Science.gov

Sample records for model species comparison

  1. Probabilistic models of species discovery and biodiversity comparisons.

    PubMed

    Edie, Stewart M; Smits, Peter D; Jablonski, David

    2017-04-04

    Inferring large-scale processes that drive biodiversity hinges on understanding the phylogenetic and spatial pattern of species richness. However, clades and geographic regions are accumulating newly described species at an uneven rate, potentially affecting the stability of currently observed diversity patterns. Here, we present a probabilistic model of species discovery to assess the uncertainty in diversity levels among clades and regions. We use a Bayesian time series regression to estimate the long-term trend in the rate of species description for marine bivalves and find a distinct spatial bias in the accumulation of new species. Despite these biases, probabilistic estimates of future species richness show considerable stability in the currently observed rank order of regional diversity. However, absolute differences in richness are still likely to change, potentially modifying the correlation between species numbers and geographic, environmental, and biological factors thought to promote biodiversity. Applied to scallops and related clades, we find that accumulating knowledge of deep-sea species will likely shift the relative richness of these three families, emphasizing the need to consider the incomplete nature of bivalve taxonomy in quantitative studies of its diversity. Along with estimating expected changes to observed patterns of diversity, the model described in this paper pinpoints geographic areas and clades most urgently requiring additional systematic study-an important practice for building more complete and accurate models of biodiversity dynamics that can inform ecological and evolutionary theory and improve conservation practice.

  2. An extensive comparison of species-abundance distribution models

    PubMed Central

    Baldridge, Elita; Harris, David J.; Xiao, Xiao

    2016-01-01

    A number of different models have been proposed as descriptions of the species-abundance distribution (SAD). Most evaluations of these models use only one or two models, focus on only a single ecosystem or taxonomic group, or fail to use appropriate statistical methods. We use likelihood and AIC to compare the fit of four of the most widely used models to data on over 16,000 communities from a diverse array of taxonomic groups and ecosystems. Across all datasets combined the log-series, Poisson lognormal, and negative binomial all yield similar overall fits to the data. Therefore, when correcting for differences in the number of parameters the log-series generally provides the best fit to data. Within individual datasets some other distributions performed nearly as well as the log-series even after correcting for the number of parameters. The Zipf distribution is generally a poor characterization of the SAD. PMID:28028483

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. Comparison of guinea pig and protozoan models for determining virulence of Legionella species.

    PubMed Central

    Fields, B S; Barbaree, J M; Shotts, E B; Feeley, J C; Morrill, W E; Sanden, G N; Dykstra, M J

    1986-01-01

    Legionella pneumophila organisms are able to infect and multiply within the ciliated protozoan Tetrahymena pyriformis. This ability may be associated with virulence, because an attenuated strain of L. pneumophila fails to multiply within this protozoan, whereas a virulent strain increases 10,000-fold in number when coincubated with T. pyriformis. Seventeen strains (11 species) of legionellae were evaluated for virulence by intraperitoneal injection of guinea pigs and inoculation of protozoan cultures. Analysis of the data indicates that there are four categories of legionellae with respect to virulence as follows: organisms that infect and kill guinea pigs and multiply in T. pyriformis; organisms that infect but do not kill guinea pigs and multiply in T. pyriformis; organisms that do not infect guinea pigs but are lethal at high concentrations and multiply in T. pyriformis; and organisms that neither infect nor kill guinea pigs and fail to multiply in T. pyriformis. Evidence suggests that these distinctions are based on two virulence factors: intracellular multiplication in a host and toxic activity. Images PMID:3744550

  8. Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

    PubMed

    Kazemian, Majid; Zhu, Qiyun; Halfon, Marc S; Sinha, Saurabh

    2011-12-01

    Despite recent advances in experimental approaches for identifying transcriptional cis-regulatory modules (CRMs, 'enhancers'), direct empirical discovery of CRMs for all genes in all cell types and environmental conditions is likely to remain an elusive goal. Effective methods for computational CRM discovery are thus a critically needed complement to empirical approaches. However, existing computational methods that search for clusters of putative binding sites are ineffective if the relevant TFs and/or their binding specificities are unknown. Here, we provide a significantly improved method for 'motif-blind' CRM discovery that does not depend on knowledge or accurate prediction of TF-binding motifs and is effective when limited knowledge of functional CRMs is available to 'supervise' the search. We propose a new statistical method, based on 'Interpolated Markov Models', for motif-blind, genome-wide CRM discovery. It captures the statistical profile of variable length words in known CRMs of a regulatory network and finds candidate CRMs that match this profile. The method also uses orthologs of the known CRMs from closely related genomes. We perform in silico evaluation of predicted CRMs by assessing whether their neighboring genes are enriched for the expected expression patterns. This assessment uses a novel statistical test that extends the widely used Hypergeometric test of gene set enrichment to account for variability in intergenic lengths. We find that the new CRM prediction method is superior to existing methods. Finally, we experimentally validate 12 new CRM predictions by examining their regulatory activity in vivo in Drosophila; 10 of the tested CRMs were found to be functional, while 6 of the top 7 predictions showed the expected activity patterns. We make our program available as downloadable source code, and as a plugin for a genome browser installed on our servers.

  9. 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.

  10. Comparison of homoeolocus organisation in paired BAC clones from white clover (Trifolium repens L.) and microcolinearity with model legume species

    PubMed Central

    2010-01-01

    Background White clover (Trifolium repens L.) is an outbreeding allotetraploid species and an important forage legume in temperate grassland agriculture. Comparison of sub-genome architecture and study of nucleotide sequence diversity within allopolyploids provides insight into evolutionary divergence mechanisms, and is also necessary for the development of whole-genome sequencing strategies. This study aimed to evaluate the degree of divergence between the O and P' sub-genomes of white clover through sequencing of BAC clones containing paired homoeoloci. The microsyntenic relationships between the genomes of white clover and the model legumes Lotus japonicus and Medicago truncatula as well as Arabidopsis thaliana were also characterised. Results A total of four paired homoeologous BACs were selected and sequenced to generate 173 kb of overlapping sequence between the O and P' sub-genomes. Equivalent gene content was generally observed, apart from small-scale deletions, in contrast to conservation of intergenic sequences, which varied between the four selected regions. Measurement of the number of synonymous substitutions between homoeologous genes led to estimation of a 4.2 million year divergence time between the two sub-genomes. Microsynteny was observed between the genomes of white clover and L. japonicus for all four targeted regions, but corresponding M. truncatula genomic regions were only identified for two BAC pairs. Conclusions This study describes the first analysis of sub-genome structural conservation across selected genomic regions in white clover. Although the high levels of sequence conservation between the O and P' sub-genomes would complicate efforts for whole genome sequence assembly, the conserved microsynteny with model legume genomes, especially that of L. japonicus, will be highly valuable for the future of white clover genomics and molecular breeding. PMID:20492736

  11. Spore Size Comparison Between Several Bacillus Species

    DTIC Science & Technology

    2005-10-01

    Spore Size Comparison Between Several Bacillus Species Ruben O. Zandomeni1, Joseph E. Fitzgibbon2, Monica Carrera1, Edward Stuebing2, James E...OCT 2005 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE Spore Size Comparison Between Several Bacillus Species 5a. CONTRACT...Systematic comparison of the size of B.anthracis spores to size of other Bacillus spores (simulants/surrogates) - all spores produced under the same

  12. 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

    2016-02-01

    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.

  13. 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].

  14. 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.

  15. 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

  16. 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

  17. 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

  18. Comparison between two meshless methods based on collocation technique for the numerical solution of four-species tumor growth model

    NASA Astrophysics Data System (ADS)

    Dehghan, Mehdi; Mohammadi, Vahid

    2017-03-01

    As is said in [27], the tumor-growth model is the incorporation of nutrient within the mixture as opposed to being modeled with an auxiliary reaction-diffusion equation. The formulation involves systems of highly nonlinear partial differential equations of surface effects through diffuse-interface models [27]. Simulations of this practical model using numerical methods can be applied for evaluating it. The present paper investigates the solution of the tumor growth model with meshless techniques. Meshless methods are applied based on the collocation technique which employ multiquadrics (MQ) radial basis function (RBFs) and generalized moving least squares (GMLS) procedures. The main advantages of these choices come back to the natural behavior of meshless approaches. As well as, a method based on meshless approach can be applied easily for finding the solution of partial differential equations in high-dimension using any distributions of points on regular and irregular domains. The present paper involves a time-dependent system of partial differential equations that describes four-species tumor growth model. To overcome the time variable, two procedures will be used. One of them is a semi-implicit finite difference method based on Crank-Nicolson scheme and another one is based on explicit Runge-Kutta time integration. The first case gives a linear system of algebraic equations which will be solved at each time-step. The second case will be efficient but conditionally stable. The obtained numerical results are reported to confirm the ability of these techniques for solving the two and three-dimensional tumor-growth equations.

  19. 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...

  20. Model comparison in ANOVA.

    PubMed

    Rouder, Jeffrey N; Engelhardt, Christopher R; McCabe, Simon; Morey, Richard D

    2016-12-01

    Analysis of variance (ANOVA), the workhorse analysis of experimental designs, consists of F-tests of main effects and interactions. Yet, testing, including traditional ANOVA, has been recently critiqued on a number of theoretical and practical grounds. In light of these critiques, model comparison and model selection serve as an attractive alternative. Model comparison differs from testing in that one can support a null or nested model vis-a-vis a more general alternative by penalizing more flexible models. We argue this ability to support more simple models allows for more nuanced theoretical conclusions than provided by traditional ANOVA F-tests. We provide a model comparison strategy and show how ANOVA models may be reparameterized to better address substantive questions in data analysis.

  1. 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

  2. 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.

  3. 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.

  4. A mechanistic inter-species comparison of flicker sensitivity.

    PubMed

    Jarvis, John R; Prescott, Neville B; Wathes, Christopher M

    2003-07-01

    The general validity of both the Rovamo [Vision Res. 39 (1999) 533] and Barten (Contrast sensitivity of the human eye, SPIE Optical Engineering Press, 1999), modulation transfer function models for describing flicker sensitivity in vertebrates was examined using published data for goldfish, chickens, tree shrews, ground squirrels, cats, pigeons and humans. Both models adequately described the flicker response in each species at frequencies greater than approximately 1 Hz. At lower frequencies, response predictions differed between the two models and this was due, in part, to dissimilar definitions of the role played by lateral inhibition in the retina. Modelled flicker sensitivity for a matched retinal illuminance condition enabled a direct inter-species comparison of signal processing response times at the photoreceptor level. The modelled results also quantified differences between species in post-retinal signal processing capability. Finally, the relationship between flicker frequency response curves and the perception of temporal signals in real visual scenes was examined for each species. It is proposed that the area under the flicker sensitivity function may offer a single "figure of merit" for specifying overall sensitivity to time signals in a species' environment.

  5. 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.

    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

  6. 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...

  7. Multi-linear regression analysis, preliminary biotic ligand modeling, and cross species comparison of the effects of water chemistry on chronic lead toxicity in invertebrates.

    PubMed

    Esbaugh, A J; Brix, K V; Mager, E M; De Schamphelaere, K; Grosell, M

    2012-03-01

    The current study examined the chronic toxicity of lead (Pb) to three invertebrate species: the cladoceran Ceriodaphnia dubia, the snail Lymnaea stagnalis and the rotifer Philodina rapida. The test media consisted of natural waters from across North America, varying in pertinent water chemistry parameters including dissolved organic carbon (DOC), calcium, pH and total CO(2). Chronic toxicity was assessed using reproductive endpoints for C. dubia and P. rapida while growth was assessed for L. stagnalis, with chronic toxicity varying markedly according to water chemistry. A multi-linear regression (MLR) approach was used to identify the relative importance of individual water chemistry components in predicting chronic Pb toxicity for each species. DOC was an integral component of MLR models for C. dubia and L. stagnalis, but surprisingly had no predictive impact on chronic Pb toxicity for P. rapida. Furthermore, sodium and total CO(2) were also identified as important factors affecting C. dubia toxicity; no other factors were predictive for L. stagnalis. The Pb toxicity of P. rapida was predicted by calcium and pH. The predictive power of the C. dubia and L. stagnalis MLR models was generally similar to that of the current C. dubia BLM, with R(2) values of 0.55 and 0.82 for the respective MLR models, compared to 0.45 and 0.79 for the respective BLMs. In contrast the BLM poorly predicted P. rapida toxicity (R(2)=0.19), as compared to the MLR (R(2)=0.92). The cross species variability in the effects of water chemistry, especially with respect to rotifers, suggests that cross species modeling of invertebrate chronic Pb toxicity using a C. dubia model may not always be appropriate.

  8. Simulating organic species with the global atmospheric chemistry general circulation model ECHAM5/MESSy1: a comparison of model results with observations

    NASA Astrophysics Data System (ADS)

    Pozzer, A.; Jöckel, P.; Tost, H.; Sander, R.; Ganzeveld, L.; Kerkweg, A.; Lelieveld, J.

    2007-01-01

    The atmospheric-chemistry general circulation model ECHAM5/MESSy1 is evaluated with observations of different organic ozone precursors. This study continues a prior analysis which focused primarily on the representation of atmospheric dynamics and ozone. We use the results of the same reference simulation and apply a statistical analysis using data from numerous field campaigns. The results serve as a basis for future improvements of the model system. ECHAM5/MESSy1 generally reproduces the spatial distribution and the seasonal cycle of carbon monoxide (CO) very well. However, for the background in the northern hemisphere we obtain a negative bias (mainly due to an underestimation of emissions from fossil fuel combustion), and in the high latitude southern hemisphere a yet unexplained positive bias. The model results agree well with observations of alkanes, whereas severe problems in the simulation of alkenes are present. For oxygenated compounds the results are ambiguous: The model results are in good agreement with observations of formaldehyde, but systematic biases are present for methanol and acetone. The discrepancies between the model results and the observations are explained (partly) by means of sensitivity studies.

  9. Simulating organic species with the global atmospheric chemistry general circulation model ECHAM5/MESSy1: a comparison of model results with observations

    NASA Astrophysics Data System (ADS)

    Pozzer, A.; Jöckel, P.; Tost, H.; Sander, R.; Ganzeveld, L.; Kerkweg, A.; Lelieveld, J.

    2007-05-01

    The atmospheric-chemistry general circulation model ECHAM5/MESSy1 is evaluated with observations of different organic ozone precursors. This study continues a prior analysis which focused primarily on the representation of atmospheric dynamics and ozone. We use the results of the same reference simulation and apply a statistical analysis using data from numerous field campaigns. The results serve as a basis for future improvements of the model system. ECHAM5/MESSy1 generally reproduces the spatial distribution and the seasonal cycle of carbon monoxide (CO) very well. However, for the background in the Northern Hemisphere we obtain a negative bias (mainly due to an underestimation of emissions from fossil fuel combustion), and in the high latitude Southern Hemisphere a yet unexplained positive bias. The model results agree well with observations of alkanes, whereas severe problems in the simulation of alkenes and isoprene are present. For oxygenated compounds the results are ambiguous: The model results are in good agreement with observations of formaldehyde, but systematic biases are present for methanol and acetone. The discrepancies between the model results and the observations are explained (partly) by means of sensitivity studies.

  10. 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.

  11. Comparison of lipid membrane-water partitioning with various organic solvent-water partitions of neutral species and ionic species: Uniqueness of cerasome as a model for the stratum corneum in partition processes.

    PubMed

    Zhang, Keda; Fahr, Alfred; Abraham, Michael H; Acree, William E; Tobin, Desmond J; Liu, Xiangli

    2015-10-15

    Lipid membrane-water partitions (e.g., immobilized artificial membrane systems where the lipid membrane is a neutral phospholipid monolayer bound to gel beads) were compared to various organic solvent-water partitions using linear free energy relationships. To this end, we also measured the retention factors of 36 compounds (including neutral and ionic species) from water to liposomes made up of 3-sn-phosphatidylcholine and 3-sn-phosphatidyl-l-serine (80:20, mol/mol), employing liposome electrokinetic chromatography in this work. The results show that lipid membranes exhibit a considerably different chemical environment from those of organic solvents. For both neutral species and ionic species, partitions into the more polar hydroxylic solvents are chemically closer to partition into the lipid membrane as compared to partitions into the less polar hydroxylic solvents and into aprotic solvents. This means that solutes partition into the polar parts of lipid membranes, regardless of whether they are charged or not. In addition, cerasome (i.e., liposome composed mainly of stratum corneum lipids) was compared with regular phospholipid liposomes as a possible model for human stratum corneum in partitions. It was found that the cerasome-water partition exhibits a better chemical similarity to skin permeation. This is probably due to the unique structures of ceramides that occur in cerasome and in the stratum corneum lipid domain. We further show that membranes in membrane-water partitions exhibit very different properties.

  12. 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.

  13. Ontogenetic comparisons of standard metabolism in three species of crocodilians

    PubMed Central

    Brien, Matthew L.; Tracy, Christopher R.; Manolis, S. Charlie; Webb, Grahame J. W.; Seymour, Roger S.; Christian, Keith A.

    2017-01-01

    Due in part to their large size, aggressive temperament, and difficulty in handling, there are few physiological studies of adult crocodilians in the literature. As a result, studies comparing individuals across an ontogenetic series and comparisons among species are also lacking. We addressed this gap in knowledge by measuring standard metabolic rates (SMR) of three species of crocodilians (Crocodylus porosus, C. johnsoni, and Alligator mississippiensis), and included individuals that ranged from 0.22 to 114 kg. Allometric scaling of SMR with body mass was similar among the species, but C. porosus had significantly higher SMR than did C. johnsoni or A. mississippiensis. Differences in SMR among species are potentially related to behavioural differences in levels of aggression; C. porosus are the most aggressive of the crocodilians measured, and have rates of standard metabolism that are approximately 36% higher at the grand mean body size than those measured for C. johnsoni or A. mississippiensis, which are among the least aggressive crocodilians. PMID:28182696

  14. 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.

  15. 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. ...

  16. Alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons.

    PubMed

    Lu, Jianguo; Peatman, Eric; Wang, Wenqi; Yang, Qing; Abernathy, Jason; Wang, Shaolin; Kucuktas, Huseyin; Liu, Zhanjiang

    2010-06-01

    Alternative splicing (AS) is a mechanism by which the coding diversity of the genome can be greatly increased. Rates of AS are known to vary according to the complexity of eukaryotic species potentially explaining the tremendous phenotypic diversity among species with similar numbers of coding genes. Little is known, however, about the nature or rate of AS in teleost fish. Here, we report the characteristics of AS in teleost fish and classification and frequency of five canonical AS types. We conducted both same-species and cross-species analysis utilizing the Genome Mapping and Alignment Program (GMAP) and an AS pipeline (ASpipe) to study AS in four genome-enabled species (Danio rerio, Oryzias latipes, Gasterosteus aculeatus, and Takifugu rubripes) and one species lacking a complete genome sequence, Ictalurus punctatus. AS frequency was lowest in the highly duplicated genome of zebrafish (17% of mapped genes). The compact genome of the pufferfish showed the highest occurrence of AS (approximately 43% of mapped genes). An inverse correlation between AS frequency and genome size was consistent across all analyzed species. Cross-species comparisons utilizing zebrafish as the reference genome allowed the identification of additional putative AS genes not revealed by zebrafish transcripts. Approximately, 50% of AS genes identified by same-species comparisons were shared among two or more species. A searchable website, the Teleost Alternative Splicing Database, was created to allow easy identification and visualization of AS transcripts in the studied teleost genomes. Our results and associated database should further our understanding of alternative splicing as an important functional and evolutionary mechanism in the genomes of teleost fish.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. Foehn diagnosis and model comparison

    NASA Astrophysics Data System (ADS)

    Duerr, B.; Sprenger, M.; Fuhrer, O.; Burri, K.; Gutermann, T.; Hächler, P.; Neururer, A.; Richner, H.; Werner, R.

    2010-09-01

    The «Alpine Research Group Foehn Rhine Valley - Lake Constance (AGF)» (Arbeitsgemeinschaft Föhnforschung Rheintal-Bodensee) is analysing meteorological parameters and investigating foehn phenomena in the Rhine valley since 1971. Their main goal is to find plausible criteria for reliable foehn forecasts and to deepen our understanding of foehn in the target area. The presentation will focus on two main topics: (a) application of a fully automated foehn diagnosis tool; and (b) comparison of model data (COSMO-2, COSMO-7, VERA, INCA) with measurements in our target area. With respect to (a), the foehn diagnosis tool is applied for different meteorological stations of the Swiss meteorological network (SMN). Although it always uses the same six criteria (relative humidity, wind sector, wind force, gale maximum, difference of potential temperature to SMN site Gütsch and wind sector Gütsch), empirical thresholds have to be determined for each site individually. In doing so, foehn can be objectively detected and automatically identified as such in the most cases. In the second part, referring to (b), the foehn case of the 8th December 2006 is considered. It brought high wind velocities as well as a unusually far-reaching foehn, which was observed even north of Lake Constance. The synoptic- to local-scale dynamics of this foehn case is presented in detail, and the further developments within the framework of COSMO-2 to a high spatial resolution of 2.2 km facilitates the comparison of model forecasts with surface measurements. This comparison will be carried out with several parameters such as wind force, potential temperature and air pressure. Furthermore, the forecasted temporal evolution of foehn will be compared to the foehn's beginning and end detected by the foehn diagnosis tool.

  2. New trends in species distribution modelling

    USGS Publications Warehouse

    Zimmermann, Niklaus E.; Edwards, Thomas C.; 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.

  3. 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

  4. 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

  5. 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.

  6. Provisional Models for Endangered Species Pesticide Assessments

    EPA Pesticide Factsheets

    The tools and models on this web page were developed for use in the Steps 1 and 2 analyses of national level assessments of the risks of chlorpyrifos, diazinon and malathion to endangered and threatened species and designated critical habitat.

  7. Can mechanism inform species' distribution models?

    PubMed

    Buckley, Lauren B; Urban, Mark C; Angilletta, Michael J; Crozier, Lisa G; Rissler, Leslie J; Sears, Michael W

    2010-08-01

    Two major approaches address the need to predict species distributions in response to environmental changes. Correlative models estimate parameters phenomenologically by relating current distributions to environmental conditions. By contrast, mechanistic models incorporate explicit relationships between environmental conditions and organismal performance, estimated independently of current distributions. Mechanistic approaches include models that translate environmental conditions into biologically relevant metrics (e.g. potential duration of activity), models that capture environmental sensitivities of survivorship and fecundity, and models that use energetics to link environmental conditions and demography. We compared how two correlative and three mechanistic models predicted the ranges of two species: a skipper butterfly (Atalopedes campestris) and a fence lizard (Sceloporus undulatus). Correlative and mechanistic models performed similarly in predicting current distributions, but mechanistic models predicted larger range shifts in response to climate change. Although mechanistic models theoretically should provide more accurate distribution predictions, there is much potential for improving their flexibility and performance.

  8. 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

  9. 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

  10. 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…

  11. Incorporating uncertainty in predictive species distribution modelling.

    PubMed

    Beale, Colin M; Lennon, Jack J

    2012-01-19

    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.

  12. Modeling species invasions in Ecopath with Ecosim: an evaluation using Laurentian Great Lakes models

    USGS Publications Warehouse

    Langseth, Brian J.; Rogers, Mark; Zhang, Hongyan

    2012-01-01

    Invasive species affect the structure and processes of ecosystems they invade. Invasive species have been particularly relevant to the Laurentian Great Lakes, where they have played a part in both historical and recent changes to Great Lakes food webs and the fisheries supported therein. There is increased interest in understanding the effects of ecosystem changes on fisheries within the Great Lakes, and ecosystem models provide an essential tool from which this understanding can take place. A commonly used model for exploring fisheries management questions within an ecosystem context is the Ecopath with Ecosim (EwE) modeling software. Incorporating invasive species into EwE models is a challenging process, and descriptions and comparisons of methods for modeling species invasions are lacking. We compared four methods for incorporating invasive species into EwE models for both Lake Huron and Lake Michigan based on the ability of each to reproduce patterns in observed data time series. The methods differed in whether invasive species biomass was forced in the model, the initial level of invasive species biomass at the beginning of time dynamic simulations, and the approach to cause invasive species biomass to increase at the time of invasion. The overall process of species invasion could be reproduced by all methods, but fits to observed time series varied among the methods and models considered. We recommend forcing invasive species biomass when model objectives are to understand ecosystem impacts in the past and when time series of invasive species biomass are available. Among methods where invasive species time series were not forced, mediating the strength of predator–prey interactions performed best for the Lake Huron model, but worse for the Lake Michigan model. Starting invasive species biomass at high values and then artificially removing biomass until the time of invasion performed well for both models, but was more complex than starting invasive species

  13. 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

  14. Connexin36 Expression in the Mammalian Retina: A Multiple-Species Comparison

    PubMed Central

    Kovács-Öller, Tamás; Debertin, Gábor; Balogh, Márton; Ganczer, Alma; Orbán, József; Nyitrai, Miklós; Balogh, Lajos; Kántor, Orsolya; Völgyi, Béla

    2017-01-01

    Much knowledge about interconnection of human retinal neurons is inferred from results on animal models. Likewise, there is a lack of information on human retinal electrical synapses/gap junctions (GJ). Connexin36 (Cx36) forms GJs in both the inner and outer plexiform layers (IPL and OPL) in most species including humans. However, a comparison of Cx36 GJ distribution in retinas of humans and popular animal models has not been presented. To this end a multiple-species comparison was performed in retinas of 12 mammals including humans to survey the Cx36 distribution. Areas of retinal specializations were avoided (e.g., fovea, visual streak, area centralis), thus observed Cx36 distribution differences were not attributed to these species-specific architecture of central retinal areas. Cx36 was expressed in both synaptic layers in all examined retinas. Cx36 plaques displayed an inhomogenous IPL distribution favoring the ON sublamina, however, this feature was more pronounced in the human, swine and guinea pig while it was less obvious in the rabbit, squirrel monkey, and ferret retinas. In contrast to the relative conservative Cx36 distribution in the IPL, the labels in the OPL varied considerably among mammals. In general, OPL plaques were rare and rather small in rod dominant carnivores and rodents, whereas the human and the cone rich guinea pig retinas displayed robust Cx36 labels. This survey presented that the human retina displayed two characteristic features, a pronounced ON dominance of Cx36 plaques in the IPL and prevalent Cx36 plaque conglomerates in the OPL. While many species showed either of these features, only the guinea pig retina shared both. The observed similarities and subtle differences in Cx36 plaque distribution across mammals do not correspond to evolutionary distances but may reflect accomodation to lifestyles of examined species. PMID:28337128

  15. 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 ...

  16. Mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes

    PubMed Central

    2012-01-01

    Background The sizes of proteins are relevant to their biochemical structure and for their biological function. The statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes. Results Using the full genomic sequences of over 1,302 prokaryotic and 140 eukaryotic species two datasets containing 1.2 and 6.1 million proteins were generated and analyzed statistically. The lengthwise distribution of proteins can be roughly described with a gamma type or log-normal model, depending on the species. However the shape parameter of the gamma model has not a fixed value of 2, as previously suggested, but varies between 1.5 and 3 in different species. A gamma model with unrestricted shape parameter described best the distributions in ~48% of the species, whereas the log-normal distribution described better the observed protein sizes in 42% of the species. The gamma restricted function and the sum of exponentials distribution had a better fitting in only ~5% of the species. Eukaryotic proteins have an average size of 472 aa, whereas bacterial (320 aa) and archaeal (283 aa) proteins are significantly smaller (33-40% on average). Average protein sizes in different phylogenetic groups were: Alveolata (628 aa), Amoebozoa (533 aa), Fornicata (543 aa), Placozoa (453 aa), Eumetazoa (486 aa), Fungi (487 aa), Stramenopila (486 aa), Viridiplantae (392 aa). Amino acid composition is biased according to protein size. Protein length correlated negatively with %C, %M, %K, %F, %R, %W, %Y and positively with %D, %E, %Q, %S and %T. Prokaryotic proteins had a different protein size bias for %E, %G, %K and %M as compared to eukaryotes. Conclusions Mathematical modeling of protein length empirical distributions can be used to asses the quality of small ORFs annotation in genomic releases (detection of too many false positive small ORFs). There is a negative correlation between average protein size and total number of proteins among

  17. 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.

  18. 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.

  19. 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

  20. Quantifying errors in trace species transport modeling

    PubMed Central

    Prather, Michael J.; Zhu, Xin; Strahan, Susan E.; Steenrod, Stephen D.; Rodriguez, Jose M.

    2008-01-01

    One expectation when computationally solving an Earth system model is that a correct answer exists, that with adequate physical approximations and numerical methods our solutions will converge to that single answer. With such hubris, we performed a controlled numerical test of the atmospheric transport of CO2 using 2 models known for accurate transport of trace species. Resulting differences were unexpectedly large, indicating that in some cases, scientific conclusions may err because of lack of knowledge of the numerical errors in tracer transport models. By doubling the resolution, thereby reducing numerical error, both models show some convergence to the same answer. Now, under realistic conditions, we identify a practical approach for finding the correct answer and thus quantifying the advection error. PMID:19066224

  1. 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...

  2. Dry deposition fluxes and deposition velocities of seven trace metal species at five sites in central Taiwan - a summary of surrogate surface measurements and a comparison with model estimations

    NASA Astrophysics Data System (ADS)

    Zhang, L.; Fang, G. C.; Liu, C. K.; Huang, Y. L.; Huang, J. H.; Huang, C. S.

    2012-04-01

    Daily air concentrations and dry deposition fluxes of seven metal species were monitored at five sites in central Taiwan for five or six days every month from September 2009 to August 2010. Annual average concentrations at the five sites were in the range of 2.8 to 3.6 ng m-3 for As, 25 to 82 ng m-3 for Mn, 1900 to 2800 ng m-3 for Fe, 69 to 109 ng m-3 for Zn, 18 to 33 ng m-3 for Cr, 60 to 110 ng m-3 for Cu, and 25 to 40 ng m-3 for Pb. Annual average dry deposition fluxes were on the order of 3, 20, 400, 50, 25, 50, and 50 μg m-2 day-1 for As, Mn, Fe, Zn, Cr, Cu, and Pb, respectively. Annual average dry deposition velocities (Vd) for the seven metal species ranged from 0.18 to 2.22 cm s-1 at these locations. Small seasonal and geographical variations, e.g. from a few percent to a factor of 2 for different species and/or at different locations, were found in the measured concentrations, fluxes, and Vds. The measured fluxes and air concentrations had moderate to good correlations for several of the species at several of the sites (e.g. Fe, Zn, and Mn at most of the sites), but had either weak or no correlations for the other species or at the other sites (e.g. As at Sites I and III, Zn and Cr at Site IV, and Cu at most of the sites). The latter cases were believed to have large uncertainties in the flux measurements using surrogate surfaces. Sensitivity tests were conducted for particle Vds using a size-segregated particle dry deposition model, assuming various combinations of three lognormal size distributions representing fine particles (PM2.5), coarse particles (PM2.5-10), and super-sized particles (PM10+), respectively. It was found that the measured dry deposition fluxes can be reproduced reasonably well using the size-segregated particle dry deposition model if the mass fractions of the metal species in PM2.5, PM2.5-10 and PM10+ were known. Significant correlations between the modeled and the measured daily fluxes were found for those cases that were believed

  3. 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.

  4. 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

  5. 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.

  6. Comparison of chitin structures isolated from seven Orthoptera species.

    PubMed

    Kaya, Murat; Erdogan, Sevil; Mol, Abbas; Baran, Talat

    2015-01-01

    Differences in the physichochemical properties of the chitin structure of the exoskeleton of seven species from four genera were investigated in this study. The same method was used to isolate the chitin structure of the seven species. The physicochemical properties of the isolated chitins were revealed by ESEM, FTIR, TGA and XRD analyses. The FTIR, TGA and XRD results from the chitin samples were similar. The surface morphologies of the chitins were investigated by ESEM and interesting results were noted. While the surface morphologies of the chitins isolated from two species within the same genus were quite different, the surface morphologies of chitins isolated from species belonging to different genera showed similarity. It was determined that the dry weight chitin contents of the grasshopper species varied between 5.3% and 8.9%. The results of molecular analysis showed that the chitins from seven Orthoptera species (between 5.2 and 6.8 kDa) have low molecular weights. Considering that these invasive and harmful species are killed with insecticides and go to waste in large amounts, this study suggests that they should be collected and evaluated as an alternative chitin source.

  7. 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.

  8. 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.

  9. Habitat classification: A comparison using avian species and guilds

    NASA Astrophysics Data System (ADS)

    Degraaf, Richard M.; Chadwick, Nan L.

    1984-11-01

    Results of breeding bird censuses in 1979 and 1980 were used to compare the relationships of both species and guilds to forest habitats in the White Mountains of New Hampshire. Several age classes of 11 forest cover types were studied: northern hard-woods ( Fagus-Betula-Acer), spruce ( Picea), spruce-fir ( Picea-Abies), birth ( Betula), swamp hardwoods ( Acer-Pinus-Tsuga), pine ( Pinus strobus and P. resinosa), balsam fir ( Abies), aspen ( Populus tremuloides and P. grandidentata), northern red oak ( Quercus), oak-pine ( Quercus-Pinus), and hemlock ( Tsuga). All types were even-aged; only northern hardwoods had an additional uneven-aged condition. Forest cover types were also pooled to consider generalized habitats: hardwoods, mixed forest, or softwoods. Results of ordinations based on censuses of 74 bird species indicate that foraging guilds are more related to general cover types than are nesting substrate guilds, but bird species reflect habitat differences to a greater degree than do either guild scheme. Also, considerable overlap occurs in bird species distribution between hardwoods and mixed forests; softwoods show little overlap with other types. Discriminant function and classification analyses revealed that bird species composition can be used to correctly classify general forest habitats more accurately (83.8%) than either foraging (63.2%) or nesting substrate guilds (58.4%). These results indicate that, of the habitats studied, avian species compositions are more characteristic than are foraging or nesting substrate guild composition, which tend to be similar across forest habitats.

  10. Inner Radiation Belt Data / Model Comparisons

    NASA Astrophysics Data System (ADS)

    Guild, Timothy; O'Brien, Paul; Selesnick, Richard

    We present detailed comparisons of a time-dependent inner radiation belt model with proton observations made by a variety of in-situ spacecraft during solar cycle 23. The recently-developed model (Selesnick et al., 2007) computes proton intensities as a function of time and of the three adiabatic invariants in the inner belt, which we convert to the observable count rate at the location of the satellite by using a nominal instrument response function. These comparisons and initial data-assimilation efforts suggest that the model performance can be improved especially during intervals containing unmodeled processes such as trapped proton losses during geomagnetic storms.

  11. Inner Radiation Belt Data / Model Comparisons

    NASA Astrophysics Data System (ADS)

    Guild, T. B.; O'Brien, T. P.; Selesnick, R.; Looper, M.

    2008-12-01

    We present detailed comparisons of a time-dependent inner radiation belt model with in-situ proton observations made by a variety of spacecraft during solar cycle 23. The recently-developed model (Selesnick et al., 2007) computes proton intensities as a function of time and of the three adiabatic invariants in the inner belt, which we convert to the observable count rate in a detector at the location of the satellite by using instrument response functions. These comparisons and initial data-assimilation efforts suggest that the model performance can be improved especially during injections of solar protons, and at L-shells above 2.

  12. Comparison of cytotoxic activities of extracts from Selaginella species

    PubMed Central

    Li, Juan; Lei, Xiang; Chen, Ke-li

    2014-01-01

    Background: Selaginella species are resurrection plants, which are known, possess various molecular bioactivities depending on species, but only a few species have been detailed observe in the advanced research. Objective: The objective of the following study is to compare the chemical profiles of different species of Selaginella and to investigate cytotoxicity and induction of apoptosis activities of some species of Selaginella. Materials and Methods: The high-performance liquid chromatography (HPLC) method was developed for chemical analysis. Ethyl acetate, ethanol and water-soluble extracts from seven Selaginella species were submitted to 3-(4,5-dimenthyl thizol-2-yl)-2,5-diphenyl tetrazolium bromide assay, flow cytometry, deoxyribonucleic acid (DNA) laddering analysis and caspase-3 expression using Bel-7402, HT-29 and HeLa cells. Results: The HPLC analysis revealed two major common peaks, which were identified as amentoflavone and robustaflavone and another three main peaks in their chromatograms. The results showed that S. labordei, Selaginella tamariscina and Selaginella uncinata had relatively stronger activities on Bel-7402 and HeLa cells and Selaginella moellendorfii had moderate antiproliferation activities, but Selaginella remotifolia and Selaginella pulvinata had almost no inhibitory activities. The main active components were in the ethyl acetate extracts which had abundant biflavonoids. The effects of these extracts on cell proliferation and apoptosis in different cells were not the same, they were more apparent on HeLa cells than on HT-29 cells. The assay of DNA laddering analysis and caspase-3 expression further confirmed that inducing cell apoptosis was one of antitumor mechanisms and antitumor activities of Selaginella species were related to apoptosis induced by caspase family. Conclusion: S. labordei, S. tamariscina and S. uncinata would be potential antitumor agents. PMID:25422557

  13. Comparison of budburst dynamics between species on altitudinal gradient

    NASA Astrophysics Data System (ADS)

    Davi, H.; Gillmann, M.; Ibanez, T.

    2009-04-01

    Phenology of plants is a key ecosystem parameter controlling carbon and water fluxes and also acting on the dynamics of communities. This parameter is highly sensitive to the climate and consequently is often used as a proxy of global change. In this paper, we attempt to analyse the dynamics of budburst every week for seven species (Fagus sylvatica L., Acer opalus Mill , Sorbus aria L., Quercus pubescens Willd. Abies alba Mill., Pinus sylvestris L., Pinus nigra Arnold) in two altitudinal gradients, one in a northern slope and one in a southern slope in the Ventoux mountain. The originality of this work is to assess not only the budburst date but to more precisely analyse the dynamics of budburst and its variation with altitude according to the species. Two important results are highlighted. First, the dynamics of budburst changes according to the species. Three distinct patterns can be drawn, a rapid sigmoid increase for the deciduous species, a short sigmoid increase for the pines and an intermediate curve for silver fir. These dynamics can be slowing down for coniferous when frost arises during the budburst. The second topic is the link between budburst and temperature by analysing respectively the year, the altitudinal and the aspect (north and south) effects. In 2007, budburst occurs earlier for Fagus, Acer, and Abies, it does not change for pines and is delayed for Sorbus. Date of beech budburst is the same between north and south in spite of higher temperature in south. The altitude effect on budburst varies greatly according to species and the year with a weak effect on Fagus and a stronger effect for the others species showing a threshold at 1200 m. By analysing the mean of temperatures at each altitude, we conclude that temperature effect acts differently between years or between altitudes. To conclude, we highlighted the complex effect of temperatures on budburst varying between species and situations.

  14. Comparison of mammalian mitochondrial ribosomal ribonucleic acid from different species.

    PubMed

    Mitra, R S; Bartoov, B; Monahan, J; Freeman, K B

    1972-08-01

    Mitochondrial ribosomal RNA species from mouse L cells, rat liver, rat hepatoma, hamster BHK-21 cells and human KB cells were examined by electrophoresis on polyacrylamide-agarose gels and sedimentation in sucrose density gradients. The S(E) (electrophoretic mobility) and S values of mitochondrial rRNA of all species were highly dependent on temperature and ionic strength of the medium; the S(E) values increased and the S values decreased with an increase in temperature at a low ionic strength. At an ionic strength of 0.3 at 23-25 degrees C or an ionic strength of 0.01 at 3-4 degrees C the S and S(E) values were almost the same being about 16.2-18.0 and 12.3-13.6 for human and mouse mitochondrial rRNA. The molecular weights under these conditions were calculated to be 3.8x10(5)-4.3x10(5) and 5.9x10(5)-6.8x10(5), depending on the technique used. At 25 degrees C in buffers of low ionic strength mouse mitochondrial rRNA species had a lower electrophoretic mobility than those of human and hamster. Under these conditions the smaller mitochondrial rRNA species of hamster had a lower electrophoretic mobility than that of human but the larger component had an identical mobility. Mouse and rat mitochondrial rRNA species had identical electrophoretic mobilities. Complex differences between human and mouse mitochondrial rRNA species were observed on sedimentation in sucrose density gradients under various conditions of temperature and ionic strength. Mouse L-cell mitochondrial rRNA was eluted after cytoplasmic rRNA on a column of methylated albumin-kieselguhr.

  15. 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.

  16. 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...

  17. Are all Linear Paired Comparison Models Equivalent

    DTIC Science & Technology

    1990-09-01

    Previous authors (Jackson and Fleckenstein 1957, Mosteller 1958, Noether 1960) have found that different models of paired comparisons data lead to simi...ponential distribution with a location parameter (Mosteller 1958, Noether 1960). Formal statements describing the limiting behavior of the gamma...that are not convolu- tion type linear models (the uniform model considered by Smith (1956), Mosteller (1958), Noether (1960)) and other convolution

  18. 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…

  19. 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.

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

    USGS Publications Warehouse

    Edwards, T.C.; 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.

  1. Place versus response learning in fish: a comparison between species.

    PubMed

    McAroe, Claire L; Craig, Cathy M; Holland, Richard A

    2016-01-01

    Place learning is thought to be an adaptive and flexible facet of navigation. Due to the flexibility of this learning, it is thought to be more complex than the simpler strategies such as learning a particular route or navigating through the use of cues. Place learning is crucial in a familiar environment as it allows an individual to successfully navigate to the same endpoint, regardless of where in the environment the journey begins. Much of the research to date focusing on different strategies employed for navigation has used human subjects or other mammals such as rodents. In this series of experiments, the spatial memory of four different species of fish (goldfish, killifish, zebrafish and Siamese fighting fish) was analysed using a plus maze set-up. Results suggest that three of the species showed a significant preference for the adoption of a place strategy during this task, whereas zebrafish showed no significant preference. Furthermore, zebrafish took significantly longer to learn the task than the other species. Finally, results suggest that zebrafish took the least amount of time (seconds) to complete trials both during training and probe.

  2. 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

  3. 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

  4. Comparison of ciliature microtubule organelles in three hypotrichous ciliate species

    NASA Astrophysics Data System (ADS)

    Li, Yisong; Shi, Lei; Gu, Fukang

    2010-05-01

    We examined the structure and spatial organization of ciliature base-associated microtubules (BAM) in three hypotrichous ciliates ( Stylonychia mytilus, Pseudourostyla cristata, Euplotes woodruffi) in fluorescence microscopy. The results revealed that BAM, including the anterior (ALM), posterior longitudinal microtubule (PLM) and the transverse microtubule (TM) bands, are composed of tubulin. The respective microtubular bands have cytoplasmic polarization patterns that are significantly asymmetric. The BAM of the midventral files in P. cristata appear cord-shaped compared with the ALM bands of transverse cirri in both S. mytilus and E. woodruffi, which extend to the left anterior side of the cell before converging. The TM bands of the left marginal cirri (MC) in S. mytilus extend to the right side of the cell, while those of the right MC bands extend to the left. Our observations suggest that BAM traits are common in hypotrichous ciliates even though different species possess different microtubule arrangements related to the conserved cirral morphogenetic patterns in the respective species. The differing development of BAM in the three ciliate suggests that the microtubules may be conserved in different hypotrichs. We have also demonstrated that the BAM, which appear polar and asymmetric, are localized in specific cytoskeletal positions and extend in different orientations within the cortex to connect with other ciliature-associated structures and, thus, strengthen the cortex. These BAM features indicate that they are directly associated with cell motion.

  5. Thermal sensation models: a systematic comparison.

    PubMed

    Koelblen, B; Psikuta, A; Bogdan, A; Annaheim, S; Rossi, R M

    2016-08-26

    Thermal sensation models, capable of predicting human's perception of thermal surroundings, are commonly used to assess given indoor conditions. These models differ in many aspects, such as the number and type of input conditions, the range of conditions in which the models can be applied, and the complexity of equations. Moreover, the models are associated with various thermal sensation scales. In this study, a systematic comparison of seven existing thermal sensation models has been performed with regard to exposures including various air temperatures, clothing thermal insulation, and metabolic rate values after a careful investigation of the models' range of applicability. Thermo-physiological data needed as input for some of the models were obtained from a mathematical model for human physiological responses. The comparison showed differences between models' predictions for the analyzed conditions, mostly higher than typical intersubject differences in votes. Therefore, it can be concluded that the choice of model strongly influences the assessment of indoor spaces. The issue of comparing different thermal sensation scales has also been discussed.

  6. Quantitative comparison of cardiac ventricular myocyte electrophysiology and response to drugs in human and nonhuman species.

    PubMed

    O'Hara, Thomas; Rudy, Yoram

    2012-03-01

    Explanations for arrhythmia mechanisms at the cellular level are usually based on experiments in nonhuman myocytes. However, subtle electrophysiological differences between species may lead to different rhythmic or arrhythmic cellular behaviors and drug response given the nonlinear and highly interactive cellular system. Using detailed and quantitatively accurate mathematical models for human, dog, and guinea pig ventricular action potentials (APs), we simulated and compared cell electrophysiology mechanisms and response to drugs. Under basal conditions (absence of β-adrenergic stimulation), Na(+)/K(+)-ATPase changes secondary to Na(+) accumulation determined AP rate dependence for human and dog but not for guinea pig where slow delayed rectifier current (I(Ks)) was the major rate-dependent current. AP prolongation with reduction of rapid delayed rectifier current (I(Kr)) and I(Ks) (due to mutations or drugs) showed strong species dependence in simulations, as in experiments. For humans, AP prolongation was 80% following I(Kr) block. It was 30% for dog and 20% for guinea pig. Under basal conditions, I(Ks) block was of no consequence for human and dog, but for guinea pig, AP prolongation after I(Ks) block was severe. However, with β-adrenergic stimulation, I(Ks) played an important role in all species, particularly in AP shortening at fast rate. Quantitative comparison of AP repolarization, rate-dependence mechanisms, and drug response in human, dog, and guinea pig revealed major species differences (e.g., susceptibility to arrhythmogenic early afterdepolarizations). Extrapolation from animal to human electrophysiology and drug response requires great caution.

  7. Landscape-based spatially explicit species index models for everglades restoration

    USGS Publications Warehouse

    Curnutt, J.L.; Comiskey, J.; Nott, M.P.; Gross, L.J.

    2000-01-01

    As part of the effort to restore the ???10 000-km2 Everglades drainage in southern Florida, USA, we developed spatially explicit species index (SESI) models of a number of species and species groups. In this paper we describe the methodology and results of three such models: those for the Cape Sable Seaside Sparrow and the Snail Kite, and the species group model of long-legged wading birds. SESI models are designed to produce relative comparisons of one management alternative to a base scenario or to another alternative. The model outputs do not provide an exact quantitative prediction of future biotic group responses, but rather, when applying the same input data and different hydrologic plans, the models provide the best available means to compare the relative response of the biotic groups. We compared four alternative hydrologic management scenarios to a base scenario (i.e., predicted conditions assuming that current water management practices continue). We ranked the results of the comparisons for each set of models. No one scenario was beneficial to all species; however, they provide a uniform assessment, based on the best available observational information, of relative species responses to alternative water-management plans. As such, these models were used extensively in the restoration planning.

  8. Comparison of essential oils from Cistus species growing in Sardinia.

    PubMed

    Mastino, Patrizia Monica; Marchetti, Mauro; Costa, Jean; Usai, Marianna

    2017-02-01

    Cistus genus is present in Sardinia with large populations of C. monspeliensis, C. salvifolius, C. creticus subsp. eriocephalus and few stations of C. albidus, C. creticus subsp. creticus and C. creticus subsp. corsicus. No chemical studies are currently being carried on Cistus species of Sardinia. The essential oils have shown six different profiles. C. creticus subsp. eriocephalus showed a high amount of manoyl oxide and its isomer (70%). C. salvifolius has pointed out the group of labdans, (20%); another consistent percentage is made of perfumed molecules as ionone and its derivate. Several linear hydrocarbons were produced by C. monspeliensis, and the heneicosane was the most represented element. In C. albidus no labdane-type diterpenes were identified. Analysis of C. creticus subsp creticus revealed several oxygenated sesquiterpenes and labdane-type diterpenes, especially manoyl oxide. C. creticus subsp. corsicus was qualitatively very similar to C. creticus subsp. creticus, notably concerning the labdane-type compounds.

  9. Comparison and evolution of the lagena in various animal species.

    PubMed

    Harada, Y; Kasuga, S; Tamura, S

    2001-04-01

    The structure of the vestibular organs of the teleost fish (bluegill), newts (Japanese fire-belly newt), frogs (black-spotted pond frog), snapping turtles and birds (chicks) was morphologically compared, with particular attention to the lagena macula, and the differences between animal species with relation to evolution were considered. Teleost fish had no striola on the lagena macula. The striola of newts were short and restricted to the central area of the macula, but those of frogs, snapping turtles and chicks extended from the anterior to posterior edges of the macula. This indicates that the frog is more highly evolved than the newt. The length of the kinocilium of sensory hairs was equal to that of the longest stereocilium in teleost fish and newts, but the kinocilia of frogs, snapping turtles and chicks were longer than the longest stereocilium. This indicates that the function of the lagena of teleost fish and newts is for hearing whilst in the other animals they are for posture. The diameter of the sensory hair bundles is small in teleost fish and frogs, but large in newts and snapping turtles. This indicates that the sensitivity of the sensory cells of the lagena towards outer force is low in teleost fish and frogs, high in newts and snapping turtles and intermediate in birds. The lagena of snapping turtles protrudes from the basilar papilla into the vestibule but the lagena of chicks lies on the tip of the long projecting basilar papilla. From observation of the locations of lagenae it is natural to speculate that there must have been some species of animal now extinct that had the evolving location of the lagena prior to that of chicks. In future it will be very interesting and useful to identify this extinct animal using DNA techniques.

  10. Estimating species richness and accumulation by modeling species occurrence and detectability

    USGS Publications Warehouse

    Dorazio, R.M.; Royle, J. Andrew; Soderstrom, B.; Glimskarc, A.

    2006-01-01

    A statistical model is developed for estimating species richness and accumulation by formulating these community-level attributes as functions of model-based estimators of species occurrence while accounting for imperfect detection of individual species. The model requires a sampling protocol wherein repeated observations are made at a collection of sample locations selected to be representative of the community. This temporal replication provides the data needed to resolve the ambiguity between species absence and nondetection when species are unobserved at sample locations. Estimates of species richness and accumulation are computed for two communities, an avian community and a butterfly community. Our model-based estimates suggest that detection failures in many bird species were attributed to low rates of occurrence, as opposed to simply low rates of detection. We estimate that the avian community contains a substantial number of uncommon species and that species richness greatly exceeds the number of species actually observed in the sample. In fact, predictions of species accumulation suggest that even doubling the number of sample locations would not have revealed all of the species in the community. In contrast, our analysis of the butterfly community suggests that many species are relatively common and that the estimated richness of species in the community is nearly equal to the number of species actually detected in the sample. Our predictions of species accumulation suggest that the number of sample locations actually used in the butterfly survey could have been cut in half and the asymptotic richness of species still would have been attained. Our approach of developing occurrence-based summaries of communities while allowing for imperfect detection of species is broadly applicable and should prove useful in the design and analysis of surveys of biodiversity.

  11. 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.

  12. Factorial Comparison of Working Memory Models

    PubMed Central

    van den Berg, Ronald; Awh, Edward; Ma, Wei Ji

    2014-01-01

    Three questions have been prominent in the study of visual working memory limitations: (a) What is the nature of mnemonic precision (e.g., quantized or continuous)? (b) How many items are remembered? (c) To what extent do spatial binding errors account for working memory failures? Modeling studies have typically focused on comparing possible answers to a single one of these questions, even though the result of such a comparison might depend on the assumed answers to both others. Here, we consider every possible combination of previously proposed answers to the individual questions. Each model is then a point in a 3-factor model space containing a total of 32 models, of which only 6 have been tested previously. We compare all models on data from 10 delayed-estimation experiments from 6 laboratories (for a total of 164 subjects and 131,452 trials). Consistently across experiments, we find that (a) mnemonic precision is not quantized but continuous and not equal but variable across items and trials; (b) the number of remembered items is likely to be variable across trials, with a mean of 6.4 in the best model (median across subjects); (c) spatial binding errors occur but explain only a small fraction of responses (16.5% at set size 8 in the best model). We find strong evidence against all 6 documented models. Our results demonstrate the value of factorial model comparison in working memory. PMID:24490791

  13. 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

  14. 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.…

  15. 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

  16. 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

  17. Sustainability in single-species population models

    PubMed Central

    Quinn, Terrance J.; Collie, Jeremy S.

    2005-01-01

    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, FMSY, which results in MSY, and a higher value, Fext, for which the population is eventually driven to extinction. For each F between 0 and Fext, 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 viewpoint 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 FMSY (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 preserving

  18. Do Stacked Species Distribution Models Reflect Altitudinal Diversity Patterns?

    PubMed Central

    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

  19. Dissolution Model of Multiple Species: Leaching of Highly Soluble Minerals

    NASA Astrophysics Data System (ADS)

    Moreno, Luis; Ordóñez, Javier I.; Cisternas, Luis A.

    2017-03-01

    Dissolution of multi-species from a solid matrix is widely extended in different processes such as leaching of minerals; however, its modeling is often focused on a single species. A model for the simultaneous dissolution of soluble species was developed, which considers different solubilities and dissolution rates and considers that particle collapses when the rapidly soluble species is depleted. The collapsed matter is formed by inert material and a fraction of the soluble species with lower dissolution rate that has not dissolved yet. The model is applied to the leaching of a water-soluble mineral (caliche) with two soluble species dissolving simultaneously with different rates. Measured outlet concentrations of nitrate and magnesium were used to validate the model. Results showed that the model reproduced adequately the leaching of species with rapid and intermediate dissolution rate. Effect of the operating and kinetic parameters on the leaching process is also shown using the actual conditions of heap leaching for caliche mineral.

  20. 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.

  1. Toxicity Comparison of Eight Repellents Against Four Species of Female Mosquitoes

    DTIC Science & Technology

    2009-01-01

    TOXICITY COMPARISON OF EIGHT REPELLENTS AGAINST FOUR SPECIES OF FEMALE MOSQUITOES JULIA W. PRIDGEON, ULRICH R. BERNIER AND JAMES J. BECNEL Center for...repellents (DMP, Rutgers 612, DEET, IR3535, Picardin, PMD, AI3-35765, and AI3-37220) were evaluated by topical application against females of Aedes aegypti...repellent toxicity, topical application INTRODUCTION Females of the mosquito species Aedes aegypti (L.) transmit viral pathogens to humans, resulting in

  2. Mid-Piacenzian Data-Model Comparison

    NASA Astrophysics Data System (ADS)

    Dowsett, Harry; Robinson, Marci; Haywood, Alan; Valdes, Paul; Salzmann, Ulrich; Hill, Dan; Foley, Kevin; Williams, Mark

    2010-05-01

    The Pliocene Research, Interpretation and Synoptic Mapping (PRISM) Project aims to accurately and comprehensively reconstruct and understand mid-Pliocene climate conditions in order to gain insight into a warmer than present world that may resemble a future climate. PRISM has demonstrated a sustained and dedicated commitment to provide the paleoclimate modeling community with a mid-Piacenzian paleoenvironmental reconstruction of important boundary conditions for use in model initialization and verification. PRISM is presently in its fourth phase as reconstructions are constantly improved, refined and updated to meet this unique goal. A summary of the development of the PRISM data set will be presented. In this presentation we compare the PRISM3D reconstruction to the HadCM3 coupled ocean atmosphere model simulation of mid-Piacenzian climate. While there is overall agreement between data and model, several regions can be highlighted where disagreement is significant and requires further analysis. For example, high latitude warming shown by multiple proxies is not reflected to the same degree in model results. Low latitude warming shown by the model is still difficult to reconcile with faunal data, but the gap between the two results has diminished relative to previous data-model comparisons. The concept of a "permanent El Nino" while evident in mean conditions, is not reflected in further analyses of either model or data. With the recognition that future climate conditions near the end of this century may be somewhat similar to conditions during the mid-Piacenzian, the PRISM reconstruction, coupled with independent paleoclimate proxy data, represents a unique and invaluable tool for paleoclimate and future global change research. Similarly, data-model comparisons such as this one are integral to refining both the data-based reconstructions and the climate models themselves in order to improve confidence in model simulations.

  3. Effectiveness of Reptile Species Identification--A Comparison of a Dichotomous Key with an Identification Book

    ERIC Educational Resources Information Center

    Randler, Christoph; Zehender, Irene

    2006-01-01

    Species identification tasks are a prerequisite for an understanding of biodiversity. Here, we focused on different educational materials to foster the identification of six European reptile species. Our educational training unit was based on natural plastic models of six species and pupils either used an illustrated identification book or a…

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  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 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.

  10. Data for Room Fire Model Comparisons

    PubMed Central

    Peacock, Richard D.; Davis, Sanford; Babrauskas, Vytenis

    1991-01-01

    With the development of models to predict fire growth and spread in buildings, there has been a concomitant evolution in the measurement and analysis of experimental data in real-scale fires. This report presents the types of analyses that can be used to examine large-scale room fire test data to prepare the data for comparison with zone-based fire models. Five sets of experimental data which can be used to test the limits of a typical two-zone fire model are detailed. A standard set of nomenclature describing the geometry of the building and the quantities measured in each experiment is presented. Availability of ancillary data (such as smaller-scale test results) is included. These descriptions, along with the data (available in computer-readable form) should allow comparisons between the experiment and model predictions. The base of experimental data ranges in complexity from one room tests with individual furniture items to a series of tests conducted in a multiple story hotel equipped with a zoned smoke control system. PMID:28184121

  11. 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.

  12. Model selection and assessment for multi­-species occupancy models

    USGS Publications Warehouse

    Broms, Kristin M.; Hooten, Mevin B.; Fitzpatrick, Ryan M.

    2016-01-01

    While multi-species occupancy models (MSOMs) are emerging as a popular method for analyzing biodiversity data, formal checking and validation approaches for this class of models have lagged behind. Concurrent with the rise in application of MSOMs among ecologists, a quiet regime shift is occurring in Bayesian statistics where predictive model comparison approaches are experiencing a resurgence. Unlike single-species occupancy models that use integrated likelihoods, MSOMs are usually couched in a Bayesian framework and contain multiple levels. Standard model checking and selection methods are often unreliable in this setting and there is only limited guidance in the ecological literature for this class of models. We examined several different contemporary Bayesian hierarchical approaches for checking and validating MSOMs and applied these methods to a freshwater aquatic study system in Colorado, USA, to better understand the diversity and distributions of plains fishes. Our findings indicated distinct differences among model selection approaches, with cross-validation techniques performing the best in terms of prediction.

  13. 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...

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

    USGS Publications Warehouse

    Hahn, D. Caldwell; Hatfield, Jeffrey S.; Abdelnabi, Mahmoud A.; Wu, Julie M.; Igl, Lawrence D.; Ottinger, Mary 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.

  15. Historical Species Distribution Models Predict Species Limits in Western Plethodon Salamanders.

    PubMed

    Pelletier, Tara A; Crisafulli, Charlie; Wagner, Steve; Zellmer, Amanda J; Carstens, Bryan C

    2015-11-01

    Allopatry is commonly used to predict boundaries in species delimitation investigations under the assumption that currently allopatric distributions are indicative of reproductive isolation; however, species ranges are known to change over time. Incorporating a temporal perspective of geographic distributions should improve species delimitation; to explore this, we investigate three species of western Plethodon salamanders that have shifted their ranges since the end of the Pleistocene. We generate species distribution models (SDM) of the current range, hindcast these models onto a climatic model 21 Ka, and use three molecular approaches to delimit species in an integrated fashion. In contrast to expectations based on the current distribution, we detect no independent lineages in species with allopatric and patchy distributions (Plethodon vandykei and Plethodon larselli). The SDMs indicate that probable habitat is more expansive than their current range, especially during the last glacial maximum (LGM) (21 Ka). However, with a contiguous distribution, two independent lineages were detected in Plethodon idahoensis, possibly due to isolation in multiple glacial refugia. Results indicate that historical SDMs are a better predictor of species boundaries than current distributions, and strongly imply that researchers should incorporate SDM and hindcasting into their investigations and the development of species hypotheses.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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].

  2. Synteny of Prunus and other model plant species

    PubMed Central

    Jung, Sook; Jiwan, Derick; Cho, Ilhyung; Lee, Taein; Abbott, Albert; Sosinski, Bryon; Main, Dorrie

    2009-01-01

    Background Fragmentary conservation of synteny has been reported between map-anchored Prunus sequences and Arabidopsis. With the availability of genome sequence for fellow rosid I members Populus and Medicago, we analyzed the synteny between Prunus and the three model genomes. Eight Prunus BAC sequences and map-anchored Prunus sequences were used in the comparison. Results We found a well conserved synteny across the Prunus species – peach, plum, and apricot – and Populus using a set of homologous Prunus BACs. Conversely, we could not detect any synteny with Arabidopsis in this region. Other peach BACs also showed extensive synteny with Populus. The syntenic regions detected were up to 477 kb in Populus. Two syntenic regions between Arabidopsis and these BACs were much shorter, around 10 kb. We also found syntenic regions that are conserved between the Prunus BACs and Medicago. The array of synteny corresponded with the proposed whole genome duplication events in Populus and Medicago. Using map-anchored Prunus sequences, we detected many syntenic blocks with several gene pairs between Prunus and Populus or Arabidopsis. We observed a more complex network of synteny between Prunus-Arabidopsis, indicative of multiple genome duplication and subsequence gene loss in Arabidopsis. Conclusion Our result shows the striking microsynteny between the Prunus BACs and the genome of Populus and Medicago. In macrosynteny analysis, more distinct Prunus regions were syntenic to Populus than to Arabidopsis. PMID:19208249

  3. 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

  4. Vocal learning in Grey parrots: A brief review of perception, production, and cross-species comparisons.

    PubMed

    Pepperberg, Irene M

    2010-10-01

    This chapter briefly reviews what is known-and what remains to be understood-about Grey parrot vocal learning. I review Greys' physical capacities-issues of auditory perception and production-then discuss how these capacities are used in vocal learning and can be recruited for referential communication with humans. I discuss cross-species comparisons where applicable and conclude with a description of recent research that integrates issues of reference, production and perception.

  5. 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

  6. Some considerations on the use of ecological models to predict species' geographic distributions

    USGS Publications Warehouse

    Peterjohn, B.G.

    2001-01-01

    Peterson (2001) used Genetic Algorithm for Rule-set Prediction (GARP) models to predict distribution patterns from Breeding Bird Survey (BBS) data. Evaluations of these models should consider inherent limitations of BBS data: (1) BBS methods may not sample species and habitats equally; (2) using BBS data for both model development and testing may overlook poor fit of some models; and (3) BBS data may not provide the desired spatial resolution or capture temporal changes in species distributions. The predictive value of GARP models requires additional study, especially comparisons with distribution patterns from independent data sets. When employed at appropriate temporal and geographic scales, GARP models show considerable promise for conservation biology applications but provide limited inferences concerning processes responsible for the observed patterns.

  7. 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.

  8. 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…

  9. 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

  10. 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...

  11. The scaling of geographic ranges: implications for species distribution models

    USGS Publications Warehouse

    Yackulic, Charles B.; Ginsberg, Joshua R.

    2016-01-01

    There is a need for timely science to inform policy and management decisions; however, we must also strive to provide predictions that best reflect our understanding of ecological systems. Species distributions evolve through time and reflect responses to environmental conditions that are mediated through individual and population processes. Species distribution models that reflect this understanding, and explicitly model dynamics, are likely to give more accurate predictions.

  12. 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.

  13. 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.

  14. 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

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

    PubMed

    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 < 0.01), and targeted sampling did detect more species than nontargeted sampling with less

  16. Construction of analytically solvable models for interacting species. [biological species competition

    NASA Technical Reports Server (NTRS)

    Rosen, G.

    1976-01-01

    The basic form of a model representation for systems of n interacting biological species is a set of essentially nonlinear autonomous ordinary differential equations. A generic canonical expression for the rate functions in the equations is reported which permits the analytical general solution to be obtained by elementary computation. It is shown that a general analytical solution is directly obtainable for models where the rate functions are prescribed by the generic canonical expression from the outset. Some illustrative examples are given which demonstrate that the generic canonical expression can be used to construct analytically solvable models for two interacting species with limit-cycle dynamics as well as for a three-species interdependence.

  17. A comparison of populations of island and adjacent mainland species of Caribbean Selenops (Araneae: Selenopidae) spiders.

    PubMed

    Crews, Sarah C; Puente-Rolón, Alberto R; Rutstein, Elliot; Gillespie, Rosemary G

    2010-03-01

    The role of the landscape in structuring populations has been the focus of numerous studies, in particular, the extent to which islands provide opportunities for isolation, and the consistency of such an effect across lineages. The current study examines this phenomenon using a series of relatively widespread taxa, all within a single genus of spiders, Selenops. We focus on the Caribbean Islands and adjacent Mesoamerican mainland to examine how the islands per se dictate structure across lineages. We use molecular genetic data from mitochondrial and nuclear genes to examine the population structure of seven species of Selenops. Comparisons are made between species found in the Greater Antilles, Lesser Antilles, and adjacent mainland. Results indicate that geography has little effect on the population structure of mainland species. In contrast, population structure appears to be partitioned by island in the insular Caribbean. Within islands, the amount of population structure for each species is variable and may be dictated more by ecological or demographic parameters, rather than geographic location. The overall conclusion is that the extent to which a given lineage is structured is highly variable across species, with this variability overwhelming any general signal of geographical isolation.

  18. Null model analysis of species nestedness patterns.

    PubMed

    Ulrich, Werner; Gotelli, Nicholas J

    2007-07-01

    Nestedness is a common biogeographic pattern in which small communities form proper subsets of large communities. However, the detection of nestedness in binary presence-absence matrices will be affected by both the metric used to quantify nestedness and the reference null distribution. In this study, we assessed the statistical performance of eight nestedness metrics and six null model algorithms. The metrics and algorithms were tested against a benchmark set of 200 random matrices and 200 nested matrices that were created by passive sampling. Many algorithms that have been used in nestedness studies are vulnerable to type I errors (falsely rejecting a true null hypothesis). The best-performing algorithm maintains fixed row and fixed column totals, but it is conservative and may not always detect nestedness when it is present. Among the eight indices, the popular matrix temperature metric did not have good statistical properties. Instead, the Brualdi and Sanderson discrepancy index and Cutler's index of unexpected presences performed best. When used with the fixed-fixed algorithm, these indices provide a conservative test for nestedness. Although previous studies have revealed a high frequency of nestedness, a reanalysis of 288 empirical matrices suggests that the true frequency of nested matrices is between 10% and 40%.

  19. 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.

  20. Null model analysis of species associations using abundance data.

    PubMed

    Ulrich, Werner; Gotelli, Nicholas J

    2010-11-01

    The influence of negative species interactions has dominated much of the literature on community assembly rules. Patterns of negative covariation among species are typically documented through null model analyses of binary presence/absence matrices in which rows designate species, columns designate sites, and the matrix entries indicate the presence (1) or absence (0) of a particular species in a particular site. However, the outcome of species interactions ultimately depends on population-level processes. Therefore, patterns of species segregation and aggregation might be more clearly expressed in abundance matrices, in which the matrix entries indicate the abundance or density of a species in a particular site. We conducted a series of benchmark tests to evaluate the performance of 14 candidate null model algorithms and six covariation metrics that can be used with abundance matrices. We first created a series of random test matrices by sampling a metacommunity from a lognormal species abundance distribution. We also created a series of structured matrices by altering the random matrices to incorporate patterns of pairwise species segregation and aggregation. We next screened each algorithm-index combination with the random and structured matrices to determine which tests had low Type I error rates and good power for detecting segregated and aggregated species distributions. In our benchmark tests, the best-performing null model does not constrain species richness, but assigns individuals to matrix cells proportional to the observed row and column marginal distributions until, for each row and column, total abundances are reached. Using this null model algorithm with a set of four covariance metrics, we tested for patterns of species segregation and aggregation in a collection of 149 empirical abundance matrices and 36 interaction matrices collated from published papers and posted data sets. More than 80% of the matrices were significantly segregated, which

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Analytically tractable model for community ecology with many species

    NASA Astrophysics Data System (ADS)

    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.

  10. Bias correction in species distribution models: pooling survey and collection data for multiple species

    PubMed Central

    Fithian, William; Elith, Jane; Hastie, Trevor; Keith, David A.

    2016-01-01

    Summary Presence-only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence–absence or count data collected in systematic, planned surveys are more reliable but typically less abundant.We proposed a probabilistic model to allow for joint analysis of presence-only and survey data to exploit their complementary strengths. Our method pools presence-only and presence–absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence-only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence-only data.We evaluate our model’s performance on data for 36 eucalypt species in south-eastern Australia. We find that presence-only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data-pooling technique substantially improves the out-of-sample predictive performance of our model when the amount of available presence–absence data for a given species is scarceIf we have only presence-only data and no presence–absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species’ geographic range. PMID:27840673

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

    PubMed Central

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

    2011-01-01

    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

  12. 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.

  13. How clonal are Neisseria species? The epidemic clonality model revisited.

    PubMed

    Tibayrenc, Michel; Ayala, Francisco J

    2015-07-21

    The three species Neisseria meningitidis, Neisseria gonorrheae, and Neisseria lactamica are often regarded as highly recombining bacteria. N. meningitidis has been considered a paradigmatic case of the "semiclonal model" or of "epidemic clonality," demonstrating occasional bouts of clonal propagation in an otherwise recombining species. In this model, occasional clonality generates linkage disequilibrium in the short term. In the long run, however, the effects of clonality are countered by recombination. We show that many data are at odds with this proposal and that N. meningitidis fits the criteria that we have proposed for predominant clonal evolution (PCE). We point out that (i) the proposed way to distinguish epidemic clonality from PCE may be faulty and (ii) the evidence of deep phylogenies by microarrays and whole-genome sequencing is at odds with the predictions of the semiclonal model. Last, we revisit the species status of N. meningitidis, N. gonorrheae, and N. lactamica in the light of the PCE model.

  14. 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

  15. Species-free species distribution models describe macroecological properties of protected area networks.

    PubMed

    Robinson, Jason L; Fordyce, James A

    2017-01-01

    Among the greatest challenges facing the conservation of plants and animal species in protected areas are threats from a rapidly changing climate. An altered climate creates both challenges and opportunities for improving the management of protected areas in networks. Increasingly, quantitative tools like species distribution modeling are used to assess the performance of protected areas and predict potential responses to changing climates for groups of species, within a predictive framework. At larger geographic domains and scales, protected area network units have spatial geoclimatic properties that can be described in the gap analysis typically used to measure or aggregate the geographic distributions of species (stacked species distribution models, or S-SDM). We extend the use of species distribution modeling techniques in order to model the climate envelope (or "footprint") of individual protected areas within a network of protected areas distributed across the 48 conterminous United States and managed by the US National Park System. In our approach we treat each protected area as the geographic range of a hypothetical endemic species, then use MaxEnt and 5 uncorrelated BioClim variables to model the geographic distribution of the climatic envelope associated with each protected area unit (modeling the geographic area of park units as the range of a species). We describe the individual and aggregated climate envelopes predicted by a large network of 163 protected areas and briefly illustrate how macroecological measures of geodiversity can be derived from our analysis of the landscape ecological context of protected areas. To estimate trajectories of change in the temporal distribution of climatic features within a protected area network, we projected the climate envelopes of protected areas in current conditions onto a dataset of predicted future climatic conditions. Our results suggest that the climate envelopes of some parks may be locally unique or have

  16. Species-free species distribution models describe macroecological properties of protected area networks

    PubMed Central

    Fordyce, James A.

    2017-01-01

    Among the greatest challenges facing the conservation of plants and animal species in protected areas are threats from a rapidly changing climate. An altered climate creates both challenges and opportunities for improving the management of protected areas in networks. Increasingly, quantitative tools like species distribution modeling are used to assess the performance of protected areas and predict potential responses to changing climates for groups of species, within a predictive framework. At larger geographic domains and scales, protected area network units have spatial geoclimatic properties that can be described in the gap analysis typically used to measure or aggregate the geographic distributions of species (stacked species distribution models, or S-SDM). We extend the use of species distribution modeling techniques in order to model the climate envelope (or “footprint”) of individual protected areas within a network of protected areas distributed across the 48 conterminous United States and managed by the US National Park System. In our approach we treat each protected area as the geographic range of a hypothetical endemic species, then use MaxEnt and 5 uncorrelated BioClim variables to model the geographic distribution of the climatic envelope associated with each protected area unit (modeling the geographic area of park units as the range of a species). We describe the individual and aggregated climate envelopes predicted by a large network of 163 protected areas and briefly illustrate how macroecological measures of geodiversity can be derived from our analysis of the landscape ecological context of protected areas. To estimate trajectories of change in the temporal distribution of climatic features within a protected area network, we projected the climate envelopes of protected areas in current conditions onto a dataset of predicted future climatic conditions. Our results suggest that the climate envelopes of some parks may be locally unique or

  17. AAV retinal transduction in a large animal model species: Comparison of a self-complementary AAV2/5 with a single-stranded AAV2/5 vector

    PubMed Central

    Bartoe, J.T.; Fischer, A.J.; Scott, M.; Boye, S.L.; Chiodo, V.; Hauswirth, W.W.

    2009-01-01

    Purpose To compare self-complementary (sc) and single-stranded (ss) adeno-associated viral 2/5 (AAV2/5) vectors for retinal cell transduction in the dog when delivered by subretinal injection. Methods ScAAV2/5 and ssAAV2/5 vectors encoding enhanced green fluorescent protein (GFP) under control of the chicken beta actin promoter were prepared to the same titer. Equal amounts of viral particles were delivered into the subretinal spaces of both eyes of two dogs. In each dog, one eye received the scAAV2/5 and the other the ssAAV2/5. In vivo expression of GFP was monitored ophthalmoscopically. The dogs were sacrificed, and their retinas were examined by fluorescent microscopy and immunohistochemistry to determine GFP expression patterns and to assay for glial reactivity. Results GFP expression in the scAAV2/5 injected eyes was detectable at a much earlier time point than in the ssAAV2/5 injected eyes. Expression of GFP was also at higher levels in the scAAV2/5-injected eyes. Expression levels remained stable for the seven month duration of the study. The types of cells transduced by both vectors were similar; there was strong reporter gene expression in the RPE and photoreceptors, although not all cones in the transduced area expressed GFP. Some horizontal and Müller cells were also transduced. Conclusions When delivered by subretinal injection in the dog, scAAV2/5 induces faster and stronger transgene expression than ssAAV2/5. The spectrum of retinal neurons transduced is similar between the two vectors. These results confirm in a large animal model those previously reported in the mouse. ScAAV2/5 shows promise for use in the treatment of conditions where a rapid transgene expression is desirable. Furthermore, it may be possible to use a lower number of viral particles to achieve the same effect compared with ssAAV2/5 vectors. PMID:19756181

  18. 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.

  19. Remote sensing and GIS applications for modeling species distributions

    NASA Astrophysics Data System (ADS)

    Harris, Grant

    Habitat loss is the leading cause of species endangerment. It fragments what remains (most harmful for habitat specialists) and isolates populations (applicable to all species). The fragments, parks and other protected areas where species remain are often too small for the long-term persistence of many species. Although these effects are more pronounced in tropical forests, where most species live, the problem is so widespread that it manifests itself across suites of ecosystems and taxa. Mitigating the problems caused by habitat and population fragmentation requires more information. Specifically, we must determine which species are most extinction prone, find ways to cheaply and quickly determine priority areas for conservation, quantify the minimum areas required for species persistence, and identify the key variables needed for species presence. Here, I analyze each of these four key points, using a spectrum of species, and a variety of remote sensing and GIS techniques. For habitat specialists, exemplified by tropical forest birds, I quantify habitat loss directly. It's simply a matter of measuring the remaining forest. To model habitat generalists, such as African elephants, I incorporate habitat and other variables (water, people, greenness) that dictate their presence. For birds, I find that habitat loss affects all forest endemic species equally. Species not threatened have large remaining ranges and high abundances in their ranges. My methods also refine conservation priorities in biological hotspots. The key lies in finding where species live now, and broad-scale natural history information plus coarse-scale imagery suits this purpose. Coarse imagery is also sufficient to understand the minimum range size at which birds become threatened. Be it habitat loss directly or induced by climate change, bird ranges must be over 20,000 km2 in lowland species, and 10,000 km2 for montane birds to avoid threat. For elephants, it is water and people that predict

  20. The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species

    PubMed Central

    Asaf, Sajjad; Waqas, Muhammad; Khan, Abdul L.; Khan, Muhammad A.; Kang, Sang-Mo; Imran, Qari M.; Shahzad, Raheem; Bilal, Saqib; Yun, Byung-Wook; Lee, In-Jung

    2017-01-01

    Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the O. minuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete O. minuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny. PMID:28326093

  1. 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

  2. Comparison of song frequency and receptor tuning in two closely related bushcricket species.

    PubMed

    Kalmring, K; Rössler, W; Jatho, M; Hoffmann, E

    1995-01-01

    The songs and the structure and physiology of the auditory organs in the closely related bushcricket species Tettigonia viridissima and Tettigonia cantans were investigated comparatively using bioacoustical, histological and neurophysiological methods. The morphology of the crista acustica, the main auditory receptor organ, is very similar in the two species in respect to both the distribution of scolopidia along the length axis of the crista and the dimensions of corresponding scolopidia and attachment structures. The only obvious difference is that T. viridissima has one more scolopidium in the crista acustica and that the overall length of the crista is by about 50 microns larger than in T. cantans. In contrast, differences were found in the physiology of individual auditory receptor cells. Comparison of the threshold characteristics of all the receptor cells of the crista acustica in both species reveals a differential sensitivity of groups of auditory receptor cells at dominant frequencies of the song. In each species, the sensitivity of auditory receptor cells is method to the energy spectrum of the song. These differences in the physiology can partly be explained by differences in transmission characteristics of the acoustic trachea.

  3. 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.

  4. 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.

  5. Considerations for building climate-based species distribution models

    USGS Publications Warehouse

    Bucklin, David N.; Basille, Mathieu; Romanach, Stephanie; Brandt, Laura A.; Mazzotti, Frank J.; Watling, James I.

    2016-01-01

    Climate plays an important role in the distribution of species. A given species may adjust to new conditions in-place, move to new areas with suitable climates, or go extinct. Scientists and conservation practitioners use mathematical models to predict the effects of future climate change on wildlife and plan for a biodiverse future. This 8-page fact sheet written by David N. Bucklin, Mathieu Basille, Stephanie S. Romañach, Laura A. Brandt, Frank J. Mazzotti, and James I. Watling and published by the Department of Wildlife Ecology and Conservation explains how, with a better understanding of species distribution models, we can predict how species may respond to climate change. The models alone cannot tell us how a certain species will actually respond to changes in climate, but they can inform conservation planning that aims to allow species to both adapt in place and (for those that are able to) move to newly suitable areas. Such planning will likely minimize loss of biodiversity due to climate change.

  6. 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

  7. 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.

  8. 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 ...

  9. 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

  10. 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

  11. Estimating and Modeling Gene Flow for a Spatially Distributed Species

    DTIC Science & Technology

    1991-01-01

    AD-A238 221/I1 Estimating and modeling gene flow for a spatially distributed species JUL1 7 1961T. Burr 1 and T. V. Kurien 2 Department of Statistics...modeling gene flow for a spatially distributed species. By T. Burr and T. V. Kurien Departmeii Of Statistics Florida State University Abstract This...chromosome (referred to as a locus) is a meaningful string of several hundred symbols called a gene . Typ- ically there are many loci on a chromosome. The

  12. Species data: National inventory of range maps and distribution models

    USGS Publications Warehouse

    Gergely, Kevin J.; McKerrow, Alexa

    2013-01-01

    The Gap Analysis Program (GAP) produces data and tools that help meet critical national challenges such as biodiversity conservation, renewable energy development, climate change adaptation, and infrastructure investment. The GAP species data includes vertebrate range maps and distribution models for the continental United States, as well as Alaska, Hawaii, Puerto Rico, and U.S. Virgin Islands. The vertebrate species include amphibians, birds, mammals, and reptiles. Furthermore, data used to create the distribution models (for example, percent canopy cover, elevation, and so forth) also are available.

  13. Quantitative comparisons of satellite observations and cloud models

    NASA Astrophysics Data System (ADS)

    Wang, Fang

    .9% in the one month 1D-Var retrievals examined. To attain better constrained cloud/rain ratios and improved retrieval quality, this study suggests the implementation of higher microwave frequency channels in the 1D-Var algorithm. Cloud Resolving Models (CRMs) offer an important pathway to interpret satellite observations of microphysical properties of storms. High frequency microwave brightness temperatures (Tbs) respond to precipitating-sized ice particles and can, therefore, be compared with simulated Tbs at the same frequencies. By clustering the Tb vectors at these frequencies, the scene can be classified into distinct microphysical regimes, in other words, cloud types. The properties for each cloud type in the simulated scene are compared to those in the observation scene to identify the discrepancies in microphysics within that cloud type. A convective storm over the Amazon observed by the Tropical Rainfall Measuring Mission (TRMM) is simulated using the Regional Atmospheric Modeling System (RAMS) in a semi-ideal setting, and four regimes are defined within the scene using cluster analysis: the 'clear sky/thin cirrus' cluster, the 'cloudy' cluster, the 'stratiform anvil' cluster and the 'convective' cluster. The relationship between Tb difference of 37 and 85 GHz and Tb at 85 GHz is found to contain important information of microphysical properties such as hydrometeor species and size distributions. Cluster-by-cluster comparison between the observations and the simulations discloses biases in the model including overproduction of supercooled water and large hail particles. The detected biases shed light on how the model should be adjusted to generate more realistic microphysical relationships for each cluster. Guided by the model/observation discrepancies in the 'convective' cloud cluster, a new simulation is performed to provide dynamic adjustments by generating more but smaller hail particles.

  14. Developing informative microsatellite makers for non-model species using reference mapping against a model species' genome.

    PubMed

    Hung, Chih-Ming; Yu, Ai-Yun; Lai, Yu-Ting; Shaner, Pei-Jen L

    2016-03-15

    Microsatellites have a wide range of applications from behavioral biology, evolution, to agriculture-based breeding programs. The recent progress in the next-generation sequencing technologies and the rapidly increasing number of published genomes may greatly enhance the current applications of microsatellites by turning them from anonymous to informative markers. Here we developed an approach to anchor microsatellite markers of any target species in a genome of a related model species, through which the genomic locations of the markers, along with any functional genes potentially linked to them, can be revealed. We mapped the shotgun sequence reads of a non-model rodent species Apodemus semotus against the genome of a model species, Mus musculus, and presented 24 polymorphic microsatellite markers with detailed background information for A. semotus in this study. The developed markers can be used in other rodent species, especially those that are closely related to A. semotus or M. musculus. Compared to the traditional approaches based on DNA cloning, our approach is likely to yield more loci for the same cost. This study is a timely demonstration of how a research team can efficiently generate informative (neutral or function-associated) microsatellite markers for their study species and unique biological questions.

  15. 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.

  16. 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

  17. 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.

  18. Iodine Species in the Marine Boundary Layer: a model study

    NASA Astrophysics Data System (ADS)

    Moldanova, J.; Sander, R.

    2003-04-01

    Multiphase chemical reactions of iodine species in marine boundary layer (MBL) were simulated using the box Model Of Chemistry Considering Aerosols (MOCCA). The chemical mechanism considers reactions both in the gas phase and in deliquesced sea-salt and sulfate aerosols. Photochemical reaction rates vary as a function of solar declination. In addition to the standard tropospheric HOx, CH4, and NOx chemistry, the reaction mechanism includes S, Cl, Br, and I compounds. A new version of the model that evaluates chemical processes involving different aerosol size fractions was developed. The particle population was partitioned into 8 monodispersed size bins with median diameters equal to the corresponding size interval of the modelled continuous distribution. Further information about the model is available at http://www.mpch-mainz.mpg.de/˜sander/mocca/. Source of the iodine in the modelled MBL was photolysis of biogenic iodinated hydrocarbons. Some of the gas phase iodine species are soluble and iodine recycles through the deliquescent aerosol particles where it interacts with other halogen species. Both the gas-phase and aqueous-phase reaction mechanism of iodine includes numerous uncertainties. Distribution of the inorganic iodine species between the gas and aqueous phase and its sensitivity to the unknown or not well defined reaction rates and equilibria is presented.

  19. 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

  20. 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

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

    PubMed

    Särkinen, Tiina; Gonzáles, Paúl; Knapp, Sandra

    2013-01-01

    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.

  2. 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

  3. 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.

  4. 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

  5. N Reactor RELAP5 model benchmark comparisons

    SciTech Connect

    Fletcher, C.D.; Bolander, M.A.

    1988-02-01

    This report documents work performed at the Idaho National Engineering Laboratory (INEL) in support of Westinghouse Hanford Company safety analyses for the N Reactor. The portion of the work reported here includes comparisons of RELAP5/MOD2-calculated data with measured plant data for: (1) a plant trip reactor transient from full power operation; and (2) a hot dump test performed prior to plant startup. These qualitative comparisons are valuable because they provide an indication of the capabilities of the RELAP5/MOD2 code to simulate operational and blowdonw transients in the N Reactor. 9 refs., 12 figs., 4 tabs.

  6. 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...

  7. 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.

  8. 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

  9. 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.

  10. Comparing niche- and process-based models to reduce prediction uncertainty in species range shifts under climate change.

    PubMed

    Morin, Xavier; Thuiller, Wilfried

    2009-05-01

    Obtaining reliable predictions of species range shifts under climate change is a crucial challenge for ecologists and stakeholders. At the continental scale, niche-based models have been widely used in the last 10 years to predict the potential impacts of climate change on species distributions all over the world, although these models do not include any mechanistic relationships. In contrast, species-specific, process-based predictions remain scarce at the continental scale. This is regrettable because to secure relevant and accurate predictions it is always desirable to compare predictions derived from different kinds of models applied independently to the same set of species and using the same raw data. Here we compare predictions of range shifts under climate change scenarios for 2100 derived from niche-based models with those of a process-based model for 15 North American boreal and temperate tree species. A general pattern emerged from our comparisons: niche-based models tend to predict a stronger level of extinction and a greater proportion of colonization than the process-based model. This result likely arises because niche-based models do not take phenotypic plasticity and local adaptation into account. Nevertheless, as the two kinds of models rely on different assumptions, their complementarity is revealed by common findings. Both modeling approaches highlight a major potential limitation on species tracking their climatic niche because of migration constraints and identify similar zones where species extirpation is likely. Such convergent predictions from models built on very different principles provide a useful way to offset uncertainties at the continental scale. This study shows that the use in concert of both approaches with their own caveats and advantages is crucial to obtain more robust results and that comparisons among models are needed in the near future to gain accuracy regarding predictions of range shifts under climate change.

  11. 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.

  12. Mechanistic species distribution modeling reveals a niche shift during invasion.

    PubMed

    Chapman, Daniel S; Scalone, Romain; Štefanić, Edita; Bullock, James M

    2017-04-02

    Niche shifts of non-native plants can occur when they colonize novel climatic conditions. However, the mechanistic basis for niche shifts during invasion is poorly understood and has rarely been captured within species distribution models. We quantified the consequence of between-population variation in phenology for invasion of common ragweed (Ambrosia artemisiifolia L.) across Europe. Ragweed is of serious concern because of its harmful effects as a crop weed and because of its impact on public health as a major aeroallergen. We developed a forward mechanistic species distribution model based on responses of ragweed development rates to temperature and photoperiod. The model was parameterized and validated from the literature and by re-analyzing data from a reciprocal common garden experiment in which native and invasive populations were grown within and beyond the current invaded range. It could therefore accommodate between-population variation in the physiological requirements for flowering, and predict the potentially-invaded ranges of individual populations. Northern-origin populations that were established outside the generally-accepted climate envelope of the species had lower thermal requirements for bud development, suggesting local adaptation of phenology had occurred during the invasion. The model predicts that this will extend the potentially-invaded range northwards and increase the average suitability across Europe by 90% in the current climate and 20% in the future climate. Therefore, trait variation observed at the population scale can trigger a climatic niche shift at the biogeographic scale. For ragweed, earlier flowering phenology in established northern populations could allow the species to spread beyond its current invasive range, substantially increasing its risk to agriculture and public health. Mechanistic species distribution models offer the possibility to represent niche shifts by varying the traits and niche responses of individual

  13. Dense gene physical maps of the non-model species Drosophila subobscura.

    PubMed

    Orengo, Dorcas J; Puerma, Eva; Papaceit, Montserrat; Segarra, Carmen; Aguadé, Montserrat

    2017-01-11

    The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism. These maps are based on 462 markers: 115, 236, and 111 markers for elements A, C, and E, respectively. The availability of these dense maps will facilitate genome assembly and will thus greatly contribute to obtaining a good reference genome, which is a required step for D. subobscura to attain the model species status. The comparative analysis of these physical maps and those obtained from the D. pseudoobscura and D. melanogaster genomes allowed us to infer the number of fixed inversions and chromosomal evolutionary rates for each pairwise comparison. For all three elements, rates inferred from the more closely related species were higher than those inferred from the more distantly related species, which together with results of relative-rate tests point to an acceleration in the D. subobscura lineage at least for elements A and E.

  14. 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.

  15. 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.

  16. 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.

  17. Comparison of vanadium-rich activity of three species fungi of basidiomycetes.

    PubMed

    Han, Chunchao; Cui, Bo; Qu, Jingran

    2009-03-01

    A comparison of vanadium-rich activity of three species fungi of Basidiomycetes, Ganoderma lucidum, Coprinus comatus, and Grifola frondosa, was studied. By fermentation and atomic absorption spectroscopy analysis, the biomass of G. lucidum and G. frondosa declined rapidly when the concentration of vanadium exceeded 0.3% but the biomass of C. comatus did not decline rapidly until the concentration of vanadium exceeded 0.4% and the content of vanadium accumulated in the mycelia was 3529.3 microg/g. After the mice were administered (intragastrically) with vanadium-rich C. comatus, the blood glucose of alloxan-induced hyperglycemic mice was decreased (p < 0.05) and the body weight of the alloxan-induced hyperglycemic mice was increased gradually. Thus, we selected C. comatus to absorb vanadium and chose 0.4% as the optimal concentration of vanadium for the pharmacological works.

  18. Variable soft sphere molecular model for air species

    NASA Astrophysics Data System (ADS)

    Koura, Katsuhisa; Matsumoto, Hiroaki

    1992-05-01

    A reliable set of cross-section parameters of the variable soft sphere (VSS) molecular model is determined for the Monte Carlo simulation of air species from the transport collision integrals or potential parameters provided by Cubley and Mason (1975) over the high-temperature range 300-15,000 K. The VSS cross-section parameters for the inverse-power-law potential are also determined from the viscosity coefficients recommended by Maitland and Smith (1972) for common species in the low (20-300 K) and high (300-2000 K) temperature ranges.

  19. Variable soft sphere molecular model for air species

    NASA Astrophysics Data System (ADS)

    Koura, Katsuhisa; Matsumoto, Hiroaki

    1992-05-01

    A reliable set of cross-section parameters of the variable soft sphere (VSS) molecular model is determined for the Monte Carlo simulation of air species from the transport collision integrals or potential parameters provided by Cubley and Mason [Phys. Fluids 18, 1109 (1975)] over the high-temperature range 300-15 000 K. The VSS cross-section parameters for the inverse-power-law potential are also determined from the viscosity coefficients recommended by Maitland and Smith [J. Chem. Eng. Data 17, 150 (1972)] for common species in the low (20-300 K) and high (300-2000 K) temperature ranges.

  20. 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

  1. 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.

  2. 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

  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. Predicting the fate of biodiversity using species' distribution models: enhancing model comparability and repeatability.

    PubMed

    Rodríguez-Castañeda, Genoveva; Hof, Anouschka R; Jansson, Roland; Harding, Larisa E

    2012-01-01

    Species distribution modeling (SDM) is an increasingly important tool to predict the geographic distribution of species. Even though many problems associated with this method have been highlighted and solutions have been proposed, little has been done to increase comparability among studies. We reviewed recent publications applying SDMs and found that seventy nine percent failed to report methods that ensure comparability among studies, such as disclosing the maximum probability range produced by the models and reporting on the number of species occurrences used. We modeled six species of Falco from northern Europe and demonstrate that model results are altered by (1) spatial bias in species' occurrence data, (2) differences in the geographic extent of the environmental data, and (3) the effects of transformation of model output to presence/absence data when applying thresholds. Depending on the modeling decisions, forecasts of the future geographic distribution of Falco ranged from range contraction in 80% of the species to no net loss in any species, with the best model predicting no net loss of habitat in Northern Europe. The fact that predictions of range changes in response to climate change in published studies may be influenced by decisions in the modeling process seriously hampers the possibility of making sound management recommendations. Thus, each of the decisions made in generating SDMs should be reported and evaluated to ensure conclusions and policies are based on the biology and ecology of the species being modeled.

  5. 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...

  6. 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

  7. 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...

  8. Biotic Interactions in the Face of Climate Change: A Comparison of Three Modelling Approaches

    PubMed Central

    Jaeschke, Anja; Bittner, Torsten; Jentsch, Anke; Reineking, Björn; Schlumprecht, Helmut; Beierkuhnlein, Carl

    2012-01-01

    Climate change is expected to alter biotic interactions, and may lead to temporal and spatial mismatches of interacting species. Although the importance of interactions for climate change risk assessments is increasingly acknowledged in observational and experimental studies, biotic interactions are still rarely incorporated in species distribution models. We assessed the potential impacts of climate change on the obligate interaction between Aeshna viridis and its egg-laying plant Stratiotes aloides in Europe, based on an ensemble modelling technique. We compared three different approaches for incorporating biotic interactions in distribution models: (1) We separately modelled each species based on climatic information, and intersected the future range overlap (‘overlap approach’). (2) We modelled the potential future distribution of A. viridis with the projected occurrence probability of S. aloides as further predictor in addition to climate (‘explanatory variable approach’). (3) We calibrated the model of A. viridis in the current range of S. aloides and multiplied the future occurrence probabilities of both species (‘reference area approach’). Subsequently, all approaches were compared to a single species model of A. viridis without interactions. All approaches projected a range expansion for A. viridis. Model performance on test data and amount of range gain differed depending on the biotic interaction approach. All interaction approaches yielded lower range gains (up to 667% lower) than the model without interaction. Regarding the contribution of algorithm and approach to the overall uncertainty, the main part of explained variation stems from the modelling algorithm, and only a small part is attributed to the modelling approach. The comparison of the no-interaction model with the three interaction approaches emphasizes the importance of including obligate biotic interactions in projective species distribution modelling. We recommend the use of

  9. Evaluation and Comparison of Computational Models

    PubMed Central

    Myung, Jay; Tang, Yun; Pitt, Mark A.

    2009-01-01

    Computational models are powerful tools that can enhance the understanding of scientific phenomena. The enterprise of modeling is most productive when the reasons underlying the adequacy of a model, and possibly its superiority to other models, are understood. This chapter begins with an overview of the main criteria that must be considered in model evaluation and selection, in particular explaining why generalizability is the preferred criterion for model selection. This is followed by a review of measures of generalizability. The final section demonstrates the use of five versatile and easy-to-use selection methods for choosing between two mathematical models of protein folding. PMID:19216931

  10. 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.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    Enßle, 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.

  13. 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.

  14. 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.

  15. Submillimeter Absorption Spectroscopy in Semiconductor Manufacturing Plasmas and Comparison to Theoretical Models

    NASA Astrophysics Data System (ADS)

    Helal, Yaser H.; Neese, Christopher F.; De Lucia, Frank C.; Ewing, Paul R.; Agarwal, Ankur; Craver, Barry; Stout, Phillip J.; Armacost, Michael D.

    2015-06-01

    Plasmas used in the semiconductor manufacturing industry are of a similar nature to the environments often created for submillimeter spectroscopic study of astrophysical species. At the low operating pressures of these plasmas, submillimeter absorption spectroscopy is a method capable of measuring the abundances and temperatures of molecules, radicals, and ions without disturbing any of the properties of the plasma. These measurements provide details and insight into the interactions and reactions occurring within the plasma and their implications for semiconductor manufacturing processes. A continuous wave, 500 to 750 GHz, absorption spectrometer was designed and used to make measurements of species in semiconductor processing plasmas. Comparisons with expectations from theoretical plasma models provide a basis for validating and improving these models, which is a complex and difficult science itself. Furthermore, these comparisons are an evaluation for the use of submillimeter spectroscopy as a diagnostic tool in manufacturing processes.

  16. 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.

  17. 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

  18. Comparison of the formation of nicotinic acid conjugates in leaves of different plant species.

    PubMed

    Ashihara, Hiroshi; Yin, Yuling; Katahira, Riko; Watanabe, Shin; Mimura, Tetsuro; Sasamoto, Hamako

    2012-11-01

    There are three metabolic fates of nicotinic acid in plants: (1) nicotinic acid mononucleotide formation for NAD synthesis by the so-called salvage pathway of pyridine nucleotide biosynthesis; (2) nicotinic acid N-glucoside formation; and (3) trigonelline (N-methylnicotinic acid) formation. In the present study, the metabolism of [carbonyl-(14)C]nicotinamide was investigated in leaves of 23 wild plant species. All species readily converted nicotinamide to nicotinic acid, and only a fraction of nicotinic acid was utilised for NAD and NADP synthesis. The remaining nicotinic acid is converted to the nicotinic acid conjugates. Only one plant species, Cycas revoluta, produced both nicotinic acid N-glucoside and trigonelline; the other 22 species produced one or other of the conjugates. The nicotinic acid N-glucoside-forming plants are Cyathea lepifera, Arenga trewmula var. englri, Barringtonia racemosa, Ilex paraguariensis, Angelica japonica, Scaevola taccada and Farfugium japonicum. In contrast, trigonelline is formed in C. lepifera, Ginkgo biloba, Pinus luchuensis, Casuarina equisetifolia, Alocasia odora, Pandanus odoratissimus, Hylocereus undatus, Kalanchoe pinnata, Kalanchoe tubiflora, Populus alba, Garcinia subelliptica, Oxalis corymbosa, Leucaena leucocephala, Vigna marina, Hibiscus tiliaceus and Melicope triphylla. The diversity of nicotinic acid conjugate formation in plants is discussed using these results and our previous investigation involving a few model plants, various crops and ferns. Nicotinic acid N-glucoside formation was restricted mostly to ferns and selected orders of angiosperms, whereas other plants produce trigonelline. In most cases the formation of both nicotinic acid conjugates is incompatible, but some exceptions have been found.

  19. 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.

  20. A Comparison of Alternative Models for Testlets

    ERIC Educational Resources Information Center

    Li, Yanmei; Bolt, Daniel M.; Fu, Jianbin

    2006-01-01

    When tests are made up of testlets, standard item response theory (IRT) models are often not appropriate due to the local dependence present among items within a common testlet. A testlet-based IRT model has recently been developed to model examinees' responses under such conditions (Bradlow, Wainer, & Wang, 1999). The Bradlow, Wainer, and…

  1. Using cross-species comparisons and a neurobiological framework to understand early social deprivation effects on behavioral development

    PubMed Central

    BRETT, ZOË H.; HUMPHREYS, KATHRYN L.; FLEMING, ALISON S.; KRAEMER, GARY W.; DRURY, STACY S.

    2017-01-01

    Building upon the transactional model of brain development, we explore the impact of early maternal deprivation on neural development and plasticity in three neural systems: hyperactivity/impulsivity, executive function, and hypothalamic–pituitary–adrenal axis functioning across rodent, nonhuman primate, and human studies. Recognizing the complexity of early maternal–infant interactions, we limit our cross-species comparisons to data from rodent models of artificial rearing, nonhuman primate studies of peer rearing, and the relations between these two experimental approaches and human studies of children exposed to the early severe psychosocial deprivation associated with institutional care. In addition to discussing the strengths and limitations of these paradigms, we present the current state of research on the neurobiological impact of early maternal deprivation and the evidence of sensitive periods, noting methodological challenges. Integrating data across preclinical animal models and human studies, we speculate about the underlying biological mechanisms; the differential impact of deprivation due to temporal factors including onset, offset, and duration of the exposure; and the possibility and consequences of reopening of sensitive periods during adolescence. PMID:25997759

  2. 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.

  3. 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.

  4. How clonal are Neisseria species? The epidemic clonality model revisited

    PubMed Central

    Tibayrenc, Michel; Ayala, Francisco J.

    2015-01-01

    The three species Neisseria meningitidis, Neisseria gonorrheae, and Neisseria lactamica are often regarded as highly recombining bacteria. N. meningitidis has been considered a paradigmatic case of the “semiclonal model” or of “epidemic clonality,” demonstrating occasional bouts of clonal propagation in an otherwise recombining species. In this model, occasional clonality generates linkage disequilibrium in the short term. In the long run, however, the effects of clonality are countered by recombination. We show that many data are at odds with this proposal and that N. meningitidis fits the criteria that we have proposed for predominant clonal evolution (PCE). We point out that (i) the proposed way to distinguish epidemic clonality from PCE may be faulty and (ii) the evidence of deep phylogenies by microarrays and whole-genome sequencing is at odds with the predictions of the semiclonal model. Last, we revisit the species status of N. meningitidis, N. gonorrheae, and N. lactamica in the light of the PCE model. PMID:26195766

  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. 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.

  7. Species comparison and pharmacological characterization of human, monkey, rat, and mouse TRPA1 channels.

    PubMed

    Bianchi, Bruce R; Zhang, Xu-Feng; Reilly, Regina M; Kym, Philip R; Yao, Betty B; Chen, Jun

    2012-05-01

    The transient receptor potential ankyrin-1 (TRPA1) channel has emerged as an attractive target for development of analgesic and anti-inflammatory drugs. However, drug discovery efforts targeting TRPA1 have been hampered by differences between human and rodent species. Many compounds have been identified to have antagonist activity at human TRPA1 (hTRPA1), but when tested at rat TRPA1 (rTRPA1) and mouse TRPA1 (mTRPA1), they show reduced potency as antagonists, no effect, or agonist activity. These compounds are excluded from further drug development because they cannot be tested in preclinical studies using conventional rat/mouse models. To broaden our understanding of species-specific differences, we cloned and functionally characterized rhesus monkey TRPA1 (rhTRPA1) and compared its pharmacological profile to hTRPA1, rTRPA1, and mTRPA1 channels. The functional activities of a diverse group of TRPA1 ligands (both reactive and nonreactive) were determined in a fluorescent Ca²⁺ influx assay, using transiently transfected human embryonic kidney 293-F cells. 4-Methyl-N-[2,2,2-trichloro-1-(4-nitro-phenylsulfanyl)-ethyl]-benzamide, menthol, and caffeine displayed species-specific differential pharmacology at TRPA1. The pharmacological profile of the rhTRPA1 channel was found to be similar to the hTRPA1 channel. In contrast, the rTRPA1 and mTRPA1 channels closely resembled each other but were pharmacologically distinct from either hTRPA1 or rhTRPA1 channels. Our findings reveal that TRPA1 function differs between primate and rodent species and suggest that rhesus monkey could serve as a surrogate species for humans in preclinical studies.

  8. 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.

  9. 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.

  10. 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.

  11. 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

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

    PubMed

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

    2015-04-21

    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

  13. Comparison of kinetic theory models of laser ablation of carbon

    SciTech Connect

    Shusser, Michael

    2010-05-15

    The paper compares the predictions of three-dimensional kinetic theory models of laser ablation of carbon. All the models are based on the moment solution of the Boltzmann equation for arbitrary strong evaporation but use different approximations. Comparison of the model predictions demonstrated that the choice of the particular model has very little influence on the results. The influence of the heat conduction from the gas to the solid phase was also found to be negligible in this problem.

  14. 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.

  15. 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.

  16. 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…

  17. 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.; 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

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

    PubMed

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

    2011-09-01

    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

  19. Analysis and comparison of three ecosystem models

    NASA Astrophysics Data System (ADS)

    Newberger, P. A.; Allen, J. S.; Spitz, Y. H.

    2003-03-01

    Three-component (NPZ), four-component (NPZD), and five-component (NNPZD) nitrogen-based ecosystem models are compared. The fixed points of the zero-dimensional systems, with no spatial variation except light attenuation by water, are determined. A linear-stability analysis shows that unstable steady solutions exist for all three models. Time-periodic solutions are found in these regions. It is shown that the choice of the values of the parameters in the zooplankton equation is critical in determining steady state concentrations. One-dimensional model studies allowing variation with depth, self-shading by phytoplankton, and vertical diffusion show that the differences among the models increase when the available light is influenced by the presence of phytoplankton. With vertical diffusion, periodic solutions, such as those in the zero-dimensional case, are not found. Finally, a set of one-dimensional depth-integrated models, with variability in time and across-shore coordinate, are formulated. These models include horizontal advection and diffusion and the sinking of detritus (or phytoplankton). Application of a constant offshore advection velocity and coastal boundary conditions consistent with upwelling, produces many of the features seen in two-dimensional experiments [, 2003]. The dependence of the resulting spatial distributions of phytoplankton and zooplankton on the values of the biological parameters is determined, helping to explain the two-dimensional results. Significant differences are found between the NPZ and the other models as a result of the sinking of phytoplankton rather than detritus.

  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. 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.

  2. Comparison of tropical and temperate freshwater animal species' acute sensitivities to chemicals: implications for deriving safe extrapolation factors.

    PubMed

    Kwok, Kevin W H; Leung, Kenneth M Y; Lui, Gilbert S G; Chu, S Vincent K H; Lam, Paul K S; Morritt, David; Maltby, Lorraine; Brock, Theo C M; Van den Brink, Paul J; Warne, Michael St J; Crane, Mark

    2007-01-01

    Toxicity data for tropical species are often lacking for ecological risk assessment. Consequently, tropical and subtropical countries use water quality criteria (WQC) derived from temperate species (e.g., United States, Canada, or Europe) to assess ecological risks in their aquatic systems, leaving an unknown margin of uncertainty. To address this issue, we use species sensitivity distributions of freshwater animal species to determine whether temperate datasets are adequately protective of tropical species assemblages for 18 chemical substances. The results indicate that the relative sensitivities of tropical and temperate species are noticeably different for some of these chemicals. For most metals, temperate species tend to be more sensitive than their tropical counterparts. However, for un-ionized ammonia, phenol, and some pesticides (e.g., chlorpyrifos), tropical species are probably more sensitive. On the basis of the results from objective comparisons of the ratio between temperate and tropical hazardous concentration values for 10% of species, or the 90% protection level, we recommend that an extrapolation factor of 10 should be applied when such surrogate temperate WQCs are used for tropical or subtropical regions and a priori knowledge on the sensitivity of tropical species is very limited or not available.

  3. INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

    PubMed

    Manda, Prashanti; Mungall, Christopher J; Balhoff, James P; Lapp, Hilmar; Vision, Todd J

    2016-01-01

    There is growing use of ontologies for the measurement of cross-species phenotype similarity. Such similarity measurements contribute to diverse applications, such as identifying genetic models for human diseases, transferring knowledge among model organisms, and studying the genetic basis of evolutionary innovations. Two organismal features, whether genes, anatomical parts, or any other inherited feature, are considered to be homologous when they are evolutionarily derived from a single feature in a common ancestor. A classic example is the homology between the paired fins of fishes and vertebrate limbs. Anatomical ontologies that model the structural relations among parts may fail to include some known anatomical homologies unless they are deliberately added as separate axioms. The consequences of neglecting known homologies for applications that rely on such ontologies has not been well studied. Here, we examine how semantic similarity is affected when external homology knowledge is included. We measure phenotypic similarity between orthologous and non-orthologous gene pairs between humans and either mouse or zebrafish, and compare the inclusion of real with faux homology axioms. Semantic similarity was preferentially increased for orthologs when using real homology axioms, but only in the more divergent of the two species comparisons (human to zebrafish, not human to mouse), and the relative increase was less than 1% to non-orthologs. By contrast, inclusion of both real and faux random homology axioms preferentially increased similarities between genes that were initially more dissimilar in the other comparisons. Biologically meaningful increases in semantic similarity were seen for a select subset of gene pairs. Overall, the effect of including homology axioms on cross-species semantic similarity was modest at the levels of divergence examined here, but our results hint that it may be greater for more distant species comparisons.

  4. Comparison of metabolic profiles and bioactivities of the leaves of three edible Congolese Hibiscus species.

    PubMed

    Kapepula, Paulin Mutwale; Kabamba Ngombe, Nadege; Tshisekedi Tshibangu, Pascal; Tsumbu, César; Franck, Thierry; Mouithys-Mickalad, Ange; Mumba, Dieudonné; Tshala-Katumbay, Désiré; Serteyn, Didier; Tits, Monique; Angenot, Luc; Kalenda, Pascal Dibungi T; Frédérich, Michel

    2017-03-21

    Methanolic and dichloromethane extracts from the leaves of Congolese Hibiscus species were characterised by chromatographic and spectroscopic techniques and their in vitro biochemical activities against ROS production were evaluated in cellular models and on an enzyme, myeloperoxidase (MPO), involved in inflammation. Hibiscus acetosella has a chemical fingerprint different from Hibiscus cannabinus and Hibiscus sabdariffa both having similar fingerprints. Major compounds were polyphenols, represented mainly by caffeoyl-hydroxycitric acid for H. acetosella and neochlorogenic acid for the two other species. All extracts displayed high cellular antioxidant activity with IC50 values ranging from 0.5 to 3 μg mL(-1) using lucigenin on neutrophils. Dichloromethane extracts showed more efficient effects on extracellular ROS production and MPO activity. Antioxidant and anti-inflammatory activities of caffeoyl-hydroxycitric acid were significantly higher than those of neochlorogenic acid. The bioactivities of Hibiscus species were positively correlated with their phytochemical content and could justify their use as local nutraceutical resources and medicines.

  5. Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts

    PubMed Central

    Eisen, Jonathan A.; Kopp, Artyom

    2012-01-01

    The combination of ecological diversity with genetic and experimental tractability makes Drosophila a powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts in Drosophila physiology, behavior, and fitness, most recent work has focused on Drosophila-bacterial interactions. In order to get a more complete understanding of the Drosophila microbiome, we characterized the yeast communities associated with different Drosophila species collected around the world. We focused on the phylum Ascomycota because it constitutes the vast majority of the Drosophila-associated yeasts. Our sampling strategy allowed us to compare the distribution and structure of the yeast and bacterial communities in the same host populations. We show that yeast communities are dominated by a small number of abundant taxa, that the same yeast lineages are associated with different host species and populations, and that host diet has a greater effect than host species on yeast community composition. These patterns closely parallel those observed in Drosophila bacterial communities. However, we do not detect a significant correlation between the yeast and bacterial communities of the same host populations. Comparative analysis of different symbiont groups provides a more comprehensive picture of host-microbe interactions. Future work on the role of symbiont communities in animal physiology, ecological adaptation, and evolution would benefit from a similarly holistic approach. PMID:22885750

  6. 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.

  7. Comparison of dark energy models after Planck 2015

    NASA Astrophysics Data System (ADS)

    Xu, Yue-Yao; Zhang, Xin

    2016-11-01

    We make a comparison for ten typical, popular dark energy models according to their capabilities of fitting the current observational data. The observational data we use in this work include the JLA sample of type Ia supernovae observation, the Planck 2015 distance priors of cosmic microwave background observation, the baryon acoustic oscillations measurements, and the direct measurement of the Hubble constant. Since the models have different numbers of parameters, in order to make a fair comparison, we employ the Akaike and Bayesian information criteria to assess the worth of the models. The analysis results show that, according to the capability of explaining observations, the cosmological constant model is still the best one among all the dark energy models. The generalized Chaplygin gas model, the constant w model, and the α dark energy model are worse than the cosmological constant model, but still are good models compared to others. The holographic dark energy model, the new generalized Chaplygin gas model, and the Chevalliear-Polarski-Linder model can still fit the current observations well, but from an economically feasible perspective, they are not so good. The new agegraphic dark energy model, the Dvali-Gabadadze-Porrati model, and the Ricci dark energy model are excluded by the current observations.

  8. 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

  9. 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.

  10. Modeling metapopulation dynamics for single species of seabirds

    USGS Publications Warehouse

    Buckley, P.A.; Downer, R.; McCullough, D.R.; Barrett, R.H.

    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

  11. Comparisons of stemflow and its bio-/abiotic influential factors between two xerophytic shrub species

    NASA Astrophysics Data System (ADS)

    Yuan, Chuan; Gao, Guangyao; Fu, Bojie

    2017-03-01

    Stemflow transports nutrient-enriched precipitation to the rhizosphere and functions as an efficient terrestrial flux in water-stressed ecosystems. However, its ecological significance has generally been underestimated because it is relatively limited in amount, and the biotic mechanisms that affect it have not been thoroughly studied at the leaf scale. This study was conducted during the 2014 and 2015 rainy seasons at the northern Loess Plateau of China. We measured the branch stemflow volume (SFb), shrub stemflow equivalent water depth (SFd), stemflow percentage of incident precipitation (SF %), stemflow productivity (SFP), funnelling ratio (FR), the meteorological characteristics and the plant traits of branches and leaves of C. korshinskii and S. psammophila. This study evaluated stemflow efficiency for the first time with the combined results of SFP and FR, and sought to determine the inter- and intra-specific differences of stemflow yield and efficiency between the two species, as well as the specific bio-/abiotic mechanisms that affected stemflow. The results indicated that C. korshinskii had a greater stemflow yield and efficiency at all precipitation levels than that of S. psammophila. The largest inter-specific difference generally occurred at the 5-10 mm branches during rains of ≤ 2 mm. Precipitation amount was the most influential meteorological characteristic that affected stemflow yield and efficiency in these two endemic shrub species. Branch angle was the most influential plant trait on FR. For SFb, stem biomass and leaf biomass were the most influential plant traits for C. korshinskii and S. psammophila, respectively. For SFP of these two shrub species, leaf traits (the individual leaf area) and branch traits (branch size and biomass allocation pattern) had a great influence during lighter rains ≤ 10 mm and heavier rains > 15 mm, respectively. The lower precipitation threshold to start stemflow allowed C. korshinskii (0.9 mm vs. 2

  12. 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.

  13. A comparison of Mott cell morphology of three avian species. II. - Bad behavior by plasmacytes?

    PubMed

    Cotter, Paul F; Bakst, Murray R

    2017-02-01

    Mott cells are atypical plasmacytes recognized microscopically by endoplasmic reticulum (ER) distensions (Russell bodies) a result of retained secretory product (antibody). Originally associated with parasitism, they are observed in a broad spectrum of immunopathology, sometimes involving hypergammaglobulinemia. Few descriptions of Mott cells appear in avian literature. The purpose of the manuscript is to provide examples identified by light microscopy in three poultry species. Transmission electron micrographs (TEM) of plasmacytes from the turkey oviduct mucosa are included for comparison with Mott cell light microscopic images. Wright's stained blood and bone marrow from commercial and specific pathogen free (SPF) chickens, ducks, and turkeys are the sources. Mott cell positive samples commonly occurred with leukocytosis or leukemoid reactions, polymicrobial bacteremia, and fungemia. Atypical granulocytes and leukocytes regularly accompanied Mott cells. It is proposed that circulating Mott cells are "sentinels" indicative of stress, dyscrasia, and pathology. Moreover, Mott cells, like other atypia, complicate the interpretation of simple heterophil/lymphocyte (H/L) ratios. As Mott cells are defective plasmacytes these observations address hematology, immunology, pathology, and welfare issues.

  14. GCM radiation model-to-observation comparison

    SciTech Connect

    Ding, Ming; Wang, Wei-Chyung

    1996-12-31

    A general circulation model radiation model is compared to the concurrent meteorological and radiative flux measurement from the Atmospheric Radiation Measurement (ARM) program for the purpose of identifying and reducing uncertainties associated with cloud treatment. Three aspects are studied: clear sky condition, single-layer overcast sky condition, and multiple-layer fractional cloud condition. The radiation parameterization used is based on the GENESIS global model with some revisions. Data from the ARM site consists of meteorological observations and radiation measurements at the top of the atmosphere and at the surface. Good agreement between the model and observations is found in the outgoing longwave and shortwave flux at the top of the atmosphere for the clear sky and single-layer overcast conditions. The model overestimates the downward shortwave flux at the surface under clear sky condition and underestimates under single-layer overcast condition. Under the multiple-layer fractional cloud condition, a large uncertainty in the shortwave radiation calculation is associated with the cloud vertical overlapping assumption. 17 refs., 2 figs., 1 tab.

  15. A comparison between egg trancriptomes of cod and salmon reveals species-specific traits in eggs for each species.

    PubMed

    Wargelius, Anna; Furmanek, Tomasz; Montfort, Jérôme; Le Cam, Aurélie; Kleppe, Lene; Juanchich, Amelie; Edvardsen, Rolf B; Taranger, Geir Lasse; Bobe, Julien

    2015-05-01

    Fish in use in aquaculture display large variation in gamete biology. To reach better understanding around this issue, this study aims at identifying if species specific "egg life history traits" can be hidden in the unfertilized egg. This was done by investigating egg transcriptome differences between Atlantic salmon and Atlantic cod. Salmon and cod eggs were selected due to their largely differencing phenotypes. An oligo microarray analysis was performed on ovulated eggs from cod (n = 8) and salmon (n = 7). The arrays were normalized to a similar spectrum for both arrays. Both arrays were re-annotated with SWISS-Prot and KEGG genes to retrieve an official gene symbol and an orthologous KEGG annotation, in salmon and cod arrays this represented 14,009 and 7,437 genes respectively. The probe linked to the highest gene expression for that particular KEGG annotation was used to compare expression between species. Differential expression was calculated for genes that had an annotation with score >300, resulting in a total of 2,457 KEGG annotations (genes) being differently expressed between the species (FD > 2). This analysis revealed that immune, signal transduction and excretory related pathways were overrepresented in salmon compared to cod. The most overrepresented pathways in cod were related to regulation of genetic information processing and metabolism. To conclude this analysis clearly point at some distinct transcriptome repertoires for cod and salmon and that these differences may explain some of the species-specific biological features for salmon and cod eggs.

  16. 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...

  17. 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...

  18. 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

  19. An evolutionary explanation of the aggregation model of species coexistence.

    PubMed Central

    Rohlfs, Marko; Hoffmeister, Thomas S

    2003-01-01

    In ecology, the 'aggregation model of coexistence' provides a powerful concept to explain the unexpectedly high species richness of insects on ephemeral resources like dung pats, fruits, etc. It suggests that females aggregate their eggs across resource patches, which leads to an increased intraspecific competition within occupied patches and a relatively large number of patches that remain unoccupied. This provides competitor-free patches for heterospecifics, facilitating species coexistence. At first glance, deliberately causing competition among the females' own offspring and leaving resources to heterospecific competitors seems altruistic and incompatible with individual fitness maximization, raising the question of how natural selection operates in favour of egg aggregation on ephemeral resource patches. Allee effects that lead to fitness maxima at intermediate egg densities have been suggested, but not yet detected. Using drosophilid flies on decaying fruits as a study system, we demonstrate a hump-shaped relationship between egg density and individual survival probability, with maximum survivorship at intermediate densities. This pattern clearly selects for egg aggregation and resolves the possible conflict between the ecological concept of species coexistence on ephemeral resources and evolutionary theory. PMID:12952629

  20. Comparison of Mixed-Model Approaches for Association Mapping

    PubMed Central

    Stich, Benjamin; Möhring, Jens; Piepho, Hans-Peter; Heckenberger, Martin; Buckler, Edward S.; Melchinger, Albrecht E.

    2008-01-01

    Association-mapping methods promise to overcome the limitations of linkage-mapping methods. The main objectives of this study were to (i) evaluate various methods for association mapping in the autogamous species wheat using an empirical data set, (ii) determine a marker-based kinship matrix using a restricted maximum-likelihood (REML) estimate of the probability of two alleles at the same locus being identical in state but not identical by descent, and (iii) compare the results of association-mapping approaches based on adjusted entry means (two-step approaches) with the results of approaches in which the phenotypic data analysis and the association analysis were performed in one step (one-step approaches). On the basis of the phenotypic and genotypic data of 303 soft winter wheat (Triticum aestivum L.) inbreds, various association-mapping methods were evaluated. Spearman's rank correlation between P-values calculated on the basis of one- and two-stage association-mapping methods ranged from 0.63 to 0.93. The mixed-model association-mapping approaches using a kinship matrix estimated by REML are more appropriate for association mapping than the recently proposed QK method with respect to (i) the adherence to the nominal α-level and (ii) the adjusted power for detection of quantitative trait loci. Furthermore, we showed that our data set could be analyzed by using two-step approaches of the proposed association-mapping method without substantially increasing the empirical type I error rate in comparison to the corresponding one-step approaches. PMID:18245847

  1. Hydrodynamical comparison test of solar models

    NASA Astrophysics Data System (ADS)

    Bach, K.; Kim, Y.-C.

    2012-12-01

    We present three dimensional radiation-hydrodynamical (RHD) simulations for solar surface convection based on three most recent solar mixtures: Grevesse & Sauval (1998), Asplund, Grevesse & Sauval (2005), and Asplund, Grevesse, Sauval & Scott (2009). The outer convection zone of the Sun is an extremely turbulent region composed of partly ionized compressible gases at high temperature. The super-adiabatic layer (SAL) is the transition region where the transport of energy changes drastically from convection to radiation. In order to describe physical processes accurately, a realistic treatment of radiation should be considered as well as convection. However, newly updated solar mixtures that are established from radiation-hydrodynamics do not generate properly internal structures estimated by helioseismology. In order to address this fundamental problem, solar models are constructed consistently based on each mixture and used as initial configurations for radiation-hydrodynamical simulations. From our simulations, we find that the turbulent flows in each model are statistically similar in the SAL.

  2. Groundwater Models: a Comparison Using Field Data

    DTIC Science & Technology

    1989-04-01

    Water , U - Uz Treatment, Solute Transport, Computer 19. ABSTRACT (Continue on reverse if necessary and identify by block number) This report evaluates the...APPENDIX A TOPOGRAPHIC MAP OF THE NORTHERN HALF OF THE OTIS SEWAGE PLUME ....... ................... .. 165 B WATER TABLE MAP OF THE NORTHERN HALF OF THE...31 Water Table Contours in the Modeled Areas at Otis ... ...... 85 32 Three-Dimensional Diagram Showing Vertical Stratification of the Otis Sewage

  3. 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.

  4. 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.

  5. 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 Canberras 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.

  6. 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.

  7. An empirical probability model of detecting species at low densities.

    PubMed

    Delaney, David G; Leung, Brian

    2010-06-01

    False negatives, not detecting things that are actually present, are an important but understudied problem. False negatives are the result of our inability to perfectly detect species, especially those at low density such as endangered species or newly arriving introduced species. They reduce our ability to interpret presence-absence survey data and make sound management decisions (e.g., rapid response). To reduce the probability of false negatives, we need to compare the efficacy and sensitivity of different sampling approaches and quantify an unbiased estimate of the probability of detection. We conducted field experiments in the intertidal zone of New England and New York to test the sensitivity of two sampling approaches (quadrat vs. total area search, TAS), given different target characteristics (mobile vs. sessile). Using logistic regression we built detection curves for each sampling approach that related the sampling intensity and the density of targets to the probability of detection. The TAS approach reduced the probability of false negatives and detected targets faster than the quadrat approach. Mobility of targets increased the time to detection but did not affect detection success. Finally, we interpreted two years of presence-absence data on the distribution of the Asian shore crab (Hemigrapsus sanguineus) in New England and New York, using our probability model for false negatives. The type of experimental approach in this paper can help to reduce false negatives and increase our ability to detect species at low densities by refining sampling approaches, which can guide conservation strategies and management decisions in various areas of ecology such as conservation biology and invasion ecology.

  8. 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 ...

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. MICS-Asia II: Model inter-comparison and evaluation of acid deposition

    NASA Astrophysics Data System (ADS)

    Wang, Zifa; Xie, Fuying; Sakurai, T.; Ueda, H.; Han, Zhiwei; Carmichael, G. R.; Streets, D.; Engardt, M.; Holloway, T.; Hayami, H.; Kajino, M.; Thongboonchoo, N.; Bennet, C.; Park, S. U.; Fung, C.; Chang, A.; Sartelet, K.; Amann, M.

    This paper focuses on the comparison of chemical deposition of eight regional chemical models used in Model Inter-Comparison Study for Asia (MICS-Asia) II. Monthly-mean depositions of chemical species simulated by these models, including dry deposition of SO 2, HNO 3, NH 3, sulfate, nitrate and ammonium and wet deposition of SO 42-, NO 3- and NH 4+, have been provided for four periods (March, July, December 2001 and March 2002) in this work. Observations at 37 sites of the Acid Deposition Monitoring Network in East Asia (EANET) are compared with SO 42-, NO 3- and NH 4+ wet deposition model results. Significant correlations appeared between the observation and computed ensemble mean of participant models. Also, differences among modeled sulfur and nitrogen dry depositions have been studied at the EANET sites. Based on the analysis of acid deposition for various species from different models, total depositions of sulfur (SO 2 and sulfate) and nitrogen (nitrate and ammonium) have been evaluated as the ensemble mean of the eight models. In general, all models capture the observed spatial distribution of sulfur and nitrogen deposition, although the absolute values may differ from measurements. High deposition often occurs in eastern China, Japan, the Republic of Korea, Thailand, Vietnam, Philippines and other parts of Southeast Asia. The magnitude of model bias is quite large for many of the models. In examining the reasons for model-measurement disagreement, we find that differences in chemical processes, deposition parameterization, and modeled precipitation are the main reasons for large model disparities.

  14. Comparisons and Evaluation of Hall Thruster Models

    DTIC Science & Technology

    2007-11-02

    electromagnets and to be unaffected by the discharge, so that it can be treated as input data. Both models calculate , to facilitate the solution of the...large number of neutrals are calculated , where collisions are treated with random numbers. This approach is realistic but takes much computation time...cos, 232 vkT mvvvvvg     −∝ (8) where v is the speed, θ the angle with the axial direction, and φ an angle in the plane perpendicular to

  15. 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.

  16. 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.

  17. Brachypodium: a promising hub between model species and cereals.

    PubMed

    Girin, Thomas; David, Laure C; Chardin, Camille; Sibout, Richard; Krapp, Anne; Ferrario-Méry, Sylvie; Daniel-Vedele, Françoise

    2014-10-01

    Brachypodium distachyon was proposed as a model species for genetics and molecular genomics in cereals less than 10 years ago. It is now established as a standard for research on C3 cereals on a variety of topics, due to its close phylogenetic relationship with Triticeae crops such as wheat and barley, and to its simple genome, its minimal growth requirement, and its short life cycle. In this review, we first highlight the tools and resources for Brachypodium that are currently being developed and made available by the international community. We subsequently describe how this species has been used for comparative genomic studies together with cereal crops, before illustrating major research fields in which Brachypodium has been successfully used as a model: cell wall synthesis, plant-pathogen interactions, root architecture, and seed development. Finally, we discuss the usefulness of research on Brachypodium in order to improve nitrogen use efficiency in cereals, with the aim of reducing the amount of applied fertilizer while increasing the grain yield. Several paths are considered, namely an improvement of either nitrogen remobilization from the vegetative organs, nitrate uptake from the soil, or nitrate assimilation by the plant. Altogether, these examples position the research on Brachypodium as at an intermediate stage between basic research, carried out mainly in Arabidopsis, and applied research carried out on wheat and barley, enabling a complementarity of the studies and reciprocal benefits.

  18. 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.

  19. Predicting environmental suitability for a rare and threatened species (Lao newt, Laotriton laoensis) using validated species distribution models.

    PubMed

    Chunco, Amanda J; Phimmachak, Somphouthone; Sivongxay, Niane; Stuart, Bryan L

    2013-01-01

    The Lao newt (Laotriton laoensis) is a recently described species currently known only from northern Laos. Little is known about the species, but it is threatened as a result of overharvesting. We integrated field survey results with climate and altitude data to predict the geographic distribution of this species using the niche modeling program Maxent, and we validated these predictions by using interviews with local residents to confirm model predictions of presence and absence. The results of the validated Maxent models were then used to characterize the environmental conditions of areas predicted suitable for L. laoensis. Finally, we overlaid the resulting model with a map of current national protected areas in Laos to determine whether or not any land predicted to be suitable for this species is coincident with a national protected area. We found that both area under the curve (AUC) values and interview data provided strong support for the predictive power of these models, and we suggest that interview data could be used more widely in species distribution niche modeling. Our results further indicated that this species is mostly likely geographically restricted to high altitude regions (i.e., over 1,000 m elevation) in northern Laos and that only a minute fraction of suitable habitat is currently protected. This work thus emphasizes that increased protection efforts, including listing this species as endangered and the establishment of protected areas in the region predicted to be suitable for L. laoensis, are urgently needed.

  20. Three-species food web model with impulsive control strategy and chaos

    NASA Astrophysics Data System (ADS)

    Yu, Hengguo; Zhong, Shouming; Agarwal, Ravi P.; Sen, S. K.

    2011-02-01

    A three-species ecological model with impulsive control strategy is developed using the theory and methods of ecology and ordinary differential equation. Conditions for extinction of the system are given based on the theory of impulsive equation and small amplitude perturbation. Using comparison involving multiple Lyapunov functions, the system is shown to be permanent. Further, the influence of the impulsive perturbation on the inherent oscillation are studied numerically and is found to depict rich dynamics, such as the period-doubling bifurcation, the period-halving bifurcation, a chaotic band, a narrow or wide periodic window, and chaotic crises. In addition, the largest Lyapunov exponent is computed. This computation demonstrates the chaotic dynamic behavior of the model. The qualitative nature of concerned strange attractors is also investigated through their computed Fourier spectra. The foregoing results have the potential to be useful for the study of the dynamic complexity of ecosystems.

  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. 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.

  3. Incorporating a Process-Based Land Use Variable into Species- Distribution Modelling and an Estimated Probability of Species Occurrence Into a Land Change Model: A Case of Albania

    NASA Astrophysics Data System (ADS)

    Laze, Kuenda

    2016-08-01

    Modelling of land use may be improved by incorporating the results of species distribution modelling and species distribution modelling may be upgraded if a variable of the process-based variable of forest cover change or accessibility of forest from human settlement is included. This work presents the results of spatially explicit analyses of the changes in forest cover from 2000 to 2007 using the method of Geographically Weighted Regression (GWR) and of the species distribution for protected species of Lynx lynx martinoi, Ursus arctos using Generalized Linear Models (GLMs). The methodological approach is separately searching for a parsimonious model for forest cover change and species distribution for the entire territory of Albania. The findings of this work show that modelling of land change and of species distribution is indeed value-added by showing higher values of model selection of corrected Akaike Information Criterion. These results provide evidences on the effects of process-based variables on species distribution modelling and on the performance of species distribution modelling as well as show an example of the incorporation of estimated probability of species occurrences in a land change modelling.

  4. 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.

  5. Global Modeling of Uranium Molecular Species Formation Using Laser-Ablated Plasmas

    NASA Astrophysics Data System (ADS)

    Curreli, Davide; Finko, Mikhail; Azer, Magdi; Armstrong, Mike; Crowhurst, Jonathan; Radousky, Harry; Rose, Timothy; Stavrou, Elissaios; Weisz, David; Zaug, Joseph

    2016-10-01

    Uranium is chemically fractionated from other refractory elements in post-detonation nuclear debris but the mechanism is poorly understood. Fractionation alters the chemistry of the nuclear debris so that it no longer reflects the chemistry of the source weapon. The conditions of a condensing fireball can be simulated by a low-temperature plasma formed by vaporizing a uranium sample via laser heating. We have developed a global plasma kinetic model in order to model the chemical evolution of U/UOx species within an ablated plasma plume. The model allows to track the time evolution of the density and energy of an uranium plasma plume moving through an oxygen atmosphere of given fugacity, as well as other relevant quantities such as average electron and gas temperature. Comparison of model predictions with absorption spectroscopy of uranium-ablated plasmas provide preliminary insights on the key chemical species and evolution pathways involved during the fractionation process. This project was sponsored by the DoD, Defense Threat Reduction Agency, Grant HDTRA1-16-1-0020. This work was performed in part under the auspices of the U.S. DoE by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  6. Biochemical adaptations of notothenioid fishes: comparisons between cold temperate South American and New Zealand species and Antarctic species.

    PubMed

    Petricorena, Zulema L Coppes; Somero, George N

    2007-07-01

    Fishes of the perciform suborder Notothenioidei afford an excellent opportunity for studying the evolution and functional importance of diverse types of biochemical adaptation to temperature. Antarctic notothenioids have evolved numerous biochemical adaptations to stably cold waters, including antifreeze glycoproteins, which inhibit growth of ice crystals, and enzymatic proteins with cold-adapted specific activities (k(cat) values) and substrate binding abilities (K(m) values), which support metabolism at low temperatures. Antarctic notothenioids also exhibit the loss of certain biochemical traits that are ubiquitous in other fishes, including the heat-shock response (HSR) and, in members of the family Channichthyidae, hemoglobins and myoglobins. Tolerance of warm temperatures is also truncated in stenothermal Antarctic notothenioids. In contrast to Antarctic notothenioids, notothenioid species found in South American and New Zealand waters have biochemistries more reflective of cold-temperate environments. Some of the contemporary non-Antarctic notothenioids likely derive from ancestral species that evolved in the Antarctic and later "escaped" to lower latitude waters when the Antarctic Polar Front temporarily shifted northward during the late Miocene. Studies of cold-temperate notothenioids may enable the timing of critical events in the evolution of Antarctic notothenioids to be determined, notably the chronology of acquisition and amplification of antifreeze glycoprotein genes and the loss of the HSR. Genomic studies may reveal how the gene regulatory networks involved in acclimation to temperature differ between stenotherms like the Antarctic notothenioids and more eurythermal species like cold-temperate notothenioids. Comparative studies of Antarctic and cold-temperate notothenioids thus have high promise for revealing the mechanisms by which temperature-adaptive biochemical traits are acquired - or through which traits that cease to be of advantage under

  7. Comparison of three officinal Chinese pharmacopoeia species of Glycyrrhiza based on separation and quantification of triterpene saponins and chemometrics analysis.

    PubMed

    Tao, Weiwei; Duan, Jinao; Zhao, Runhuai; Li, Xueyu; Yan, Hui; Li, Jianping; Guo, Sheng; Yang, Nianyun; Tang, Yuping

    2013-12-01

    The dried roots and rhizomes of Glycyrrhiza species, named licorice, have been utilized as food as well as crude drugs in China for thousands of years. Glycyrrhiza species can be differentiated based on the morphologic features of their aerial part, i.e. leaf and fruit morphologies, but not on their root morphology, even though that is the medicinal part. In this paper, a fast and effective UPLC-TQ-MS/MS method was explored for better identification and quantitative investigation of triterpene saponins in licorice, which laid basis for chemical comparison of three officinal Chinese pharmacopoeia Glycyrrhiza species. The results showed that all of these licorice samples were rich in triterpene saponins but with significant difference corresponding to different Glycyrrhiza species. The proposed method could be useful in quality control and standardization of licorice raw materials and its products.

  8. Comparison and correlation of Simple Sequence Repeats distribution in genomes of Brucella species

    PubMed Central

    Kiran, Jangampalli Adi Pradeep; Chakravarthi, Veeraraghavulu Praveen; Kumar, Yellapu Nanda; Rekha, Somesula Swapna; Kruti, Srinivasan Shanthi; Bhaskar, Matcha

    2011-01-01

    Computational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested that over expressed tri-nucleotide SSRs in genomic and coding regions might be responsible in the generation of functional variation of proteins expressed which in turn may lead to different pathogenicity, virulence determinants, stress response genes, transcription regulators and host adaptation proteins of Brucella genomes. Abbreviations SSRs - Simple Sequence Repeats, ORFs - Open Reading Frames. PMID:21738309

  9. 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.

  10. 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.

  11. 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 ...

  12. 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.

  13. 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.

  14. 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.

  15. Reactivity of inorganic sulfide species toward a heme protein model.

    PubMed

    Bieza, Silvina A; Boubeta, Fernando; Feis, Alessandro; Smulevich, Giulietta; Estrin, Darío A; Boechi, Leonardo; Bari, Sara E

    2015-01-20

    The reactivity of inorganic sulfide species toward heme peptides was explored under biorelevant conditions in order to unravel the molecular details of the reactivity of the endogenous hydrogen sulfide toward heme proteins. Unlike ferric porphyrinates, which are reduced by inorganic sulfide, some heme proteins can form stable Fe(III)-sulfide adducts. To isolate the protein factors ruling the redox chemistry, we used as a system model, the undecapeptide microperoxidase (MP11), a heme peptide derived from cytochrome c proteolysis that retains the proximal histidine bound to the Fe(III) atom. Upon addition of gaseous hydrogen sulfide (H2S) at pH 6.8, the UV-vis spectra of MP11 closely resembled those of the low-spin ferric hydroxo complex (only attained at an alkaline pH) and cysteine or alkylthiol derivatives, suggesting that the Fe(III) reduction was prevented. The low-frequency region of the resonance Raman spectrum revealed the presence of an Fe(III)-S band at 366 cm(-1) and the general features of a low-spin hexacoordinated heme. Anhydrous sodium sulfide (Na2S) was the source of sulfide of choice for the kinetic evaluation of the process. Theoretical calculations showed no distal stabilization mechanisms for bound sulfide species in MP11, highlighting a key role of the proximal histidine for the stabilization of the Fe(III)-S adducts of heme compounds devoid of distal counterparts, which is significant with regard to the biochemical reactivity of endogenous hydrogen sulfide.

  16. 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.

  17. 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

  18. Defining Predictive Probability Functions for Species Sampling Models.

    PubMed

    Lee, Jaeyong; Quintana, Fernando A; Müller, Peter; Trippa, Lorenzo

    2013-01-01

    We review the class of species sampling models (SSM). In particular, we investigate the relation between the exchangeable partition probability function (EPPF) and the predictive probability function (PPF). It is straightforward to define a PPF from an EPPF, but the converse is not necessarily true. In this paper we introduce the notion of putative PPFs and show novel conditions for a putative PPF to define an EPPF. We show that all possible PPFs in a certain class have to define (unnormalized) probabilities for cluster membership that are linear in cluster size. We give a new necessary and sufficient condition for arbitrary putative PPFs to define an EPPF. Finally, we show posterior inference for a large class of SSMs with a PPF that is not linear in cluster size and discuss a numerical method to derive its PPF.

  19. 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.

  20. MODEL COMPARISON FOR THE DENSITY STRUCTURE ACROSS SOLAR CORONAL WAVEGUIDES

    SciTech Connect

    Arregui, I.; Asensio Ramos, A.

    2015-10-01

    The spatial variation of physical quantities, such as the mass density, across solar atmospheric waveguides governs the timescales and spatial scales for wave damping and energy dissipation. The direct measurement of the spatial distribution of density, however, is difficult, and indirect seismology inversion methods have been suggested as an alternative. We applied Bayesian inference, model comparison, and model-averaging techniques to the inference of the cross-field density structuring in solar magnetic waveguides using information on periods and damping times for resonantly damped magnetohydrodynamic transverse kink oscillations. Three commonly employed alternative profiles were used to model the variation of the mass density across the waveguide boundary. Parameter inference enabled us to obtain information on physical quantities such as the Alfvén travel time, the density contrast, and the transverse inhomogeneity length scale. The inference results from alternative density models were compared and their differences quantified. Then, the relative plausibility of the considered models was assessed by performing model comparison. Our results indicate that the evidence in favor of any of the three models is minimal, unless the oscillations are strongly damped. In such a circumstance, the application of model-averaging techniques enables the computation of an evidence-weighted inference that takes into account the plausibility of each model in the calculation of a combined inversion for the unknown physical parameters.

  1. Model Comparison for the Density Structure across Solar Coronal Waveguides

    NASA Astrophysics Data System (ADS)

    Arregui, I.; Soler, R.; Asensio Ramos, A.

    2015-10-01

    The spatial variation of physical quantities, such as the mass density, across solar atmospheric waveguides governs the timescales and spatial scales for wave damping and energy dissipation. The direct measurement of the spatial distribution of density, however, is difficult, and indirect seismology inversion methods have been suggested as an alternative. We applied Bayesian inference, model comparison, and model-averaging techniques to the inference of the cross-field density structuring in solar magnetic waveguides using information on periods and damping times for resonantly damped magnetohydrodynamic transverse kink oscillations. Three commonly employed alternative profiles were used to model the variation of the mass density across the waveguide boundary. Parameter inference enabled us to obtain information on physical quantities such as the Alfvén travel time, the density contrast, and the transverse inhomogeneity length scale. The inference results from alternative density models were compared and their differences quantified. Then, the relative plausibility of the considered models was assessed by performing model comparison. Our results indicate that the evidence in favor of any of the three models is minimal, unless the oscillations are strongly damped. In such a circumstance, the application of model-averaging techniques enables the computation of an evidence-weighted inference that takes into account the plausibility of each model in the calculation of a combined inversion for the unknown physical parameters.

  2. 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

  3. 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.

  4. 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)…

  5. 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.

  6. 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

  7. 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.

  8. Comparison of single neuron models in terms of synchronization propensity

    NASA Astrophysics Data System (ADS)

    Sungar, N.; Allaria, E.; Leyva, I.; Arecchi, F. T.

    2008-09-01

    A plausible model for coherent perception is the synchronization of chaotically distributed neural spike trains over wide cortical areas. A recently introduced propensity criterion provides a tool for a quantitative comparison of different neuron models in terms of their ability to synchronize to an applied perturbation. We explore the propensity of several systems and indicate the requirements to be satisfied by a plausible candidate for modeling neuronal activity. Our results show that the conflicting requirements of stability and sensitivity leading to high propensity to synchronization can be satisfied by a strongly nonuniform attractor made of two distinct regions: a saddle focus plus a sufficiently separated saddle node.

  9. Quantitative analysis of neocortical gyrencephaly in African elephants (Loxodonta africana) and six species of cetaceans: comparison with other mammals.

    PubMed

    Manger, Paul R; Prowse, Michelle; Haagensen, Mark; Hemingway, Jason

    2012-08-01

    This study provides quantitative data on the extent of gyrencephaly in the large-brained African elephant and several species of cetaceans (from smaller to larger brained) in comparison with other mammals. Across three mammalian orders (primates, carnivores, and artiodactyls), the species with the larger brains are more gyrencephalic with each order, exhibiting a specific negative allometry. The African elephant, with a 5-kg brain, has a gyrencephalic index (GI) of 3.89, which, though highly gyrencephalic, is not more so than would be predicted for a mammal with a 5-kg brain. The cetaceans had an average GI of 5.43, are the most gyrencephalic mammals studied to date, and are more gyrencephalic than one would predict based on comparison with other mammals. No relationship between brain mass and GI was evident in the cetaceans as seen in other mammals, with all cetaceans showing similar GIs irrespective of brain mass (range of GI 5.23-5.70, range of brain mass 577-5617 g). This is yet another parameter indicating cetaceans to be neuroanatomical outliers. Two species of pinnipeds studied had GIs that were well above those seen for terrestrial carnivores, and the aquatic manatee was close to lissencephalic. Thus, all three groups of marine mammals showed unusual extents of cortical gyrencephaly, indicating a morphological alteration of the telencephalon associated with the return to the marine environment. The analysis suggests that cortical thickness and neuronal density are important factors in determining the extent of gyrencephaly across mammalian species.

  10. Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.

    PubMed

    Latouche, G N; Daniel, H M; Lee, O C; Mitchell, T G; Sorrell, T C; Meyer, W

    1997-12-01

    A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers.

  11. Comparison of use of phenotypic and genotypic characteristics for identification of species of the anamorph genus Candida and related teleomorph yeast species.

    PubMed Central

    Latouche, G N; Daniel, H M; Lee, O C; Mitchell, T G; Sorrell, T C; Meyer, W

    1997-01-01

    A total of 49 type and neotype isolates and 32 clinical isolates of the anamorph genus Candida and related teleomorph genera were obtained from different culture collections and clinical laboratories. Isolates were subjected to two phenotypic methods of identification, Vitek yeast biochemical card (YBC) and API ID 32C, both based on carbohydrate assimilation, and one genotypic method, PCR fingerprinting, based on the detection of DNA polymorphisms between minisatellite-specific sequences with the primer M13 (5' GAGGGTGGCGGTTCT 3'). The correct identification of a strain at the Centraalbureau voor Schimmelcultures was used as the gold standard for the identification of an isolate. When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively. When uncommon species were added to the study, several of which are not included in the databases, the identification efficiencies were 76.5 and 77.5%, respectively. By comparison, all isolates were correctly identified by PCR fingerprinting, with 63 reference species profiles in the databank. Sufficient polymorphisms among the total set of banding patterns were observed, with adequate similarity in the major patterns obtained from a given species, to allow each isolate to be assigned unambiguously to a particular species. In addition, variations in minor bands allowed for differentiation to the strain level. PCR fingerprinting was found to be rapid, reproducible, and more cost-effective than either biochemical approach. Our results provide reference laboratories with an improved identification method for yeasts based on genotypic rather than phenotypic markers. PMID:9399515

  12. 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

  13. 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.

  14. No more non-model species: the promise of next generation sequencing for comparative immunology.

    PubMed

    Dheilly, Nolwenn M; Adema, Coen; Raftos, David A; Gourbal, Benjamin; Grunau, Christoph; Du Pasquier, Louis

    2014-07-01

    Next generation sequencing (NGS) allows for the rapid, comprehensive and cost effective analysis of entire genomes and transcriptomes. NGS provides approaches for immune response gene discovery, profiling gene expression over the course of parasitosis, studying mechanisms of diversification of immune receptors and investigating the role of epigenetic mechanisms in regulating immune gene expression and/or diversification. NGS will allow meaningful comparisons to be made between organisms from different taxa in an effort to understand the selection of diverse strategies for host defence under different environmental pathogen pressures. At the same time, it will reveal the shared and unique components of the immunological toolkit and basic functional aspects that are essential for immune defence throughout the living world. In this review, we argue that NGS will revolutionize our understanding of immune responses throughout the animal kingdom because the depth of information it provides will circumvent the need to concentrate on a few "model" species.

  15. 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.

  16. Comparison of endemic and exotic entomopathogenic nematode species for control of Colorado potato beetle (Coleoptera: Chrysomelidae).

    PubMed

    Berry, R E; Liu, J; Reed, G

    1997-12-01

    We compared the efficacy of 2 endemic strains of entomopathogenic nematodes isolated from Hermiston, OR, with that of 3 exotic nematode species for control of Colorado potato beetle, Leptinotarsa decemlineata (Say). In laboratory experiments, the exotic Heterorhabditis species were more pathogenic to Colorado potato beetle than were the endemic Heterorhabditis strains. Exotic Steinernema species were less pathogenic to Colorado potato beetle than the exotic Heterorhabditis species. No Colorado potato beetle adults emerged from soil treated with H. marelatus Liu & Berry, a new species collected from Seaside, OR. Nematode pathogenicity was detected up to 14 wk after application in Galleria mellonella (L.) in soil taken from field plots treated with endemic and exotic nematode species.

  17. 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.

  18. Comparison of Observed and Modelled Thermospheric Winds Above Northern Scandinavia

    NASA Astrophysics Data System (ADS)

    Henley, E.; Bushell, A. C.; Jackson, D.; Guio, P.; Aruliah, A. L.; Häggström, I.

    2015-12-01

    ESPAS (www.espas-fp7.eu) is an EU FP7 e-infrastructure project which provides a platform to access many different observations and model results for the near-Earth space environment, and through metadata allows searching for different data sharing a common time, spatial volume, or phenomenon etc. As part of work to demonstrate a use case for ESPAS, the Met Office has compared modelled thermospheric winds above northern Scandinavia with observations available through ESPAS. This has principally relied upon winds from UCL's CMAT2 model (also available through ESPAS), which are compared to wind observations made using UCL's Fabry-Perot interferometer (FPI) measurements of airglow above sites such as Svalbard and Kiruna. We will present the results of these comparisons, discussing them in the context of assessing thermospheric model performance, notably as independent measurements when considering data assimilation experiments, but also for gross model issues such as polar cap convection cell positions. Further work will also be presented, refining the FPI-model comparison using collocated incoherent scatter radar measurements from EISCAT to distinguish times where the FPI measurements are likely to be contaminated by auroral emissions at lower altitudes than the airglow emissions, thereby ensuring FPI measurements are only compared to model winds at the appropriate altitude.

  19. 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.

  20. A comparison of inbreeding depression in tropical and widespread Drosophila species.

    PubMed

    Bechsgaard, Jesper S; Hoffmann, Ary A; Sgró, Carla; Loeschcke, Volker; Bilde, Trine; Kristensen, Torsten N

    2013-01-01

    The evolutionary history of widespread and specialized species is likely to cause a different genetic architecture of key ecological traits in the two species groups. This may affect how these two groups respond to inbreeding. Here we investigate inbreeding effects in traits related to performance in 5 widespread and 5 tropical restricted species of Drosophila with the aim of testing whether the two species groups suffered differently from inbreeding depression. The traits investigated were egg-to-adult viability, developmental time and resistance to heat, cold and desiccation. Our results showed that levels of inbreeding depression were species and trait specific and did not differ between the species groups for stress resistance traits. However, for the life history traits developmental time and egg-to adult viability, more inbreeding depression was observed in the tropical species. The results reported suggest that for life history traits tropical species of Drosophila will suffer more from inbreeding depression than widespread species in case of increases in the rate of inbreeding e.g. due to declines in population sizes.

  1. Cognitive representation in transitive inference: a comparison of four corvid species.

    PubMed

    Bond, Alan B; Wei, Cynthia A; Kamil, Alan C

    2010-10-01

    During operant transitive inference experiments, subjects are trained on adjacent stimulus pairs in an implicit linear hierarchy in which responses to higher ranked stimuli are rewarded. Two contrasting forms of cognitive representation are often used to explain resulting choice behavior. Associative representation is based on memory for the reward history of each stimulus. Relational representation depends on memory for the context in which stimuli have been presented. Natural history characteristics that require accurate configural memory, such as social complexity or reliance on cached food, should tend to promote greater use of relational representation. To test this hypothesis, four corvid species with contrasting natural histories were trained on the transitive inference task: pinyon jays, Gymnorhinus cyanocephalus; Clark's nutcrackers, Nucifraga columbiana; azure-winged magpies, Cyanopica cyanus; and western scrub jays, Aphelocoma californica. A simplified computer model of associative representation displayed a characteristic pattern of accuracy as a function of position in the hierarchy. Analysis of the deviation of each subject's performance from this predicted pattern yielded an index of reliance on relational representation. Regression of index scores against rankings of social complexity and caching reliance indicated that both traits were significantly and independently associated with greater use of relational representation.

  2. ACAT-selective and nonselective DGAT1 inhibition: adrenocortical effects--a cross-species comparison.

    PubMed

    Floettmann, Jan Eike; Buckett, Linda K; Turnbull, Andrew V; Smith, Tim; Hallberg, Carina; Birch, Alan; Lees, David; Jones, Huw B

    2013-01-01

    Acyl-coenzyme A: cholesterol O-Acyltransferase (ACAT) and Acyl-coenzyme A: diacylglycerol O-acyltransferase (DGAT) enzymes play important roles in synthesizing neutral lipids, and inhibitors of these enzymes have been investigated as potential treatments for diabetes and other metabolic diseases. Administration of a Acyl-coenzyme A: diacylglycerol O-acyltransferase 1 (DGAT1) inhibitor with very limited cellular selectivity over ACAT resulted in significant adrenocortical degenerative changes in dogs. These changes included macrosteatotic vacuolation associated with adrenocyte cell death in the zonae glomerulosa and fasciculata and minimal to substantial mixed inflammatory cell infiltration and were similar to those described previously for some ACAT inhibitors in dogs. In the mouse, similar but only transient adrenocortical degenerative changes were seen as well as a distinctive nondegenerative reduction in cortical fine vacuolation. In the marmoset, only the distinctive nondegenerative reduction in cortical fine vacuolation was observed, suggesting that the dog, followed by the mouse, is the most sensitive species for cortical degeneration. Biochemical analysis of adrenal cholesterol and cholesteryl ester indicated that the distinctive reduction in cortical fine vacuolation correlated with a significant reduction in cholesteryl ester in the mouse and marmoset, whereas no significant reduction in cholestryl ester, but an increase in free cholesterol was observed in dogs. Administration of a DGAT1 inhibitor with markedly improved selectivity over ACAT to the marmoset and the mouse resulted in no adrenal pathology at exposures sufficient to cause substantial DGAT1 but not ACAT inhibition, thereby implicating ACAT rather than DGAT1 inhibition as the probable cause of the observed adrenal changes. Recognizing that the distinctive nondegenerative reduction in cortical fine vacuolation in the mouse could be used as a histopathological biomarker for an in vivo model of

  3. Mechanisms underlying the toxic effects of antimony species in human embryonic kidney cells (HEK-293) and their comparison with arsenic species.

    PubMed

    Verdugo, Marcelo; Ogra, Yasumitsu; Quiroz, Waldo

    2016-01-01

    Antimony cytotoxicity was assessed in human embryonic kidney cells (HEK-293). Uptake, mitochondrial respiratory activity, ROS generation and diffusional kinetics were measured using fluorescence recovery after photobleaching (FRAP). Furthermore, the toxic effect induced by Sb was compared with As toxicity in regard to ROS generation and diffusional kinetics, which provides information on the protein aggregation process. Our results show a favored uptake of Sb(III) and a more severe effect, decreasing the mitochondrial activity more than in the presence of Sb(V). In comparison with As, the Sb species did not generate a significant increase in ROS generation, which was observed with As(III) and As(V). FRAP analysis yielded important information on the diffusion and binding dynamics of live cells in presence of these metalloids. The mobile fraction showed a strong decrease with the As species and Sb(III). The diffusion rate and the koff-rate were significantly decreased for the As and Sb species but were more strong in the presence of As(III).

  4. Protein structure comparison using the markov transition model of evolution.

    PubMed

    Kawabata, T; Nishikawa, K

    2000-10-01

    A number of automatic protein structure comparison methods have been proposed; however, their similarity score functions are often decided by the researchers' intuition and trial-and-error, and not by theoretical background. We propose a novel theory to evaluate protein structure similarity, which is based on the Markov transition model of evolution. Our similarity score between structures i and j is defined as log P(j --> i)/P(i), where P(j --> i) is the probability that structure j changes to structure i during the evolutionary process, and P(i) is the probability that structure i appears by chance. This is a reasonable definition of structure similarity, especially for finding evolutionarily related (homologous) similarity. The probability P(j --> i) is estimated by the Markov transition model, which is similar to the Dayhoff's substitution model between amino acids. To estimate the parameters of the model, homologous protein structure pairs are collected using sequence similarity, and the numbers of structure transitions within the pairs are counted. Next these numbers are transformed to a transition probability matrix of the Markov transition. Transition probabilities for longer time are obtained by multiplying the probability matrix by itself several times. In this study, we generated three types of structure similarity scores: an environment score, a residue-residue distance score, and a secondary structure elements (SSE) score. Using these scores, we developed the structure comparison program, Matras (MArkovian TRAnsition of protein Structure). It employs a hierarchical alignment algorithm, in which a rough alignment is first obtained by SSEs, and then is improved with more detailed functions. We attempted an all-versus-all comparison of the SCOP database, and evaluated its ability to recognize a superfamily relationship, which was manually assigned to be homologous in the SCOP database. A comparison with the FSSP database shows that our program can

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

    PubMed Central

    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

  6. Classifiers as a model-free group comparison test.

    PubMed

    Kim, Bommae; Oertzen, Timo von

    2017-04-03

    The conventional statistical methods to detect group differences assume correct model specification, including the origin of difference. Researchers should be able to identify a source of group differences and choose a corresponding method. In this paper, we propose a new approach of group comparison without model specification using classification algorithms in machine learning. In this approach, the classification accuracy is evaluated against a binomial distribution using Independent Validation. As an application example, we examined false-positive errors and statistical power of support vector machines to detect group differences in comparison to conventional statistical tests such as t test, Levene's test, K-S test, Fisher's z-transformation, and MANOVA. The SVMs detected group differences regardless of their origins (mean, variance, distribution shape, and covariance), and showed comparably consistent power across conditions. When a group difference originated from a single source, the statistical power of SVMs was lower than the most appropriate conventional test of the study condition; however, the power of SVMs increased when differences originated from multiple sources. Moreover, SVMs showed substantially improved performance with more variables than with fewer variables. Most importantly, SVMs were applicable to any types of data without sophisticated model specification. This study demonstrates a new application of classification algorithms as an alternative or complement to the conventional group comparison test. With the proposed approach, researchers can test two-sample data even when they are not certain which statistical test to use or when data violates the statistical assumptions of conventional methods.

  7. 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...

  8. Comparison and analysis of tropospheric scintillation models for Northern Malaysia

    NASA Astrophysics Data System (ADS)

    Mandeep, J. S.; Yee, Anthony Cheng Chen; Abdullah, M.; Tariqul, M.

    2011-07-01

    This paper presents the results of a study on tropospheric scintillation on satellite link that has been performed at University Sains Malaysia (USM) to obtain statistics of scintillation from the 12.255 GHz Superbird-C satellite with an elevation angle of 40.1°. Comparison of existing tropospheric scintillation models, namely the International Telecommunication Union (ITU), Direct Physical-Statistical Prediction (DPSP), Modeled Physical-Statistical Prediction (MPSP), Kamp-Tervonen-Salonen (KVS), and Karasawa were done for the measurement site. Then, cumulative distributions of measured scintillation intensity compared to the result of the prediction models for tropospheric scintillation were plotted and analyzed. ITU-R model gave the best prediction of 5.8% of error at 0.1% of fading time, compared with the other models.

  9. 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.

  10. 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.

  11. Comparison of Solar Energetic Particle Flux Mapping Models

    NASA Astrophysics Data System (ADS)

    Young, S. L.; Roth, C. M.; Brodowski, C. M.; Kress, B. T.; Johnston, W. R.; Huston, S. L.; McCollough, J. P., II; Wilson, G.; Selesnick, R.

    2015-12-01

    Previous work using the Tsyganenko-Sitnov 2005 (TS05) magnetic field model combined withthe Dartmouth-CISM (DC) cutoff code to map GOES-7 SEM observations to CRRES locationshas demonstrated that, for reasonably static magnetospheric conditions, solar energetic particleobservations at GOES-7 can be mapped relatively accurately to locations inside of geosynchronouswhere L > 4.5. Also a good correlation with observations continues to approximately L = 3.5. Aprevious comparison of the TS05-DC combination with two other cutoff models found it to be themost accurate of the set when compared to SAMPEX observations in a LEO orbit. However, theTS05-DC combination requires significant computational resources compared to other models soit is important to quantify the difference in accuracy for operational purposes. In this study wecharacterize the Smart and Shea (SS) cutoff code and the Selesnick-Neal-Ogliore (SNO) model andcompare them to the TS05-DC cutoff model.

  12. 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

  13. 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

    2016-04-14

    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).

  14. Hydrogen species

    NASA Technical Reports Server (NTRS)

    Schiff, H. I.; Burnett, C.; Carli, B.; Dezafra, R.; Evans, W. F. J.; Guthrie, P. D.; Hampson, R. F.; Heaps, W.; Jones, R.; Kley, D.

    1985-01-01

    Measurements of the members of the HO(x) family (OH, HO2, and H2O2) and their major source gases, H2O, and CH4 are discussed. Emphasis is placed on measurements which were made since the 1982 World Meteorologic Organization (WMO) report. Measurement techniques, available data, an assessment of data reliability, and a comparison of the data with theoretical distributions of stratospheric HO(x) species predicted from one and two dimensional photochemical models are discussed.

  15. 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.

  16. 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.

  17. 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

  18. 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.

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

    DOE PAGES

    Jozefik, Zoltan; Kerstein, Alan R.; Schmidt, Heiko; ...

    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

  20. 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.

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

    PubMed

    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.

  2. 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.

  3. Comparison of the prevalence of Mycoplasma species in dogs with and without respiratory disease.

    PubMed

    Schulz, Bianka S; Raufeisen, Katharina; Weber, Karin; Laberke, Siija; Hartmann, Katrin

    2015-01-01

    Aim of the study was to investigate the prevalence of Mycoplasma species in dogs with and without signs of respiratory disease. Bronchoalveolarlavage fluid (BALF) and pharyngeal swabs were collected from 29 dogs with respiratory diseases (RD) and 16 dogs without signs of RD that were euthanised because of other diseases. Samples were tested for Mycoplasma species by PCR and culture, and sequencing was performed in Mycoplasma species-positive BALF samples. Pharyngeal swabs were positive for Mycoplasma species by PCR in 91.7% of dogs with RD and 86.7% of dogs without signs of RD (p = 1.000); BALF samples were PCR-positive in 37.9% of dogs with RD and 18.8% of dogs without signs of RD (p = 0.194) Mycoplasmo culture of BALF was positive in 28.6% of dogs with RD and in 18.8% without signs of RD (p = 0.730). When culture and PCR were compared, there was no significant difference in the detection rate of Mycoplasma species (p = 0.658) Sequencing detected different Mycoplasma species. Out of these, however, Mycoplasma cynos was isolated from four dogs with RD. There is no significant difference in the prevalence of Mycoplasma species between dogs with RD and dogs without evidence of RD; however, Mycoplasma cynos seems to be associated with respiratory disease.

  4. Comparison of specific versus literature species sensitivity distributions for herbicides risk assessment.

    PubMed

    Larras, Floriane; Gregorio, Vincent; Bouchez, Agnès; Montuelle, Bernard; Chèvre, Nathalie

    2016-02-01

    Species sensitivity distributions (SSDs) are an important predictive tool in risk assessment. Usually, literature data are used to build SSDs that are mostly based on planktonic species. But, to get adequate protective thresholds for environmental communities, one could argue that SSD should be built on ecotoxicological data obtained from species found in the ecosystem that should be protected. This is particularly true when benthic algae are of concern. Due to the lack of literature data, building SSD on benthic microalgae is difficult. This paper aims in comparing SSDs, and thus protective thresholds (hazardous concentration that affects 5% of the species of a community, HC5), built on ecotoxicological data obtained (1) from literature and (2) with specific bioassays on benthic diatoms from a lake. Thresholds were derived for protection against four herbicides separately and for a mixture of them. Sensitivity data obtained from literature were statistically lower than the specific data for all herbicides: Species tested in the literature were usually more sensitive (mainly chlorophytes), leading to more protective lower HC5. The HC5 thresholds (literature or specific) derived for protection against the mixture were also compared to the observed sensitivity of an assemblage of benthic diatom species exposed to an increasing range of herbicide mixture concentrations. We observed that one species within the assemblage (Fragilaria rumpens) was affected at a concentration below both the literature and the specific HC5 thresholds.

  5. [The Littorina species of the European coasts: No model for the evolution of terrestrial gastropods].

    PubMed

    Remmert, Hermann

    1968-12-01

    The Littorina-species of the European coasts are completely isoosmotic with their environment.Small specimens (species) have very small gills; with increasing size the gills grow rapidly. The gills of different species of identical size show no difference. The reproduction does not trend towards direct development parallel to the habitat of the species.Therefore the Littorina species are no model for the evolution of terrestrial gastropods, their characteristics are merely those of intertidal animals.

  6. Use of dynamic soil-vegetation models to assess impacts of nitrogen deposition on plant species composition: an overview.

    PubMed

    De Vries, W; Wamelink, G W W; Van Dobben, H; Kros, J; Reinds, G J; Mol-Dijkstra, J P; Smart, S M; Evans, C D; Rowe, E C; Belyazid, S; Sverdrup, H U; Van Hinsberg, A; Posch, M; Hettelingh, J-P; Spranger, T; Bobbink, R

    2010-01-01

    Field observations and experimental data of effects of nitrogen (N) deposition on plant species diversity have been used to derive empirical critical N loads for various ecosystems. The great advantage of such an approach is the inclusion of field evidence, but there are also restrictions, such as the absence of explicit criteria regarding significant effects on the vegetation, and the impossibility to predict future impacts when N deposition changes. Model approaches can account for this. In this paper, we review the possibilities of static and dynamic multispecies models in combination with dynamic soil-vegetation models to (1) predict plant species composition as a function of atmospheric N deposition and (2) calculate critical N loads in relation to a prescribed protection level of the species composition. The similarities between the models are presented, but also several important differences, including the use of different indicators for N and acidity and the prediction of individual plant species vs. plant communities. A summary of the strengths and weaknesses of the various models, including their validation status, is given. Furthermore, examples are given of critical load calculations with the model chains and their comparison with empirical critical N loads. We show that linked biogeochemistry-biodiversity models for N have potential for applications to support European policy to reduce N input, but the definition of damage thresholds for terrestrial biodiversity represents a major challenge. There is also a clear need for further testing and validation of the models against long-term monitoring or long-term experimental data sets and against large-scale survey data. This requires a focused data collection in Europe, combing vegetation descriptions with variables affecting the species diversity, such as soil acidity, nutrient status and water availability. Finally, there is a need for adaptation and upscaling of the models beyond the regions for which

  7. Comparison of models for predicting landfill methane recovery. Final report

    SciTech Connect

    Vogt, W.G.; Augenstein, D.

    1997-03-01

    Landfill methane models are tools used to project methane generation over time from a mass of landfilled waste. These models are used for sizing landfill gas (LFG) collection systems, evaluations and projections of LFG energy uses, and regulatory purposes. The objective of this project was to select various landfill methane models and to provide a comparison of model outputs to actual long-term gas recovery data from a number of well managed and suitable landfills. Another objective was to use these data to develop better estimates of confidence limits that can be assigned to model projections. This project assessed trial model forms against field data from available landfills where methane extraction was maximized, waste filling history was well-documented, and other pertinent site information was of superior quality. Data were obtained from 18 US landfills. Four landfill methane models were compared: a zero-order, a simple first order, a modified first order, and a multi-phase first order model. Models were adjusted for best fit to field data to yield parameter combinations based on the minimized residual errors between predicted and experienced methane recovery. The models were optimized in this way using two data treatments: absolute value of the differences (arithmetic error minimization) and absolute value of the natural log of the ratios (logarithmic error minimization).

  8. Immigration rates and species niche characteristics affect the relationship between species richness and habitat heterogeneity in modeled meta-communities.

    PubMed

    Bar-Massada, Avi

    2015-01-01

    The positive relationship between habitat heterogeneity and species richness is a cornerstone of ecology. Recently, it was suggested that this relationship should be unimodal rather than linear due to a tradeoff between environmental heterogeneity and population sizes. Increased environmental heterogeneity will decrease effective habitat sizes, which in turn will increase the rate of local species extinctions. The occurrence of the unimodal richness-heterogeneity relationship at the habitat scale was confirmed in both empirical and theoretical studies. However, it is unclear whether it can occur at broader spatial scales, for meta-communities in diverse and patchy landscapes. Here, I used a spatially explicit meta-community model to quantify the roles of two species-level characteristics, niche width and immigration rates, on the type of the richness-heterogeneity relationship at the landscape scale. I found that both positive and unimodal richness-heterogeneity relationships can occur in meta-communities in patchy landscapes. The type of the relationship was affected by the interactions between inter-patch immigration rates and species' niche widths. Unimodal relationships were prominent in meta-communities comprising species with wide niches but low inter-patch immigration rates. In contrast, meta-communities consisting of species with narrow niches and high immigration rates exhibited positive relationships. Meta-communities comprising generalist species are therefore likely to exhibit unimodal richness-heterogeneity relationships as long as low immigration rates prevent rescue effects and patches are small. The richness-heterogeneity relationship at the landscape scale is dictated by species' niche widths and inter-patch immigration rates. These immigration rates, in turn, depend on the interaction between species dispersal capabilities and habitat connectivity, highlighting the roles of both species traits and landscape structure in generating the richness

  9. Comparison of software models for energy savings from cool roofs

    DOE PAGES

    New, Joshua; Miller, William A.; Huang, Yu; ...

    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

  10. 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.

  11. 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.

  12. 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.

  13. Comparison of fecal microbiota of three captive carnivore species inhabiting Korea

    PubMed Central

    AN, Choa; OKAMOTO, Yumiko; XU, Siyu; EO, Kyung Yeon; KIMURA, Junpei; YAMAMOTO, Naomichi

    2016-01-01

    This study aimed at characterizing fecal microbiota of three captive carnivore species of leopard cats Prionailurus bengalensis, Eurasian otters Lutra lutra and raccoon dogs Nyctereutes procyonoides. We used DNA barcoding sequencing to analyze 16S rRNA genes of uncultured bacteria in the feces collected in the Seoul Zoo. The sequencing analyses revealed that: 1) Firmicutes was the most dominant phylum for all three animals; 2) bacterial genus-rank compositions were distinct across species of the animals; and 3) bacterial community memberships were different across species of the studied animals. We expect such baseline information is useful for better understanding of these endangered species and future management of their health in zoos. PMID:28049922

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. A Model-Model and Data-Model Comparison for the Early Eocene Hydrological Cycle

    NASA Technical Reports Server (NTRS)

    Carmichael, Matthew J.; Lunt, Daniel J.; Huber, Matthew; Heinemann, Malte; Kiehl, Jeffrey; LeGrande, Allegra; Loptson, Claire A.; Roberts, Chris D.; Sagoo, Navjit; Shields, Christine

    2016-01-01

    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

  19. 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.

  20. 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.

  1. 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

  2. A Generalized Approach to the Modeling of the Species-Area Relationship

    PubMed Central

    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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. Comparison of Hall Thruster Plume Expansion Model with Experimental Data

    DTIC Science & Technology

    2006-05-23

    focus of this study, is a hybrid particle- in-cell ( PIC ) model that tracks particles along an unstructured tetrahedral mesh. * Research Engineer...measurements of the ion current density profile, ion energy distributions, and ion species fraction distributions using a nude Faraday probe, retarding...Vol.37 No.1. 6 Oh, D. and Hastings, D., “Three Dimensional PIC -DSMC Simulations of Hall Thruster Plumes and Analysis for Realistic Spacecraft

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. Acute Toxicity Prediction to Threatened and Endangered Species Using Interspecies Correlation Estimation (ICE) Models.

    PubMed

    Willming, Morgan M; Lilavois, Crystal R; Barron, Mace G; Raimondo, Sandy

    2016-10-04

    Evaluating contaminant sensitivity of threatened and endangered (listed) species and protectiveness of chemical regulations often depends on toxicity data for commonly tested surrogate species. The U.S. EPA's Internet application Web-ICE is a suite of Interspecies Correlation Estimation (ICE) models that can extrapolate species sensitivity to listed taxa using least-squares regressions of the sensitivity of a surrogate species and a predicted taxon (species, genus, or family). Web-ICE was expanded with new models that can predict toxicity to over 250 listed species. A case study was used to assess protectiveness of genus and family model estimates derived from either geometric mean or minimum taxa toxicity values for listed species. Models developed from the most sensitive value for each chemical were generally protective of the most sensitive species within predicted taxa, including listed species, and were more protective than geometric means models. ICE model estimates were compared to HC5 values derived from Species Sensitivity Distributions for the case study chemicals to assess protectiveness of the two approaches. ICE models provide robust toxicity predictions and can generate protective toxicity estimates for assessing contaminant risk to listed species.

  16. A natural M RNA reassortant arising from two species of plant- and insect-infecting bunyaviruses and comparison of its sequence and biological properties to parental species.

    PubMed

    Webster, Craig G; Reitz, Stuart R; Perry, Keith L; Adkins, Scott

    2011-05-10

    Reassortment allows multicomponent viruses to exchange genome segments, a process well-documented in the vertebrate- and arthropod-infecting members of the family Bunyaviridae but not between distinct species of the plant- and insect-infecting members of the genus Tospovirus. Genome sequence comparisons of a virus causing severe tospovirus-like symptoms in Florida tomato with Groundnut ringspot virus (GRSV) and Tomato chlorotic spot virus (TCSV) demonstrated that reassortment has occurred, with the large (L) and small (S) RNAs coming from GRSV and the medium (M) RNA coming from TCSV (i.e. L(G)M(T)S(G)). Neither parental genotype is known to occur in the U.S. suggesting that L(G)M(T)S(G) was introduced as a reassortant. L(G)M(T)S(G) was transmitted by western flower thrips (Frankliniella occidentalis [Pergande]), and was not able to overcome the Sw5 resistance gene of tomato. Our demonstration of reassortment between GRSV and TCSV suggests caution in defining species within the family Bunyaviridae based on their ability to reassort.

  17. 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

  18. The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes.

    PubMed

    Brown, Emily J; Bachtrog, Doris

    2014-07-01

    The chromatin landscape is key for gene regulation, but little is known about how it differs between sexes or between species. Here, we study the sex-specific chromatin landscape of Drosophila miranda, a species with young sex chromosomes, and compare it with Drosophila melanogaster. We analyze six histone modifications in male and female larvae of D. miranda (H3K4me1, H3K4me3, H3K36me3, H4K16ac, H3K27me3, and H3K9me2), and define seven biologically meaningful chromatin states that show different enrichments for transcribed and silent genes, repetitive elements, housekeeping, and tissue-specific genes. The genome-wide distribution of both active and repressive chromatin states differs between males and females. In males, active chromatin is enriched on the X, relative to females, due to dosage compensation of the hemizygous X. Furthermore, a smaller fraction of the euchromatic portion of the genome is in a repressive chromatin state in males relative to females. However, sex-specific chromatin states appear not to explain sex-biased expression of genes. Overall, conservation of chromatin states between male and female D. miranda is comparable to conservation between D. miranda and D. melanogaster, which diverged >30 MY ago. Active chromatin states are more highly conserved across species, while heterochromatin shows very low levels of conservation. Divergence in chromatin profiles contributes to expression divergence between species, with ∼26% of genes in different chromatin states in the two species showing species-specific or species-biased expression, an enrichment of approximately threefold over null expectation. Our data suggest that heteromorphic sex chromosomes in males (that is, a hypertranscribed X and an inactivated Y) may contribute to global redistribution of active and repressive chromatin marks between chromosomes and sexes.

  19. 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

  20. Modelling ecological complexity for marine species conservation: the effect of variable connectivity on species spatial distribution and age-structure.

    PubMed

    Guizien, Katell; Bramanti, Lorenzo

    2014-01-01

    Connectivity is currently emphasized as a key factor in conservation for its role in enhancing biodiversity of an area and giving benefit to the adjacent areas. For most marine species, connectivity is synonomous of larval dispersal. We applied a spatially explicit meta-population model to test the hypothesis that larval dispersal can affect local demographical features, consequently misleading conservation practice in the marine environment. Simulations were carried out in the Gulf of Lions where coastal circulation displays highly variable temporal and spatial submeso-scale structures. Two different benthic invertebrate species were considered: a soft bottom short lived species and a hard bottom long lived one. In the first case, simulations showed that highest densities at equilibrium do not inform on self-persistent populations location. In the second case, simulations showed that connectivity effects may result in out-of-equilibria demographical structure. We emphasized the caveats in the parameterization of demographical models when local demography is controlled by connectivity.

  1. A comparison of major petroleum life cycle models | Science ...

    EPA Pesticide Factsheets

    Many organizations have attempted to develop an accurate well-to-pump life cycle model of petroleum products in order to inform decision makers of the consequences of its use. Our paper studies five of these models, demonstrating the differences in their predictions and attempting to evaluate their data quality. Carbon dioxide well-to-pump emissions for gasoline showed a variation of 35 %, and other pollutants such as ammonia and particulate matter varied up to 100 %. Differences in allocation do not appear to explain differences in predictions. Effects of these deviations on well-to-wheels passenger vehicle and truck transportation life cycle models may be minimal for effects such as global warming potential (6 % spread), but for respiratory effects of criteria pollutants (41 % spread) and other impact categories, they can be significant. A data quality assessment of the models’ documentation revealed real differences between models in temporal and geographic representativeness, completeness, as well as transparency. Stakeholders may need to consider carefully the tradeoffs inherent when selecting a model to conduct life cycle assessments for systems that make heavy use of petroleum products. This is a qualitative and quantitative comparison of petroleum LCA models intended for an expert audience interested in better understanding the data quality of existing petroleum life cycle models and the quantitative differences between these models.

  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 in simulation codes which will be used for BBU experiments at Jefferson Lab and improve BBU simulation results. We review two RF cavity models in the simulation codes elegant and TDBBU (a BBU simulation code developed at Jefferson Lab). elegant can include the Rosenzweig-Serafini (R-S) model for the RF focusing effect. Whereas TDBBU uses a model from the code TRANSPORT which considers the adiabatic damping effect, but not the RF focusing effect. Quantitative comparisons are discussed for the CEBAF beamline. We also compare the R-S model with the results from numerical simulations for a CEBAF-type 5-cell superconducting cavity to validate the use of the R-S model as an improved low-energy RF cavity transport model in TDBBU. We have implemented the R-S model in TDBBU. It will improve BBU simulation results to be more matched with analytic calculations and experimental results.

  3. 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

  4. 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.

  5. 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.

  6. Thermal acclimation of photosynthesis: a comparison of boreal and temperate tree species along a latitudinal transect.

    PubMed

    Dillaway, Dylan N; Kruger, Eric L

    2010-06-01

    Common gardens were established along a approximately 900 km latitudinal transect to examine factors limiting geographical distributions of boreal and temperate tree species in eastern North America. Boreal representatives were trembling aspen (Populus tremuloides Michx.) and paper birch (Betula papyrifera Marsh.), while temperate species were eastern cottonwood (Populus deltoides Bartr ex. Marsh var. deltoides) and sweetgum (Liquidambar styraciflua L.). The species were compared with respect to adjustments of leaf photosynthetic metabolism along the transect, with emphasis on temperature sensitivities of the maximum rate of ribulose bisphosphate (RuBP) carboxylation (E(V)) and regeneration (E(J)). During leaf development, the average air temperature (T(growth)) differed between the coolest and warmest gardens by 12 degrees C. Evidence of photosynthetic thermal acclimation (metabolic shifts compensating for differences in T(growth)) was generally lacking in all species. Namely, neither E(V) nor E(J) was positively related to T(growth). Correspondingly, the optimum temperature (T(opt)) of ambient photosynthesis (A(sat)) did not vary significantly with T(growth). Modest variation in T(opt) was explained by the combination of E(V) plus the slope and curvature of the parabolic temperature response of mesophyll conductance (g(m)). All in all, species differed little in photosynthetic responses to climate. Furthermore, the adaptive importance of photosynthetic thermal acclimation was overshadowed by g(m)'s influence on A(sat)'s temperature response.

  7. The cosmological Janus model: comparison with observational data

    NASA Astrophysics Data System (ADS)

    Petit, Jean-Pierre; Dagostini, Gilles

    2017-01-01

    In 2014 we presented a model based on a system of two coupled field equations to describe two populations of particles, one positive and the other mass of negative mass. The analysis of this system by Newtonian approximation show that the masses of the same signs attract according to Newton's law while the masses of opposite signs repel according to an anti-Newton law. This eliminates the runaway phenomenon. It uses the time-dependent exact solution of this system to build the bolometric magnitude distribution of the red-shift. Comparing the prediction of our model -which requires adjustment with a single parameter- with the data from 740 supernovae highlighting the acceleration of the universe gives an excellent agreement. The comparison is then made with the multi-parametric Λ CDM model.

  8. Future mission studies: Preliminary comparisons of solar flux models

    NASA Technical Reports Server (NTRS)

    Ashrafi, S.

    1991-01-01

    The results of comparisons of the solar flux models are presented. (The wavelength lambda = 10.7 cm radio flux is the best indicator of the strength of the ionizing radiations such as solar ultraviolet and x-ray emissions that directly affect the atmospheric density thereby changing the orbit lifetime of satellites. Thus, accurate forecasting of solar flux F sub 10.7 is crucial for orbit determination of spacecrafts.) The measured solar flux recorded by National Oceanic and Atmospheric Administration (NOAA) is compared against the forecasts made by Schatten, MSFC, and NOAA itself. The possibility of a combined linear, unbiased minimum-variance estimation that properly combines all three models into one that minimizes the variance is also discussed. All the physics inherent in each model are combined. This is considered to be the dead-end statistical approach to solar flux forecasting before any nonlinear chaotic approach.

  9. 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.

  10. 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.

  11. Exotic annual Bromus invasions: comparisons among species and ecoregions in the western United States

    USGS Publications Warehouse

    Brooks, Matthew L.; Brown, Cynthia S.; Chambers, Jeanne C.; D'Antonio, Carla M.; Keeley, Jon E.; Belnap, Jayne

    2016-01-01

    Exotic annual Bromus species are widely recognized for their potential to invade, dominate, and alter the structure and function of ecosystems. In this chapter, we summarize the invasion potential, ecosystem threats, and management strategies for different Bromus species within each of five ecoregions of the western United States. We characterize invasion potential and threats in terms of ecosystem resistance to Bromus invasion and ecosystem resilience to disturbance with an emphasis on the importance of fi re regimes. We also explain how soil temperature and moisture regimes can be linked to patterns of resistance and resilience and provide a conceptual framework that can be used to evaluate the relative potential for invasion and ecological impact of the dominant exotic annual Bromus species in the western United States.

  12. A Comparison of Photosynthetic Characteristics of Encelia Species Possessing Glabrous and Pubescent Leaves 1

    PubMed Central

    Ehleringer, James R.; Björkman, Olle

    1978-01-01

    Measurements of the dependence of photosynthesis on light, CO2, and temperature are reported for two species of Encelia (Compositae) which differ in leaf pubescence and in geographical distribution. Encelia californica is glabrous and occurs in relatively mild, but arid habitats and Encelia farinosa is heavily pubescent and occurs in hot, arid habitats. Both species possess the C3 photosynthetic pathway. Under high irradiances and normal atmospheric conditions the two species have high photosynthetic rates, exceeding 3 nanomoles of CO2 per square centimeter per second (48 milligrams of CO2 per square decimeter per hour) and complete light saturation does not occur by full noon sunlight. The high photosynthetic capacity is related to a high efficiency of utilization of intercellular CO2 combined with high stomatal conductance. Leaf estimates of total soluble protein and fraction I protein are higher in these species than in most plants, although the proportion of fraction I protein is not higher. Both E. californica and E. farinosa attain a maximum rate of photosynthesis between 25 and 30 C, despite the fact that the two species grow in very different thermal habitats. Neither E. californica nor E. farinosa shows significant acclimation in the temperature dependence of photosynthesis when grown under different temperature regimes. The presence of leaf hairs which reduce leaf absorptance and consequently leaf temperature plays an important part in the ability of E. farinosa to survive in its native high temperature environment. When the effects of pubescence are taken into account, there are few if any significant differences in the photosynthetic characteristics of the two species. PMID:16660483

  13. Social complexity parallels vocal complexity: a comparison of three non-human primate species.

    PubMed

    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.

  14. 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

  15. Modification of benthic communities by territorial damselfish: a multi-species comparison

    NASA Astrophysics Data System (ADS)

    Ceccarelli, D. M.

    2007-12-01

    The effects of territorial damselfish on coral reef benthos have been well-studied for a few relatively large-bodied species with visually distinct territories. Despite a growing body of research demonstrating their abundance, and their effects on algae, corals and other grazers, there has been little research on the effects of the territorial damselfish community as a whole. This study investigated the space occupation, territory composition, and diet of ten damselfish species at three locations: Magnetic and Orpheus Islands (Great Barrier Reef), and Kimbe Bay (Papua New Guinea). Territories were measured, and the composition of benthic communities inside and outside territories was assessed both in situ and from algal collections. The stomach contents of territorial damselfishes were also quantified. Although the larger, previously well-studied species had the most visible effect on the benthic community in their territories, all the smaller species also significantly affected the algal composition, normally with an increase of palatable algae. However, the composition of algal assemblages inside the territories of different species varied considerably. Damselfish territories were highly individual, not just among species, but also among locations. Diets were diverse and indicated a greater degree of omnivory and detritivory than previously thought. At all locations, territories occupied a substantial proportion of the substratum: >25% on Magnetic Island, >50% at Orpheus Island, and ˜50% in Kimbe Bay. Within individual zones, this figure was as high as 70%. The contribution of territorial damselfishes to a range of benthic patterns and processes is considerable, and future benthic studies may need to distinguish more closely between territory and non-territory areas.

  16. Data-Model Comparison of Pliocene Sea Surface Temperature

    NASA Astrophysics Data System (ADS)

    Dowsett, H. J.; Foley, K.; Robinson, M. M.; Bloemers, J. T.

    2013-12-01

    The mid-Piacenzian (late Pliocene) climate represents the most geologically recent interval of long-term average warmth and shares similarities with the climate projected for the end of the 21st century. As such, its fossil and sedimentary record represents a natural experiment from which we can gain insight into potential climate change impacts, enabling more informed policy decisions for mitigation and adaptation. We present the first systematic comparison of Pliocene sea surface temperatures (SST) between an ensemble of eight climate model simulations produced as part of PlioMIP (Pliocene Model Intercomparison Project) and the PRISM (Pliocene Research, Interpretation and Synoptic Mapping) Project mean annual SST field. Our results highlight key regional (mid- to high latitude North Atlantic and tropics) and dynamic (upwelling) situations where there is discord between reconstructed SST and the PlioMIP simulations. These differences can lead to improved strategies for both experimental design and temporal refinement of the palaeoenvironmental reconstruction. Scatter plot of multi-model-mean anomalies (squares) and PRISM3 data anomalies (large blue circles) by latitude. Vertical bars on data anomalies represent the variability of warm climate phase within the time-slab at each locality. Small colored circles represent individual model anomalies and show the spread of model estimates about the multi-model-mean. While not directly comparable in terms of the development of the means nor the meaning of variability, this plot provides a first order comparison of the anomalies. Encircled areas are a, PRISM low latitude sites outside of upwelling areas; b, North Atlantic coastal sequences and Mediterranean sites; c, large anomaly PRISM sites from the northern hemisphere. Numbers identify Ocean Drilling Program sites.

  17. COMPARISON OF PBPK MODELING SOFTWARE FEATURES AND APPROACHES TO MODELING IMPORTNAT PHYSIOLOGICAL AND BIOCHEMICAL BEHAVIORS

    EPA Science Inventory

    Abstract for 40th Annual Meeting of the Society of Toxicology, March 25-29, 2001

    COMPARISON OF PBPK MODELING SOFTWARE FEATURES AND APPROACHES TO MODELING IMPORTANT PHYSIOLOGICAL AND BIOCHEMICAL BEHAVIORS. R S DeWoskin and R W Setzer. USEPA/ORD/NHEERL, RTP, NC, USA.

    ...

  18. Interplanetary flux enhancements - Comparison with cometary models and observations

    NASA Technical Reports Server (NTRS)

    Russell, C. T.; Phillips, J. L.; Luhmann, J. G.; Fedder, J. A.

    1986-01-01

    Interplanetary field enhancements (IFE's) are unusual nearly symmetric increases in the strength of the interplanetary magnetic field lasting tens of minutes to hours. Examples of interplanetary field enhancements are compared with MHD models and with the data obtained by the ICE spacecraft at Giacobini-Zinner. These comparisons suggest that the varying properties of IFE's are due to the fact that some events are due to passages in front of the nucleus, others in the near tail and yet others in the distant tail.

  19. Comparison of Three Optical Methods for Measuring Model Deformation

    NASA Technical Reports Server (NTRS)

    Burner, A. W.; Fleming, G. A.; Hoppe, J. C.

    2000-01-01

    The objective of this paper is to compare the current state-of-the-art of the following three optical techniques under study by NASA for measuring model deformation in wind tunnels: (1) video photogrammetry, (2) projection moire interferometry, and (3) the commercially available Optotrak system. An objective comparison of these three techniques should enable the selection of the best technique for a particular test undertaken at various NASA facilities. As might be expected, no one technique is best for all applications. The techniques are also not necessarily mutually exclusive and in some cases can be complementary to one another.

  20. An atmospheric tritium release database for model comparisons. Revision 1

    SciTech Connect

    Murphy, C.E. Jr.; Wortham, G.R.

    1995-01-01

    A database of vegetation, soil, and air tritium concentrations at gridded coordinate locations following nine accidental atmospheric releases is described. While none of the releases caused a significant dose to the public, the data collected are valuable for comparison with the results of tritium transport models used for risk assessment. The largest, potential, individual off-site dose from any of the releases was calculated to be 1.6 mrem. The population dose from this same release was 46 person-rem which represents 0.04% of the natural background radiation dose to the population in the path of the release.

  1. Model/Data Comparisons of NO2 and HNO3

    NASA Astrophysics Data System (ADS)

    Remsberg, E. E.; Natarajan, M.; Thompson, R. E.; Gordley, L. L.

    2001-05-01

    NASA Reference Publication 1292 [Prather and Remsberg, 1993] contains reports of the stratospheric model simulations of NOy for 1980, when the effects of volcanic aerosols on the partitioning of NOy should have been minimal. Those model runs included heterogeneous chemistry on background aerosols. Model values of NO2 and HNO3 were compared with those from the archived Nimbus 7 LIMS dataset, and the models exhibited the seasonal asymmetry that was observed for the LIMS HNO3. Still there were model/data differences that did not seem to be related solely to the variations among the model transport fields. Since then, we have updated the LIMS emissivity tables (spectroscopic parameters) and developed new algorithms for retrieving the profiles of the LIMS species, and we will show that there is improved agreement between these new data and the early results from most of the models. However, because there have also been improvements since 1992 in model transport of N2O and in the relevant chemical mechanisms for the generation and partitioning of NOy, it is recommended that the various models be rerun for the 1980 case and recompared with this latest version of the LIMS dataset.

  2. Patch reef modeling: a comparison of Devonian and recent examples

    SciTech Connect

    Precht, W.F.

    1983-09-01

    In reef research, models have been developed to define variations in the lithic and biotic development of facies. Walker and Alberstadt, and Hoffman and Narkiewicz developed models for growth of ancient reef communities. Although these models form a solid foundation by which patch reefs can be classed and zoned, they are neither complete nor accurate for all reef types. A comparison was made of Lower Devonian patch reefs from the Appalachian basin of New York, New Jersey, and Pennsylvania, and Holocene examples from the Bahamas and Florida Keys to identify the structure, orientation, community variability, and succession of the reef biofacies. The complexion and genesis of the carbonate lithofacies were also studied. Results show similarities; these include the size, areal distribution, 3-D geometry, wave-resistance potential, lateral sequences of facies, sedimentary textures and structures, vertical zonation explained by growth from low-energy to high-energy regimes, biotic diversity, growth habit and form, and postmortem alteration. Thus, when used in conjunction with the traditional models, the recent can serve as the basis for a general model which include most patch reef types. However, these models should not be used as explicit analogs for all Phanerozoic reefs. Knowing and understanding the limitations of these comparative studies are essential to a fuller comprehension of the potential for variations which exist within and between the traditional models.

  3. Nanoparticles of selenium as species with stronger physiological effects in sheep in comparison with sodium selenite.

    PubMed

    Sadeghian, Sirous; Kojouri, Gholam Ali; Mohebbi, Abdonnaser

    2012-06-01

    The present study was designed to compare the effects of nano red selenium and sodium selenite on the antioxidative activities of neutrophils and the hematological parameters in sheep. Fifteen sheep were randomly allocated into three groups. Groups 1 and 2 received selenium nanoparticles orally at 1 mg/kg and sodium selenite at 1 mg Se/kg for 10 consecutive days; group 3 served as the control. To assess the degrees of oxidative stress and of lipid peroxidation of the cellular membranes, the levels of thiobarbituric acid reactive substances (TBARS) were determined in serum samples that were collected at different supplementation intervals, i.e., after 0, 10, 20, and 30 days. In addition, hematological parameters in the serum samples were measured by routine procedures. It was found that TBARS levels in groups 1 and 2 were significantly higher on days 20 and 30 compared to the basal level on day 0. It was also found that on day 30, the TBARS activities in both treated groups were significantly higher than those of the controls (P < 0.05). These findings may explain the seemingly paradoxical effects of supplemental selenium on the indicators of oxidative stress, as the levels of TBARS were generally expected to decrease in the presence of selenium. There were no significant differences between the PCV and RBC values in the three groups. The white blood cell count (WBC) in group 1 showed a significant increase on days 20 and 30 in comparison with the control group. However, in group 2, there was a significant increase of the WBC value just on day 20 in comparison with the control group. Also, there were significant increases of the neutrophil counts and significant decreases of the lymphocyte counts on day 10 in group 1, in comparison with those in group 2 and controls, and on days 20 and 30 in groups 1 and 2 in comparison with those in the control group.

  4. Comparison between realistic and spherical approaches in EEG forward modelling.

    PubMed

    Meneghini, Fabio; Vatta, Federica; Esposito, Fabrizio; Mininel, Stefano; Di Salle, Francesco

    2010-06-01

    In electroencephalography (EEG) a valid conductor model of the head (forward model) is necessary for predicting measurable scalp voltages from intra-cranial current distributions. All inverse models, capable of inferring the spatial distribution of the neural sources generating measurable electrical and magnetic signals outside the brain are normally formulated in terms of a pre-estimated forward model, which implies considering one (or more) current dipole(s) inside the head and computing the electrical potentials generated at the electrode sites on the scalp surface. Therefore, the accuracy of the forward model strongly affects the reliability of the source reconstruction process independently of the specific inverse model. So far, it is as yet unclear which brain regions are more sensitive to the choice of different model geometry, from both quantitative and qualitative points of view. In this paper, we compare the finite difference method-based realistic model with the four-layers sensor-fitted spherical model using simulated cortical sources in the MNI152 standard space. We focused on the investigation of the spatial variation of the lead fields produced by simulated cortical sources which were placed on the reconstructed mesh of the neocortex along the surface electrodes of a 62-channel configuration. This comparison is carried out by evaluating a point spread function all over the brain cortex, with the aim of finding the lead fields mismatch between realistic and spherical geometry. Realistic geometry turns out to be a relevant factor of improvement which is particularly important when considering sources placed in the temporal or in the occipital cortex. In these situations, using a realistic head model will allow a better spatial discrimination of neural sources when compared to the spherical model.

  5. Power law cosmology model comparison with CMB scale information

    NASA Astrophysics Data System (ADS)

    Tutusaus, Isaac; Lamine, Brahim; Blanchard, Alain; Dupays, Arnaud; Zolnierowski, Yves; Cohen-Tanugi, Johann; Ealet, Anne; Escoffier, Stéphanie; Le Fèvre, Olivier; Ilić, Stéphane; Pisani, Alice; Plaszczynski, Stéphane; Sakr, Ziad; Salvatelli, Valentina; Schücker, Thomas; Tilquin, André; Virey, Jean-Marc

    2016-11-01

    Despite the ability of the cosmological concordance model (Λ CDM ) to describe the cosmological observations exceedingly well, power law expansion of the Universe scale radius, R (t )∝tn, has been proposed as an alternative framework. We examine here these models, analyzing their ability to fit cosmological data using robust model comparison criteria. Type Ia supernovae (SNIa), baryonic acoustic oscillations (BAO) and acoustic scale information from the cosmic microwave background (CMB) have been used. We find that SNIa data either alone or combined with BAO can be well reproduced by both Λ CDM and power law expansion models with n ˜1.5 , while the constant expansion rate model (n =1 ) is clearly disfavored. Allowing for some redshift evolution in the SNIa luminosity essentially removes any clear preference for a specific model. The CMB data are well known to provide the most stringent constraints on standard cosmological models, in particular, through the position of the first peak of the temperature angular power spectrum, corresponding to the sound horizon at recombination, a scale physically related to the BAO scale. Models with n ≥1 lead to a divergence of the sound horizon and do not naturally provide the relevant scales for the BAO and the CMB. We retain an empirical footing to overcome this issue: we let the data choose the preferred values for these scales, while we recompute the ionization history in power law models, to obtain the distance to the CMB. In doing so, we find that the scale coming from the BAO data is not consistent with the observed position of the first peak of the CMB temperature angular power spectrum for any power law cosmology. Therefore, we conclude that when the three standard probes (SNIa, BAO, and CMB) are combined, the Λ CDM model is very strongly favored over any of these alternative models, which are then essentially ruled out.

  6. 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

  7. 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

  8. 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.

  9. Comparison of Systems for Identification and Differentiation of Species within the Genus Yersinia

    PubMed Central

    Neubauer, Heinrich; Sauer, Thomas; Becker, Heinz; Aleksic, Stojanca; Meyer, Hermann

    1998-01-01

    Of four tested identification systems (API 20E, API Rapid 32 IDE, Micronaut E, and the PCR-based Yersinia enterocolitica Amplification Set), API 20E is still the system of choice for identifying pathogenic Yersinia isolates. It provides the highest sensitivity both at the genus and at the species level and has the best cost-effectiveness correlation. PMID:9774596

  10. Comparison of polyphenol oxidase expression in glandular trichomes of solanum and lycopersicon species.

    PubMed

    Yu, H; Kowalski, S P; Steffens, J C

    1992-12-01

    Tetralobulate glandular trichomes are present on the foliage of many solanaceous species. Resistance of many of these species to insects is conditioned by the ability of trichomes to rupture upon contact and to rapidly polymerize their contents, resulting in entrapment of insects in hardened trichome exudate. In the wild potato, Solanum berthaultii, polymerization of trichome exudate is initiated by a soluble M(r) 59,000 polyphenol oxidase (PPO), which is a dominant protein constituent of the organ. PPOs, although ubiquitous in angiosperms, typically display great heterogeneity in molecular weight and are found at low levels in plant cells. Because of the unusually high accumulation and tissue-specific expression of the M(r) 59,000 PPO in S. berthaultii glandular trichomes, we analyzed trichome proteins of a number of Lycopersicon and Solanum species to assess the extent to which possession of the M(r) 59,000 PPO is conserved. Trichomes were collected manually and examined for PPO activity, immuno-cross-reactivity with S. berthaultiiM(r) 59,000 PPO, and protein content. In addition, N-terminal amino acid sequences were obtained for five trichome PPOs. All species analyzed possessed trichome PPOs similar in structure and level of expression to that of S. berthaultii. The relationship between sequences and structures of these conserved PPOs and the variable PPOs of leaf is discussed.

  11. Comparison of biofilm ecology supporting growth of individual Naegleria species in a drinking water distribution system.

    PubMed

    Puzon, Geoffrey J; Wylie, Jason T; Walsh, Tom; Braun, Kalan; Morgan, Matthew J

    2017-02-21

    Free-living amoebae (FLA) are common components of microbial communities in drinking water distribution systems (DWDS). FLA are of clinical importance both as pathogens and as reservoirs for bacterial pathogens, so identifying the conditions promoting amoebae colonisation of DWDSs is an important public health concern for water utilities. We used high-throughput amplicon sequencing to compare eukaryotic and bacterial communities associated with DWDS biofilms supporting distinct FLA species (N. fowleri, N. lovaniensis or Vermamoeba sp.) at sites with similar physical/chemical conditions. Eukaryote and bacterial communities were characteristic of different FLA species presence, and biofilms supporting Naegleria growth had higher bacterial richness and higher abundance of Proteobacteria, Bacteroidetes (bacteria), Nematoda and Rotifera (eukaryota). The eukaryotic community in the biofilms had the greatest difference in relation to the presence of N. fowleri, while the bacterial community identified individual bacterial families associated with the presence of different Naegleria species. Our results demonstrate that ecogenomics data provide a powerful tool for studying the microbial and meiobiotal content of biofilms, and, in these samples can effectively discriminate biofilm communities supporting pathogenic N. fowleri. The identification of microbial species associated with N. fowleri could further be used in the management and control of N. fowleri in DWDSs.

  12. 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...

  13. 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...

  14. 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 ...

  15. 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.

  16. Comparison of Polyphenol Oxidase Expression in Glandular Trichomes of Solanum and Lycopersicon Species 1

    PubMed Central

    Yu, Haifeng; Kowalski, Stanley P.; Steffens, John C.

    1992-01-01

    Tetralobulate glandular trichomes are present on the foliage of many solanaceous species. Resistance of many of these species to insects is conditioned by the ability of trichomes to rupture upon contact and to rapidly polymerize their contents, resulting in entrapment of insects in hardened trichome exudate. In the wild potato, Solanum berthaultii, polymerization of trichome exudate is initiated by a soluble Mr 59,000 polyphenol oxidase (PPO), which is a dominant protein constituent of the organ. PPOs, although ubiquitous in angiosperms, typically display great heterogeneity in molecular weight and are found at low levels in plant cells. Because of the unusually high accumulation and tissue-specific expression of the Mr 59,000 PPO in S. berthaultii glandular trichomes, we analyzed trichome proteins of a number of Lycopersicon and Solanum species to assess the extent to which possession of the Mr 59,000 PPO is conserved. Trichomes were collected manually and examined for PPO activity, immuno-cross-reactivity with S. berthaultiiMr 59,000 PPO, and protein content. In addition, N-terminal amino acid sequences were obtained for five trichome PPOs. All species analyzed possessed trichome PPOs similar in structure and level of expression to that of S. berthaultii. The relationship between sequences and structures of these conserved PPOs and the variable PPOs of leaf is discussed. Images Figure 1 Figure 2 Figure 3 PMID:16653213

  17. Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs.

    PubMed

    de Vries, Jan; Woehle, Christian; Christa, Gregor; Wägele, Heike; Tielens, Aloysius G M; Jahns, Peter; Gould, Sven B

    2015-03-07

    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.

  18. 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 ...

  19. Topographic variables improve climate models of forage species abundance in the northeastern United States

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species distribution modeling has most commonly been applied to presence-only data and to woody species, but detailed predicted abundance maps for forage species would be of great value for agricultural management and land use planning. We used field data from 107 farms across the northeastern Unite...

  20. Hierarchical modeling of population stability and species group attributes from survey data

    USGS Publications Warehouse

    Sauer, J.R.; Link, W.A.

    2002-01-01

    Many ecological studies require analysis of collections of estimates. For example, population change is routinely estimated for many species from surveys such as the North American Breeding Bird Survey (BBS), and the species are grouped and used in comparative analyses. We developed a hierarchical model for estimation of group attributes from a collection of estimates of population trend. The model uses information from predefined groups of species to provide a context and to supplement data for individual species; summaries of group attributes are improved by statistical methods that simultaneously analyze collections of trend estimates. The model is Bayesian; trends are treated as random variables rather than fixed parameters. We use Markov Chain Monte Carlo (MCMC) methods to fit the model. Standard assessments of population stability cannot distinguish magnitude of trend and statistical significance of trend estimates, but the hierarchical model allows us to legitimately describe the probability that a trend is within given bounds. Thus we define population stability in terms of the probability that the magnitude of population change for a species is less than or equal to a predefined threshold. We applied the model to estimates of trend for 399 species from the BBS to estimate the proportion of species with increasing populations and to identify species with unstable populations. Analyses are presented for the collection of all species and for 12 species groups commonly used in BBS summaries. Overall, we estimated that 49% of species in the BBS have positive trends and 33 species have unstable populations. However, the proportion of species with increasing trends differs among habitat groups, with grassland birds having only 19% of species with positive trend estimates and wetland birds having 68% of species with positive trend estimates.

  1. 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

  2. Mitochondrial genomic comparison of Clonorchis sinensis from South Korea with other isolates of this species.

    PubMed

    Wang, Daxi; Young, Neil D; Koehler, Anson V; Tan, Patrick; Sohn, Woon-Mok; Korhonen, Pasi K; Gasser, Robin B

    2017-02-22

    Clonorchiasis is a neglected tropical disease that affects >35 million people mainly in China, Vietnam, South Korea and some parts of Russia. The disease-causing agent, Clonorchis sinensis, is a liver fluke of humans and other piscivorous animals, and has a complex aquatic life cycle involving snails and fish intermediate hosts. Chronic infection in humans causes liver disease and associated complications including malignant bile duct cancer. Central to control and to understanding the epidemiology of this disease is knowledge of the specific identity of the causative agent as well as genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species and that genetic variation within the species is limited, karyotypic variation within C. sinensis among China, Korea (2n=56) and Russian Far East (2n=14) suggests that this taxon might contain sibling species. Here, we assessed and applied a deep sequencing-bioinformatic approach to sequence and define a reference mitochondrial (mt) genome for a particular isolate of C. sinensis from Korea (Cs-k2), to confirm its specific identity, and compared this mt genome with homologous data sets available for this species. Comparative analyses revealed consistency in the number and structure of genes as well as in the lengths of protein-coding genes, and limited genetic variation among isolates of C. sinensis. Phylogenetic analyses of amino acid sequences predicted from mt genes showed that representatives of C. sinensis clustered together, with absolute nodal support, to the exclusion of other liver fluke representatives, but sub-structuring within C. sinensis was not well supported. The plan now is to proceed with the sequencing, assembly and annotation of a high quality draft nuclear genome of this defined isolate (Cs-k2) as a basis for a detailed investigation of molecular variation within C. sinensis from disparate

  3. Control of food intake by metabolism of fuels: a comparison across species.

    PubMed

    Allen, Michael S; Bradford, Barry J

    2012-08-01

    Research with laboratory species suggests that meals can be terminated by peripheral signals carried to brain feeding centres via hepatic vagal afferents, and that these signals are affected by oxidation of fuels. Pre-gastric fermentation in ruminants greatly alters fuels, allowing mechanisms conserved across species to be studied with different types and temporal absorption of fuels. These fuels include SCFA, glucose, lactate, amino acids and long-chain fatty acid (FA) isomers, all of which are absorbed and metabolised by different tissues at different rates. Propionate is produced by rumen microbes, absorbed within the timeframe of meals, and quickly cleared by the liver. Its hypophagic effects are variable, likely due to its fate; propionate is utilised for gluconeogenesis or oxidised and also stimulates oxidation of acetyl-CoA by anapleurosis. In contrast, acetate has little effect on food intake, likely because its uptake by the ruminant liver is negligible. Glucose is hypophagic in non-ruminants but not ruminants and unlike non-ruminant species, uptake of glucose by ruminant liver is negligible, consistent with the differences in hypophagic effects between them. Inhibition of FA oxidation increases food intake, whereas promotion of FA oxidation suppresses food intake. Hypophagic effects of fuel oxidation also vary with changes in metabolic state. The objective of this paper is to compare the type and utilisation of fuels and their effects on feeding across species. We believe that the hepatic oxidation theory allows insight into mechanisms controlling feeding behaviour that can be used to formulate diets to optimise energy balance in multiple species.

  4. Comparison of phylogeny, venom composition and neutralization by antivenom in diverse species of bothrops complex.

    PubMed

    Sousa, Leijiane F; Nicolau, Carolina A; 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.

  5. 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.; 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.

  6. 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

  7. 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...

  8. 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

  9. Comparison of CME radial velocities from a flux rope model and an ice cream cone model

    NASA Astrophysics Data System (ADS)

    Kim, T.; Moon, Y.; Na, H.

    2011-12-01

    Coronal Mass Ejections (CMEs) on the Sun are the largest energy release process in the solar system and act as the primary driver of geomagnetic storms and other space weather phenomena on the Earth. So it is very important to infer their directions, velocities and three-dimensional structures. In this study, we choose two different models to infer radial velocities of halo CMEs since 2008 : (1) an ice cream cone model by Xue et al (2005) using SOHO/LASCO data, (2) a flux rope model by Thernisien et al. (2009) using the STEREO/SECCHI data. In addition, we use another flux rope model in which the separation angle of flux rope is zero, which is morphologically similar to the ice cream cone model. The comparison shows that the CME radial velocities from among each model have very good correlations (R>0.9). We will extending this comparison to other partial CMEs observed by STEREO and SOHO.

  10. Comparison of particular logistic models' adoption in the Czech Republic

    NASA Astrophysics Data System (ADS)

    Vrbová, Petra; Cempírek, Václav

    2016-12-01

    Managing inventory is considered as one of the most challenging tasks facing supply chain managers and specialists. Decisions related to inventory locations along with level of inventory kept throughout the supply chain have a fundamental impact on the response time, service level, delivery lead-time and the total cost of the supply chain. The main objective of this paper is to identify and analyse the share of a particular logistic model adopted in the Czech Republic (Consignment stock, Buffer stock, Safety stock) and also compare their usage and adoption according to different industries. This paper also aims to specify possible reasons of particular logistic model preferences in comparison to the others. The analysis is based on quantitative survey held in the Czech Republic.

  11. Data-model comparison using FORWARD and CoMP

    NASA Astrophysics Data System (ADS)

    Gibson, Sarah

    2015-10-01

    The FORWARD SolarSoft IDL package is a community resource for model-data comparison, with a particular emphasis on analyzing coronal magnetic fields. FORWARD allows the synthesis of coronal polarimetric signals at visible, infrared, and radio frequencies, and will soon be augmented for ultraviolet polarimetry. In this paper we focus on observations of the infrared (IR) forbidden lines of Fe XIII, and describe how FORWARD may be used to directly access these data from the Mauna Loa Solar Observatory Coronal Multi-channel Polarimeter (MLSO/CoMP), to put them in the context of other space- and ground-based observations, and to compare them to synthetic observables generated from magnetohydrodynamic (MHD) models.

  12. Comparison of Histograms for Use in Cloud Observation and Modeling

    NASA Technical Reports Server (NTRS)

    Green, Lisa; Xu, Kuan-Man

    2005-01-01

    Cloud observation and cloud modeling data can be presented in histograms for each characteristic to be measured. Combining information from single-cloud histograms yields a summary histogram. Summary histograms can be compared to each other to reach conclusions about the behavior of an ensemble of clouds in different places at different times or about the accuracy of a particular cloud model. As in any scientific comparison, it is necessary to decide whether any apparent differences are statistically significant. The usual methods of deciding statistical significance when comparing histograms do not apply in this case because they assume independent data. Thus, a new method is necessary. The proposed method uses the Euclidean distance metric and bootstrapping to calculate the significance level.

  13. Model/data comparison of typhoon-generated noise

    NASA Astrophysics Data System (ADS)

    Wang, Jing-Yan; Li, Feng-Hua

    2016-12-01

    Ocean noise recorded during a typhoon can be used to monitor the typhoon and investigate the mechanism of the wind-generated noise. An analytical expression for the typhoon-generated noise intensity is derived as a function of wind speed. A “bi-peak” structure was observed in an experiment during which typhoon-generated noise was recorded. Wind speed dependence and frequency dependence were also observed in the frequency range of 100 Hz-1000 Hz. The model/data comparison shows that results of the present model of 500 Hz and 1000 Hz are in reasonable agreement with the experimental data, and the typhoon-generated noise intensity has a dependence on frequency and a power-law dependence on wind speed. Project supported by the National Natural Science Foundation of China (Grant Nos. 11434012, 41561144006, and 11125420).

  14. Diffusive shock acceleration - comparison of a unified shock model to bow shock observations

    SciTech Connect

    Ellison, D.C.; Moebius, E.

    1987-07-01

    A comparison is made between recent AMPTE/IRM observations of diffuse ions detected upstream of the earth's bow shock when the interplanetary magnetic field was nearly parallel to the solar wind direction and a known collisionless quasi-parallel shock model. These observations, which provide the proton spectrum for all of velocity space, give a direct measure of the shock acceleration efficiency and show how thermal solar winds are injected into the diffusive shock acceleration mechanism. The model accurately describes the proton spectrum; moreover, it predicts the shock structure, the complete particle spectrum, the relative velocity distributions of different ion species in the down stream region, and the enhancement of heavy ions over protons relative to the unshocked solar wind. 68 references.

  15. Diffusive shock acceleration - Comparison of a unified shock model to bow shock observations

    NASA Technical Reports Server (NTRS)

    Ellison, Donald C.; Moebius, Eberhard

    1987-01-01

    A comparison is made between recent AMPTE/IRM observations of diffuse ions detected upstream of the earth's bow shock when the interplanetary magnetic field was nearly parallel to the solar wind direction and a known collisionless quasi-parallel shock model. These observations, which provide the proton spectrum for all of velocity space, give a direct measure of the shock acceleration efficiency and show how thermal solar winds are injected into the diffusive shock acceleration mechanism. The model accurately describes the proton spectrum; moreover, it predicts the shock structure, the complete particle spectrum, the relative velocity distributions of different ion species in the down stream region, and the enhancement of heavy ions over protons relative to the unshocked solar wind.

  16. Comparison of four molecular approaches to identify Candida parapsilosis complex species

    PubMed Central

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2017-01-01

    Since the description of Candida orthopsilosis and C. metapsilosis in 2005, several methods have been proposed to identify and differentiate these species from C. parapsilosis sensu stricto. Species-specific uniplex polymerase chain reaction (PCR) was performed and compared with sequencing of the D1/D2 region of the LSU 28S rDNA gene, microsatellite typing of C. parapsilosis sensu stricto, and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. There was agreement between results of testing of 98 clinical isolates with the four PCR-based methods, with 59 isolates identified as C. parapsilosis sensu stricto, 37 as C. orthopsilosis, and two as C. metapsilosis. PMID:28225905

  17. Comparison of four molecular approaches to identify Candida parapsilosis complex species.

    PubMed

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2017-03-01

    Since the description of Candida orthopsilosis and C. metapsilosis in 2005, several methods have been proposed to identify and differentiate these species from C. parapsilosis sensu stricto. Species-specific uniplex polymerase chain reaction (PCR) was performed and compared with sequencing of the D1/D2 region of the LSU 28S rDNA gene, microsatellite typing of C. parapsilosis sensu stricto, and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. There was agreement between results of testing of 98 clinical isolates with the four PCR-based methods, with 59 isolates identified as C. parapsilosis sensu stricto, 37 as C. orthopsilosis, and two as C. metapsilosis.

  18. Comparison of four molecular approaches to identify Candida parapsilosis complex species.

    PubMed

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2017-02-16

    Since the description of Candida orthopsilosis and C. metapsilosis in 2005, several methods have been proposed to identify and differentiate these species from C. parapsilosis sensu stricto. Species-specific uniplex polymerase chain reaction (PCR) was performed and compared with sequencing of the D1/D2 region of the LSU 28S rDNA gene, microsatellite typing of C. parapsilosis sensu stricto, and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. There was agreement between results of testing of 98 clinical isolates with the four PCR-based methods, with 59 isolates identified as C. parapsilosis sensu stricto, 37 as C. orthopsilosis, and two as C. metapsilosis.

  19. 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.

  20. 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

  1. A Comparison of Multiple Esterases as Biomarkers of Organophosphate Exposure and Effect in Two Earthworm Species

    PubMed Central

    Schneider, Ashley; Stoskopf, Michael K.

    2011-01-01

    Two different earthworm species, Eisenia fetida and Lumbricus terrestris, were exposed to 5 μg/cm2 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

  2. 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.

  3. Carbonaceous species methods comparison study: University of Minnesota results. Final report

    SciTech Connect

    McMurry, P.H.; Zhang, X.

    1988-10-01

    The Carbon Methods Comparison Study conducted during August 12-20, 1986 at Citrus College, Glendora, CA in the Los Angeles basin compared analytical methodologies for analyzing the carbon content of aerosol samples, as well as compared measurements acquired with different samples. Five samplers, including a multistage microorifice uniform deposit impactor (MOUDI), a conventional quartz filter, a specially designed electrostatic precipitator (ESP), and 2 identical single stage MOUDIs were used. One of the single stage MOUDIs was used as a fine particle sampler; the second was used in experiments to investigate possible sampling articles. The results are summarized and discussed.

  4. A comparison of floral integration between selfing and outcrossing species: a meta-analysis

    PubMed Central

    Fornoni, Juan; Ordano, Mariano; Pérez-Ishiwara, Rubén; Boege, Karina; Domínguez, César A.

    2016-01-01

    Background and Aims Floral integration is thought to be an adaptation to promote cross-fertilization, and it is often assumed that it increases morphological matching between flowers and pollinators, increasing the efficiency of pollen transfer. However, the evidence for this role of floral integration is limited, and recent studies have suggested a possible positive association between floral integration and selfing. Although a number of explanations exist to account for this inconsistency, to date there has been no attempt to examine the existence of an association between floral integration and mating system. This study hypothesized that if pollinator-mediated pollen movement among plants (outcrossing) is the main factor promoting floral integration, species with a predominantly outcrossing mating system should present higher levels of floral integration than those with a predominantly selfing mating system. Methods A phylogenetically informed meta-analysis of published data was performed in order to evaluate whether mating system (outcrossing vs. selfing) accounts for the variation in floral integration among 64 species of flowering plants. Morphometric floral information was used to compare intra-floral integration among traits describing sexual organs (androecium and gynoecium) and those corresponding to the perianth (calix and corolla). Key Results The analysis showed that outcrossing species have lower floral integration than selfing species. This pattern was caused by significantly higher integration of sexual traits than perianth traits, as integration of the latter group remained unchanged across mating categories. Conclusions The results suggest that the evolution of selfing is associated with concomitant changes in intra-floral integration. Thus, floral integration of sexual traits should be considered as a critical component of the selfing syndrome. PMID:26578721

  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. 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.

  7. 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

  8. Comparison of methods for in vitro testing of susceptibility of porcine Mycoplasma species to antimicrobial agents.

    PubMed

    Ter Laak, E A; Pijpers, A; Noordergraaf, J H; Schoevers, E C; Verheijden, J H

    1991-02-01

    The MICs of 18 antimicrobial agents used against strains of three porcine Mycoplasma species were determined by a serial broth dilution method. Twenty field strains of M. hyorhinis, ten field strains of M. hyopneumoniae, six field strains of M. flocculare, and the type strains of these species were tested. Twelve field strains and the type strain of M. hyorhinis were also tested by an agar dilution method. Tests were read at various time points. When the broth dilution method was used, the final MIC had to be read 2 days after color changes had stopped. MICs of tetracycline, oxytetracycline, doxycycline, and minocycline were low for the three Mycoplasma species tested. MICs of chlortetracycline were 8 to 16 times higher than MICs of the other tetracyclines. Spiramycin, tylosin, kitasamycin, spectinomycin, tiamulin, lincomycin, and clindamycin were effective against all strains of M. hyorhinis and M. hyopneumoniae. The quinolones were highly effective against M. hyopneumoniae but less effective against M. hyorhinis. The susceptibility patterns for M. hyopneumoniae and M. flocculare were similar.

  9. Comparison of methods for in vitro testing of susceptibility of porcine Mycoplasma species to antimicrobial agents.

    PubMed Central

    Ter Laak, E A; Pijpers, A; Noordergraaf, J H; Schoevers, E C; Verheijden, J H

    1991-01-01

    The MICs of 18 antimicrobial agents used against strains of three porcine Mycoplasma species were determined by a serial broth dilution method. Twenty field strains of M. hyorhinis, ten field strains of M. hyopneumoniae, six field strains of M. flocculare, and the type strains of these species were tested. Twelve field strains and the type strain of M. hyorhinis were also tested by an agar dilution method. Tests were read at various time points. When the broth dilution method was used, the final MIC had to be read 2 days after color changes had stopped. MICs of tetracycline, oxytetracycline, doxycycline, and minocycline were low for the three Mycoplasma species tested. MICs of chlortetracycline were 8 to 16 times higher than MICs of the other tetracyclines. Spiramycin, tylosin, kitasamycin, spectinomycin, tiamulin, lincomycin, and clindamycin were effective against all strains of M. hyorhinis and M. hyopneumoniae. The quinolones were highly effective against M. hyopneumoniae but less effective against M. hyorhinis. The susceptibility patterns for M. hyopneumoniae and M. flocculare were similar. PMID:2024954

  10. 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).

  11. 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

  12. Toxicity of ivermectin on cladocerans: comparison of toxic effects on Daphnia and Ceriodaphnia species.

    PubMed

    Lopes, Christelle; Charles, Sandrine; Vollat, Bernard; Garric, Jeanne

    2009-10-01

    Interspecies differences in contaminant sensitivity are measured to assess environmental risk based on species sensitivity distribution. The present study was intended to demonstrate the importance of studying the effects of contaminants on the life-history traits of various species. To do this, we compared the effects of ivermectin on the survival, growth, and reproduction of two cladoceran species (Daphnia magna and Ceriodaphnia dubia) and two strains of D. magna (one Japanese and one European). Ivermectin is widely used against endo- and ectoparasites in livestock and pets and is known for its high toxicity. Local aquatic ecosystems can be contaminated due to direct excretion into surface waters, but few data are available about the chronic effects of ivermectin on aquatic organisms. Adult daphnids were exposed to concentrations from 0 to 1 ng/L. Our results show a significant effect on all the life-history traits measured and reveal inter- and intraspecies differences. The no-observed-effect concentration found for growth and reproduction is 0.0003 ng/L for D. magna versus 0.001 ng/L for C. dubia, and the lowest-observed-effect concentration is 0.001 ng/L for D. magna versus 0.01 ng/L for C. dubia. C. dubia is smaller than D. magna and appeared to be less sensitive to ivermectin. The European strain of D. magna exhibited less resistance than the Japanese strain. A bias in the sex ratio was observed for all strains tested.

  13. A comparison of Frost expression among species and life stages of Drosophila.

    PubMed

    Bing, X; Zhang, J; Sinclair, Brent J

    2012-02-01

    Frost (Fst) is a gene associated with cold exposure in Drosophila melanogaster. We used real-time PCR to assess whether cold exposure induces expression of Fst in 10 different life stages of D. melanogaster, and adults of seven other Drosophila species. We exposed groups of individuals to 0 °C (2 h), followed by 1 h recovery (22 °C). Frost was significantly upregulated in response to cold in eggs, third instar larvae, and 2- and 5-day-old male and female adults in D. melanogaster. Life stages in which cold did not upregulate Fst had high constitutive expression. Frost is located on the opposite strand of an intron of Diuretic hormone (DH), but cold exposure did not upregulate DH. Frost orthologues were identified in six other species within the Melanogaster group (Drosophila sechellia, Drosophila simulans, Drosophila yakuba, Drosophila erecta, Drosophila ananassae and Drosophila mauritiana). Frost orthologues were upregulated in response to cold exposure in both sexes in adults of all of these species. The predicted structure of a putative Frost consensus protein shows highly conserved tandem repeats of motifs involved in cell signalling (PEST and TRAF2), suggesting that Fst might encode an adaptor protein involved in acute stress or apoptosis signalling in vivo.

  14. Comparison of the hemolytic activity between C. albicans and non-albicans Candida species.

    PubMed

    Rossoni, Rodnei Dennis; Barbosa, Júnia Oliveira; Vilela, Simone Furgeri Godinho; Jorge, Antonio Olavo Cardoso; Junqueira, Juliana Campos

    2013-01-01

    The ability to produce enzymes, such as hemolysins, is an important virulence factor for the genus Candida.The objective of this study was to compare the hemolytic activity between C. albicansand non-albicans Candida species. Fifty strains of Candida species, isolated from the oral cavity of patients infected with HIV were studied. The isolates included the following species: C. albicans, C. dubliniensis, C. glabrata, C. tropicalis, C. krusei, C. parapsilosis, C. dubliniensis, C. norvegensis, C. lusitaniae, and C. guilliermondii. Hemolysin production was evaluated on Sabouraud dextrose agar containing chloramphenicol, blood, and glucose. A loop-full of pure Candidaculture was spot-inoculated onto plates and incubated at 37 ºC for 24 h in a 5% CO2 atmosphere. Hemolytic activity was defined as the formation of a translucent halo around the colonies. All C. albicansstrains that were studied produced hemolysins. Among the non-albicans Candidaspecies, 86% exhibited hemolytic activity. Only C. guilliermondiiand some C. parapsilosis isolates were negative for this enzyme. In conclusion, most non-albicans Candidaspecies had a similar ability to produce hemolysins when compared to C. albicans.

  15. 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.

  16. 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

  17. BACE1 across species: a comparison of the in vivo consequences of BACE1 deletion in mice and rats

    PubMed Central

    Weber, Martin; Wu, Tiffany; Meilandt, William J.; Dominguez, Sara L.; Solanoy, Hilda O.; Maloney, Janice A.; Ngu, Hai; Baca, Miriam; Kung, Chung; Lima, Lisa; Earr, Timothy K.; Fleck, Daniel; Shields, Shannon D.; Forrest, William F.; Foreman, Oded; Warming, Søren; Watts, Ryan J.; Scearce-Levie, Kimberly

    2017-01-01

    Assessing BACE1 (β-site APP cleaving enzyme 1) knockout mice for general health and neurological function may be useful in predicting risks associated with prolonged pharmacological BACE1 inhibition, a treatment approach currently being developed for Alzheimer’s disease. To determine whether BACE1 deletion-associated effects in mice generalize to another species, we developed a novel Bace1−/− rat line using zinc-finger nuclease technology and compared Bace1−/− mice and rats with their Bace1+/+ counterparts. Lack of BACE1 was confirmed in Bace1−/− animals from both species. Removal of BACE1 affected startle magnitude, balance beam performance, pain response, and nerve myelination in both species. While both mice and rats lacking BACE1 have shown increased mortality, the increase was smaller and restricted to early developmental stages for rats. Bace1−/− mice and rats further differed in body weight, spontaneous locomotor activity, and prepulse inhibition of startle. While the effects of species and genetic background on these phenotypes remain difficult to distinguish, our findings suggest that BACE1’s role in myelination and some sensorimotor functions is consistent between mice and rats and may be conserved in other species. Other phenotypes differ between these models, suggesting that some effects of BACE1 inhibition vary with the biological context (e.g. species or background strain). PMID:28281673

  18. Bringing modeling to the masses: A web based system to predict potential species distributions

    USGS Publications Warehouse

    Graham, Jim; Newman, Greg; Kumar, Sunil; Jarnevich, Catherine S.; Young, Nick; Crall, Alycia W.; Stohlgren, Thomas J.; Evangelista, Paul

    2010-01-01

    Predicting current and potential species distributions and abundance is critical for managing invasive species, preserving threatened and endangered species, and conserving native species and habitats. Accurate predictive models are needed at local, regional, and national scales to guide field surveys, improve monitoring, and set priorities for conservation and restoration. Modeling capabilities, however, are often limited by access to software and environmental data required for predictions. To address these needs, we built a comprehensive web-based system that: (1) maintains a large database of field data; (2) provides access to field data and a wealth of environmental data; (3) accesses values in rasters representing environmental characteristics; (4) runs statistical spatial models; and (5) creates maps that predict the potential species distribution. The system is available online at www.niiss.org, and provides web-based tools for stakeholders to create potential species distribution models and maps under current and future climate scenarios.

  19. 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.

  20. 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 ...

  1. 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 ...

  2. Phylogeny and development of marine model species: strongylocentrotid sea urchins.

    PubMed

    Biermann, Christiane H; Kessing, Bailey D; Palumbi, Stephen R

    2003-01-01

    The phylogenetic relationships of ten strongy-locentrotid sea urchin species were determined using mitochondrial DNA sequences. This phylogeny provides a backdrop for the evolutionary history of one of the most studied groups of sea urchins. Our phylogeny indicates that a major revision of this group is in order. All else remaining unchanged, it supports the inclusion of three additional species into the genus Strongylocentrotus (Hemicentrotus pulcherrimus, Allocentrotus fragilis, and Pseudocentrotus depressus). All were once thought to be closely related to this genus, but subsequent revisions separated them into other taxonomic groupings. Most strongylocentrotid species are the result of a recent burst of speciation in the North Pacific that resulted in an ecological diversification. There has been a steady reduction in the complexity of larval skeletons during the expansion of this group. Gamete attributes like egg size, on the other hand, are not correlated with phylogenetic position. In addition, our results indicate that the rate of replacement substitutions is highly variable among phylogenetic lineages. The branches leading to S. purpuratus and S. franciscanus were three to six times longer than those leading to closely related species.

  3. A Comparison of the Sensitivities of Dominant Plant Species to Experimental Drought

    NASA Astrophysics Data System (ADS)

    Felton, A. J.; Smith, M.; Griffin-Nolan, R.; Slette, I.

    2015-12-01

    Locally and globally, climate extremes are expected to become an increasingly important determinant of terrestrial ecosystem structure and functioning. In particular, extreme drought events are likely to have the most pronounced and negative impact on biodiversity (Tilman and El haddi 1992), carbon storage (Ciais et al. 2005) and cycling (Reichstein et al. 2013). As a consequence, an expressed need has been for a next generation of experiments designed to elucidate the causes and consequences of ecosystem sensitivity to drought (Smith 2011, Reichstein et al. 2013). A recent analysis of the 2012 U.S. Southwest drought revealed different sensitivities in primary production across five grassland ecosystems positioned along a precipitation gradient, with the most mesic (wet) grassland less sensitive than the most xeric (dry) grassland (Knapp et al. 2015). While this analysis suggests increasing sensitivity to drought with decreasing mean annual precipitation (MAP), an understanding of the relative roles of the abiotic (e.g., resource availability) and biotic (e.g., species identity) ecosystem components in driving this sensitivity trend is unclear. To address this uncertainty, we conducted a soil moisture manipulation study using the dominant grass species from the tallgrass prairie (892mm MAP), the shortgrass steppe (372mm MAP), and desert grassland (246mm MAP). The study imposed a "dry-down" to four target levels of volumetric soil water content at 25%, 20%, 15% and 10% t