

  7. Comparison of saline tolerance among genetically similar species of Fusarium and Meloidogyne recovered from marine and terrestrial habitats

    NASA Astrophysics Data System (ADS)

    Elmer, W. H.; LaMondia, J. A.

    2014-08-01

    Successful plant pathogens co-evolve and adapt to the environmental constraints placed on host plants. We compared the salt tolerance of two salt marsh pathogens, Fusarium palustre and Meloidogyne spartinae, to genetically related terrestrial species, F. sporotrichioides and Meloidogyne hapla, to assess whether the salt marsh species had acquired selective traits for persisting in saline environments or if salt tolerance was comparable among Fusarium and Meloidogyne species. Comparisons of both species were made in vitro in vessels containing increasing concentration of NaCl. We observed that F. palustre was more tolerant to NaCl than F. sporotrichioides. The radial expansion of F. palustre on NaCl-amended agar plates was unaffected by increasing concentrations up to 0.3 M. F. sporotrichioides showed large reductions in growth at the same concentrations. Survival of M. hapla was greatest at 0 M, and reduced by half in a 0.3 M solution for 4 days. No juveniles survived exposure to 0.3 M NaCl for 12 days. M. spartinae survived at all NaCl concentrations tested, including 1.0 M for at least 12 days. These findings are consistent with the hypothesis that marine organisms in the upper tidal zone must osmoregulate to withstand a wide range of salinity and provide evidence that these pathogens evolved in saline conditions and are not recent introductions from terrestrial niches.

  8. Comparison of aerodynamic models for Vertical Axis Wind Turbines

    NASA Astrophysics Data System (ADS)

    Simão Ferreira, C.; Aagaard Madsen, H.; Barone, M.; Roscher, B.; Deglaire, P.; Arduin, I.

    2014-06-01

    Multi-megawatt Vertical Axis Wind Turbines (VAWTs) are experiencing an increased interest for floating offshore applications. However, VAWT development is hindered by the lack of fast, accurate and validated simulation models. This work compares six different numerical models for VAWTS: a multiple streamtube model, a double-multiple streamtube model, the actuator cylinder model, a 2D potential flow panel model, a 3D unsteady lifting line model, and a 2D conformal mapping unsteady vortex model. The comparison covers rotor configurations with two NACA0015 blades, for several tip speed ratios, rotor solidity and fixed pitch angle, included heavily loaded rotors, in inviscid flow. The results show that the streamtube models are inaccurate, and that correct predictions of rotor power and rotor thrust are an effect of error cancellation which only occurs at specific configurations. The other four models, which explicitly model the wake as a system of vorticity, show mostly differences due to the instantaneous or time averaged formulation of the loading and flow, for which further research is needed.

  9. Comparison of Models for Ball Bearing Dynamic Capacity and Life

    NASA Technical Reports Server (NTRS)

    Gupta, Pradeep K.; Oswald, Fred B.; Zaretsky, Erwin V.

    2015-01-01

    Generalized formulations for dynamic capacity and life of ball bearings, based on the models introduced by Lundberg and Palmgren and Zaretsky, have been developed and implemented in the bearing dynamics computer code, ADORE. Unlike the original Lundberg-Palmgren dynamic capacity equation, where the elastic properties are part of the life constant, the generalized formulations permit variation of elastic properties of the interacting materials. The newly updated Lundberg-Palmgren model allows prediction of life as a function of elastic properties. For elastic properties similar to those of AISI 52100 bearing steel, both the original and updated Lundberg-Palmgren models provide identical results. A comparison between the Lundberg-Palmgren and the Zaretsky models shows that at relatively light loads the Zaretsky model predicts a much higher life than the Lundberg-Palmgren model. As the load increases, the Zaretsky model provides a much faster drop off in life. This is because the Zaretsky model is much more sensitive to load than the Lundberg-Palmgren model. The generalized implementation where all model parameters can be varied provides an effective tool for future model validation and enhancement in bearing life prediction capabilities.

  10. Comparison of two laryngeal tissue fiber constitutive models

    NASA Astrophysics Data System (ADS)

    Hunter, Eric J.; Palaparthi, Anil Kumar Reddy; Siegmund, Thomas; Chan, Roger W.

    2014-02-01

    Biological tissues are complex time-dependent materials, and the best choice of the appropriate time-dependent constitutive description is not evident. This report reviews two constitutive models (a modified Kelvin model and a two-network Ogden-Boyce model) in the characterization of the passive stress-strain properties of laryngeal tissue under tensile deformation. The two models are compared, as are the automated methods for parameterization of tissue stress-strain data (a brute force vs. a common optimization method). Sensitivity (error curves) of parameters from both models and the optimized parameter set are calculated and contrast by optimizing to the same tissue stress-strain data. Both models adequately characterized empirical stress-strain datasets and could be used to recreate a good likeness of the data. Nevertheless, parameters in both models were sensitive to measurement errors or uncertainties in stress-strain, which would greatly hinder the confidence in those parameters. The modified Kelvin model emerges as a potential better choice for phonation models which use a tissue model as one component, or for general comparisons of the mechanical properties of one type of tissue to another (e.g., axial stress nonlinearity). In contrast, the Ogden-Boyce model would be more appropriate to provide a basic understanding of the tissue's mechanical response with better insights into the tissue's physical characteristics in terms of standard engineering metrics such as shear modulus and viscosity.

  11. Social complexity parallels vocal complexity: a comparison of three non-human primate species

    PubMed Central

    Bouchet, Hélène; Blois-Heulin, Catherine; Lemasson, Alban

    2013-01-01

    Social factors play a key role in the structuring of vocal repertoires at the individual level, notably in non-human primates. Some authors suggested that, at the species level too, social life may have driven the evolution of communicative complexity, but this has rarely been empirically tested. Here, we use a comparative approach to address this issue. We investigated vocal variability, at both the call type and the repertoire levels, in three forest-dwelling species of Cercopithecinae presenting striking differences in their social systems, in terms of social organization as well as social structure. We collected female call recordings from twelve De Brazza's monkeys (Cercopithecus neglectus), six Campbell's monkeys (Cercopithecus campbelli) and seven red-capped mangabeys (Cercocebus torquatus) housed in similar conditions. First, we noted that the level of acoustic variability and individual distinctiveness found in several call types was related to their importance in social functioning. Contact calls, essential to intra-group cohesion, were the most individually distinctive regardless of the species, while threat calls were more structurally variable in mangabeys, the most “despotic” of our three species. Second, we found a parallel between the degree of complexity of the species' social structure and the size, diversity, and usage of its vocal repertoire. Mangabeys (most complex social structure) called twice as often as guenons and displayed the largest and most complex repertoire. De Brazza's monkeys (simplest social structure) displayed the smallest and simplest repertoire. Campbell's monkeys displayed an intermediate pattern. Providing evidence of higher levels of vocal variability in species presenting a more complex social system, our results are in line with the theory of a social-vocal coevolution of communicative abilities, opening new perspectives for comparative research on the evolution of communication systems in different animal taxa. PMID

  12. Modeling mass transfer in solid oxide fuel cell anode: I. Comparison between Fickian, Stefan-Maxwell and dusty-gas models

    NASA Astrophysics Data System (ADS)

    Bao, Cheng; Jiang, Zeyi; Zhang, Xinxin

    2016-04-01

    Fickian, Stefan-Maxwell and dusty-gas model have been widely used in modeling mass transfer in porous electrodes of solid oxide fuel cells. Suwanwarangkul et al. (J. Power Sources 122 (2003) 9-18) implement a survey for performance comparison among these models to predict the concentration overpotential of a solid oxide fuel cell anode. In their work, the flux ratio of species is calculated by Graham's law and contradictorily the equimolar counter transport is used for isobaric assumption. Focused on the flux-ratio approaches and usually neglected pressure gradient, a comparison between Fickian, Stefan-Maxwell and dusty-gas model is done again in this article. The dusty gas model combined with the 'Stoich' flux-ratio approach, i.e. the species flux is dictated by its stoichiometry of the electrochemical reaction, is validated to make the best performance. And all models by the 'Graham' flux-ratio approach, i.e. the flux of species satisfies Graham's law, underestimate the concentration overpotential when the molecular weights of species are quite different. The extended Stefan-Maxwell model is an alternative, although it generally exaggerates the role of Knudsen diffusion. The effect of pore size on the Knudsen diffusion and pressure gradient is also discussed.

  13. Distributed hydrological models: comparison between TOPKAPI, a physically based model and TETIS, a conceptually based model

    NASA Astrophysics Data System (ADS)

    Ortiz, E.; Guna, V.

    2009-04-01

    The present work aims to carry out a comparison between two distributed hydrological models, the TOPKAPI (Ciarapica and Todini, 1998; Todini and Ciarapica, 2001) and TETIS (Vélez, J. J.; Vélez J. I. and Francés, F, 2002) models, obtaining the hydrological solution computed on the basis of the same storm events. The first model is physically based and the second one is conceptually based. The analysis was performed on the 21,4 km2 Goodwin Creek watershed, located in Panola County, Mississippi. This watershed extensively monitored by the Agricultural Research Service (ARS) National Sediment Laboratory (NSL) has been chosen because it offers a complete database compiling precipitation (16 rain gauges), runoff (6 discharge stations) and GIS data. Three storm events were chosen to evaluate the performance of the two models: the first one was chosen to calibrate the models, and the other two to validate them. Both models performed a satisfactory hydrological response both in calibration and validation events. While for the TOPKAPI model it wasn't a real calibration, due to its really good performance with parameters modal values derived of watershed characteristics, for the TETIS model it has been necessary to perform a previous automatic calibration. This calibration was carried out using the data provided by the observed hydrograph, in order to adjust the modeĺs 9 correction factors. Keywords: TETIS, TOPKAPI, distributed models, hydrological response, ungauged basins.

  14. Comparison of seed bank estimation techniques using six weed species in two soil types

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tests of three different seed bank estimation techniques were performed on six different weed species. Petri plate germination was compared to two emergence methods, each on two different soil types (stony loam vs. silt loam). Soil types produced equal emergence proportions, however both emergence...

  15. INTERSPECIES COMPARISONS OF A/D RATIOS: A/D RATIOS ARE NOT CONSTANT ACROSS SPECIES

    EPA Science Inventory

    The hypothesis that the ratio of the adult (A) and developmental (D) toxicity of a chemical is constant across animal species has been proposed as the basis for identifying developmental hazards, both from traditional developmental toxicity screens using laboratory mammals and fr...

  16. Bat Species Comparisons Based on External Morphology: A Test of Traditional versus Geometric Morphometric Approaches

    PubMed Central

    Schmieder, Daniela A.; Benítez, Hugo A.; Borissov, Ivailo M.; Fruciano, Carmelo

    2015-01-01

    External morphology is commonly used to identify bats as well as to investigate flight and foraging behavior, typically relying on simple length and area measures or ratios. However, geometric morphometrics is increasingly used in the biological sciences to analyse variation in shape and discriminate among species and populations. Here we compare the ability of traditional versus geometric morphometric methods in discriminating between closely related bat species – in this case European horseshoe bats (Rhinolophidae, Chiroptera) – based on morphology of the wing, body and tail. In addition to comparing morphometric methods, we used geometric morphometrics to detect interspecies differences as shape changes. Geometric morphometrics yielded improved species discrimination relative to traditional methods. The predicted shape for the variation along the between group principal components revealed that the largest differences between species lay in the extent to which the wing reaches in the direction of the head. This strong trend in interspecific shape variation is associated with size, which we interpret as an evolutionary allometry pattern. PMID:25965335

  17. Cross-species comparison of mammalian saliva using an LC-MALDI based proteomic approach.

    PubMed

    de Sousa-Pereira, Patrícia; Cova, Marta; Abrantes, Joana; Ferreira, Rita; Trindade, Fábio; Barros, António; Gomes, Pedro; Colaço, Bruno; Amado, Francisco; Esteves, Pedro J; Vitorino, Rui

    2015-05-01

    Despite the importance of saliva in the regulation of oral cavity homeostasis, few studies have been conducted to quantitatively compare the saliva of different mammal species. Aiming to define a proteome signature of mammals' saliva, an in-depth SDS-PAGE-LC coupled to MS/MS (GeLC-MS/MS) approach was used to characterize the saliva from primates (human), carnivores (dog), glires (rat and rabbit), and ungulates (sheep, cattle, horse). Despite the high variability in the number of distinct proteins identified per species, most protein families were shared by the mammals studied with the exception of cattle and horse. Alpha-amylase is an example that seems to reflect the natural selection related to digestion efficacy and food recognition. Casein protein family was identified in all species but human, suggesting an alternative to statherin in the protection of hard tissues. Overall, data suggest that different proteins might assure a similar role in the regulation of oral cavity homeostasis, potentially explaining the specific mammals' salivary proteome signature. Moreover, some protein families were identified for the first time in the saliva of some species, the presence of proline-rich proteins in rabbit's saliva being a good example. PMID:25641928

  18. A toxicokinetic comparison of two species of low larkspur (Delphinium spp.) in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Low larkspurs can have different toxic potentials to livestock due to variation in the individual alkaloids present in the plants. Two species of low larkspur, Delphinium nuttallianum and D. andersonii were dosed to 10 Holstein steers at 10mg and 12mg toxic alkaloids/kg, respectively. Blood samples ...

  19. Morphometrical and genetic comparison of two nematode species: H. spumosa and H. dahomensis (Nematoda, Heterakidae).

    PubMed

    Ribas, Alexis; de Bellocq, Jöelle Gouy; Ros, Albert; Ndiaye, Papa Ibnou; Miquel, Jordi

    2013-09-01

    Heterakis is a genus of parasitic nematodes, the majority of which are found in ground-feeding birds and only rarely in mammals. The best-known species is Heterakis spumosa, a parasite associated with the cosmopolitan invasive rodent Rattus rattus of Asiatic origin. Heterakis dahomensis was described in 1911 as a parasite of the Gambian giant rat (Cricetomys gambianus) from Benin (Africa), subsequently synonymized to H. spumosa by Hall (1916). The study of helminths in African rodents is scarce and patchy. Since the original description of H. dahomensis, there have been only a few reports from Africa of species belonging to the genus Heterakis and the validity of this species has never in fact been confirmed or rejected. In the present study individual Heterakis spp. were collected from C. gambianus from Senegal. The morphological data taken point to differences between Heterakis dahomensis and H. spumosa, specifically in the number of tail papillae in males and in the vulva cuticular processes of females. In addition, molecular data revealed differences between these taxa and so H. dahomensis should be considered as a valid species. Moreover, recent changes in the systematics of the genus Cricetomys mean that it is now necessary to study the morphology and genetics of the Heterakis specimens collected from Cricetomys spp. (previously assigned to C. gambianus) in order to determine their taxonomic status as either H. dahomensis o H. spumosa. PMID:23990438

  20. Comparison of the emergence of three Brassicaceae species of different origins grown in Spain and USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thlaspi arvense, Camelina sativa, C. microcarpa and Neslia paniculata are four Brassicaceae family species that are becoming rare in North-Eastern Spain. Conversely, both T. arvense and C. sativa are being investigated as oilseed crops in North America for industrial/biofuel purposes. C. microcarpa ...

  1. Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs

    PubMed Central

    de Vries, Jan; Woehle, Christian; Christa, Gregor; Wägele, Heike; Tielens, Aloysius G. M.; Jahns, Peter; Gould, Sven B.

    2015-01-01

    The only animal cells known that can maintain functional plastids (kleptoplasts) in their cytosol occur in the digestive gland epithelia of sacoglossan slugs. Only a few species of the many hundred known can profit from kleptoplasty during starvation long-term, but why is not understood. The two sister taxa Elysia cornigera and Elysia timida sequester plastids from the same algal species, but with a very different outcome: while E. cornigera usually dies within the first two weeks when deprived of food, E. timida can survive for many months to come. Here we compare the responses of the two slugs to starvation, blocked photosynthesis and light stress. The two species respond differently, but in both starvation is the main denominator that alters global gene expression profiles. The kleptoplasts' ability to fix CO2 decreases at a similar rate in both slugs during starvation, but only E. cornigera individuals die in the presence of functional kleptoplasts, concomitant with the accumulation of reactive oxygen species (ROS) in the digestive tract. We show that profiting from the acquisition of robust plastids, and key to E. timida's longer survival, is determined by an increased starvation tolerance that keeps ROS levels at bay. PMID:25652835

  2. Comparisons of electronic and visual ratings of strawberry leaves inoculated with two colletotrichum species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inoculation of detached strawberry leaves with Colletotrichum species may provide a rapid and accurate method for identifying anthracnose resistant germplasm. The purpose of this study was to compare electronic and visual rating methods of screening for anthracnose resistance. Eight to 17 detached...

  3. Comparison of virulence plasmid (pYV/pCD)-associated phenotypes in Yersinia species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phenotypic expression of several virulence plasmid (pYV/pCD; 70-kb)-associated genetic determinants were compared among Yesinia species; Yesinia pestis, (an attenuated strain which does not cause plague designated to be used in BSL2 facility), Y. pseudotuberculosis and Y. enterocolitica including lo...

  4. Visual and electronic comparisons of detached strawberry leaves inoculated with two Colletotrichum species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Inoculation of detached strawberry leaves with Colletotrichum species may provide an accurate, rapid, non-destructive method of identifying anthracnose resistant germplasm. The purpose of this study was to compare two methods for screening anthracnose resistance. Detached leaves of 60 susceptible an...

  5. Comparison of the Morphology and Histomorphometry of Spermatogenic Cyst of Three Sharks Species With Diametric Testes.

    PubMed

    Gomes do Rêgo, Mariana; Fitzpatrick, John L; Hissa V Hazin, Fabio; Araujo, Maria Lucia G; Barros, Maria Edna Gomes; Evêncio Neto, Joaquim

    2016-06-01

    Characterization of the reproductive anatomy of elasmobranchs (sharks, skates, rays, and sawfish) offers unique insights into the evolution of reproductive traits in animals due to their phylogenetic position at the base of the vertebrate tree of life. Yet, despite advances in our understanding of male elasmobranch reproductive physiology and testes histology, very little is known about how testes histomorphometrics varies with male maturation. In this study, we characterize and contrast testes morphology and histomorphology of males at different maturation stages in three shark species with diametric testes development: Prionaceglauca, Rhizoprionodon lalandii, and Mustelus canis. All stages of spermatogenesis were observed in P. glauca and R. lalandii, while for M. canis, only males at early stages of maturation were examined and therefore all the spermatogenesis cells lineage were not present. The number of Sertoli cells increased with cell development by six times in R. lalandii and roughly four times in P. glauca, and were statistically different among stages of spermatogenesis cysts in both species. Statistical differences in cyst diameter and Sertoli cell numbers were observed between P. glauca and R. lalandii. The increase of spermatocyte II cell diameter described for R. Lalandii in this study was not usual to elasmobranch species as compared, for example, to P. glauca. This information proves the importance of studying the testicular development and the process of spermatogenesis is necessary for understanding the reproductive biology of the species, including life cycles and history, variation of reproductive morphology. Anat Rec, 299:759-768, 2016. © 2016 Wiley Periodicals, Inc. PMID:26864330

  6. Comparison of the chemical compositions and nutritive values of various pumpkin (Cucurbitaceae) species and parts.

    PubMed

    Kim, Mi Young; Kim, Eun Jin; Kim, Young-Nam; Choi, Changsun; Lee, Bog-Hieu

    2012-02-01

    Pumpkins have considerable variation in nutrient contents depending on the cultivation environment, species, or part. In this study, the general chemical compositions and some bioactive components, such as tocopherols, carotenoids, and β-sitosterol, were analyzed in three major species of pumpkin (Cucurbitaceae pepo, C. moschata, and C. maxima) grown in Korea and also in three parts (peel, flesh, and seed) of each pumpkin species. C. maxima had significantly more carbohydrate, protein, fat, and fiber than C. pepo or C. moschata (P < 0.05). The moisture content as well as the amino acid and arginine contents in all parts of the pumpkin was highest in C. pepo. The major fatty acids in the seeds were palmitic, stearic, oleic, and linoleic acids. C. pepo and C. moschata seeds had significantly more γ-tocopherol than C. maxima, whose seeds had the highest β-carotene content. C. pepo seeds had significantly more β-sitosterol than the others. Nutrient compositions differed considerably among the pumpkin species and parts. These results will be useful in updating the nutrient compositions of pumpkin in the Korean food composition database. Additional analyses of various pumpkins grown in different years and in different areas of Korea are needed. PMID:22413037

  7. Comparison of Campylobacter species Using flaA Short Variable Region DNA Sequence Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Although the relative rates of Campylobacter infections have been declining in the U.S. over the last decade, Campylobacter species continue to be one of the primary bacterial agents responsible for gastroenteritis worldwide. Infections are usually considered foodborne as Campylobacter...

  8. Comparison of numerical models of a pyrotechnic device

    SciTech Connect

    Pierce, K.G.

    1986-01-01

    The predictions of two numerical models of a hot-wire initiated pyrotechnic device are compared to each other and to experimental results. Both models employ finite difference approximations to the heat diffusion equation in cylindrical coordinates. The temperature dependence of the thermal properties of the pyrotechnic materials and of the bridgewire are modeled. An Arrhenius' model is used to describe the exothermic reaction in the powder. One model employs a single radial coordinate and predicts the radial temperature distribution in the bridgewire and surrounding powder mass. In addition to the radial coordinate, the other model also employs a longitudinal coordinate to predict the temperature distribution parallel to the axis of the bridgewire. The predictions of the two-dimensional model concerning the energy requirements for ignition and the energy losses from the ends of the bridgewire are presented. A comparison of the predictions of the two models and the development of thermal gradients are employed to define the regime where the assumption, in the one-dimensional model, of negligible heat transfer axial to the bridgewire does not lead to significant error. The general problems associated with predicting ignition from a diffusion model are also discussed.

  9. Model comparison for the density structure along solar prominence threads

    NASA Astrophysics Data System (ADS)

    Arregui, I.; Soler, R.

    2015-06-01

    Context. Quiescent solar prominence fine structures are typically modelled as density enhancements, called threads, which occupy a fraction of a longer magnetic flux tube. This is justified from the spatial distribution of the imaged plasma emission or absorption of prominences at small spatial scales. The profile of the mass density along the magnetic field is unknown, however, and several arbitrary alternatives are employed in prominence wave studies. The identification and measurement of period ratios from multiple harmonics in standing transverse thread oscillations offer a remote diagnostics method to probe the density variation of these structures. Aims: We present a comparison of theoretical models for the field-aligned density along prominence fine structures. They aim to imitate density distributions in which the plasma is more or less concentrated around the centre of the magnetic flux tube. We consider Lorentzian, Gaussian, and parabolic profiles. We compare theoretical predictions based on these profiles for the period ratio between the fundamental transverse kink mode and the first overtone to obtain estimates for the density ratios between the central part of the tube and its foot-points and to assess which one would better explain observed period ratio data. Methods: Bayesian parameter inference and model comparison techniques were developed and applied. To infer the parameters, we computed the posterior distribution for the density gradient parameter that depends on the observable period ratio. The model comparison involved computing the marginal likelihood as a function of the period ratio to obtain the plausibility of each density model as a function of the observable. We also computed the Bayes factors to quantify the relative evidence for each model, given a period ratio observation. Results: A Lorentzian density profile, with plasma density concentrated around the centre of the tube, seems to offer the most plausible inversion result. A

  10. Comparison of the physicochemical surface properties of Streptococcus rattus with those of other mutans streptococcal species.

    PubMed

    van der Mei, H C; de Soet, J J; de Graaff, J; Rouxhet, P G; Busscher, H J

    1991-01-01

    Mutans streptococci comprise a group of seven closely related, yet distinct species. The distinction between the four species used in this study, namely Streptococcus sobrinus, Streptococcus cricetus, Streptococcus rattus, and Streptococcus mutans, has been made only recently on the basis of DNA homologies. In order to determine if there is a difference in the physicochemical surface properties of these species, strains were characterized by contact angles, zeta potentials and isoelectric points (IEP), elemental surface compositions by X-ray photoelectron spectroscopy, and molecular moieties by infrared spectroscopy. Contact angles, particularly when measured with water, can be considered a measure of cell surface hydrophobicity; zeta potentials reflect the charge of the outermost cell surface; X-ray photoelectron spectroscopy yields the relative abundance of carbon, oxygen, nitrogen, and phosphorus over the outer 5 nm of the bacterial cell surface; infrared spectroscopy enables a molecular characterization in terms of proteins, phosphates, and polysaccharides. All four species were homogeneous with regard to their physicochemical surface properties. However, the S. rattus species were clearly different from the others on the basis of the low water contact angle (21 +/- 2 vs. 26-31 degrees), highly negative zeta potential and lack of IEP, and high oxygen/carbon (0.50 +/- 0.02 vs. 0.41-0.43) and phosphorus/carbon (0.016 +/- 0.001 vs. 0.006-0.008) surface concentration ratios. Amongst the other differences observed, each species had a characteristic pH dependence of their zeta potential measured in phosphate buffer, yielding an IEP of 1.7, 2.1, and 2.5 for S. cricetus, S. sobrinus, and S. mutans, respectively. However, a cluster analysis on the zeta potential data showed only an isolated cluster for the S. rattus species. Thus it is likely that the higher cariogenicity of S. sobrinus with respect to S. cricetus and S. mutans is, in addition to a higher acidogenicity

  11. Comparison of software models for energy savings from cool roofs

    DOE PAGESBeta

    New, Joshua; Miller, William A.; Huang, Yu; Levinson, Ronnen

    2015-06-07

    For this study, a web-based Roof Savings Calculator (RSC) has been deployed for the United States Department of Energy as an industry-consensus tool to help building owners, manufacturers, distributors, contractors and researchers easily run complex roof and attic simulations. RSC simulates multiple roof and attic technologies for side-by-side comparison including reflective roofs, different roof slopes, above sheathing ventilation, radiant barriers, low-emittance roof surfaces, duct location, duct leakage rates, multiple substrate types, and insulation levels. Annual simulations of hour-by-hour, whole-building performance are used to provide estimated annual energy and cost savings from reduced HVAC use. While RSC reported similar cooling savingsmore » to other simulation engines, heating penalty varied significantly. RSC results show reduced cool roofing cost-effectiveness, thus mitigating expected economic incentives for this countermeasure to the urban heat island effect. This paper consolidates comparison of RSC's projected energy savings to other simulation engines including DOE-2.1E, AtticSim, Micropas, and EnergyPlus. Also included are comparisons to previous simulation-based studies, analysis of RSC cooling savings and heating penalties, the role of radiative heat exchange in an attic assembly, and changes made for increased accuracy of the duct model. Finally, radiant heat transfer and duct interaction not previously modeled is considered a major contributor to heating penalties.« less

  12. Comparison of software models for energy savings from cool roofs

    SciTech Connect

    New, Joshua; Miller, William A.; Huang, Yu; Levinson, Ronnen

    2015-06-07

    For this study, a web-based Roof Savings Calculator (RSC) has been deployed for the United States Department of Energy as an industry-consensus tool to help building owners, manufacturers, distributors, contractors and researchers easily run complex roof and attic simulations. RSC simulates multiple roof and attic technologies for side-by-side comparison including reflective roofs, different roof slopes, above sheathing ventilation, radiant barriers, low-emittance roof surfaces, duct location, duct leakage rates, multiple substrate types, and insulation levels. Annual simulations of hour-by-hour, whole-building performance are used to provide estimated annual energy and cost savings from reduced HVAC use. While RSC reported similar cooling savings to other simulation engines, heating penalty varied significantly. RSC results show reduced cool roofing cost-effectiveness, thus mitigating expected economic incentives for this countermeasure to the urban heat island effect. This paper consolidates comparison of RSC's projected energy savings to other simulation engines including DOE-2.1E, AtticSim, Micropas, and EnergyPlus. Also included are comparisons to previous simulation-based studies, analysis of RSC cooling savings and heating penalties, the role of radiative heat exchange in an attic assembly, and changes made for increased accuracy of the duct model. Finally, radiant heat transfer and duct interaction not previously modeled is considered a major contributor to heating penalties.

  13. Comparison of Software Models for Energy Savings from Cool Roofs

    SciTech Connect

    New, Joshua Ryan; Miller, William A; Huang, Yu; Levinson, Ronnen

    2016-01-01

    A web-based Roof Savings Calculator (RSC) has been deployed for the United States Department of Energy as an industry-consensus tool to help building owners, manufacturers, distributors, contractors and researchers easily run complex roof and attic simulations. RSC simulates multiple roof and attic technologies for side-by-side comparison including reflective roofs, different roof slopes, above sheathing ventilation, radiant barriers, low-emittance roof surfaces, duct location, duct leakage rates, multiple substrate types, and insulation levels. Annual simulations of hour-by-hour, whole-building performance are used to provide estimated annual energy and cost savings from reduced HVAC use. While RSC reported similar cooling savings to other simulation engines, heating penalty varied significantly. RSC results show reduced cool roofing cost-effectiveness, thus mitigating expected economic incentives for this countermeasure to the urban heat island effect. This paper consolidates comparison of RSC s projected energy savings to other simulation engines including DOE-2.1E, AtticSim, Micropas, and EnergyPlus. Also included are comparisons to previous simulation-based studies, analysis of RSC cooling savings and heating penalties, the role of radiative heat exchange in an attic assembly, and changes made for increased accuracy of the duct model. Radiant heat transfer and duct interaction not previously modeled is considered a major contributor to heating penalties.

  14. Modelling invasion for a habitat generalist and a specialist plant species

    USGS Publications Warehouse

    Evangelista, P.H.; Kumar, S.; Stohlgren, T.J.; Jarnevich, C.S.; Crall, A.W.; Norman, J. B., III; Barnett, D.T.

    2008-01-01

    Predicting suitable habitat and the potential distribution of invasive species is a high priority for resource managers and systems ecologists. Most models are designed to identify habitat characteristics that define the ecological niche of a species with little consideration to individual species' traits. We tested five commonly used modelling methods on two invasive plant species, the habitat generalist Bromus tectorum and habitat specialist Tamarix chinensis, to compare model performances, evaluate predictability, and relate results to distribution traits associated with each species. Most of the tested models performed similarly for each species; however, the generalist species proved to be more difficult to predict than the specialist species. The highest area under the receiver-operating characteristic curve values with independent validation data sets of B. tectorum and T. chinensis was 0.503 and 0.885, respectively. Similarly, a confusion matrix for B. tectorum had the highest overall accuracy of 55%, while the overall accuracy for T. chinensis was 85%. Models for the generalist species had varying performances, poor evaluations, and inconsistent results. This may be a result of a generalist's capability to persist in a wide range of environmental conditions that are not easily defined by the data, independent variables or model design. Models for the specialist species had consistently strong performances, high evaluations, and similar results among different model applications. This is likely a consequence of the specialist's requirement for explicit environmental resources and ecological barriers that are easily defined by predictive models. Although defining new invaders as generalist or specialist species can be challenging, model performances and evaluations may provide valuable information on a species' potential invasiveness.

  15. Comparison of Phylogeny, Venom Composition and Neutralization by Antivenom in Diverse Species of Bothrops Complex

    PubMed Central

    Peixoto, Pedro S.; Bernardoni, Juliana L.; Oliveira, Sâmella S.; Portes-Junior, José Antonio; Mourão, Rosa Helena V.; Lima-dos-Santos, Isa; Sano-Martins, Ida S.; Chalkidis, Hipócrates M.; Valente, Richard H.; Moura-da-Silva, Ana M.

    2013-01-01

    In Latin America, Bothrops snakes account for most snake bites in humans, and the recommended treatment is administration of multispecific Bothrops antivenom (SAB – soro antibotrópico). However, Bothrops snakes are very diverse with regard to their venom composition, which raises the issue of which venoms should be used as immunizing antigens for the production of pan-specific Bothrops antivenoms. In this study, we simultaneously compared the composition and reactivity with SAB of venoms collected from six species of snakes, distributed in pairs from three distinct phylogenetic clades: Bothrops, Bothropoides and Rhinocerophis. We also evaluated the neutralization of Bothrops atrox venom, which is the species responsible for most snake bites in the Amazon region, but not included in the immunization antigen mixture used to produce SAB. Using mass spectrometric and chromatographic approaches, we observed a lack of similarity in protein composition between the venoms from closely related snakes and a high similarity between the venoms of phylogenetically more distant snakes, suggesting little connection between taxonomic position and venom composition. P-III snake venom metalloproteinases (SVMPs) are the most antigenic toxins in the venoms of snakes from the Bothrops complex, whereas class P-I SVMPs, snake venom serine proteinases and phospholipases A2 reacted with antibodies in lower levels. Low molecular size toxins, such as disintegrins and bradykinin-potentiating peptides, were poorly antigenic. Toxins from the same protein family showed antigenic cross-reactivity among venoms from different species; SAB was efficient in neutralizing the B. atrox venom major toxins. Thus, we suggest that it is possible to obtain pan-specific effective antivenoms for Bothrops envenomations through immunization with venoms from only a few species of snakes, if these venoms contain protein classes that are representative of all species to which the antivenom is targeted. PMID

  16. Functional comparison of plasma-membrane Na+/H+ antiporters from two pathogenic Candida species

    PubMed Central

    Krauke, Yannick; Sychrova, Hana

    2008-01-01

    Background The virulence of Candida species depends on many environmental conditions. Extracellular pH and concentration of alkali metal cations belong among important factors. Nevertheless, the contribution of transporters mediating the exchange of alkali metal cations for protons across the plasma membrane to the cell salt tolerance and other physiological properties of various Candida species has not been studied so far. Results The tolerance/sensitivity of four pathogenic Candida species to alkali metal cations was tested and the role of one of the cation transporters in that tolerance (presumed to be the plasma-membrane Na+/H+ antiporter) was studied. The genes encoding these antiporters in the most and least salt sensitive species, C. dubliniensis and C. parapsilosis respectively, were identified, cloned and functionally expressed in the plasma membranes of Saccharomyces cerevisiae cells lacking their own cation exporters. Both CpCnh1 and CdCnh1 antiporters had broad substrate specificity and transported Na+, K+, Li+, and Rb+. Their activity in S. cerevisiae cells differed; CpCnh1p provided cells with a much higher salt tolerance than the CdCnh1 antiporter. The observed difference in activity was confirmed by direct measurements of sodium and potassium efflux mediated by these antiporters. Conclusion We have cloned two genes encoding putative Na+/H+ antiporters in C. parapsilosis and C. dubliniensis, and characterized the transport properties of encoded proteins. Our results show that the activity of plasma-membrane Na+/H+ antiporters is one of the factors determining the tolerance of pathogenic Candida species to high external concentrations of alkali metal cations. PMID:18492255

  17. Unified phenology model with Bayesian calibration for several European species in Belgium

    NASA Astrophysics Data System (ADS)

    Fu, Y. S. H.; Demarée, G.; Hamdi, R.; Deckmyn, A.; Deckmyn, G.; Janssens, I. A.

    2009-04-01

    Plant phenology is a good bio-indicator for climate change, and this has brought a significant increase of interest. Many kinds of phenology models have been developed to analyze and predict the phenological response to climate change, and those models have been summarized into one kind of unified model, which could be applied to different species and environments. In our study, we selected seven European woody plant species (Betula verrucosa, Quercus robur pedunculata, Fagus sylvatica, Fraxinus excelsior, Symphoricarpus racemosus, Aesculus hippocastanum, Robinia pseudoacacia) occurring in five sites distributed across Belgium. For those sites and tree species, phenological observations such as bud burst were available for the period 1956 - 2002. We also obtained regional downscaled climatic data for each of these sites, and combined both data sets to test the unified model. We used a Bayesian approach to generate distributions of model parameters from the observation data. In this poster presentation, we compare parameter distributions between different species and between different sites for individual species. The results of the unified model show a good agreement with the observations, except for Fagus sylvatica. The failure to reproduce the bud burst data for Fagus sylvatica suggest that the other factors not included in the unified model affect the phenology of this species. The parameter series show differences among species as we expected. However, they also differed strongly for the same species among sites.Further work should elucidate the mechanism that explains why model parameters differ among species and sites.

  18. The Model Organism Hermissenda crassicornis (Gastropoda: Heterobranchia) Is a Species Complex

    PubMed Central

    Lindsay, Tabitha

    2016-01-01

    Hermissenda crassicornis is a model organism used in various fields of research including neurology, ecology, pharmacology, and toxicology. In order to investigate the systematics of this species and the presence of cryptic species in H. crassicornis, we conducted a comprehensive molecular and morphological analysis of this species covering its entire range across the North Pacific Ocean. We determined that H. crassicornis constitutes a species complex of three distinct species. The name Hermissensa crassicornis is retained for the northeast Pacific species, occurring from Alaska to Northern California. The name H. opalescens is reinstated for a species occurring from the Sea of Cortez to Northern California. Finally, the name H. emurai is maintained for the northwestern species, found in Japan and in the Russian Far East. These three species have consistent morphological and color pattern differences that can be used for identification in the field. PMID:27105319

  19. Minor loops modelling with a modified Jiles-Atherton model and comparison with the Preisach model

    NASA Astrophysics Data System (ADS)

    Benabou, A.; Leite, J. V.; Clénet, S.; Simão, C.; Sadowski, N.

    When modelling electrical devices, one has to estimate quite accurately the iron losses for the sake of efficiency. The use of non-sinusoidal electrical sources increases the harmonic content in electrical systems and, consequently, increases significantly the magnetic losses in devices feed by these sources. The harmonic content adds non-centred minor hysteresis loops over the classical major one. The numerical tool used for the material modelling must be able to represent the magnetic behaviour in such conditions. Then, the use of a hysteresis model is the more suited solution, but the chosen model has to take into account correctly the minor loops. The Jiles-Atherton hysteresis model is one of the most employed, due its well-known properties, but it is not able to represent closed minor loops. In this work, we propose a simple approach based on experimental observations and empirical considerations, to improve the representation of minor loops in this model by keeping its simplicity of use and implementation in a FE calculation code. Differently to other approaches found in the literature, the previous knowledge of the magnetic field evolution is not needed. A comparison between measured and calculated curves, as well with the Preisach model, is performed to validate the model.

  20. Animal Models of Osteoarthritis: Comparisons and Key Considerations.

    PubMed

    McCoy, A M

    2015-09-01

    Osteoarthritis (OA) is unquestionably one of the most important chronic health issues in humans, affecting millions of individuals and costing billions of dollars annually. Despite widespread awareness of this disease and its devastating impact, the pathogenesis of early OA is not completely understood, hampering the development of effective tools for early diagnosis and disease-modifying therapeutics. Most human tissue available for study is obtained at the time of joint replacement, when OA lesions are end stage and little can be concluded about the factors that played a role in disease development. To overcome this limitation, over the past 50 years, numerous induced and spontaneous animal models have been utilized to study disease onset and progression, as well as to test novel therapeutic interventions. Reflecting the heterogeneity of OA itself, no single "gold standard" animal model for OA exists; thus, a challenge for researchers lies in selecting the most appropriate model to answer a particular scientific question of interest. This review provides general considerations for model selection, as well as important features of species such as mouse, rat, guinea pig, sheep, goat, and horse, which researchers should be mindful of when choosing the "best" animal model for their intended purpose. Special consideration is given to key variations in pathology among species as well as recommended guidelines for reporting the histologic features of each model. PMID:26063173

  1. Radicals and Reservoirs in the GMI Chemistry and Transport Model: Comparison to Measurements

    NASA Technical Reports Server (NTRS)

    Douglass, Anne R.; Stolarski, Richard S.; Strahan, Susan E.; Connell, Peter S.

    2004-01-01

    We have used a three-dimensional chemistry and transport model (CTM), developed under the Global Modeling Initiative (GMI), to carry out two simulations of the composition of the stratosphere under changing halogen loading for 1995 through 2030. The two simulations differ only in that one uses meteorological fields from a general circulation model while the other uses meteorological fields from a data assimilation system. A single year's winds and temperatures are repeated for each 36-year simulation. We compare results from these two simulations with an extensive collection of data from satellite and ground-based measurements for 1993-2000. Comparisons of simulated fields with observations of radical and reservoir species for some of the major ozone-destroying compounds are of similar quality for both simulations. Differences in the upper stratosphere, caused by transport of total reactive nitrogen and methane, impact the balance among the ozone loss processes and the sensitivity of the two simulations to the change in composition.

  2. Overall Energy Considerations for Algae Species Comparison and Selection in Algae-to-Fuels Processes

    SciTech Connect

    Link, D.; Kail, B.; Curtis, W.; Tuerk,A.

    2011-01-01

    The controlled growth of microalgae as a feedstock for alternative transportation fuel continues to receive much attention. Microalgae have the characteristics of rapid growth rate, high oil (lipid) content, and ability to be grown in unconventional scenarios. Algae have also been touted as beneficial for CO{sub 2} reuse, as algae can be grown using CO{sub 2} emissions from fossil-based energy generation. Moreover, algae does not compete in the food chain, lessening the 'food versus fuel' debate. Most often, it is assumed that either rapid production rate or high oii content should be the primary factor in algae selection for algae-to-fuels production systems. However, many important characteristics of algae growth and lipid production must be considered for species selection, growth condition, and scale-up. Under light limited, high density, photoautotrophic conditions, the inherent growth rate of an organism does not affect biomass productivity, carbon fixation rate, and energy fixation rate. However, the oil productivity is organism dependent, due to physiological differences in how the organisms allocate captured photons for growth and oil production and due to the differing conditions under which organisms accumulate oils. Therefore, many different factors must be considered when assessing the overall energy efficiency of fuel production for a given algae species. Two species, Chlorella vulgaris and Botryococcus braunii, are popular choices when discussing algae-to-fuels systems. Chlorella is a very robust species, often outcompeting other species in mixed-culture systems, and produces a lipid that is composed primarily of free fatty acids and glycerides. Botryococcus is regarded as a slower growing species, and the lipid that it produces is characterized by high hydrocarbon content, primarily C28-C34 botryococcenes. The difference in growth rates is often considered to be an advantage oiChlorella. However, the total energy captured by each algal species in

  3. Predicting recycling behaviour: Comparison of a linear regression model and a fuzzy logic model.

    PubMed

    Vesely, Stepan; Klöckner, Christian A; Dohnal, Mirko

    2016-03-01

    In this paper we demonstrate that fuzzy logic can provide a better tool for predicting recycling behaviour than the customarily used linear regression. To show this, we take a set of empirical data on recycling behaviour (N=664), which we randomly divide into two halves. The first half is used to estimate a linear regression model of recycling behaviour, and to develop a fuzzy logic model of recycling behaviour. As the first comparison, the fit of both models to the data included in estimation of the models (N=332) is evaluated. As the second comparison, predictive accuracy of both models for "new" cases (hold-out data not included in building the models, N=332) is assessed. In both cases, the fuzzy logic model significantly outperforms the regression model in terms of fit. To conclude, when accurate predictions of recycling and possibly other environmental behaviours are needed, fuzzy logic modelling seems to be a promising technique. PMID:26774211

  4. A model-model and data-model comparison for the early Eocene hydrological cycle

    NASA Astrophysics Data System (ADS)

    Carmichael, Matthew J.; Lunt, Daniel J.; Huber, Matthew; Heinemann, Malte; Kiehl, Jeffrey; LeGrande, Allegra; Loptson, Claire A.; Roberts, Chris D.; Sagoo, Navjit; Shields, Christine; Valdes, Paul J.; Winguth, Arne; Winguth, Cornelia; Pancost, Richard D.

    2016-02-01

    A range of proxy observations have recently provided constraints on how Earth's hydrological cycle responded to early Eocene climatic changes. However, comparisons of proxy data to general circulation model (GCM) simulated hydrology are limited and inter-model variability remains poorly characterised. In this work, we undertake an intercomparison of GCM-derived precipitation and P - E distributions within the extended EoMIP ensemble (Eocene Modelling Intercomparison Project; Lunt et al., 2012), which includes previously published early Eocene simulations performed using five GCMs differing in boundary conditions, model structure, and precipitation-relevant parameterisation schemes. We show that an intensified hydrological cycle, manifested in enhanced global precipitation and evaporation rates, is simulated for all Eocene simulations relative to the preindustrial conditions. This is primarily due to elevated atmospheric paleo-CO2, resulting in elevated temperatures, although the effects of differences in paleogeography and ice sheets are also important in some models. For a given CO2 level, globally averaged precipitation rates vary widely between models, largely arising from different simulated surface air temperatures. Models with a similar global sensitivity of precipitation rate to temperature (dP/dT) display different regional precipitation responses for a given temperature change. Regions that are particularly sensitive to model choice include the South Pacific, tropical Africa, and the Peri-Tethys, which may represent targets for future proxy acquisition. A comparison of early and middle Eocene leaf-fossil-derived precipitation estimates with the GCM output illustrates that GCMs generally underestimate precipitation rates at high latitudes, although a possible seasonal bias of the proxies cannot be excluded. Models which warm these regions, either via elevated CO2 or by varying poorly constrained model parameter values, are most successful in simulating a

  5. Bayesian inference and model comparison for metallic fatigue data

    NASA Astrophysics Data System (ADS)

    Babuška, Ivo; Sawlan, Zaid; Scavino, Marco; Szabó, Barna; Tempone, Raúl

    2016-06-01

    In this work, we present a statistical treatment of stress-life (S-N) data drawn from a collection of records of fatigue experiments that were performed on 75S-T6 aluminum alloys. Our main objective is to predict the fatigue life of materials by providing a systematic approach to model calibration, model selection and model ranking with reference to S-N data. To this purpose, we consider fatigue-limit models and random fatigue-limit models that are specially designed to allow the treatment of the run-outs (right-censored data). We first fit the models to the data by maximum likelihood methods and estimate the quantiles of the life distribution of the alloy specimen. To assess the robustness of the estimation of the quantile functions, we obtain bootstrap confidence bands by stratified resampling with respect to the cycle ratio. We then compare and rank the models by classical measures of fit based on information criteria. We also consider a Bayesian approach that provides, under the prior distribution of the model parameters selected by the user, their simulation-based posterior distributions. We implement and apply Bayesian model comparison methods, such as Bayes factor ranking and predictive information criteria based on cross-validation techniques under various a priori scenarios.

  6. STRUCTURE-ACTIVITY COMPARISON OF ORGANOTIN SPECIES: DIBUTYLTIN IS A DEVELOPMENTAL NEUROTOXICANT IN VITRO AND IN VIVO.

    EPA Science Inventory

    This manuscript compares the toxicity of a number of organotin species present in drinking water using a set of in vitro assays that model neuronal differentiation, and viability and apoptosis. Dibutyltin (DBT), dimethyltin (DMT), monomethyltin (MMT), and the positive control tri...

  7. Comparison between analytical and numerical solution of mathematical drying model

    NASA Astrophysics Data System (ADS)

    Shahari, N.; Rasmani, K.; Jamil, N.

    2016-02-01

    Drying is often related to the food industry as a process of shifting heat and mass inside food, which helps in preserving food. Previous research using a mass transfer equation showed that the results were mostly concerned with the comparison between the simulation model and the experimental data. In this paper, the finite difference method was used to solve a mass equation during drying using different kinds of boundary condition, which are equilibrium and convective boundary conditions. The results of these two models provide a comparison between the analytical and the numerical solution. The result shows a close match between the two solution curves. It is concluded that the two proposed models produce an accurate solution to describe the moisture distribution content during the drying process. This analysis indicates that we have confidence in the behaviour of moisture in the numerical simulation. This result demonstrated that a combined analytical and numerical approach prove that the system is behaving physically. Based on this assumption, the model of mass transfer was extended to include the temperature transfer, and the result shows a similar trend to those presented in the simpler case.

  8. Resonance scattering by fish schools: A comparison of two models.

    PubMed

    Raveau, M; Feuillade, C

    2016-01-01

    The effective medium method is used to investigate resonance scattering from schools of fish with gas-filled swim bladders, as a function of frequency and azimuth. Calculations are also performed with a coupled differential equation model, which incorporates both multiple scattering between fish and wave interference interactions of their scattered fields [Feuillade, Nero, and Love, J. Acoust. Soc. Am. 99, 196-208 (1996)]. A theoretical comparison of the models for idealized spherical schools shows good agreement over the entire resonance region in the forward direction, where interference interactions have a minimal effect. Good agreement is also seen in back scattering at low frequencies, where the wavelength λ≥4s, and s is the average nearest neighbor fish separation. If λ<4s, the models diverge in back scattering, and the effective medium method fails. This can be critically important when migrations of schools to deeper water cause the collective resonance frequency to increase. Multiple scattering interactions are negligible when |4πnf(b)(2)/k|⪅0.01, where n is the fish number density, f(b) is the individual fish scattering amplitude, and k=2π/λ. A comparison with forward scattering data shows very good agreement for both models, and indicates a method for estimating fish abundance. For back scattering data, the effective medium method diverges strongly when λ<4s. PMID:26827014

  9. The Evolution of SN 1997eg Through Spectropolarimetric Model Comparisons

    NASA Astrophysics Data System (ADS)

    Huk, Leah N.; Peters, C. L.; Hoffman, J. L.

    2013-01-01

    Spectra of the interacting SNe type IIn show strong and narrow emission lines along with complex polarization signatures. The degeneracy in total light line profiles that normally obscures the differences among objects in the IIn subclass can be overcome through analysis of polarized line profiles instead. A new technique involving reverse analysis of the polarized line profiles through model comparison allows us to extract information about the circumstellar material (CSM) and progenitor wind. Using a three-dimensional radiative transfer code called SLIP, we have created the first quantitative simulations of polarized line profiles in SNe IIn. By varying CSM parameters such as geometry, optical depth, brightness, and temperature, we constructed a grid of 1296 simulated H-alpha line profiles in both total light and polarized light. Previous comparisons of the total light H-alpha line profiles of the type IIn SN 1997eg with this model grid suggested an optically thick disk-like scattering region viewed nearly edge on and becoming brighter over time. Extending this work, we here present results obtained by comparing the observed line profiles of SN 1997eg with the model grid in polarized light alone, and in polarized and total light simultaneously. Preliminary results suggest that simultaneous fitting yields more consistent results than fitting using flux profiles or polarized flux profiles alone. This process produces the best fits for a radially thick disk-like circumstellar scattering region. Future comparisons of additional interacting supernovae with our models will provide insight into common trends amongst CSM characteristics in SNe IIn and reveal properties of the winds of their massive progenitors. This research is supported by the National Science Foundation, Sigma Xi, University of Denver, and Vanderbilt University.

  10. Depressive-like behavioral profiles in captive-bred single- and socially-housed rhesus and cynomolgus macaques: a species comparison

    PubMed Central

    Camus, Sandrine M. J.; Rochais, Céline; Blois-Heulin, Catherine; Li, Qin; Hausberger, Martine; Bezard, Erwan

    2014-01-01

    Background: To unravel the causes of major depressive disorder (MDD), the third leading cause of disease burden around the world, ethological animal models have recently been proposed. Our previous studies highlighted a depressive-like profile among single- and socially-housed farm-bred cynomolgus macaques. Although phylogenetically close, cynomolgus and rhesus macaques, the two most commonly used macaque species in biomedical research, differ on several levels such as patterns of aggression, reconciliation, temperament, or dominance styles. The question of whether one captive macaque species was more vulnerable than another in the development of a pathological profile reminiscent of MDD symptoms was explored. Methods: Behavioral data (including body postures, orientations, gaze directions, inter-individual distances, and locations in the cage) were collected in farming conditions. Using an unbiased validated ethological scan-sampling method, followed by multiple correspondence and hierarchical clustering analyses, 40 single- and 35 socially-housed rhesus macaques were assessed. Independently, for each housing condition, inter-species comparisons were made with previously acquired data on farm-bred cynomolgus monkeys. Results: Consistent with our previous studies, we found depressive-like characteristics (e.g., inactivity, low level of investigation and maintenance, long time spent inactive while facing the wall) among single- and socially-housed rhesus macaques. Species-specificities were reported in non-depressive time budgets and in the prevalence of the pathological profiles. Conclusions: Our results suggest that rhesus may be more vulnerable to developing a despair-like state than cynomolgus macaques, both in single- and in social-housing conditions. Therefore, rhesus macaques are more suitable for use as a “spontaneous” model of depressive disorders. PMID:24600363

  11. Long-term, large scale banking of citrus species embryos: comparisons between cryopreservation and other seed banking temperatures.

    PubMed

    Malik, S K; Chaudhury, R; Pritchard, H W

    2012-01-01

    The long-term, large scale application of embryo cryopreservation has been assessed rarely and comparisons of viability loss for partially dried material with conventional seed bank storage conditions infrequently made. Five citrus species were cryopreserved following air drying of embryos (seed minus the testa) and embryonic axes: rough lemon (Citrus jambhiri), pommelo (C. grandis), mandarin (C. reticulata), citron (C. medica) and kagzi lime (C. aurantifolia). Although drying rates to c. 10 percent moisture content (MC) were approximately 10-times faster for isolated axes compared to embryos, the optimum MCs for cryopreservation were generally similar within a species, varying from c. 10 percent (C. jambhiri) to c. 20 percent (C. medica). Nonetheless, the hydration window for cryopreservation of the axis was usually wider than for the embryo. For all species, embryo or axis survival after cryopreservation ranged from 65 to 96 percent (C. medica axes), producing normal healthy seedlings from embryos and plantlets from axes without intervening callus growth in vitro. Whilst partially dried embryos of all five species survived fully liquid nitrogen vapour storage for 120 days, viability loss was rapid at -20 degree C, 5 degree C and ambient temperature, with a maximum interpolated half-life across these temperatures of c. 80 days for C. grandis at 5 degree C. The developed cryopreservation protocols were applied routinely to cryobank 377 accessions of Citrus germplasm from field genebanks, farmer's orchards, semi-wild and wild sources. After an average of 6.3 to 8.4 years cryo-storage, between 69 and 81 percent of accessions per species retained > 70 percent of the viability after desiccation. The results provide irrevocable evidence for the importance of cryopreservation for the banking of seeds of higher plants. PMID:23250405

  12. Model parameterization to simulate and compare the PAR absorption potential of two competing plant species

    PubMed Central

    Silva, Brenner; Roos, Kristin; Göttlicher, Dietrich Otto; Rollenbeck, Rütger; Nauß, Thomas; Beck, Erwin

    2009-01-01

    Mountain pastures dominated by the pasture grass Setaria sphacelata in the Andes of southern Ecuador are heavily infested by southern bracken (Pteridium arachnoideum), a major problem for pasture management. Field observations suggest that bracken might outcompete the grass due to its competitive strength with regard to the absorption of photosynthetically active radiation (PAR). To understand the PAR absorption potential of both species, the aims of the current paper are to (1) parameterize a radiation scheme of a two-big-leaf model by deriving structural (LAI, leaf angle parameter) and optical (leaf albedo, transmittance) plant traits for average individuals from field surveys, (2) to initialize the properly parameterized radiation scheme with realistic global irradiation conditions of the Rio San Francisco Valley in the Andes of southern Ecuador, and (3) to compare the PAR absorption capabilities of both species under typical local weather conditions. Field data show that bracken reveals a slightly higher average leaf area index (LAI) and more horizontally oriented leaves in comparison to Setaria. Spectrometer measurements reveal that bracken and Setaria are characterized by a similar average leaf absorptance. Simulations with the average diurnal course of incoming solar radiation (1998–2005) and the mean leaf–sun geometry reveal that PAR absorption is fairly equal for both species. However, the comparison of typical clear and overcast days show that two parameters, (1) the relation of incoming diffuse and direct irradiance, and (2) the leaf–sun geometry play a major role for PAR absorption in the two-big-leaf approach: Under cloudy sky conditions (mainly diffuse irradiance), PAR absorption is slightly higher for Setaria while under clear sky conditions (mainly direct irradiance), the average bracken individual is characterized by a higher PAR absorption potential. (∼74 MJ m−2 year−1). The latter situation which occurs if the maximum daily

  13. Model parameterization to simulate and compare the PAR absorption potential of two competing plant species.

    PubMed

    Bendix, Jörg; Silva, Brenner; Roos, Kristin; Göttlicher, Dietrich Otto; Rollenbeck, Rütger; Nauss, Thomas; Beck, Erwin

    2010-05-01

    Mountain pastures dominated by the pasture grass Setaria sphacelata in the Andes of southern Ecuador are heavily infested by southern bracken (Pteridium arachnoideum), a major problem for pasture management. Field observations suggest that bracken might outcompete the grass due to its competitive strength with regard to the absorption of photosynthetically active radiation (PAR). To understand the PAR absorption potential of both species, the aims of the current paper are to (1) parameterize a radiation scheme of a two-big-leaf model by deriving structural (LAI, leaf angle parameter) and optical (leaf albedo, transmittance) plant traits for average individuals from field surveys, (2) to initialize the properly parameterized radiation scheme with realistic global irradiation conditions of the Rio San Francisco Valley in the Andes of southern Ecuador, and (3) to compare the PAR absorption capabilities of both species under typical local weather conditions. Field data show that bracken reveals a slightly higher average leaf area index (LAI) and more horizontally oriented leaves in comparison to Setaria. Spectrometer measurements reveal that bracken and Setaria are characterized by a similar average leaf absorptance. Simulations with the average diurnal course of incoming solar radiation (1998-2005) and the mean leaf-sun geometry reveal that PAR absorption is fairly equal for both species. However, the comparison of typical clear and overcast days show that two parameters, (1) the relation of incoming diffuse and direct irradiance, and (2) the leaf-sun geometry play a major role for PAR absorption in the two-big-leaf approach: Under cloudy sky conditions (mainly diffuse irradiance), PAR absorption is slightly higher for Setaria while under clear sky conditions (mainly direct irradiance), the average bracken individual is characterized by a higher PAR absorption potential. (approximately 74 MJ m(-2) year(-1)). The latter situation which occurs if the maximum daily

  14. PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species[W][OA

    PubMed Central

    Mutwil, Marek; Klie, Sebastian; Tohge, Takayuki; Giorgi, Federico M.; Wilkins, Olivia; Campbell, Malcolm M.; Fernie, Alisdair R.; Usadel, Björn; Nikoloski, Zoran; Persson, Staffan

    2011-01-01

    The model organism Arabidopsis thaliana is readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer acquired knowledge from Arabidopsis to crop species. However, the identification of functional equivalents of well-characterized Arabidopsis genes in other plants is a nontrivial task. It is well documented that transcriptionally coordinated genes tend to be functionally related and that such relationships may be conserved across different species and even kingdoms. To exploit such relationships, we constructed whole-genome coexpression networks for Arabidopsis and six important plant crop species. The interactive networks, clustered using the HCCA algorithm, are provided under the banner PlaNet (http://aranet.mpimp-golm.mpg.de). We implemented a comparative network algorithm that estimates similarities between network structures. Thus, the platform can be used to swiftly infer similar coexpressed network vicinities within and across species and can predict the identity of functional homologs. We exemplify this using the PSA-D and chalcone synthase-related gene networks. Finally, we assessed how ontology terms are transcriptionally connected in the seven species and provide the corresponding MapMan term coexpression networks. The data support the contention that this platform will considerably improve transfer of knowledge generated in Arabidopsis to valuable crop species. PMID:21441431

  15. Comparison of the physico-chemical and phytochemical characteristics of the oil of two Plukenetia species.

    PubMed

    Chirinos, Rosana; Pedreschi, Romina; Domínguez, Gilberto; Campos, David

    2015-04-15

    A physico-chemical and phytochemical characterisation of the oil of two rich sources of polyunsaturated fatty acids, tocopherols and phytosterols is presented for two close species of Plukenetia, endemic to the Amazon Region of Peru. Plukenetia huayllabambana presented approximately 9% more oil yield than Plukenetia volubilis. Fatty acid profiles were pretty similar for both species but P. huayllabambana presented a significantly higher content of α-linolenic acid than P. volubilis (51.3 and 45.6 g/100 g oil, respectively). Important contents of γ- and δ-tocopherol were evidenced in both oils (127.6 and 84.0 and, 93.3 and 47.5 mg/100 g oil, for P. volubilis and P. huayllabambana, respectively). β-Sitosterol was the most important and representative phytosterol in both oils (∼127 mg/100 g oil). The results of this study indicate P. huayllabambana as an important dietary source of health promoting phytochemicals. PMID:25466144

  16. Hyperaccumulative property comparison of 24 weed species to heavy metals using a pot culture experiment.

    PubMed

    Wei, Shuhe; Zhou, Qixing; Xiao, Hong; Yang, Chuanjie; Hu, Yahu; Ren, Liping

    2009-05-01

    The screening of hyperaccumulators is still very much needed for phytoremediation. With properties such as strong tolerance to adverse environment, fast growing and highly reproductive rate, weed species may be an ideal plant for phytoremediation. The objectives of this study were to examine the tolerance and hyperaccumulative characteristics of 24 species in 9 families to Cd, Pb, Cu and Zn by using the outdoor pot-culture experiment. In the screening experiment, only Conyza canadensis and Rorippa globosa displayed Cd-hyperaccumulative characteristics. In a further concentration gradient experiment, C. canadensis was affirmed that it is not a Cd hyperaccumulator. Only R. globosa, indicated all Cd hyperaccumulative characteristics, especially Cd concentration in its stems and leaves were higher than 100 mg/kg, the minimum Cd concentration what a Cd-hyperaccumulator should accumulate. Thus, R. globosa was further validated as a Cd-hyperaccumulator. PMID:18483772

  17. Comparison of species-rich cover crop mixtures in Hungarian vineyards

    NASA Astrophysics Data System (ADS)

    Donkó, Adam; Miglécz, Tamas; Valkó, Orsolya; Török, Peter; Deák, Balazs; Kelemen, Andras; Zanathy, Gabor; Drexler, Dora

    2014-05-01

    In case of vine growing, agricultural practices of the past decades - as mechanical cultivation on steep vineyard slopes - can endanger the soil of vineyards. Moreover, climate change scenarios predict heavier rainstorms, which can also promote the degradation of the soil. These are some of the reasons why sustainable floor management plays an increasingly important role in viticulture recently. The use of cover crops in the inter-row has a special importance, especially on steep slopes and in case of organic farming to provide conditions for environmental friendly soil management. Species-rich cover crop seed mixtures may help to prevent erosion and create easier cultivation circumstances. Furthermore they have a positive effect on soil structure, soil fertility and ecosystem functions. However, it is important to find suitable seed mixtures for specific production sites, consisting ideally of native species from local provenance, adapted to the local climate/vine region/vineyard. Requirements for suitable cover crop species are as follows: they should save the soil from erosion and also from compaction caused by the movement of workers and machines, they should not compete significantly with the grapevines, or influence produce quality. We started to develop and apply several species-rich cover crop seed mixtures in spring 2012. During the experiments, three cover crop seed mixtures (Biocont-Ecovin mixture, mixture of legumes, mixture of grasses and herbs) were compared in vineyards of the Tokaj and Szekszárd vine regions of Hungary. Each mixture was sown in three consecutive inter-rows at each experimental site (all together 10 sites). Besides botanical measurements, yield, must quality, and pruning weight was studied in every treatment. The botanical survey showed that the following species of the mixtures established successfully and prospered during the years 2012 and 2013: Coronilla varia, Lotus corniculatus, Medicago lupulina, Onobrychis viciifolia

  18. A comparison of multiple esterases as biomarkers of organophosphate exposure and effect in two earthworm species.

    PubMed

    Henson-Ramsey, Heather; Schneider, Ashley; Stoskopf, Michael K

    2011-04-01

    Two different earthworm species, Eisenia fetida and Lumbricus terrestris, were exposed to 5 μg/cm(2) of malathion to evaluate their usefulness as sentinels of organophosphate exposure and to assess three different esterases, as biomarkers of malathion exposure and effect. Tissue xenobiotic burdens and esterase activity were determined for each species and each esterase in order to assess variability. E. fetida exhibited 4-fold less variability in tissue burdens than did L. terrestris and had less variable basal esterase activities. An attempt was made to correlate malathion and malaoxon tissue burdens with esterase activity post-exposure. There was no malaoxon present in the earthworm tissues. No significant correlations were determined by comparing acetylcholinesterase, butyrylcholinesterase, nor carboxylesterase activities with malathion burdens. PMID:21404045

  19. Comparison of the Essential Oil Composition of Selected Impatiens Species and Its Antioxidant Activities.

    PubMed

    Szewczyk, Katarzyna; Kalemba, Danuta; Komsta, Łukasz; Nowak, Renata

    2016-01-01

    The present paper describes the chemical composition of the essential oils obtained by hydrodistillation from four Impatiens species, Impatiens glandulifera Royle, I. parviflora DC., I. balsamina L. and I. noli-tangere L. The GC and GC-MS methods resulted in identification of 226 volatile compounds comprising from 61.7%-88.2% of the total amount. The essential oils differed significantly in their composition. Fifteen compounds were shared among the essential oils of all investigated Impatiens species. The majority of these constituents was linalool (0.7%-15.1%), hexanal (0.2%-5.3%) and benzaldehyde (0.1%-10.2%). Moreover, the antioxidant activity of the essential oils was investigated using different methods. The chemical composition of the essential oils and its antioxidant evaluation are reported for the first time from the investigated taxon. PMID:27598111

  20. A comparison of {sup 137}Cs radioactivity in localized evergreen and deciduous plant species

    SciTech Connect

    Rangel, R.C.

    1996-05-01

    A vegetation study at the Comanche Peak Steam Electric Station (CPSES) near Glen Rose, Texas was conducted in 1991 and 1992. The CPSES is a commercial nuclear power plant owned and operated by Texas Utilities Electric of Dallas, Texas. The US Nuclear Regulatory Commission (USNRC) requires the CPSES to routinely sample broadleaf vegetation in place of milk samples. Few commercial dairies exist in the vicinity. Broadleaf tree species are scarce because the climate and local limestone geology have produced a dry rolling hill topography. An evergreen juniper is the dominant tree species. Few broadleaves during the winter season have hindered year-round sampling. This study compares the environmental {sup 137}Cs concentrations between broadleaf and evergreen foliage at CPSES. Soil {sup 137}Cs concentrations from each vegetation location were also compared to the foliage {sup 137}Cs concentrations. The study`s objective was to determine if the deciduous and evergreen vegetation {sup 137}Cs concentrations are statistically the same.

  1. Estimating size and composition of biological communities by modeling the occurrence of species

    USGS Publications Warehouse

    Dorazio, R.M.; Royle, J. Andrew

    2005-01-01

    We develop a model that uses repeated observations of a biological community to estimate the number and composition of species in the community. Estimators of community-level attributes are constructed from model-based estimators of occurrence of individual species that incorporate imperfect detection of individuals. Data from the North American Breeding Bird Survey are analyzed to illustrate the variety of ecologically important quantities that are easily constructed and estimated using our model-based estimators of species occurrence. In particular, we compute site-specific estimates of species richness that honor classical notions of species-area relationships. We suggest extensions of our model to estimate maps of occurrence of individual species and to compute inferences related to the temporal and spatial dynamics of biological communities.

  2. Commensalism facilitates gene flow in mountains: a comparison between two Rattus species

    PubMed Central

    Varudkar, A; Ramakrishnan, U

    2015-01-01

    Small mammal dispersal is strongly affected by geographical barriers. However, commensal small mammals may be passively transported over large distances and strong barriers by humans (often with agricultural products). This pattern should be especially apparent in topographically complex landscapes, such as mountain ranges, where valleys and/or peaks can limit dispersal of less vagile species. We predict that commensal species would have lower genetic differentiation and higher migration rates than related non-commensals in such landscapes. We contrasted population genetic differentiation in two sympatric Rattus species (R. satarae and R. rattus) in the Western Ghats mountains in southern India. We sampled rats from villages and adjacent forests in seven locations (20–640 km apart). Capture-based statistics confirmed that R. rattus is abundant in human settlements in this region, whereas R. satarae is non-commensal and found mostly in forests. Population structure analyses using ~970-bp mitochondrial control region and 17 microsatellite loci revealed higher differentiation for the non-commensal species (R. satarae F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034; mitochondrial DNA, microsatellites, respectively). Genetic clustering analyses confirm that clusters in R. satarae are more distinct and less admixed than those in R. rattus. R. satarae shows higher slope for isolation-by-distance compared with R. rattus. Although mode of migration estimates do not strongly suggest higher rates in R. rattus than in R. satarae, they indicate that migration over long distances could still be higher in R. rattus. We suggest that association with humans could drive the observed pattern of differentiation in the commensal R. rattus, consequently impacting not only their dispersal abilities, but also their evolutionary trajectories. PMID:25944468

  3. Oenanthe incrassans: An enigmatic species from Turkey and its comparison with Oenanthe pimpinelloides (Apiaceae).

    PubMed

    Güner, Ebru Doğan

    2016-01-01

    Oenanthe incrassans (Apiaceae) was discovered in Istanbul, Turkey. It is related to Oenanthe pimpinelloides, but it clearly differs in terms of leaves, inflorescence (ray, bracts, and bracteoles) and fruit features. A taxonomic description, some photographs of the species, geographical distribution and habitat features are given. Additionally, fruit micromorphology, stem, ray and fruit anatomy, and pollen features are studied for the first time and compared to Oenanthe pimpinelloides. PMID:27212886

  4. A between-Species Comparison of Antimicrobial Resistance in Enterobacteria in Fecal Flora

    PubMed Central

    Österblad, Monica; Hakanen, Antti; Manninen, Raija; Leistevuo, Tiina; Peltonen, Reijo; Meurman, Olli; Huovinen, Pentti; Kotilainen, Pirkko

    2000-01-01

    Enterobacteria in fecal flora are often reported to be highly resistant. Escherichia coli is the main species; resistance data on other species are rare. To assess the effect of the host's environment, antimicrobial resistance was determined in fecal species of the family Enterobacteriaceae from three populations: healthy people (HP)(n = 125) with no exposure to antimicrobials for 3 months preceding sampling, university hospital patients (UP) (n = 159) from wards where the antibiotic use was 112 defined daily doses (DDD)/bed/month, and geriatric long-term patients (LTP) (n = 74) who used 1.8 DDD/bed/month. The mean length of hospital stay was 5 days for the UP and 22 months for the LTP. The isolates were identified to at least genus level, and MICs of 16 antimicrobials were determined. From the university hospital, resistance data on clinical Enterobacteriaceae isolates were also collected. Resistance data for on average two different isolates per sample (range, 1 to 5) were analyzed: 471 E. coli isolates and 261 other Enterobacteriaceae spp. Resistance was mainly found among E. coli; even in HP, 18% of E. coli isolates were resistant to two or more antimicrobial groups, with MIC patterns indicative of transferable resistance. Other fecal enterobacteria were generally susceptible, with little typically transferable multiresistance. Clinical Klebsiella and Enterobacter isolates were significantly more resistant than fecal isolates. The resistance patterns at both hospitals mirrored the patterns of antibiotic use, but LTP E. coli isolates were significantly more resistant than those from UP. Conditions permitting an efficient spread may have been more important in sustaining high resistance levels in the LTP. E. coli was the main carrier of antimicrobial resistance in fecal flora; resistance in other species was rare in the absence of antimicrobial selection. PMID:10817696

  5. Oenanthe incrassans: An enigmatic species from Turkey and its comparison with Oenanthe pimpinelloides (Apiaceae)

    PubMed Central

    Güner, Ebru Doğan

    2016-01-01

    Abstract Oenanthe incrassans (Apiaceae) was discovered in Istanbul, Turkey. It is related to Oenanthe pimpinelloides, but it clearly differs in terms of leaves, inflorescence (ray, bracts, and bracteoles) and fruit features. A taxonomic description, some photographs of the species, geographical distribution and habitat features are given. Additionally, fruit micromorphology, stem, ray and fruit anatomy, and pollen features are studied for the first time and compared to Oenanthe pimpinelloides. PMID:27212886

  6. Building and analyzing protein interactome networks by cross-species comparisons

    PubMed Central

    2010-01-01

    Background A genomic catalogue of protein-protein interactions is a rich source of information, particularly for exploring the relationships between proteins. Numerous systems-wide and small-scale experiments have been conducted to identify interactions; however, our knowledge of all interactions for any one species is incomplete, and alternative means to expand these network maps is needed. We therefore took a comparative biology approach to predict protein-protein interactions across five species (human, mouse, fly, worm, and yeast) and developed InterologFinder for research biologists to easily navigate this data. We also developed a confidence score for interactions based on available experimental evidence and conservation across species. Results The connectivity of the resultant networks was determined to have scale-free distribution, small-world properties, and increased local modularity, indicating that the added interactions do not disrupt our current understanding of protein network structures. We show examples of how these improved interactomes can be used to analyze a genome-scale dataset (RNAi screen) and to assign new function to proteins. Predicted interactions within this dataset were tested by co-immunoprecipitation, resulting in a high rate of validation, suggesting the high quality of networks produced. Conclusions Protein-protein interactions were predicted in five species, based on orthology. An InteroScore, a score accounting for homology, number of orthologues with evidence of interactions, and number of unique observations of interactions, is given to each known and predicted interaction. Our website http://www.interologfinder.org provides research biologists intuitive access to this data. PMID:20353594

  7. MODELING TOXICOKINETICS FOR CROSS-SPECIES EXTRAPOLATION OF DEVELOPMENTAL EFFECTS

    EPA Science Inventory

    Animal toxicology studies used to evaluate the potential for effects due to exposures during developmental periods are extrapolated to humans based upon the maternal exposure dose. The approach does not address whether the toxicokinetics are similar across species during the rel...

  8. Modeling of Valued Fish Species in River Networks

    EPA Science Inventory

    Riverine fish provide many ecosystem services in support of human well-being, including food, recreation, and biodiversity. Under future drivers of land use and climate change, inland waters are likely to be impaired, and conservation and protection of fish species and services ...

  9. Integrative modelling reveals mechanisms linking productivity and plant species richness

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For 40 years ecologists have sought a canonical productivity-species richness relationship 48 (PRR) for ecosystems, despite continuing disagreements about expected form and 49 interpretation. Using a large global dataset of terrestrial grasslands, we consider how 50 productivity and richness relate ...

  10. Molecular Cytogenetic Analysis of Podocarpus and Comparison with Other Gymnosperm Species

    PubMed Central

    MURRAY, BRIAN G.; FRIESEN, NIKOLAI; HESLOP‐HARRISON, J. S. (PAT)

    2002-01-01

    DNA sequences have been mapped to the chromosomes of Podocarpus species from New Zealand and Australia by fluorescent in situ hybridization. Unlike other conifers, these species show only one pair of major sites of 45S rDNA genes, and two additional minor sites were seen in the Australian P. lawrencei. Unusually, 45S sequences collocalize to the same chromosomal region as the 5S rDNA. The telomere probe (TTTAGGG)n hybridizes to the ends of all chromosomes as well as to a large number of small sites distributed along the length of all chromosomes. Two other simple sequence repeats, (AAC)5 and (GATA)4, show a diffuse pattern of hybridization sites distributed along chromosomes. Southern blots using a variety of probes obtained from the reverse transcriptase of retroelements (gypsy, copia and LINE) from P. totara, P. nivalis and Dacrycarpus dacrydioides show that these retroelements are abundant and widespread in Podocarpaceae and also in others conifers. Some retroelements such as copia pPonty3 and gypsy pPot1li are more abundant in the genome of Picea abies and Ginkgo biloba than in the species from which they were amplified. PMID:12096809

  11. Female social response to male sexual harassment in poeciliid fish: a comparison of six species

    PubMed Central

    Dadda, Marco

    2015-01-01

    Sexual harassment is common among poeciliid fish. In some fishes, males show a high frequency of sneak copulation; such sexual activity is costly to the females in terms of foraging efficiency. In mosquitofish (Gambusia holbrooki), when males are present, the distance between females tends to decrease, and this behavior has been interpreted as an adaptive strategy to dilute the costs of male sexual activity. In this study, the tendency to reduce distance in the presence of a male has been investigated in females of six poeciliid species (Girardinus metallicus, Girardinus falcatus, G. holbrooki, Poecilia reticulata, Xiphophorus hellerii, and Xiphophorus mayae) that exhibit different male mating strategies and different levels of sexual activity. Results revealed large interspecific differences in the pattern of female aggregation. Females of species with a high frequency of sneak copulations tended to reduce their social distance in the presence of a male. By contrast, species that rely mainly on courtship showed little or no variation in social distance. The proportion of sneak copulations predicts the degree of variation in female social response, but the amount of total sexual activity does not, suggesting that the change in females' social distance when a male is present may indeed serve to reduce the costs of male sexual harassment. PMID:26483719

  12. Mapping species distributions: a comparison of skilled naturalist and lay citizen science recording.

    PubMed

    van der Wal, René; Anderson, Helen; Robinson, Annie; Sharma, Nirwan; Mellish, Chris; Roberts, Stuart; Darvill, Ben; Siddharthan, Advaith

    2015-11-01

    To assess the ability of traditional biological recording schemes and lay citizen science approaches to gather data on species distributions and changes therein, we examined bumblebee records from the UK's national repository (National Biodiversity Network) and from BeeWatch. The two recording approaches revealed similar relative abundances of bumblebee species but different geographical distributions. For the widespread common carder (Bombus pascuorum), traditional recording scheme data were patchy, both spatially and temporally, reflecting active record centre rather than species distribution. Lay citizen science records displayed more extensive geographic coverage, reflecting human population density, thus offering better opportunities to account for recording effort. For the rapidly spreading tree bumblebee (Bombus hypnorum), both recording approaches revealed similar distributions due to a dedicated mapping project which overcame the patchy nature of naturalist records. We recommend, where possible, complementing skilled naturalist recording with lay citizen science programmes to obtain a nation-wide capability, and stress the need for timely uploading of data to the national repository. PMID:26508346

  13. Sexual comparisons in immune ability, survival and parasite intensity in two damselfly species.

    PubMed

    Córdoba-Aguilar, A; Contreras-Garduño, J; Peralta-Vázquez, H; Luna-González, A; Campa-Córdova, A I; Ascencio, F

    2006-08-01

    Recent evolutionary studies have suggested that females have a more robust immune system than males. Using two damselfly species (Hetaerina americana and Argia tezpi), we tested if females produced higher immune responses (as phenoloxidase and hydrolytic enzymes), had a higher survival (using a nylon implant inserted in the abdomen and measuring survival after 24h) and fewer parasites (gregarines and water mites) than males. We also tested whether immune differences should emerge in different body areas (thorax vs. abdomen) within each sex with the prediction that only females will differ with the abdomen having a higher immune response than their thorax since the former area, for ecological and physiological reasons, may be a target zone for increased immune investment. Animals were adults of approximately the same age. In both species, females were more immunocompetent than males, but only in H. americana females were immune responses greater in the abdomen than in the thorax. However, there were no differences in survival and parasite intensity or the probability of being parasitised between the sexes in either of the two species. Thus, this study lends partial support to the principle that females are better at defending than males despite the null difference in parasitism and survival. PMID:16843483

  14. Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia.

    PubMed

    Meganathan, P R; Dubey, Bhawna; Batzer, Mark A; Ray, David A; Haque, Ikramul

    2011-06-01

    Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii, Crocodylus johnstoni and Crocodylus palustris, and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii, C. johnstoni and C. palustris are 16,827 bp, 16,851 bp and 16,852 bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus. The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution. PMID:21310220

  15. Comparison of rumen microbial inhibition resulting from various essential oils isolated from relatively unpalatable plant species.

    PubMed

    Oh, H K; Jones, M B; Longhurst, W M

    1968-01-01

    Essential oils were isolated from eight plant species which were relatively unpalatable to sheep and deer. The inhibitory potency of these essential oils upon sheep and deer rumen microorganisms was compared, in terms of total gas and volatile fatty acid (VFA) production, by use of an anaerobic manometric technique. Inhibitory effects of oils from the eight plant species may be placed in four groups: (i) essential oils from vinegar weed (Trichostema lanceoletum) and California bay (Umbellularia californica) inhibited rumen microbial activity most; (ii) lesser inhibition was exhibited by rosemary (Rosmarinus officinalis) and California mugwort (Artemisia douglasiana) oils, followed by (iii) blue-gum eucalyptus (Eucalyptus globulus) and sagebrush (Artemisia tridentata) oils; and (iv) oils from Douglas fir (Psuedotsuga menziesii) and Jerusalem oak (chenopodium botrys) resulted in the least inhibition, when 0.3 ml of each oil was used. A highly significant correlation coefficient (r = 0.98(**)) between total gas and VFA production indicated the validity of either method to measure the activity of rumen microorganisms. Our results are discussed in relation to the hypothesis that the selectivity and voluntary consumption of ruminants are related to the characteristic odor and antibacterial action of essential oils isolated from relatively unpalatable plant species. PMID:5636470

  16. Functional Ecology of the Ciliate Glaucomides bromelicola, and Comparison with the Sympatric Species Bromeliothrix metopoides

    PubMed Central

    Weisse, Thomas; Scheffel, Ulrike; Stadler, Peter; Foissner, Wilhelm

    2013-01-01

    We investigated the ecology and life strategy of Glaucomides bromelicola (family Bromeliophryidae), a very common ciliate in the reservoirs (tanks) of bromeliads, assessing its response to food quality and quantity and pH. Further, we conducted competition experiments with the frequently coexisting species Bromeliothrix metopoides (family Colpodidae). In contrast to B. metopoides and many other colpodean ciliates, G. bromelicola does not form resting cysts, which jeopardizes this ciliate when its small aquatic habitats dry out. Both species form bactivorous microstomes and flagellate-feeding macrostomes. However, only G. bromelicola has a low feeding threshold and is able to adapt to different protist food. The higher affinity to the local bacterial and flagellate food renders it the superior competitor relative to B. metopoides. Continuous encystment and excystment of the latter may enable stable coexistence of both species in their natural habitat. Both are tolerant to a wide range of pH (4–9). These ciliates appear to be limited to tank bromeliads because they either lack resting cysts and vectors for long distance dispersal (G. bromelicola) and/or have highly specific food requirements (primarily B. metopoides). PMID:23865693

  17. Female social response to male sexual harassment in poeciliid fish: a comparison of six species.

    PubMed

    Dadda, Marco

    2015-01-01

    Sexual harassment is common among poeciliid fish. In some fishes, males show a high frequency of sneak copulation; such sexual activity is costly to the females in terms of foraging efficiency. In mosquitofish (Gambusia holbrooki), when males are present, the distance between females tends to decrease, and this behavior has been interpreted as an adaptive strategy to dilute the costs of male sexual activity. In this study, the tendency to reduce distance in the presence of a male has been investigated in females of six poeciliid species (Girardinus metallicus, Girardinus falcatus, G. holbrooki, Poecilia reticulata, Xiphophorus hellerii, and Xiphophorus mayae) that exhibit different male mating strategies and different levels of sexual activity. Results revealed large interspecific differences in the pattern of female aggregation. Females of species with a high frequency of sneak copulations tended to reduce their social distance in the presence of a male. By contrast, species that rely mainly on courtship showed little or no variation in social distance. The proportion of sneak copulations predicts the degree of variation in female social response, but the amount of total sexual activity does not, suggesting that the change in females' social distance when a male is present may indeed serve to reduce the costs of male sexual harassment. PMID:26483719

  18. Functional ecology of the ciliate Glaucomides bromelicola, and comparison with the sympatric species Bromeliothrix metopoides.

    PubMed

    Weisse, Thomas; Scheffel, Ulrike; Stadler, Peter; Foissner, Wilhelm

    2013-01-01

    We investigated the ecology and life strategy of Glaucomides bromelicola (family Bromeliophryidae), a very common ciliate in the reservoirs (tanks) of bromeliads, assessing its response to food quality and quantity and pH. Further, we conducted competition experiments with the frequently coexisting species Bromeliothrix metopoides (family Colpodidae). In contrast to B. metopoides and many other colpodean ciliates, G. bromelicola does not form resting cysts, which jeopardizes this ciliate when its small aquatic habitats dry out. Both species form bactivorous microstomes and flagellate-feeding macrostomes. However, only G. bromelicola has a low feeding threshold and is able to adapt to different protist food. The higher affinity to the local bacterial and flagellate food renders it the superior competitor relative to B. metopoides. Continuous encystment and excystment of the latter may enable stable coexistence of both species in their natural habitat. Both are tolerant to a wide range of pH (4-9). These ciliates appear to be limited to tank bromeliads because they either lack resting cysts and vectors for long distance dispersal (G. bromelicola) and/or have highly specific food requirements (primarily B. metopoides). PMID:23865693

  19. Midpoint attractors and species richness: Modelling the interaction between environmental drivers and geometric constraints.

    PubMed

    Colwell, Robert K; Gotelli, Nicholas J; Ashton, Louise A; Beck, Jan; Brehm, Gunnar; Fayle, Tom M; Fiedler, Konrad; Forister, Matthew L; Kessler, Michael; Kitching, Roger L; Klimes, Petr; Kluge, Jürgen; Longino, John T; Maunsell, Sarah C; McCain, Christy M; Moses, Jimmy; Noben, Sarah; Sam, Katerina; Sam, Legi; Shapiro, Arthur M; Wang, Xiangping; Novotny, Vojtech

    2016-09-01

    We introduce a novel framework for conceptualising, quantifying and unifying discordant patterns of species richness along geographical gradients. While not itself explicitly mechanistic, this approach offers a path towards understanding mechanisms. In this study, we focused on the diverse patterns of species richness on mountainsides. We conjectured that elevational range midpoints of species may be drawn towards a single midpoint attractor - a unimodal gradient of environmental favourability. The midpoint attractor interacts with geometric constraints imposed by sea level and the mountaintop to produce taxon-specific patterns of species richness. We developed a Bayesian simulation model to estimate the location and strength of the midpoint attractor from species occurrence data sampled along mountainsides. We also constructed midpoint predictor models to test whether environmental variables could directly account for the observed patterns of species range midpoints. We challenged these models with 16 elevational data sets, comprising 4500 species of insects, vertebrates and plants. The midpoint predictor models generally failed to predict the pattern of species midpoints. In contrast, the midpoint attractor model closely reproduced empirical spatial patterns of species richness and range midpoints. Gradients of environmental favourability, subject to geometric constraints, may parsimoniously account for elevational and other patterns of species richness. PMID:27358193

  20. Multi-species occurrence models to evaluate the effects of conservation and management actions

    USGS Publications Warehouse

    Zipkin, E.F.; Andrew, Royle J.; Dawson, D.K.; Bates, S.

    2010-01-01

    Conservation and management actions often have direct and indirect effects on a wide range of species. As such, it is important to evaluate the impacts that such actions may have on both target and non-target species within a region. Understanding how species richness and composition differ as a result of management treatments can help determine potential ecological consequences. Yet it is difficult to estimate richness because traditional sampling approaches detect species at variable rates and some species are never observed. We present a framework for assessing management actions on biodiversity using a multi-species hierarchical model that estimates individual species occurrences, while accounting for imperfect detection of species. Our model incorporates species-specific responses to management treatments and local vegetation characteristics and a hierarchical component that links species at a community-level. This allows for comprehensive inferences on the whole community or on assemblages of interest. Compared to traditional species models, occurrence estimates are improved for all species, even for those that are rarely observed, resulting in more precise estimates of species richness (including species that were unobserved during sampling). We demonstrate the utility of this approach for conservation through an analysis comparing bird communities in two geographically similar study areas: one in which white-tailed deer (Odocoileus virginianus) densities have been regulated through hunting and one in which deer densities have gone unregulated. Although our results indicate that species and assemblage richness were similar in the two study areas, point-level richness was significantly influenced by local vegetation characteristics, a result that would have been underestimated had we not accounted for variability in species detection.

  1. Refreezing on the Greenland ice sheet: a model comparison

    NASA Astrophysics Data System (ADS)

    Steger, Christian; Reijmer, Carleen; van den Broeke, Michiel; Ligtenberg, Stefan; Kuipers Munneke, Peter; Noël, Brice

    2016-04-01

    Mass loss of the Greenland ice sheet (GrIS) is an important contributor to global sea level rise. Besides calving, surface melt is the dominant source of mass loss. However, only part of the surface melt leaves the ice sheet as runoff whereas the other part percolates into the snow cover and refreezes. Due to this process, part of the meltwater is (intermediately) stored. Refreezing thus impacts the surface mass balance of the ice sheet but it also affects the vertical structure of the snow cover due to transport of mass and energy. Due to the sparse availability of in situ data and the demand of future projections, it is inevitable to use numerical models to simulate refreezing and related processes. Currently, the magnitude of refrozen mass is neither well constrained nor well validated. In this study, we model the snow and firn layer, and compare refreezing on the GrIS as modelled with two different numerical models. Both models are forced with meteorological data from the regional climate model RACMO 2 that has been shown to simulate realistic conditions for Greenland. One model is the UU/IMAU firn densification model (FDM) that can be used both in an on- and offline mode with RACMO 2. The other model is SNOWPACK; a model originally designed to simulate seasonal snow cover in alpine conditions. In contrast to FDM, SNOWPACK accounts for snow metamorphism and microstructure and contains a more physically based snow densification scheme. A first comparison of the models indicates that both seem to be able to capture the general spatial and temporal pattern of refreezing. Spatially, refreezing occurs mostly in the ablation zone and decreases in the accumulation zone towards the interior of the ice sheet. Below the equilibrium line altitude (ELA) where refreezing occurs in seasonal snow cover on bare ice, the storage effect is only intermediate. Temporal patterns on a seasonal range indicate two peaks in refreezing; one at the beginning of the melt season where

  2. COMPARISON OF RF CAVITY TRANSPORT MODELS FOR BBU SIMULATIONS

    SciTech Connect

    Ilkyoung Shin,Byung Yunn,Todd Satogata,Shahid Ahmed

    2011-03-01

    The transverse focusing effect in RF cavities plays a considerable role in beam dynamics for low-energy beamline sections and can contribute to beam breakup (BBU) instability. The purpose of this analysis is to examine RF cavity models