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Sample records for model species comparison

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2016-03-16

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

  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 model results transporting the odd nitrogen family with results transporting separate odd nitrogen species

    NASA Technical Reports Server (NTRS)

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

    1989-01-01

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

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

    SciTech Connect

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

    2001-11-01

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

  6. 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.

  7. 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.

  8. Strain rate and fuel composition dependence of chemiluminescent species profiles in non-premixed counterflow flames: comparison with model results

    NASA Astrophysics Data System (ADS)

    Prabasena, B.; Röder, M.; Kathrotia, T.; Riedel, U.; Dreier, T.; Schulz, C.

    2012-06-01

    A detailed comparison has been conducted between chemiluminescence (CL) species profiles of OH∗, CH∗, and C2 ∗, obtained experimentally and from detailed flame kinetics modeling, respectively, of atmospheric pressure non-premixed flames formed in the forward stagnation region of a fuel flow ejected from a porous cylinder and an air counterflow. Both pure methane and mixtures of methane with hydrogen (between 10 and 30 % by volume) were used as fuels. By varying the air-flow velocities methane flames were operated at strain rates between 100 and 350 s-1, while for methane/hydrogen flames the strain rate was fixed at 200 s-1. Spatial profiles perpendicular to the flame front were extracted from spectrograms recorded with a spectrometer/CCD camera system and evaluating each spectral band individually. Flame kinetics modeling was accomplished with an in-house chemical mechanism including C1-C4 chemistry, as well as elementary steps for the formation, removal, and electronic quenching of all measured active species. In the CH4/air flames, experiments and model results agree with respect to trends in profile peak intensity and position. For the CH4/H2/air flames, with increasing H2 content in the fuel the experimental CL peak intensities decrease slightly and their peak positions shift towards the fuel side, while for the model the drop in mole fraction is much stronger and the peak positions move closer to the fuel side. For both fuel compositions the modeled profiles peak closer to the fuel side than in the experiments. The discrepancies can only partly be attributed to the limited attainable spatial resolution but may also necessitate revised reaction mechanisms for predicting CL species in this type of flame.

  9. Simulation and Comparison of Particle Injection in an Indoor Environment Using the Species Transport and Discrete Phase Models

    SciTech Connect

    Zheng, Zhongquan C.; Wei, Zhenglun A.; Bennett, James S.; Yang, Xiaofan

    2012-12-11

    In simulating fluid/solid-particle multiphase -flows, various methods are available. One approach is the combined Euler-Lagrange method, which simulates the fluid phase flow in the Eulerian framework and the discrete phase (particle) motion in the Lagrangian framework simultaneously. The Lagrangian approach, where particle motion is determined by the current state of the fluid phase flow, is also called the discrete phase model (DPM), in the context of numerical flow simulation. In this method, the influence of the particle motions on the fluid flow can be included (two-way interactions) but are more commonly excluded (one-way interactions, when the discrete phase concentration is dilute. The other approach is to treat the particle number concentration as a continuous species, a necessarily passive quantity determined by the fluid flow, with no influences from the particles on the fluid flow (one-way interactions only), except to the extent the discrete phase “continuum” alters the overall fluid properties, such as density. In this paper, we compare these two methods with experimental data for an indoor environmental chamber. The effects of injection particle numbers and the related boundary conditions are investigated. In the Euler-Lagrange interaction or DPM model for incompressible flow, the Eulerian continuous phase is governed by the Reynolds-averaged N-S (RANS) equations. The motions of particles are governed by Newton’s second law. The effects of particle motions are communicated to the continuous phase through a force term in the RANS equations. The second formulation is a pure Eulerian type, where only the particle-number concentration is addressed, rather than the motion of each individual particle. The fluid flow is governed by the same RANS equations without the particle force term. The particle-number concentration is simulated by a species transport equation. Comparisons among the models and with experimental and literature data are presented

  10. 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.

  11. 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.

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

    PubMed

    Shabani, Farzin; Kumar, Lalit; Ahmadi, Mohsen

    2016-08-01

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

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

    PubMed

    Shabani, Farzin; Kumar, Lalit; Ahmadi, Mohsen

    2016-08-01

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

  14. A comparison of two schemes for the convective transport of chemical species in a Lagrangian global chemistry model

    NASA Astrophysics Data System (ADS)

    Collins, W. J.; Derwent, R. G.; Johnson, C. E.; Stevenson, D. S.

    2002-04-01

    We have developed a detailed parametrization scheme to represent the effects of subgrid-scale convective transport in a three-dimensional chemistry-transport model (CTM). The CTM utilizes the meteorological fields generated by a general-circulation model (GCM) to redistribute over 70 chemical species. The convective transport is implemented using the convective mass fluxes, entrainment rates and detrainment rates from the GCM. We compare the modelled distributions of 222Rn with observations. This shows that the vertical profile of this species is affected by the choice of convective-transport parametrization. The new parametrization is found to improve significantly the simulation of 222Rn over the summertime continents.

  15. 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.

  16. Bounding Species Distribution Models

    NASA Technical Reports Server (NTRS)

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

    2011-01-01

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

  17. 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

  18. 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...

  19. Evaluation of the Models-3 Community Multi-scale Air Quality (CMAQ) modeling system with observations obtained during the TRACE-P experiment: Comparison of ozone and its related species

    NASA Astrophysics Data System (ADS)

    Zhang, Meigen; Uno, Itsushi; Zhang, Renjian; Han, Zhiwei; Wang, Zifa; Pu, Yifen

    The Models-3 Community Multi-scale Air Quality (CMAQ) modeling system with meteorological fields calculated by the Regional Atmospheric Modeling System (RAMS) was applied to East Asia to investigate the transport and photochemical transformation of tropospheric ozone during the Transport and Chemical Evolution over the Pacific (TRACE-P) field campaign. Modeled concentrations of hydroxyl radical, hydroperoxyl radical, nitric oxide, nitrogen dioxide, ethene, ethane, carbon monoxide, and ozone were compared with observations obtained onboard of two aircrafts in order to evaluate the model performance. Comparison indicates that the model reproduced the tempo-spatial distributions of ozone and its related chemical species reasonably well, and most model results were within a factor of 2 of the observations.

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

    PubMed

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

    2014-12-15

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

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

    PubMed

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

    2014-10-01

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

  2. 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.

  3. 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

  4. 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...

  5. 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.

  6. 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.

  7. Comparison of the antiproliferative activity of crude ethanol extracts of nine salvia species grown in Jordan against breast cancer cell line models

    PubMed Central

    Abu-Dahab, Rana; Afifi, Fatma; Kasabri, Violet; Majdalawi, Lara; Naffa, Randa

    2012-01-01

    Background: The antiproliferative activity of Salvia species grown in Jordan has not been fully evaluated yet. The aim of this work was to study the antiproliferative activity of crude ethanol extracts from nine Salvia species grown in Jordan against a panel of breast cancer cell lines. Material and Methods: Cytotoxic activity was evaluated in human tumor models of breast cancer; MCF-7, T47D, ZR-75-1, and BT 474 by the sulforhodamine B assay. In addition, the extracts were evaluated using a non-transformed cell line (Vero) and normal fibroblast cells in order to demonstrate their selectivity and safety. Results: From the nice ethanol extracts under investigation, those of S. dominica and S. fruticosa showed an inhibitory concentration of 50% of cells (IC50) in concentrations less than 30μg/mL against the four cell lines under investigation. S. syriaca and S. hormium showed an IC50 below 30μg/ml for two out of the four cell lines. S. fruticosa, S. hormium and S. syriaca showed selectivity in their antiproliferative activity against estrogen receptor positive cell lines with minimal toxicity against normal human periodontal fibroblasts. Phytochemical screening using thin layer chromatography indicated the presence of terpenoids, flavonoids and coumarins in all examined extracts. Conclusion: Three of the plant extracts under investigation exhibited antiproliferative activity against breast cancer cells and were shown to be safe and selective. These could be considered as a potential source for novel anticancer therapy. PMID:24082637

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

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

  9. 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.

  10. Humans as cucinivores: comparisons with other species.

    PubMed

    Furness, John B; Bravo, David M

    2015-12-01

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

  11. Humans as cucinivores: comparisons with other species.

    PubMed

    Furness, John B; Bravo, David M

    2015-12-01

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

  12. Confronting species distribution model predictions with species functional traits.

    PubMed

    Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

    2016-02-01

    Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

  13. 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.

  14. 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. ...

  15. Water Relations and Hydraulic Architecture of a Tropical Tree (Schefflera morototoni) : Data, Models, and a Comparison with Two Temperate Species (Acer saccharum and Thuja occidentalis).

    PubMed

    Tyree, M T; Snyderman, D A; Wilmot, T R; Machado, J L

    1991-08-01

    The water relations and hydraulic architecture of a tropical tree (Schefflera morototoni) and of two temperate species (Acer saccharum and Thuja occidentalis) are reported. Among the water relations parameters measured were leaf and stem water storage capacity, leaf water potential, transpiration, and vulnerability of stems to cavitation and loss of hydraulic conductivity by embolisms. Among the hydraulic architecture parameters measured were hydraulic conductivity per unit pressure gradient, specific conductivity, leaf-specific conductivity, and Huber value. In terms of vulnerability of stems to cavitation, stem and leaf capacitances, and leaf-specific conductivity, all three species followed the same sequence: Schefflera > Acer > Thuja. It is argued here that the high stem capacitance and high leaf-specific conductivity of Schefflera are necessary to compensate for its high vulnerability to cavitation. Extractable water storage per unit leaf area in Schefflera stems is >100 times that of Acer and may permit the species to survive unusually long, dry seasons in Panama. Although Schefflera frequently grows >20 meters, the biggest resistance to water flow in the shoots resides in the leaves.

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

    PubMed

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

    1998-01-01

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

  17. 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.

  18. 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.

  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. Species comparison of acute inhalation toxicity of ozone and phosgene

    SciTech Connect

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

    1986-01-01

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

  1. 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

  2. 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

  3. 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.

  4. 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

  5. Applying various algorithms for species distribution modelling.

    PubMed

    Li, Xinhai; Wang, Yuan

    2013-06-01

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

  6. Applying various algorithms for species distribution modelling.

    PubMed

    Li, Xinhai; Wang, Yuan

    2013-06-01

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

  7. 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.

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

    PubMed Central

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

    2014-01-01

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

  9. Species Distribution Modeling of Deep Pelagic Eels.

    PubMed

    DeVaney, Shannon C

    2016-10-01

    The ocean's midwaters (the mesopelagic and bathypelagic zones) make up the largest living space on the planet, but are undersampled and relatively poorly understood. The true distribution of many midwater species, let alone the abiotic factors most important in determining that distribution, is not well known. Because collecting specimens and data from the deep ocean is expensive and logistically difficult, it would be useful to be able to predict where species of interest are likely to occur so that sampling effort can be concentrated in appropriate areas. The distribution of two representative midwater fishes, the gulper eel Eurypharynx pelecanoides and the bobtail eel Cyema atrum (Teleostei: Saccopharyngiformes), were modeled with MaxEnt software to examine the viability of species distribution modeling (SDM) for globally distributed midwater fishes using currently available environmental data from the ocean surface and bottom. These species were chosen because they are relatively abundant, easily recognized, and unlikely to have been misidentified in database records, and are true midwater fishes, not known to undertake significant vertical diurnal migration. Models for both species show a generally worldwide distribution with some exceptions, including the Southern Ocean and Bering Sea. Variable contributions show that surface and bottom environmental variables correlate with species presence. Both species are more likely to be found in areas with low levels of silicate. SDM is a promising method for better understanding the ecology of midwater organisms.

  10. 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

  11. 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…

  12. Species Tree Inference Using a Mixture Model.

    PubMed

    Ullah, Ikram; Parviainen, Pekka; Lagergren, Jens

    2015-09-01

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

  13. Incorporating uncertainty in predictive species distribution modelling

    PubMed Central

    Beale, Colin M.; Lennon, Jack J.

    2012-01-01

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

  14. 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

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

    PubMed

    Whitten, P L; Patisaul, H B

    2001-03-01

    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.

  16. 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

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

    PubMed Central

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

    2012-01-01

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

  18. 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 ...

  19. Comparison of Experimental Respiratory Tularemia in Three Nonhuman Primate Species

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-04-01

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

  1. 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

  2. In Silico Modeling of Geobacter Species.

    SciTech Connect

    Lovley, Derek, R.

    2008-01-29

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

  3. 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.

  4. 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

  5. Comparison between different cosmological models

    SciTech Connect

    Panotopoulos, Grigoris

    2008-05-15

    Several cosmological models have been proposed in order to explain the current acceleration of the Universe. Recently, the normal branch of the DGP (after Dvali, Gabadadze, and Porrati) brane model with a generalized Chaplygin gas was studied as a model which can cross the phantom divide line avoiding the future singularity. In the present work, we wish to address the question of whether or not the aforementioned model has a better fit to supernovae data compared to cold dark matter with a cosmological constant, the (generalized) Chaplygin gas, and the DGP model with the self-accelerating branch without extra fluid for dark energy. We have found that the Chaplygin-DGP model has the worst fit, while the two-fluid model with Chaplygin gas and dust (baryons) has the best fit among the theoretical cosmological models considered here.

  6. Direct Comparison of Bibliometric Models.

    ERIC Educational Resources Information Center

    Kinnucan, Mark T.; Wolfram, Dietmar

    1990-01-01

    Describes a technique for statistically comparing bibliometric models and illustrates its use with two examples using Lotka's hypothesis of author productivity and one example using library circulation frequencies. Topics discussed include nested statistical models, analysis of variance, regression, log-linear models, and the likelihood ratio…

  7. 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.

  8. 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...

  9. Comparison of microsclerotia production by various Metarhizium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsclerotia (MS) production by various species and strains of Metarhizium was evaluated by growing cultures in liquid media with 36 g L-1 carbon and carbon-to-nitrogen ratios (CN) of 10:1. 30:1, or 50:1. Species evaluated included M. anisopliae, M. brunneum, M. pingshaense, and M. robertsii. Biom...

  10. Motif content comparison between monocot and dicot species

    PubMed Central

    Cserhati, Matyas

    2015-01-01

    While a number of DNA sequence motifs have been functionally characterized, the full repertoire of motifs in an organism (the motifome) is yet to be characterized. The present study wishes to widen the scope of motif content analysis in different monocot and dicot species that include both rice species, Brachypodium, corn, wheat as monocots and Arabidopsis, Lotus japonica, Medicago truncatula, and Populus tremula as dicots. All possible existing motifs were analyzed in different regions of genomes such as were found in different sets of sequences in these species: the whole genome, core proximal and distal promoters, 5′ and 3′ UTRs, and the 1st introns. Due to the increased number of species involved in this study compared to previous works, species relationships were analyzed based on the similarity of common motif content. Certain secondary structure elements were inferred in the genomes of these species as well as new unknown motifs. The distribution of 20 motifs common to the studied species were found to have a significantly larger occurrence within the promoters and 3′ UTRs of genes, both being regulatory regions. Motifs common to the promoter regions of japonica rice, Brachypodium, and corn were also found in a number of orthologous and paralogous genes. Some of our motifs were found to be complementary to miRNA elements in Brachypodium distachyon and japonica rice. PMID:26484161

  11. 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

  12. 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.

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2015-03-01

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

  15. Compound leaf development in model plant species.

    PubMed

    Bar, Maya; Ori, Naomi

    2015-02-01

    Plant leaves develop in accordance with a common basic program, which is flexibly adjusted to the species, developmental stage and environment. Two key stages of leaf development are morphogenesis and differentiation. In the case of compound leaves, the morphogenesis stage is prolonged as compared to simple leaves, allowing for the initiation of leaflets. Here, we review recent advances in the understanding of how plant hormones and transcriptional regulators modulate compound leaf development, yielding a substantial diversity of leaf forms, focusing on four model compound leaf organisms: cardamine (Cardamine hirsuta), tomato (Solanum lycopersicum), medicago (Medicago truncatula) and pea (Pisum sativum).

  16. Rodent nutrition: digestive comparisons of 4 common rodent species.

    PubMed

    Grant, Kerrin

    2014-09-01

    This article summarizes the literature regarding digestive strategies and captive diets of common rodent pocket pets. A comparison is made between the 2 suborders in which chinchillas, guinea pigs, hamsters, and gerbils occur, highlighting digestive anatomy and dietary adaptations. Recommended captive diets are provided, as well as common nutritionally related health issues that may be presented to veterinary clinics.

  17. Rodent nutrition: digestive comparisons of 4 common rodent species.

    PubMed

    Grant, Kerrin

    2014-09-01

    This article summarizes the literature regarding digestive strategies and captive diets of common rodent pocket pets. A comparison is made between the 2 suborders in which chinchillas, guinea pigs, hamsters, and gerbils occur, highlighting digestive anatomy and dietary adaptations. Recommended captive diets are provided, as well as common nutritionally related health issues that may be presented to veterinary clinics. PMID:25155666

  18. 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

  19. Chronological aging in conidia of pathogenic Aspergillus: Comparison between species.

    PubMed

    Oliveira, Manuela; Pereira, Clara; Bessa, Cláudia; Araujo, Ricardo; Saraiva, Lucília

    2015-11-01

    Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus and Aspergillus niger are common airborne fungi, and the most frequent causative agents of human fungal infections. However, the resistance and lifetime persistence of these fungi in the atmosphere, and the mechanism of aging of Aspergillus conidia are unknown.With this work, we intended to study the processes underlying conidial aging of these four relevant and pathogenic Aspergillus species. Chronological aging was therefore evaluated in A. fumigatus, A. flavus, A. terreus and A. niger conidia exposed to environmental and human body temperatures. The results showed that the aging process in Aspergillus conidia involves apoptosis,with metacaspase activation, DNA fragmentation, and reactive oxygen species production, associated with secondary necrosis. Distinct results were observed for the selected pathogenic species. At environmental conditions, A. niger was the species with the highest resistance to aging, indicating a higher adaption to environmental conditions, whereas A. flavus followed by A. terreus were the most sensitive species. At higher temperatures (37 °C), A. fumigatus presented the longest lifespan, in accordance with its good adaptation to the human body temperature. Altogether,with this work new insights regarding conidia aging are provided, which may be useful when designing treatments for aspergillosis.

  20. 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…

  1. 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.

  2. 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.

  3. Comparison of antigens of pneumonia-associated mycoplasma species by gel diffusion.

    PubMed

    Ball, H J; Todd, D

    1978-09-01

    Comparison of fluorocarbon-extracted antigens of six mycoplasma species by double immunodiffusion and counterimmunodiffusion techniques revealed a close reciprocal relationship among Mycoplasma dispar, M. ovipneumoniae, and M. hyopneumoniae. A lesser degree of cross-reaction was also demonstrated between these three species and M. hyorhinis and M. bovoculi. The interrelationships were more clearly demonstrated by double immunodiffusion than by counterimmunodiffusion.

  4. Comparison of antigens of pneumonia-associated mycoplasma species by gel diffusion.

    PubMed Central

    Ball, H J; Todd, D

    1978-01-01

    Comparison of fluorocarbon-extracted antigens of six mycoplasma species by double immunodiffusion and counterimmunodiffusion techniques revealed a close reciprocal relationship among Mycoplasma dispar, M. ovipneumoniae, and M. hyopneumoniae. A lesser degree of cross-reaction was also demonstrated between these three species and M. hyorhinis and M. bovoculi. The interrelationships were more clearly demonstrated by double immunodiffusion than by counterimmunodiffusion. Images PMID:101469

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

    PubMed

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

    2014-07-01

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

  6. 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. PMID:26385107

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

    PubMed

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

    2012-08-01

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

  8. 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.

  9. ConSite: web-based prediction of regulatory elements using cross-species comparison.

    PubMed

    Sandelin, Albin; Wasserman, Wyeth W; Lenhard, Boris

    2004-07-01

    ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis. ConSite offers several unique features, including an interactive expert system for retrieving orthologous regulatory sequences. Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/www.phylofoot.org/consite.

  10. Identification of four Aconitum species used as "Caowu" in herbal markets by 3D reconstruction and microstructural comparison.

    PubMed

    Liu, Chan-Chan; Cheng, Ming-En; Peng, Huasheng; Duan, Hai-Yan; Huang, Luqi

    2015-05-01

    Authentication is the first priority when evaluating the quality of Chinese herbal medicines, particularly highly toxic medicines. The most commonly used authentication methods are morphological identification and microscopic identification. Unfortunately, these methods could not effectively evaluate some herbs with complex interior structures, such as root of Aconitum species with a circular conical shape and an interior structure with successive changes. Defining the part that should be selected as the standard plays an essential role in accurate microscopic identification. In this study, we first present a visual 3D model of Aconitum carmichaeli Debx. constructed obtained from microscopic analysis of serial sections. Based on this model, we concluded that the point of largest root diameter should be used as the standard for comparison and identification. The interior structure at this point is reproducible and its shape and appearance can easily be used to distinguish among species. We also report details of the interior structures of parts not shown in the 3D model, such as stone cells and cortical thickness. To demonstrate the usefulness of the results from the 3D model, we have distinguished the microscopic structures, at their largest segments, of the other three Aconitum species used for local habitat species of Caowu. This work provides the basis for resolution of some debate regarding the microstructural differences among these species. Thus, we conclude that the 3D model composed of serial sections has enabled the selection of a standard cross-section that will enable the accurate identification of Aconitum species in Chinese medicine.

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

    PubMed

    Dutrillaux, Anne-Marie; Dutrillaux, Bernard

    2016-01-01

    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

  12. 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

  13. Species comparison of enantioselective oral bioavailability and pharmacokinetics of ketoprofen.

    PubMed

    Neirinckx, E; Croubels, S; De Boever, S; Remon, J P; Bosmans, T; Daminet, S; De Backer, P; Vervaet, C

    2011-12-01

    As a part of ongoing research to further elucidate frequent and species-specific causes of differences in oral bioavailability, a 3mg/kg dose of racemic ketoprofen, a high permeability/low solubility compound in the human biopharmaceutics classification system, was administered intravenously and orally to different species. Due to possible enantioselective disposition kinetics and inversion, enantiomers were quantitated separately using a stereospecific HPLC assay. The absolute bioavailability of R(-) and S(+) ketoprofen in chickens, turkeys, dogs and pigs was 31.5% and 52.6%, 42.6% and 32.5%, 33.6% and 89.1%, and 85.9% and 83.5% respectively. Incomplete bioavailability in poultry is probably due to incomplete absorption in addition to first-pass elimination. Low bioavailability of R(-) ketoprofen in dogs, strongly indicates first-pass metabolism. High bioavailability of S(+) ketoprofen in dogs and both enantiomers in pigs confirms that absorption of these substances is complete and controlled by gastric emptying rather than dissolution.

  14. 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

  15. Whole-genome sequence comparison as a method for improving bacterial species definition.

    PubMed

    Zhang, Wen; Du, Pengcheng; Zheng, Han; Yu, Weiwen; Wan, Li; Chen, Chen

    2014-01-01

    We compared pairs of 1,226 bacterial strains with whole genome sequences and calculated their average nucleotide identity (ANI) between genomes to determine whether whole genome comparison can be directly used for bacterial species definition. We found that genome comparisons of two bacterial strains from the same species (SGC) have a significantly higher ANI than those of two strains from different species (DGC), and that the ANI between the query and the reference genomes can be used to determine whether two genomes come from the same species. Bacterial species definition based on ANI with a cut-off value of 0.92 matched well (81.5%) with the current bacterial species definition. The ANI value was shown to be consistent with the standard for traditional bacterial species definition, and it could be used in bacterial taxonomy for species definition. A new bioinformatics program (ANItools) was also provided in this study for users to obtain the ANI value of any two bacterial genome pairs (http://genome.bioinfo-icdc.org/). This program can match a query strain to all bacterial genomes, and identify the highest ANI value of the strain at the species, genus and family levels respectively, providing valuable insights for species definition.

  16. 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.

  17. 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.

  18. 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.

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

    PubMed

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

    2016-06-01

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

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

    PubMed

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

    2016-06-01

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

  1. 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

  2. Cross-Species Comparison of Genes Related to Nutrient Sensing Mechanisms Expressed along the Intestine

    PubMed Central

    van der Wielen, Nikkie; van Avesaat, Mark; de Wit, Nicole J. W.; Vogels, Jack T. W. E.; Troost, Freddy; Masclee, Ad; Koopmans, Sietse-Jan; van der Meulen, Jan; Boekschoten, Mark V.; Müller, Michael; Hendriks, Henk F. J.; Witkamp, Renger F.; Meijerink, Jocelijn

    2014-01-01

    Introduction Intestinal chemosensory receptors and transporters are able to detect food-derived molecules and are involved in the modulation of gut hormone release. Gut hormones play an important role in the regulation of food intake and the control of gastrointestinal functioning. This mechanism is often referred to as “nutrient sensing”. Knowledge of the distribution of chemosensors along the intestinal tract is important to gain insight in nutrient detection and sensing, both pivotal processes for the regulation of food intake. However, most knowledge is derived from rodents, whereas studies in man and pig are limited, and cross-species comparisons are lacking. Aim To characterize and compare intestinal expression patterns of genes related to nutrient sensing in mice, pigs and humans. Methods Mucosal biopsy samples taken at six locations in human intestine (n = 40) were analyzed by qPCR. Intestinal scrapings from 14 locations in pigs (n = 6) and from 10 locations in mice (n = 4) were analyzed by qPCR and microarray, respectively. The gene expression of glucagon, cholecystokinin, peptide YY, glucagon-like peptide-1 receptor, taste receptor T1R3, sodium/glucose cotransporter, peptide transporter-1, GPR120, taste receptor T1R1, GPR119 and GPR93 was investigated. Partial least squares (PLS) modeling was used to compare the intestinal expression pattern between the three species. Results and conclusion The studied genes were found to display specific expression patterns along the intestinal tract. PLS analysis showed a high similarity between human, pig and mouse in the expression of genes related to nutrient sensing in the distal ileum, and between human and pig in the colon. The gene expression pattern was most deviating between the species in the proximal intestine. Our results give new insights in interspecies similarities and provide new leads for translational research and models aiming to modulate food intake processes in man. PMID:25216051

  3. 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.…

  4. 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

  5. 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

  6. 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

  7. Modeling Nitrogen Species as Pollutants: Thermochemical Influences.

    PubMed

    Bugler, John; Somers, Kieran P; Simmie, John M; Güthe, Felix; Curran, Henry J

    2016-09-15

    To simulate emissions of nitrogen-containing compounds in practical combustion environments, it is necessary to have accurate values for their thermochemical parameters, as well as accurate kinetic values to describe the rates of their formation and decomposition. Significant disparity is observed in the literature for the former, and we therefore present herein high-accuracy ab initio gas-phase thermochemistry for 60 nitrogenous compounds, many of which are important in the formation and consumption chemistry of NOx species. Several quantum-chemical composite methods (CBS-APNO, G3, and G4) were utilized to derive enthalpies of formation via the atomization method. Entropies and heat capacities were calculated from traditional statistical thermodynamics, with oscillators treated as anharmonic based on ro-vibrational property analyses carried out at the B3LYP/cc-pVTZ level of theory. The use of quantum chemical methods, along with the treatments of anharmonicities and hindered rotors, ensures accurate enthalpy of formation, entropy, and heat capacity values across the temperature range 298.15-3000 K. The implications of these results for atmospheric and combustion modeling are discussed. PMID:27547977

  8. Bayesian model comparison of solar flare spectra

    NASA Astrophysics Data System (ADS)

    Ireland, J.; Holman, G.

    2012-12-01

    The detailed understanding of solar flares requires an understanding of the physics of accelerated electrons, since electrons carry a large fraction of the total energy released in a flare. Hard X-ray energy flux spectral observations of solar flares can be fit with different parameterized models of the interaction of the flare-accelerated electrons with the solar plasma. Each model describes different possible physical effects that may occur in solar flares. Bayesian model comparison provides a technique for assessing which model best describes the data. The advantage of this technique over others is that it can fully account for the different number and type of parameters in each model. We demonstrate this using Ramaty High Energy Solar Spectroscopic Imager (RHESSI) spectral data from the GOES (Geostationary Operational Environmental Satellite) X4.8 flare of 23-July-2002. We suggest that the observed spectrum can be reproduced using two different parameterized models of the flare electron content. The first model assumes that the flare-accelerated electron spectrum consisting of a single power law with a fixed low energy cutoff assumed to be below the range of fitted X-ray energies, interacting with a non-uniformly ionized target. The second model assumes that the flare-accelerated electron spectrum has a broken power law and a low energy cutoff, which interacts with a fully ionized target plasma. The low energy cutoff in this model is a parameter used in fitting the data. We will introduce and use Bayesian model comparison techniques to decide which model best explains the observed data. This work is funded by the NASA Solar and Heliospheric Physics program.

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

    PubMed Central

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

    1999-01-01

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

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

    PubMed

    Xu, Chaoqun; Yuan, Sanling

    2016-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Xia, Yonghui; Han, Maoan; Huang, Zhenkun

    2008-01-01

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

  12. 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.

  13. 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

  14. Comparison of Biomass Burning Smoke Plume Models

    NASA Astrophysics Data System (ADS)

    Carlson, L. J.; Mason, S. A.; Trentmann, J.; Winterrath, T.; Christian, T. J.; Yokelson, R. J.; Andreae, M. O.; Hobbs, P. V.

    2003-12-01

    Biomass burning is known to inject considerable quantities of trace gases into the atmosphere. Recent laboratory, field, and modeling studies have shown that significant atmospheric transformations occur within the vicinity of fire events before these emissions are released into the regional atmosphere. Understanding the local-scale transformations is an important parameter for inclusion into larger, global tropospheric models. An inter-model comparison was carried out between two independently developed zero-dimensional, gas-phase tropospheric models used to describe the photochemical evolution of young biomass burning smoke plumes. One of these models was developed and operated at the Max Planck Institute in Mainz, Germany; the second was constructed at the University of Montana- Missoula and is currently run at SUNY Fredonia. Identical initial parameters used in both models were taken from field measurements of biomass burning events under very different fire conditions (African savanna and Alaskan forest/shrub/bog mixture). The Fredonia model predicts slightly different chemistry than the Mainz model, which results in higher radical concentrations and lower PAN production when the same initial conditions are applied. Differences in the simulated results may be attributed to subtle differences in the calculation of photolytic rate constants and the modeled tropospheric chemistry. We survey the differences in model construction and the outcomes.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed

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

    2015-01-01

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

  2. 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.

  3. Process-based modeling of species' distributions: what limits temperate tree species' range boundaries?

    PubMed

    Morin, Xavier; Augspurger, Carol; Chuine, Isabelle

    2007-09-01

    Niche-based models are widely used to understand what environmental factors determine species' distributions, but they do not provide a clear framework to study the processes involved in defining species' ranges. Here we used a process-based model to identify these processes and to assess the potential distribution of 17 North American boreal/temperate tree species. Using input of only climate and soil properties, the model reproduced the 17 species' distributions accurately. Our results allowed us to identify the climatic factors as well as the biological processes involved in limiting species' ranges. The model showed that climatic constraints limit species' distributions mainly through their impact on phenological processes, and secondarily through their impact on drought and frost mortality. The northern limit of species' ranges appears to be caused mainly by the inability to undergo full fruit ripening and/or flowering, while the southern limit is caused by the inability to flower or by frost injury to flowers. These findings about the ecological processes shaping tree species' distribution represent a crucial step toward obtaining a more complete picture of the potential impact of climate on species' ranges. PMID:17918406

  4. 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.

  5. Richards-like two species population dynamics model.

    PubMed

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

    2014-12-01

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

  6. Richards-like two species population dynamics model.

    PubMed

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

    2014-12-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

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

    2011-12-14

    Rigorous numerical description of multi-species 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 for imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multi-species diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multi-species diffusion. Numerical simulations found that a diffusion model with a single, common diffusion coefficient for all species was sufficient to describe multi-species U(VI) diffusion under steady-state condition of major chemical composition, but not under transient chemical conditions. Simulations revealed that a fully coupled diffusion model can be well approximated by a component-based diffusion model, which considers 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 rigorously enforced, if necessary, by adding an artificial kinetic reaction term induced by the charge separation. The diffusion models were applied to describe U(VI) diffusive mass transfer in intragranular domains in two sediments collected from US Department of Energy's Hanford 300A where intragrain diffusion is a rate-limiting process controlling U(VI) adsorption and desorption. The grain-scale reactive diffusion model was able to describe U(VI) adsorption/desorption kinetics that has been described using a semi-empirical, multi-rate model

  9. 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...

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

    USGS Publications Warehouse

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

    2005-01-01

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

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  13. 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

  14. 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

  15. 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].

  16. Effects of species evenness and dominant species identity on multiple ecosystem functions in model grassland communities.

    PubMed

    Orwin, Kate H; Ostle, Nick; Wilby, Andrew; Bardgett, Richard D

    2014-03-01

    Ecosystems provide multiple services upon which humans depend. Understanding the drivers of the ecosystem functions that support these services is therefore important. Much research has investigated how species richness influences functioning, but we lack knowledge of how other community attributes affect ecosystem functioning. Species evenness, species spatial arrangement, and the identity of dominant species are three attributes that could affect ecosystem functioning, by altering the relative abundance of functional traits and the probability of synergistic species interactions such as facilitation and complementary resource use. We tested the effect of these three community attributes and their interactions on ecosystem functions over a growing season, using model grassland communities consisting of three plant species from three functional groups: a grass (Anthoxanthum odoratum), a forb (Plantago lanceolata), and a N-fixing forb (Lotus corniculatus). We measured multiple ecosystem functions that support ecosystem services, including ecosystem gas exchange, water retention, C and N loss in leachates, and plant biomass production. Species evenness and dominant species identity strongly influenced the ecosystem functions measured, but spatial arrangement had few effects. By the end of the growing season, evenness consistently enhanced ecosystem functioning and this effect occurred regardless of dominant species identity. The identity of the dominant species under which the highest level of functioning was attained varied across the growing season. Spatial arrangement had the weakest effect on functioning, but interacted with dominant species identity to affect some functions. Our results highlight the importance of understanding the role of multiple community attributes in driving ecosystem functioning. PMID:24213721

  17. Effects of species evenness and dominant species identity on multiple ecosystem functions in model grassland communities.

    PubMed

    Orwin, Kate H; Ostle, Nick; Wilby, Andrew; Bardgett, Richard D

    2014-03-01

    Ecosystems provide multiple services upon which humans depend. Understanding the drivers of the ecosystem functions that support these services is therefore important. Much research has investigated how species richness influences functioning, but we lack knowledge of how other community attributes affect ecosystem functioning. Species evenness, species spatial arrangement, and the identity of dominant species are three attributes that could affect ecosystem functioning, by altering the relative abundance of functional traits and the probability of synergistic species interactions such as facilitation and complementary resource use. We tested the effect of these three community attributes and their interactions on ecosystem functions over a growing season, using model grassland communities consisting of three plant species from three functional groups: a grass (Anthoxanthum odoratum), a forb (Plantago lanceolata), and a N-fixing forb (Lotus corniculatus). We measured multiple ecosystem functions that support ecosystem services, including ecosystem gas exchange, water retention, C and N loss in leachates, and plant biomass production. Species evenness and dominant species identity strongly influenced the ecosystem functions measured, but spatial arrangement had few effects. By the end of the growing season, evenness consistently enhanced ecosystem functioning and this effect occurred regardless of dominant species identity. The identity of the dominant species under which the highest level of functioning was attained varied across the growing season. Spatial arrangement had the weakest effect on functioning, but interacted with dominant species identity to affect some functions. Our results highlight the importance of understanding the role of multiple community attributes in driving ecosystem functioning.

  18. Dickeya species relatedness and clade structure determined by comparison of recA sequences.

    PubMed

    Parkinson, Neil; Stead, David; Bew, Janice; Heeney, John; Tsror Lahkim, Leah; Elphinstone, John

    2009-10-01

    Using sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe

  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. PMID:22833799

  20. 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.

  1. 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

  2. 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.

  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. 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

  5. Comparisons between physical model and numerical model results

    SciTech Connect

    Sagasta, P.F.

    1986-04-01

    Physical modeling scaling laws provide the opportunity to compare results among numerical modeling programs, including two- and three-dimensional interactive-raytracing and more sophisticated wave-equation-approximation methods, and seismic data collected over a known, three-dimensional model in a water tank. The sixfold closely spaced common-midpoint water-tank data modeled for this study simulate a standard marine three-dimensional survey shot over a three-layered physical model (a structured upper layer overlying two flat layers. Using modeling theory, the physical-tank model dimensions scale to realistic exploration dimensions, and the ultrasonic frequencies scale to seismic frequencies of 2-60 Hz. A comparison of P and converted-S events and amplitudes among these physical tank data and numerical modeling results illustrates many of the advantages and limitations of modeling methods available to the exploration geophysicist. The ability of three-dimensional raytracing to model off-line events and more closely predict waveform phase due to geometric effects shows the greater usefulness of three-dimensional modeling methods over two-dimensional methods in seismic interpretation. Forward modeling of P to Sv-converted events and multiples predicts their presence in the seismic data. The geometry of the physical model leads to examples where raytracing approximations are limited and the more time-consuming finite-element technique is useful to better understand wave propagation within the physical model. All of the numerical modeling programs used show limitations in matching the amplitudes and phase of events in the physical-model seismic data.

  6. 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.

  7. 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…

  8. What makes us human (Homo sapiens)? The challenge of cognitive cross-species comparison.

    PubMed

    Boesch, Christophe

    2007-08-01

    Two major theoretical approaches have dominated the quest for uniquely human cognitive abilities: a developmentalist approach stressing the importance of environmental and social conditions, and a predominant approach in experimental and comparative psychology, the deterministic approach suggesting the effect of environmental and social conditions to be minimal. As a consequence, most claims of human cognitive uniqueness are based on comparisons of White middle class Westerner humans (Homo sapiens) with captive chimpanzees (Pan troglodytes). However, humans are much more than only White middle class Westerners, and chimpanzees are much more than only captives. A review of some data available on different populations of humans and chimpanzees reveals that only the predictions of the developmentalist approach are supported. In addition, systematic biases are too often introduced in experiment protocols when comparing humans with apes that further cast doubts on cross-species comparisons. The author argues that only with consideration of within-species population differences in the cognitive domains and the use of well-matched cross-species experimental procedures will an objective understanding of the different cognitive abilities between species emerge. This will require a shift in the theoretical approach adopted by many in experimental and comparative psychology.

  9. 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.

  10. GCSS Cirrus Parcel Model Comparison Project

    NASA Technical Reports Server (NTRS)

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

    2000-01-01

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

  11. 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...

  12. 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

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

    PubMed

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

    2015-01-01

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

  14. 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.

  15. Species clustering in competitive Lotka-Volterra models.

    PubMed

    Pigolotti, Simone; López, Cristóbal; Hernández-García, Emilio

    2007-06-22

    We study the properties of general Lotka-Volterra models with competitive interactions. The intensity of the competition depends on the position of species in an abstract niche space through an interaction kernel. We show analytically and numerically that the properties of these models change dramatically when the Fourier transform of this kernel is not positive definite, due to a pattern-forming instability. We estimate properties of the species distributions, such as the steady number of species and their spacings, for different types of interactions, including stretched exponential and constant kernels.

  16. 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

  17. Modeling transformations of neurodevelopmental sequences across mammalian species.

    PubMed

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

    2013-04-24

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

  18. 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.

  19. 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.

  20. Morphological Comparison and Taxonomic Utility of Copulatory Structures of Selected Nematode Species

    PubMed Central

    Rammah, Abdallah; Hirschmann, Hedwig

    1987-01-01

    Spicules of 9 Meloidogyne, 2 Heterodera, 3 Globodera, and 12 other plant-parasitic, insect-parasitic, and free-living nematodes were excised and examined using scanning electron microscopy (SEM). Gubernacula of some of the species were also excised, and their structure was determined. The two spicules of all species examined were symmetrically identical in morphology. The spicule typically consisted of three parts: head, shaft, and blade with dorsal and ventral vela. The spicular nerve entered through the cytoplasmic core opening on the lateral outer surface of the spicule head and generally communicated with the exterior through one or two pores at the spicule tip. Spicules of Xiphinema sp. and Aporcelaimellus sp. were not composed of three typical parts, were less sclerotized, and lacked a cytoplasmic core opening and distal pores. Spicules of Aphelenchoides spp. had heads expanded into apex and rostrum and had very arcuate blades with thick dorsal and ventral edges (limbs). Gubernaculum shapes were stable within a species, but differed among species examined. The accessory structures of Hoplolaimus galeatus consisted of a tongue-shaped gubernaculum with two titillae at its distal end and a plate-like capitulum terminating distally in two flat, wing-like structures. A comparison of spicules of several species of Meloidogyne by SEM and light microscopy revealed no striking morphological differences. PMID:19290150

  1. The characteristics of species in an evolutionary food web model.

    PubMed

    Lugo, Carlos A; McKane, Alan J

    2008-06-21

    We explore the consequences of modifying the way in which species are defined in an evolutionary food web model. In the original version of the model, the species were defined in terms of a fixed number of features, chosen from a large number of possibilities. These features represented phenotypic and behavioural characteristics of the species. Speciation consisted in occasionally replacing one of the features by another. Here we modify this scheme by firstly allowing for a richer structure and secondly by testing whether we are able to eliminate the need for an explicit choice of features altogether. In the first case we allow for changing the number of features which define a species, as well as their nature, and find that in the resulting webs the higher trophic levels typically contain species with the greatest number of features. In the second case, by a simplification of the mechanisms for inter and intra-species competition, we construct a model without any explicit features and find that we are still able to grow model food webs. We assess the quality of the food webs produced and discuss the consequences of our findings for the future modelling of food webs.

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

    NASA Astrophysics Data System (ADS)

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

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

  3. 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.

  4. 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.

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

    PubMed Central

    2011-01-01

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

  6. 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

  7. 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.

  8. Enhancing species distribution modeling by characterizing predator-prey interactions.

    PubMed

    Trainor, Anne M; Schmitz, Oswald J; Ivan, Jacob S; Shenk, Tanya M

    2014-01-01

    Niche theory is a well-established concept integrating a diverse array of environmental variables and multispecies interactions used to describe species geographic distribution. It is now customary to employ species distribution models (SDMs) that use environmental variables in conjunction with species location information to characterize species' niches and map their geographic ranges. The challenge remains, however, to account for the biotic interactions of species with other community members on which they depend. We show here how to connect species spatial distribution and their dependence with other species by modeling spatially explicit predator-prey interactions, which we call a trophic interaction distribution model (TIDM). To develop the principles, we capitalized on data from Canada lynx (Lynx canadensis) reintroduced into Colorado. Spatial location information for lynx obtained from telemetry was used in conjunction with environmental data to construct an SDM. The spatial locations of lynx-snowshoe hare encounters obtained from snow-tracking in conjunction with environmental data were used to construct a TIDM. The environmental conditions associated with lynx locations and lynx-hare encounters identified through both SDM and TIDM revealed an initial transient phase in habitat use that settled into a steady state. Nevertheless, despite the potential for the SDM to broadly encompass all lynx hunting and nonhunting spatial locations, the spatial extents of the SDM and TIDM differed; about 40% of important lynx-snowshoe hare locations identified in the TIDM were not identified in the lynx-only SDM. Our results encourage greater effort to quantify spatial locations of trophic interactions among species in a community and the associated environmental conditions when attempting to construct models aimed at projecting current and future species geographic distributions.

  9. 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.

  10. 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

  11. 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

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

    SciTech Connect

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

    2013-07-15

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

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

    PubMed

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

    2016-08-01

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

  14. 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.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

    Suweis, Samir; Rinaldo, Andrea; Maritan, Amos

    2012-07-01

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

  17. Benchmarking novel approaches for modelling species range dynamics.

    PubMed

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

    2016-08-01

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

  18. 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

  19. Modeling symbiosis by interactions through species carrying capacities

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. GIS-based niche modeling for mapping species' habitat.

    PubMed

    Rotenberry, John T; Preston, Kristine L; Knick, Steven T

    2006-06-01

    Ecological "niche modeling" 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.

  5. 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.

  6. 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

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

    PubMed

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

    2016-01-01

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

  8. 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.

  9. 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.

  10. 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

  11. 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 ...

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

    PubMed

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

    2016-06-01

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

  13. Engineering Large Animal Species to Model Human Diseases.

    PubMed

    Rogers, Christopher S

    2016-07-01

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

  14. Engineering Large Animal Species to Model Human Diseases.

    PubMed

    Rogers, Christopher S

    2016-01-01

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

  15. Comparison of different phosphate species adsorption by ferric and alum water treatment residuals.

    PubMed

    Gao, Sijia; Wang, Changhui; Pei, Yuansheng

    2013-05-01

    As safe byproducts of drinking water treatment processes, ferric and alum water treatment residuals (FARs) have the potential to be new phosphate (P) immobilization materials. In this study, batch experiments were conducted to investigate and compare the adsorption characteristics of three P species by FARs. The results showed that the kinetic processes of different P species' adsorption by FARs could be described by a pseudo second-order model. The ranking list of the initial adsorption rates with respect to different phosphates was pyrophosphate, phytate, orthophosphate, hexametaphosphate and glycerophosphate. Of the six models considered, the two-site Langmuir model most effectively described the adsorption characteristics of the various P species. Upon fitting the results, the maximum adsorption capacities were determined to be 40.24 mg/g for phytate, 18.04 mg/g for pyrophosphate, 17.14 mg/g for orthophosphate, 15.86 mg/g for hexametaphosphate and 10.81 mg/g for glycerophosphate. In addition, the adsorption processes of the different P species were spontaneous endothermic processes and were favored at lower pH values. The pH dependency was found to be especially true for orthophosphate, where the adsorption capacity decreased by 1.22 mg/g with an increase in pH from 5 to 9. Fractionation of the adsorbed P species from the FARs demonstrated that Al-P and Fe-P were the dominating forms, constituting approximately 80%-90% of the total P fractions, which indicated that the adsorbed P species had a low leaching risk and could stably exist in the FARs. Therefore, the FARs could be effective in controlling pollution in water caused by different P species.

  16. 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

  17. 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

  18. 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.

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

    USGS Publications Warehouse

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

    2006-01-01

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

  20. 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.

  1. 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

  2. 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

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

    PubMed

    Reza, Mohammad; Motlagh, Safari

    2015-07-01

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

  4. 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. PMID:24399901

  5. 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

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

    PubMed

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

    2012-06-23

    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.

  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. The co-occurrence of species and the co-diversity of sites in neutral models of biodiversity.

    PubMed

    Trejo-Barocio, Paulina; Arita, Héctor T

    2013-01-01

    Patterns of co-occurrence of species are widely used to assess the fit of ecological neutral models to empirical patterns. The mathematically equivalent patterns of co-diversity of sites, in contrast, have been considered only indirectly and analyses normally are focused on the spatial distribution of species richness, rather than on the patterns of species sharing. Here we use two analytical tools (range-diversity plots and rank plots) to assess the predictions of simple neutral models in relation to patterns of co-occurrence and co-diversity. Whereas a fully stochastic null model predicts zero average among species and among sites, neutral models generate systems with low levels of covariance among species and high levels of positive covariance among sites. These patterns vary with different combinations of dispersal and speciation rates, but are always linked to the shape, symmetry, and spread of the range-size and species-richness frequency distributions. Non-homogeneous patterns of diversity and distribution arise in neutral models because of the spatial arrangement of sites and their concomitant similarity, which is reflected also in the spread of the range-size frequency distribution. The nearly null covariance among species, in contrast, implies low variance in species richness of sites and very slim frequency distributions. In real world assemblages of Mexican volant and non-volant mammals, patterns of range-size and species-richness frequency distribution are similar to those generated by neutral models. However, when the comparison includes the covariance both for species (co-occurrence) and for sites (co-diversity), empirical patterns differ significantly from the predictions of neutral models. Because of the mathematical links between the covariance in the distribution of species and the variance of species-richness values and between the covariance in species sharing among sites and the variance of range-size values, a full understanding of patterns

  9. 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.

  10. 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.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  13. Benchmarking novel approaches for modelling species range dynamics

    PubMed Central

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

    2016-01-01

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

  14. 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.

  15. 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.

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

    PubMed

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

    2007-03-01

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

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

    NASA Technical Reports Server (NTRS)

    Niedermaier, Dan; Kaouk, Mo

    2010-01-01

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

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

    SciTech Connect

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

    1987-10-21

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

  19. 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

  20. 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

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

    PubMed

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

    2015-01-01

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

  2. 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

  3. CARBON-CHAIN SPECIES IN WARM-UP MODELS

    SciTech Connect

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

    2011-12-20

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

  4. 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

  5. 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.

  6. 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...

  7. 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

  8. 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.

  9. 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.

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

    PubMed

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

    2011-04-01

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

  11. 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.

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

    PubMed

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

    2015-01-01

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

  13. 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.

  14. Confirmatory Measurement Model Comparisons Using Latent Means.

    ERIC Educational Resources Information Center

    Millsap, Roger E.; Everson, Howard

    1991-01-01

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

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

    USGS Publications Warehouse

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

    2005-01-01

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

  16. 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.

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

    PubMed Central

    2012-01-01

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

  18. 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.

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

    PubMed

    Chao, Anne; Bunge, John

    2002-09-01

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

  20. Traffic flow forecasting: Comparison of modeling approaches

    SciTech Connect

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

    1997-08-01

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

  1. nIFTy cosmology: comparison of galaxy formation models

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  2. 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.

  3. Comparison of Thermal Modeling Approaches for Complex Measurement Equipment

    NASA Astrophysics Data System (ADS)

    Schalles, M.; Thewes, R.

    2014-04-01

    Thermal modeling is used for thermal investigation and optimization of sensors, instruments, and structures. Here, results depend on the chosen modeling approach, the complexity of the model, the quality of material data, and the information about the heat transport conditions of the object of investigation. Despite the widespread application, the advantages and limits of the modeling approaches are partially unknown. For comparison of different modeling approaches, a simplified and analytically describable demonstration object is used. This object is a steel rod at well-defined heat exchange conditions with the environment. For this, analytically describable models, equivalent electrical circuits, and simple and complex finite-element-analysis models are presented. Using the different approaches, static and dynamic simulations are performed and temperatures and temperature fields in the rod are estimated. The results of those calculations, comparisons with measurements, and identification of the sensitive points of the approaches are shown. General conclusions for thermal modeling of complex equipment are drawn.

  4. Modeling of Species Transport and Macrosegregation in Heavy Steel Ingots

    NASA Astrophysics Data System (ADS)

    Li, Wensheng; Shen, Houfa; Zhang, Xiong; Liu, Baicheng

    2014-04-01

    In the current study, two significant phenomena involved in heavy steel ingot casting, i.e., species transport and macrosegregation, were numerically simulated. First, a ladle-tundish-mold species transport model describing the entire multiple pouring process of heavy steel ingots was proposed. Carbon distribution and variation in both the tundish and the mold of a 292-ton steel ingot were predicted. Results indicate high carbon concentration in the bottom of the mold while low concentration carbon at the top of mold after the pouring process. Such concentration distribution helps in reducing both negative segregation in the bottom of the solidified ingot and positive segregation at the top. Second, a two-phase multiscale macrosegregation model was used to simulate the solidification process of industrial steel ingots. This model takes into account heat transfer, fluid flow, solute transport, and equiaxed grain motion on a system scale, as well as grain nucleation and growth on a microscopic scale. The model was first used to analyze a three-dimensional industry-scale steel ingot as a benchmark. Then, it was applied to study macrosegregation formation in a 53-ton steel ingot. Macrosegregation predicted by the numerical model was presented and compared with experimental measurements. Typical macrosegregation patterns in heavy steel ingots are found to be well reproduced with the two-phase model.

  5. Comparison of models of odor interaction.

    PubMed

    Cain, W S; Schiet, F T; Olsson, M J; de Wijk, R A

    1995-12-01

    Subjects rated the overall perceived intensity of concentrations of the odorants cineole, geraniol, hexyl salicylate, and linalyl acetate smelled alone and in binary mixtures. The subjects also rated intensity of specified constituents (e.g. amount of cineole in cineole, and in mixtures of cineole and linalyl acetate). The intensity of the stronger component alone offered a close description of perceived intensity. In addition to the Stronger Component model, two other psychological models (Vector and U model) and two psychophysical models (UPL2 and Equiratio Mixture model) offered descriptions ranging from fair to very good. Psychological models gave better fits, but lack explanatory power. Some results indicated that weaker odors add more potently than stronger odors, an outcome incompatible with these models. The psychophysical models, based on the additivity of single components, generally overestimated perceived intensity. Judgments of individual qualities gave only slight encouragement to any expectation of differences in masking or maskability among odorants. The results highlight the need to test particular critical hypotheses regarding how people perceive mixtures.

  6. 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.

  7. 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

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

    PubMed

    Rodríguez, Abel; Quintana, Fernando A

    2015-02-01

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

  9. Comparison of Two Analysis Approaches for Measuring Externalized Mental Models

    ERIC Educational Resources Information Center

    Al-Diban, Sabine; Ifenthaler, Dirk

    2011-01-01

    Mental models are basic cognitive constructs that are central for understanding phenomena of the world and predicting future events. Our comparison of two analysis approaches, SMD and QFCA, for measuring externalized mental models reveals different levels of abstraction and different perspectives. The advantages of the SMD include possibilities…

  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. 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.

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

    PubMed

    MacKenzie, Darryl I; Nichols, James D; Seamans, Mark E; Gutiérrez, R J

    2009-03-01

    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. PMID:19341151

  13. Numerical comparison of strong Langmuir turbulence models

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

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

  14. 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

  15. 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

  16. 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

  17. 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.

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

    PubMed

    Abraham, Michael H; Acree, William E

    2016-07-01

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

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

    PubMed

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

    2016-01-15

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

  20. Enchytraeus crypticus as model species in soil ecotoxicology.

    PubMed

    Castro-Ferreira, Marta P; Roelofs, Dick; van Gestel, Cornelis A M; Verweij, Rudo A; Soares, Amadeu M V M; Amorim, Mónica J B

    2012-06-01

    Enchytraeids are ecologically relevant soil organisms, due to their activity in decomposition and bioturbation in many soil types worldwide. The enchytraeid reproduction test (ERT) guidelines ISO 16387 and OECD 220 are exclusive to the genus Enchytraeus and recommend using the species E. albidus with a 6-week test period. The suggested alternative, E. crypticus has a shorter generation time which may enable the ERT to be twice as fast. To confirm the suitability of a 3-week test period for E. crypticus, the toxicity of five chemicals, with distinct properties and modes of action, was assessed in LUFA 2.2 soil. In all controls the validity criteria were met, as survival of E. crypticus was above 92% and more than 772 juveniles were produced. The good performance supports its appropriateness as model species. Reproduction was more sensitive than survival, with only cadmium and 3,5-dichloroaniline causing significant lethal effects in the tested concentration ranges. The effect concentration causing 50% reduction in the number of juveniles (EC50) was 35 mg kg(-1) for cadmium, <1.0 mg kg(-1) for carbendazim, 145 mg kg(-1) for phenanthrene, 275 mg kg(-1) for pentachloroaniline and 102 mg kg(-1) for 3,5-dichloroaniline. To evaluate the sensitivity of E. crypticus, the present results were compared to literature data for E. albidus. In conclusion, E. crypticus is a suitable model species in soil ecotoxicology, with advantages such as good control performance and speed, leading to a reliable and faster ERT.

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

    PubMed

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

    2001-01-01

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

  2. 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

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

    PubMed

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

    2007-09-01

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

  4. Simulation of the present-day atmospheric ozone, odd nitrogen, chlorine and other species using a coupled 2-D model in isentropic coordinates

    NASA Technical Reports Server (NTRS)

    Yang, H.; Olaguer, E.; Tung, K. K.

    1991-01-01

    A zonally averaged two-dimensional model for chemical species in the atmosphere (Olaguer et al., 1990), with coupled dynamics, radiation transfer, and chemistry, is used to study the present-day atmospheric ozone, odd nitrogen, chlorine, other species. The model utilizes all zonally averaged physical equations of momentum, energy, and mass and determines self-consistently the advective and diffusive tranasport parameters from the temperature specific to the period of observation. A comparison of the model results with observations showed good agreement.

  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. Germplasm cryobanking in zebrafish and other aquarium model species.

    PubMed

    Robles, Vanesa; Cabrita, Elsa; Herráez, M Paz

    2009-09-01

    During the last few years zebrafish and other aquarium fish have become more important model system species. In zebrafish valuable biotechnological lines are constantly emerging, and the creation of cryobanks of viable fish sperm, oocytes, and embryos from those lines is a constant and important demand. Cryopreservation is an essential tool for storing specific genetic material and would significantly help in the conservation of such lines, facilitating daily procedures in labs and companies working with this species. In this review, all advances achieved in this field are presented. Protocols for sperm cryopreservation are described, and the new directions of approaches in embryo and oocyte cryopreservation and also in blastomeres, and primordial germ cell cryopreservation are discussed.

  7. 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.

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

    PubMed

    Wallmo, Kristy; Lew, Daniel K

    2016-09-01

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

  9. Comparisons of Airborne HSRL and Modeled Aerosol Profiles

    NASA Astrophysics Data System (ADS)

    Ferrare, R. A.; Burton, S. P.; Hostetler, C. A.; Hair, J. W.; Ismail, S.; Rogers, R. R.; Notari, A.; Berkoff, T.; Butler, C. F.; Collins, J. E., Jr.; Fenn, M. A.; Scarino, A. J.; Clayton, M.; Mueller, D.; Chemyakin, E.; Fast, J. D.; Berg, L. K.; Randles, C. A.; Colarco, P. R.; daSilva, A.

    2014-12-01

    Aerosol profiles derived from a regional and a global model are compared with aerosol profiles acquired by NASA Langley Research Center (LaRC) airborne High Spectral Resolution Lidars (HSRLs) during recent field missions. We compare simulated aerosol profiles obtained from the WRF-Chem regional model with those measured by the airborne HSRL-2 instrument over the Atlantic Ocean east of Cape Cod in July 2012 during the Department of Energy Two-Column Aerosol Project (TCAP). While deployed on the LaRC King Air during TCAP, HSRL-2 acquired profiles of aerosol extinction at 355 and 532 nm, as well as aerosol backscatter and depolarization at 355, 532, and 1064 nm. Additional HSRL-2 data products include profiles of aerosol type, mixed layer depth, and aerosol microphysical parameters (e.g. effective radius, concentration). The HSRL-2 and WRF-Chem aerosol profiles are compared along the aircraft flight tracks. HSRL-2 profiles acquired during the NASA Deriving Information on Surface Conditions from COlumn and VERtically Resolved Observations Relevant to Air Quality (DISCOVER-AQ) mission over Houston during September 2013 are compared with the NASA Goddard Earth Observing System global model, version 5 (GEOS-5) profiles. In addition to comparing backscatter and extinction profiles, the fraction of aerosol extinction and optical thickness from various aerosol species from GEOS-5 are compared with aerosol extinction and optical thickness contributed by aerosol types derived from HSRL-2 data. We also compare aerosol profiles modeled by GEOS-5 with those measured by the airborne LaRC DIAL/HSRL instrument during August and September 2013 when it was deployed on the NASA DC-8 for the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) mission. DIAL/HSRL measured extinction (532 nm), backscatter (532 and 1064 nm), and depolarization profiles (532 and 1064 nm) in both nadir and zenith directions during long transects over the

  10. 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. PMID:22983143

  11. 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.

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

    PubMed Central

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

    1988-01-01

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

  13. microRNA target predictions across seven Drosophila species and comparison to mammalian targets.

    PubMed

    Grün, Dominic; Wang, Yi-Lu; Langenberger, David; Gunsalus, Kristin C; Rajewsky, Nikolaus

    2005-06-01

    microRNAs are small noncoding genes that regulate the protein production of genes by binding to partially complementary sites in the mRNAs of targeted genes. Here, using our algorithm PicTar, we exploit cross-species comparisons to predict, on average, 54 targeted genes per microRNA above noise in Drosophila melanogaster. Analysis of the functional annotation of target genes furthermore suggests specific biological functions for many microRNAs. We also predict combinatorial targets for clustered microRNAs and find that some clustered microRNAs are likely to coordinately regulate target genes. Furthermore, we compare microRNA regulation between insects and vertebrates. We find that the widespread extent of gene regulation by microRNAs is comparable between flies and mammals but that certain microRNAs may function in clade-specific modes of gene regulation. One of these microRNAs (miR-210) is predicted to contribute to the regulation of fly oogenesis. We also list specific regulatory relationships that appear to be conserved between flies and mammals. Our findings provide the most extensive microRNA target predictions in Drosophila to date, suggest specific functional roles for most microRNAs, indicate the existence of coordinate gene regulation executed by clustered microRNAs, and shed light on the evolution of microRNA function across large evolutionary distances. All predictions are freely accessible at our searchable Web site http://pictar.bio.nyu.edu.

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Information-theoretic model comparison unifies saliency metrics.

    PubMed

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

    2015-12-29

    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.

  5. 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...

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

    PubMed

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

    2016-01-01

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

  7. 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

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

    PubMed

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

    2016-06-25

    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.

  9. 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.

  10. Systematic comparison of model polymer nanocomposite mechanics.

    PubMed

    Xiao, Senbo; Peter, Christine; Kremer, Kurt

    2016-01-01

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

  11. DFT models of molecular species in carbonate molten salts.

    PubMed

    Carper, W Robert; Wahlbeck, Phillip G; Griffiths, Trevor R

    2012-05-10

    Raman spectra of high temperature carbonate melts are correlated with carbonate species modeled at 923 K using B3LYP/(6-311+G(2d,p)) density functional calculations. Species that are theoretically stable at 923 K include O(2-), O(2)(-), O(2)(2-), CO(3)(2-), C(2)O(6)(2-), CO(4)(-), CO(4)(2-), CO(4)(4-), CO(5)(2-), KCO(4)(-), LiCO(4)(-), KO(2)(-), LiO(2)(-), NaO(2)(-), KO(2), LiO(2), NaO(2), KCO(3)(-), LiCO(3)(-), and NaCO(3)(-). Triangular, linear, and bent forms are theoretically possible for KO(2)(-) and NaO(2)(-). Triangular and linear forms may exist for LiO(2)(-). Linear and triangular versions are theoretically possible for LiO(2)(-) and KO(2). A triangular version of NaO(2) may exist. The correlation between measured and theoretical Raman spectra indicate that monovalent cations are to be included in several of the species that produce Raman spectra.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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 ...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Gonadotropin hormone and receptor sequences from model teleost species.

    PubMed

    Wong, Andrew C; Van Eenennaam, Alison L

    2004-01-01

    Fish offer some advantages for the study of vertebrate reproductive physiology. Only a few of the genes encoding the components of the hypothalamic-pituitary-gonadal axis have been identified from model teleosts. This study describes a combination of database searching and molecular approaches to identify the FSH and LH gonadotropin beta-subunits (fshb and lhb, respectively), and the LH receptor (lhr) from two model teleost species: zebrafish (Danio rerio) and Fugu (Takifugu rubripes). Sequence and phylogenetic analyses were used to examine the relationships that exist between gonadotropins and their receptors from species representing several piscine orders. The gonadotropin alpha-subunit (Cga) is highly conserved among teleosts and tetrapods. The presence of a genomic pseudogene (cgap) was also noted in zebrafish. Generally, teleostean FSHbeta protein sequences share less identity with each other than do LHbeta protein sequences, supporting the hypothesis that FSHbeta diverged more rapidly during teleost evolution. Interestingly, and uniquely, zebrafish Fshb lacked two highly conserved cysteine residues in the "determinant loop" which is thought to contribute towards receptor binding and specificity. Teleost gonadotropin receptor sequences clearly diverged into two distinct groups, FSHR and LHR. As has been seen with mammalian gonadotropin receptor transcripts, splice variants of zebrafish lhr were also observed.

  2. 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.

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

    PubMed

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

    2016-01-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

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

    PubMed Central

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

    2016-01-01

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

  12. 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.

  13. Predicting the species abundance distribution using a model food web.

    PubMed

    Powell, Craig R; McKane, Alan J

    2008-12-21

    A large number of models of the species abundance distribution (SAD) have been proposed, many of which are generically similar to the log-normal distribution, from which they are often indistinguishable when describing a given data set. Ecological data sets are necessarily incomplete samples of an ecosystem, subject to statistical noise, and cannot readily be combined to yield a closer approximation to the underlying distribution. In this paper, we adopt the Webworld ecosystem model to study the predicted SAD in detail. The Webworld model is complex, and does not allow analytic examination of such features; rather, we use simulation data and an approach similar to that of ecologists analysing empirical data. By examining large sets of fully described data we are able to resolve features which can distinguish between models but which have not been investigated in detail in field data. We find that the power-law normal distribution is superior to both the log-normal and logit-normal distributions, and that the data can improve on even this at the high-population cut-off.

  14. 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 ...

  15. 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.

  16. A comparison of ionospheric model predictions with MITHRAS observations

    NASA Astrophysics Data System (ADS)

    Schunk, Robert W.

    1987-01-01

    MITHRAS is a coordinated multiradar program to study the interactions between the magnetosphere, ionosphere, and thermosphere, as well as the phenomena that result from these interactions. The program is based on a data set acquired by the Chatanika, Millstone Hill, and Eiscat incoherent scatter radars. A large portion of the data is unique in that it was the only time when the radars, well separated in local and magnetic time, simultaneously probed the high latitude ionosphere. Our effect concerned model data comparisons. Specifically, we compared the predictions of our three-dimensional, time dependent model of the high latitude ionosphere with MITHRAS data sets. Of particular interest were the variations of the ionosphere with altitude, latitude, longitude, universal time, season, and magnetic activity. Model data comparisons enabled us to determine the adequacy of our current understanding of high latitude ionosphere dynamics as well as certain magnetosphere ionosphere atmosphere coupling processes.

  17. 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.

  18. 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.

  19. A model for improving endangered species recovery programs

    NASA Astrophysics Data System (ADS)

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

    1994-09-01

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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. Defining Predictive Probability Functions for Species Sampling Models

    PubMed Central

    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. PMID:24368874

  5. 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.

  6. Comparison for non-local hydrodynamic thermal conduction models

    SciTech Connect

    Marocchino, A.; Atzeni, S.; Schiavi, A.; Tzoufras, M.; Nicolaie, Ph. D.; Mallet, J.; Tikhonchuk, V.; Feugeas, J.-L.

    2013-02-15

    Inertial confinement fusion and specifically shock ignition involve temperatures and temperature gradients for which the classical Spitzer-Haerm thermal conduction breaks down and a non-local operator is required. In this article, two non-local electron thermal conduction models are tested against kinetic Vlasov-Fokker-Planck simulations. Both models are shown to reproduce the main features of thermal heat front propagation at kinetic timescales. The reduction of the thermal conductivity as a function of the scalelength of the temperature gradient is also recovered. Comparisons at nanosecond timescales show that the models agree on the propagation velocity of the heat front, but major differences appear in the thermal precursor.

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  9. 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

  10. Comparison of modelled and observed Arctic sea ice

    NASA Astrophysics Data System (ADS)

    Bobylev, Leonid; Kuzmina, Svetlana; Johannessen, Ola M.

    2010-05-01

    When considering the climate projections one of the most important issues is how well models reproduce variability and change of the main climate parameters, e.g. sea ice. To address this issue the comparative analysis of observed and modelled sea ice coverage and thickness was performed. Modelled sea ice extent and thickness data for the comparison are represented by results of simulation runs of IPCC AR4 models. Observed data for sea ice coverage - area and extent, are Chapman and Walsh data and data from satellite passive microwave measurements available continuously since November 1978. Observed sea ice thickness data are Kwok and Rothrock data from submarines for 1975-2000 and from ICESat satellite for 2003-2008. Annual cycle of observed and modelled monthly mean sea ice extent (SIE) showed that, generally, models overestimate SIE. Disagreement between simulated and observed results is larger during late winter, spring and earlier summer. Annual cycle of observed and modelled linear trends of SIE showed that negative trend rates reach their maxima in July-August, revealing significant decreases in summer SIE. Simulated trend rates are two times smaller then observed. Thus, the observed sea ice extent decreases faster than modelled. Comparison of observed and modelled annual cycle of SIE for the different Arctic seas showed that for the Barents sea models overestimate sea ice during the whole year. For other seas models overestimate SIE only for summer and early fall. For all other seasons they underestimate Arctic sea ice. The mean differences between observed and modelled sea ice concentration in the Arctic is the largest in Barents, Kara, Laptev and East-Siberian seas and exceeds 80%. The comparison of observed and modelled sea ice thickness showed that, generally, observed values lie within the area of the model spread. But the negative trend of observed thicknesses significantly higher than that of models. So, the Arctic sea ice thickness, like its area

  11. 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.

  12. General-linear-models approach for comparing the response of several species in acute-toxicity tests

    SciTech Connect

    Daniels, K.L.; Goyert, J.C.; Farrell, M.P.; Strand, R.H.

    1982-01-01

    Acute toxicity tests (bioassays) estimate the concentration of a chemical required to produce a response (usually death) in fifty percent of a population (the LC50). Simple comparisons of LC5C values among several species are often inadequate because species can have identical LC50 values while their overall response to a chemical may differ in either the threshold concentration (intercept) or the rate of response (slope). A sequential approach using a general linear model is presented for testing differences among species in their overall response to a chemical. This method tests for equality of slopes followed by a test for equality of regression lines. This procedure employs the Statistical Analysis System's General Linear Models procedure for conducting a weighted least squares analysis with a convariable.

  13. 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.

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

    PubMed

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

    2016-06-21

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

  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 compounds of three Rubus species and their antioxidant activity.

    PubMed

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

    2015-12-01

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

  17. A Statistical Comparison of PSC Model Simulations and POAM Observations

    NASA Technical Reports Server (NTRS)

    Strawa, A. W.; Drdla, K.; Fromm, M.; Bokarius, K.; Gore, Warren J. (Technical Monitor)

    2002-01-01

    A better knowledge of PSC composition and formation mechanisms is important to better understand and predict stratospheric ozone depletion. Several past studies have attempted to compare modeling results with satellite observations. These comparisons have concentrated on case studies. In this paper we adopt a statistical approach. POAM PSC observations from several Arctic winters are categorized into Type Ia and Ib PSCs using a technique based on Strawa et al. The discrimination technique has been modified to employ the wavelengths dependence of the extinction signal at all wavelengths rather than only at 603 and 10 18 nm. Winter-long simulations for the 1999-2000 Arctic winter have been made using the IMPACT model. These simulations have been constrained by aircraft observations made during the SOLVE/THESEO 2000 campaign. A complete set of winter-long simulations was run for several different microphysical and PSC formation scenarios. The simulations give us perfect knowledge of PSC type (Ia, Ib, or II), composition, especially condensed phase HNO3 which is important for denitrification, and condensed phase H2O. Comparisons are made between the simulation and observation of PSC extinction at 1018 rim versus wavelength dependence, winter-long percentages of Ia and Ib occurrence, and temporal and altitude trends of the PSCs. These comparisons allow us to comment on how realistic some modeling scenarios are.

  18. 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.

  19. 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.

  20. Meridional Winds derived from ionosonde measurements: comparison of different models

    NASA Astrophysics Data System (ADS)

    Katamzi, Zama; Bosco Habarulema, John; Aruliah, Anasuya

    2016-07-01

    Thermospheric meridional winds are derived from ionospheric F2 region peak parameters (i.e. F2 maximum density, NmF2, and F2 peak height, hmF2) obtained using South African ionosonde for solar maximum (2001 and 2014) and solar minimum (2009). The study uses several different techniques and models to investigate the climatology behaviour of the winds in order to understand wind variability over South Africa. Detailed solar cycle, seasonal and diurnal trends will help establish how the winds influence ionospheric behaviour at this latitude. Comparisons of ionosonde derived neutral winds with empirical and numerical models such as the Coupled Middle Atmosphere Thermosphere Model (CMAT2) and Thermosphere-Ionosphere-Electrodynamics General Circulation Model (TIE-GCM) are important to understand the validity of theoretical and empirical models.

  1. A Comparison Between Models of Gravity Induced Decoherence

    NASA Astrophysics Data System (ADS)

    Bera, Sayantani; Donadi, Sandro; Lochan, Kinjalk; Singh, Tejinder P.

    2015-12-01

    It has been suggested in the literature that spatial coherence of the wave function can be dynamically suppressed by fluctuations in the spacetime geometry. These fluctuations represent the minimal uncertainty that is present when one probes spacetime geometry with a quantum probe. Two similar models have been proposed, one by Diósi (D-model) and one by Karolyhazy and collaborators (K-model), based on apparently unrelated minimal spacetime bounds. The two models arrive at somewhat different expressions for the dependence of the localization coherence length on the mass and size of the quantum object. In the present article we compare and contrast the two models from three aspects: (i) comparison of the spacetime bounds, (ii) method of calculating decoherence time, (iii) comparison of noise correlation. We show that under certain conditions the minimal spacetime bounds in the two models can be derived one from the other. We argue that the methods of calculating the decoherence time are equivalent. We re-derive the two-point correlation for the fluctuation potential in the K-model, and confirm the earlier result of Diósi and Lukács that it is non-white noise, unlike in the D-model, where the corresponding correlation is white noise in time. This seems to be the origin of the different results in the two models. We derive the non-Markovian master equation for the K-model. We argue that the minimal spacetime bound cannot predict the noise correlation uniquely, and additional criteria are necessary to accurately determine the effects of gravitationally induced decoherence.

  2. Comparison of two laryngeal tissue fiber constitutive models

    NASA Astrophysics Data System (ADS)

    Hunter, Eric J.; Palaparthi, Anil Kumar Reddy; Siegmund, Thomas; Chan, Roger W.

    2014-02-01

    Biological tissues are complex time-dependent materials, and the best choice of the appropriate time-dependent constitutive description is not evident. This report reviews two constitutive models (a modified Kelvin model and a two-network Ogden-Boyce model) in the characterization of the passive stress-strain properties of laryngeal tissue under tensile deformation. The two models are compared, as are the automated methods for parameterization of tissue stress-strain data (a brute force vs. a common optimization method). Sensitivity (error curves) of parameters from both models and the optimized parameter set are calculated and contrast by optimizing to the same tissue stress-strain data. Both models adequately characterized empirical stress-strain datasets and could be used to recreate a good likeness of the data. Nevertheless, parameters in both models were sensitive to measurement errors or uncertainties in stress-strain, which would greatly hinder the confidence in those parameters. The modified Kelvin model emerges as a potential better choice for phonation models which use a tissue model as one component, or for general comparisons of the mechanical properties of one type of tissue to another (e.g., axial stress nonlinearity). In contrast, the Ogden-Boyce model would be more appropriate to provide a basic understanding of the tissue's mechanical response with better insights into the tissue's physical characteristics in terms of standard engineering metrics such as shear modulus and viscosity.

  3. 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.

  4. 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

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

    PubMed

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

    2016-01-01

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

  6. Dispersal kernel estimation: A comparison of empirical and modelled particle dispersion in a coastal marine system

    NASA Astrophysics Data System (ADS)

    Hrycik, Janelle M.; Chassé, Joël; Ruddick, Barry R.; Taggart, Christopher T.

    2013-11-01

    Early life-stage dispersal influences recruitment and is of significance in explaining the distribution and connectivity of marine species. Motivations for quantifying dispersal range from biodiversity conservation to the design of marine reserves and the mitigation of species invasions. Here we compare estimates of real particle dispersion in a coastal marine environment with similar estimates provided by hydrodynamic modelling. We do so by using a system of magnetically attractive particles (MAPs) and a magnetic-collector array that provides measures of Lagrangian dispersion based on the time-integration of MAPs dispersing through the array. MAPs released as a point source in a coastal marine location dispersed through the collector array over a 5-7 d period. A virtual release and observed (real-time) environmental conditions were used in a high-resolution three-dimensional hydrodynamic model to estimate the dispersal of virtual particles (VPs). The number of MAPs captured throughout the collector array and the number of VPs that passed through each corresponding model location were enumerated and compared. Although VP dispersal reflected several aspects of the observed MAP dispersal, the comparisons demonstrated model sensitivity to the small-scale (random-walk) particle diffusivity parameter (Kp). The one-dimensional dispersal kernel for the MAPs had an e-folding scale estimate in the range of 5.19-11.44 km, while those from the model simulations were comparable at 1.89-6.52 km, and also demonstrated sensitivity to Kp. Variations among comparisons are related to the value of Kp used in modelling and are postulated to be related to MAP losses from the water column and (or) shear dispersion acting on the MAPs; a process that is constrained in the model. Our demonstration indicates a promising new way of 1) quantitatively and empirically estimating the dispersal kernel in aquatic systems, and 2) quantitatively assessing and (or) improving regional hydrodynamic

  7. 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.

  8. 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...

  9. Temperature tolerance and energetics: a dynamic energy budget-based comparison of North Atlantic marine species

    PubMed Central

    Freitas, Vânia; Cardoso, Joana F. M. F.; Lika, Konstadia; Peck, Myron A.; Campos, Joana; Kooijman, Sebastiaan A. L. M.; van der Veer, Henk W.

    2010-01-01

    Temperature tolerance and sensitivity were examined for some North Atlantic marine species and linked to their energetics in terms of species-specific parameters described by dynamic energy budget (DEB) theory. There was a general lack of basic information on temperature tolerance and sensitivity for many species. Available data indicated that the ranges in tolerable temperatures were positively related to optimal growth temperatures. However, no clear relationships with temperature sensitivity were established and no clear differences between pelagic and demersal species were observed. The analysis was complicated by the fact that for pelagic species, experimental data were completely absent and even for well-studied species, information was incomplete and sometimes contradictory. Nevertheless, differences in life-history strategies were clearly reflected in parameter differences between related species. Two approaches were used in the estimation of DEB parameters: one based on the assumption that reserve hardly contributes to physical volume; the other does not make this assumption, but relies on body-size scaling relationships, using parameter values of a generalized animal as pseudo-data. Temperature tolerance and sensitivity seemed to be linked with the energetics of a species. In terms of growth, relatively high temperature optima, sensitivity and/or tolerance were related to lower relative assimilation rates as well as lower maintenance costs. Making the step from limited observations to underlying mechanisms is complicated and extrapolations should be carefully interpreted. Special attention should be devoted to the estimation of parameters using body-size scaling relationships predicted by the DEB theory. PMID:20921053

  10. Comparison of CLSI broth macrodilution and microdilution methods for echinocandin susceptibility testing of 5 Candida species.

    PubMed

    Bopp, Lawrence H; Baltch, Aldona L; Ritz, William J; Smith, Raymond P

    2011-11-01

    In order to compare the Clinical and Laboratory Standards Institute (CLSI) broth macrodilution and microdilution methods of susceptibility testing for echinocandins and yeast, 55 strains of Candida representing 5 species were tested using the CLSI-recommended broth macro- and microdilution methods. Small (1-3 log(2)) but potentially important method-, species-, and drug-dependent differences in MICs were observed.

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

    DOE PAGESBeta

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

    2015-06-01

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

  12. 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).

  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

    2016-01-01

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

  14. Using Virtual Observatories for Data-Model Comparisons

    NASA Astrophysics Data System (ADS)

    Ridley, A.; de Zeeuw, D.

    2007-12-01

    Global models of the geospace environment allow researchers to better understand how the environment behaves under different conditions. In order to trust whether the model is accurate, it is crucial to compare the model results to data - i.e., validate the model. Also, models are very good at placing measurements into a global context, so the data can be better understood. With the advent of Virtural Observatories, it will become much easier to conduct data-model comparisons. This is because the model results will have similar descriptors as the data, and reside in model repositories (similar to data repositories), allowing the data and the model results to be cross-linked. In this presentation, we will describe our efforts on creating an environment in which data and models can be easily compared. We will provide real-world examples of how this can be used to better understand the geospace environment, and out progress in realizing the goal of creating such an environment.

  15. Distinguishing between cancer driver and passenger gene alteration candidates via cross-species comparison: a pilot study

    PubMed Central

    2010-01-01

    Background We are developing a cross-species comparison strategy to distinguish between cancer driver- and passenger gene alteration candidates, by utilizing the difference in genomic location of orthologous genes between the human and other mammals. As an initial test of this strategy, we conducted a pilot study with human colorectal cancer (CRC) and its mouse model C57BL/6J ApcMin/+, focusing on human 5q22.2 and 18q21.1-q21.2. Methods We first performed bioinformatics analysis on the evolution of 5q22.2 and 18q21.1-q21.2 regions. Then, we performed exon-targeted sequencing, real time quantitative polymerase chain reaction (qPCR), and real time quantitative reverse transcriptase PCR (qRT-PCR) analyses on a number of genes of both regions with both human and mouse colon tumors. Results These two regions (5q22.2 and 18q21.1-q21.2) are frequently deleted in human CRCs and encode genuine colorectal tumor suppressors APC and SMAD4. They also encode genes such as MCC (mutated in colorectal cancer) with their role in CRC etiology unknown. We have discovered that both regions are evolutionarily unstable, resulting in genes that are clustered in each human region being found scattered at several distinct loci in the genome of many other species. For instance, APC and MCC are within 200 kb apart in human 5q22.2 but are 10 Mb apart in the mouse genome. Importantly, our analyses revealed that, while known CRC driver genes APC and SMAD4 were disrupted in both human colorectal tumors and tumors from ApcMin/+ mice, the questionable MCC gene was disrupted in human tumors but appeared to be intact in mouse tumors. Conclusions These results indicate that MCC may not actually play any causative role in early colorectal tumorigenesis. We also hypothesize that its disruption in human CRCs is likely a mere result of its close proximity to APC in the human genome. Expanding this pilot study to the entire genome may identify more questionable genes like MCC, facilitating the discovery of

  16. 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

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

    PubMed

    Schwarzfeld, Marla D; Sperling, Felix A H

    2015-12-01

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

  18. 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.

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

    DOE PAGESBeta

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

    2015-06-07

    For this study, a web-based Roof Savings Calculator (RSC) has been deployed for the United States Department of Energy as an industry-consensus tool to help building owners, manufacturers, distributors, contractors and researchers easily run complex roof and attic simulations. RSC simulates multiple roof and attic technologies for side-by-side comparison including reflective roofs, different roof slopes, above sheathing ventilation, radiant barriers, low-emittance roof surfaces, duct location, duct leakage rates, multiple substrate types, and insulation levels. Annual simulations of hour-by-hour, whole-building performance are used to provide estimated annual energy and cost savings from reduced HVAC use. While RSC reported similar cooling savingsmore » to other simulation engines, heating penalty varied significantly. RSC results show reduced cool roofing cost-effectiveness, thus mitigating expected economic incentives for this countermeasure to the urban heat island effect. This paper consolidates comparison of RSC's projected energy savings to other simulation engines including DOE-2.1E, AtticSim, Micropas, and EnergyPlus. Also included are comparisons to previous simulation-based studies, analysis of RSC cooling savings and heating penalties, the role of radiative heat exchange in an attic assembly, and changes made for increased accuracy of the duct model. Finally, radiant heat transfer and duct interaction not previously modeled is considered a major contributor to heating penalties.« less

  20. 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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

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

  3. 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.

  4. Model reduction for stochastic chemical systems with abundant species

    NASA Astrophysics Data System (ADS)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2015-12-01

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

  5. Xenobiotic biotransformation in livestock: comparison to other species commonly used in toxicity testing.

    PubMed

    Watkins, J B; Klaassen, C D

    1986-09-01

    Wildlife, domesticated animals and humans are exposed daily to myriad chemicals present in our environment. The risk posed by these chemicals to one species is often determined by extrapolation from data gathered from another species. Several extensive studies have examined the capability of the liver to biotransform xenobiotics in animals commonly used in toxicity testing and in livestock. The present paper is a compilation of these data into a single source to permit comprehensive examination of inter-species variation in rates of hepatic biotransformation. Several substrates were studied for each enzyme system, including cytochrome P-450-dependent monooxygenases, epoxide hydrolases, UDP-glucuronosyltransferases, N-acetyltransferases, glutathione S-transferases and sulfotransferases. The numerous differences in substrate specificity for an individual enzymatic pathway reflect the apparent multiplicity of these enzymes in all 11 species studied. Several hundred- to several thousand-fold differences between species in enzymatic activities for certain substrates under well-defined conditions emphasize the need for caution and the risk of error in extrapolation of xenobiotic metabolism from one species to another. In spite of these uncertainties, knowledge of the rate of biotransformation may help us predict the fate of new chemicals in various species.

  6. 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.

  7. 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.

  8. Comparison of the evolutionary distances among syngens and sibling species of Paramecium.

    PubMed

    Hori, Manabu; Tomikawa, Izumi; Przyboś, Ewa; Fujishima, Masahiro

    2006-03-01

    The morphospecies of the genus Paramecium have several mating type groups, so-called syngens, composed of cells of complementary mating types. The Paramecium aurelia complex is composed of 15 sibling species assigned to the species from the syngen. To increase our understanding of the evolutionary relationships among syngen and sibling species of the genus Paramecium, we investigated the gene sequences of cytosol-type hsp70 from 7 syngens of Paramecium caudatum and 15 sibling species of P. aurelia. Molecular phylogenetic trees indicated that the P. aurelia complex could be divided into four lineages and separated into each sibling species. However, we did not find any obvious genetic distance among syngens of P. caudatum, and they could only be separated into two closely related groups. These results indicated that the concept of syngens in P. caudatum differs quite markedly from that of the P. aurelia complex. In addition, we also discuss the relationships among these species and other species, Paramecium jenningsi and Paramecium multimicronucleatum, which were once classified as varieties of P. aurelia.

  9. Modeling Stratospheric Constituents: Reactive Species That Regulate Ozone

    NASA Technical Reports Server (NTRS)

    Salawitch, Ross J.

    2000-01-01

    Photochemical loss of stratospheric ozone occurs primarily by catalytic cycles whose rates are limited by the concentration of OH, HO2, NO2, ClO, and/or BrO as well as the concentration of either atomic oxygen or of ozone itself. Once the concentrations of these gases are established, the photochemical loss rate of O3 depends on the rate coefficient of only a handful of key reactions. We have developed a method for testing our understanding of stratospheric ozone photochemistry by comparing measured and modeled concentrations of reactive hydrogen, nitrogen, chlorine and bromine radicals using a photochemical steady state model constrained by observed concentrations of long-lived precursors (e.g., NO(y), Cl(y), Br(y), O3, H2O, CH4) and environmental parameters such as ozone column, reflectivity, and aerosol surface area. We will show based on analyses of observations obtained by aircraft, balloon, and satellite platforms during the POLARIS campaign that our overall understanding of the processes that regulate these radical species is very good. The most notable current discrepancies are the tendency to underestimate observed NO2 by 15 to 30% for air masses that experience near continuous solar illumination over a 24 hour period and the tendency to underestimate observed OH and H02 by about 10 to 20% during midday and by much larger amounts at high solar zenith angle (SZA > 85). Possible resolutions to these discrepancies will be discussed. This study was carried out in close collaboration with many members of the POLARIS science team.

  10. Predicting recycling behaviour: Comparison of a linear regression model and a fuzzy logic model.

    PubMed

    Vesely, Stepan; Klöckner, Christian A; Dohnal, Mirko

    2016-03-01

    In this paper we demonstrate that fuzzy logic can provide a better tool for predicting recycling behaviour than the customarily used linear regression. To show this, we take a set of empirical data on recycling behaviour (N=664), which we randomly divide into two halves. The first half is used to estimate a linear regression model of recycling behaviour, and to develop a fuzzy logic model of recycling behaviour. As the first comparison, the fit of both models to the data included in estimation of the models (N=332) is evaluated. As the second comparison, predictive accuracy of both models for "new" cases (hold-out data not included in building the models, N=332) is assessed. In both cases, the fuzzy logic model significantly outperforms the regression model in terms of fit. To conclude, when accurate predictions of recycling and possibly other environmental behaviours are needed, fuzzy logic modelling seems to be a promising technique. PMID:26774211

  11. 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.

  12. 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

  13. 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.

  14. Bayesian inference and model comparison for metallic fatigue data

    NASA Astrophysics Data System (ADS)

    Babuška, Ivo; Sawlan, Zaid; Scavino, Marco; Szabó, Barna; Tempone, Raúl

    2016-06-01

    In this work, we present a statistical treatment of stress-life (S-N) data drawn from a collection of records of fatigue experiments that were performed on 75S-T6 aluminum alloys. Our main objective is to predict the fatigue life of materials by providing a systematic approach to model calibration, model selection and model ranking with reference to S-N data. To this purpose, we consider fatigue-limit models and random fatigue-limit models that are specially designed to allow the treatment of the run-outs (right-censored data). We first fit the models to the data by maximum likelihood methods and estimate the quantiles of the life distribution of the alloy specimen. To assess the robustness of the estimation of the quantile functions, we obtain bootstrap confidence bands by stratified resampling with respect to the cycle ratio. We then compare and rank the models by classical measures of fit based on information criteria. We also consider a Bayesian approach that provides, under the prior distribution of the model parameters selected by the user, their simulation-based posterior distributions. We implement and apply Bayesian model comparison methods, such as Bayes factor ranking and predictive information criteria based on cross-validation techniques under various a priori scenarios.

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

    PubMed Central

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

    2015-01-01

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters. OrthoVenn provides coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn. PMID:25964301

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

    PubMed

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

    2015-07-01

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters. OrthoVenn provides coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn.

  17. 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.

  18. 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

  19. Animal Models of Osteoarthritis: Comparisons and Key Considerations.

    PubMed

    McCoy, A M

    2015-09-01

    Osteoarthritis (OA) is unquestionably one of the most important chronic health issues in humans, affecting millions of individuals and costing billions of dollars annually. Despite widespread awareness of this disease and its devastating impact, the pathogenesis of early OA is not completely understood, hampering the development of effective tools for early diagnosis and disease-modifying therapeutics. Most human tissue available for study is obtained at the time of joint replacement, when OA lesions are end stage and little can be concluded about the factors that played a role in disease development. To overcome this limitation, over the past 50 years, numerous induced and spontaneous animal models have been utilized to study disease onset and progression, as well as to test novel therapeutic interventions. Reflecting the heterogeneity of OA itself, no single "gold standard" animal model for OA exists; thus, a challenge for researchers lies in selecting the most appropriate model to answer a particular scientific question of interest. This review provides general considerations for model selection, as well as important features of species such as mouse, rat, guinea pig, sheep, goat, and horse, which researchers should be mindful of when choosing the "best" animal model for their intended purpose. Special consideration is given to key variations in pathology among species as well as recommended guidelines for reporting the histologic features of each model. PMID:26063173

  20. 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.

  1. Feeding ecology and trophic comparisons of six shark species in a coastal ecosystem off southern Brazil.

    PubMed

    Bornatowski, H; Braga, R R; Abilhoa, V; Corrêa, M F M

    2014-08-01

    The diets of six shark species, Sphyrna lewini, Sphyrna zygaena, Carcharhinus obscurus, Carcharhinus limbatus, Rhizoprionodon lalandii and Galeocerdo cuvier, were investigated in a subtropical coastal ecosystem of southern Brazil. Stomach content data were obtained to assess foraging niche segregation and ontogenetic shifts in the diets of these sharks. Five of the shark species off the Paraná coast were ichthyophagous, with the exception of S. zygaena, which was teutophagous. With the exception of G. cuvier, which had a generalist diet, the other five species displayed specialization in their feeding. Ontogenetic shifts were observed in C. obscurus and S. lewini with large individuals consuming elasmobranchs. Owing to the diet overlap between C. obscurus and S. lewini, C. obscurus and C. limbatus and R. lalandii and C. limbatus, future studies on the spatial and temporal distributions of these species are needed to understand the extent of competitive interactions. PMID:24919949

  2. Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species

    PubMed Central

    Christianson, Jed A; Llewellyn, Danny J; Dennis, Elizabeth S

    2010-01-01

    Waterlogging is a serious impediment to crop productivity worldwide which acts to reduce oxygen levels in the rhizosphere due to the low diffusion rate of molecular oxygen in water. Plants respond to low oxygen through rapid and specific changes at both the transcriptional and translational levels. Transcriptional changes to low-oxygen (hypoxia) stress have been studied in a number of plant species using whole genome microarrays. Using transcriptome data from root tissue from early time points (4–5 h) from cotton (Gossypium hirsutum), Arabidopsis and gray poplar (Populus x canescens), we have identified a core set of orthologous genes that responded to hypoxia in similar ways between species, and others that showed species specific responses. Responses to hypoxia were most similar between Arabidopsis and cotton, while the waterlogging tolerant poplar species exhibited some significant differences. PMID:20724824

  3. Species comparisons of bronchoalveolar lavages from guinea pigs and rats exposed in vivo to diesel exhaust for one year

    SciTech Connect

    Chen, S.; Weller, M.A.; Barnhart, M.I.

    1982-01-01

    Male Hartly guinea pigs and Fischer rats 344 were exposed to diesel exhaust (DE) concentrations at 0, 250, and 1500 micrograms/m3 in short terms, as well as long term experiments up to one year. The effects of inhaled DE on these rodents were evaluated using bronchoalveolar lavage technique. Both the morphological and functional studies of free lung cells and the biochemical and immunologic studies of the supernatant lavage fluid provided the basis for a quantitative species comparison of the pulmonary responses of exposed guinea pigs and rats versus age matched controls. Following inhalation of 250 micrograms DE/m3, there were little or no significant changes in either species. In contrast, at higher DE concentration, leukocytic infiltration and elevation of specific proteins in lavage fluids were observed in both species. The findings occurred and persisted in both species. Some of the responses were species specific (e.g., the specific type of exudative leukocytes, appearance of reactive monocytes, and different amounts of free DE particles and debris in the lavage fluid). Other responses were similar in both species. Among them, the emergence and increase of lymphocytes was evidence of immunologic responses. Biochemical data from the supernatant fluid correlates with the changes in cellular population in the lavage. The responses appear to be dose and duration dependent. These data indicate that species differences occur. However, it is clear that the alveolar macrophage and granulocytic leukocytes continue to exert effective defense at the DE dose-durations studied. In general, rats appeared more resistant to DE exposure than guinea pigs.

  4. 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.

  5. 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.

  6. A comparison of the short-term toxicity of cadmium to indigenous and alien gammarid species.

    PubMed

    Boets, Pieter; Lock, Koen; Goethals, Peter L M; Janssen, Colin R; De Schamphelaere, Karel A C

    2012-05-01

    Amphipods play an important role in many aquatic ecosystems and are commonly used in ecotoxicology and ecosystem health assessment. Several alien gammarids have been introduced in many regions of the world during the last decades. In this study, we investigated if differences in cadmium sensitivity occurred between (1) different species belonging to the family Gammaridae and (2) different populations of the same species originating from a polluted or a non-polluted site. The acute cadmium toxicity to two indigenous (Gammarus pulex and Gammarus fossarum) and four alien (Dikerogammarus villosus, Echinogammarus berilloni, Gammarus roeseli and Gammarus tigrinus) gammarids occurring in Belgium was tested. Significant differences (P < 0.05) in median lethal concentrations (LC(50)) were found between the different species, with 72 h-LC50s ranging from 6.3 to 268 μg/l and 96 h-LC50s from 4.7 to 88.9 μg/l. No clear trend in Cd sensitivity was found when comparing indigenous and alien gammarids. D. villosus, an alien invasive species, was the most sensitive to Cd toxicity and E. berilloni, another alien species, the least sensitive. In addition, larger Gammarid species were more sensitive to Cd toxicity than smaller ones. No significant differences were found between populations of the same species originating from metal polluted sites or non-polluted sites. Overall, our results showed that considerable differences in Cd sensitivity exist between gammarid species, which should be taken into consideration in environmental risk assessment and water quality standard setting. Finally, our data suggest that alien gammarids would not have an advantage over indigenous gammarids in Cd contaminated environments.

  7. Comparison of water-effect ratios for species ranging in copper sensitivity

    SciTech Connect

    Cohen, A.S.; Stubblefield, W.A.

    1995-12-31

    USEPA guidance on the determination and use of water-effect ratios (WER) suggests that WERs (numerical representation of the relative toxicity of a metal when tested side-by-side in a natural surface water and in a laboratory reconstituted water) will increase with increasing sensitivity of test species. Guidelines on the selection of WER test species, and comments about the over- or under-protectiveness of WER-modified site-specific metals criteria, are based on this suggested tendency. A comprehensive testing program evaluated the site-specific toxicity of copper in a western Montana river system. Initially, surface water samples were collected from 3 river sites during 5 seasonal events. WER tests were conducted using 3 species (rainbow trout (RGT), fathead minnow (FHMI), and Ceriodaphnia dubia) and 5 test endpoints (RBT, FHM, and C. dubia acute toxicity; FHM and C. dubia chronic toxicity). Additional rainbow trout and C. dubia acute WER tests were conducted using water samples collected from another 13 river drainage sites. Sensitivity patterns of test species were consistent with the literature record (i.e., C. dubia acute > C. dubia chronic > RBT acute > FHM chronic > FHM acute). However, the magnitude of calculated WERs was not correlated with species sensitivity. Study-wide mean WERs (i.e., averaged for a given species over multiple sampling events and sites), expressed as dissolved copper, for RBT, FHM, and C. dubia acute tests were 2.4, 3.5, and 3.4, respectively. Similar values for FHM and C. dubia chronic tests were 3.4 and 2.9, respectively. Thus, values were generally consistent among species and followed no trend with increasing sensitivity to copper. These results highlight the complexity of chemical factors controlling the toxicity of metals in natural waters and question the validity of the assumption that lower test species sensitivities equate with higher WERs.

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

    PubMed

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

    2016-07-01

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

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

    PubMed

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

    2016-07-01

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

  10. Thematic and spatial resolutions affect model-based predictions of tree species distribution.

    PubMed

    Liang, Yu; He, Hong S; Fraser, Jacob S; Wu, ZhiWei

    2013-01-01

    Subjective decisions of thematic and spatial resolutions in characterizing environmental heterogeneity may affect the characterizations of spatial pattern and the simulation of occurrence and rate of ecological processes, and in turn, model-based tree species distribution. Thus, this study quantified the importance of thematic and spatial resolutions, and their interaction in predictions of tree species distribution (quantified by species abundance). We investigated how model-predicted species abundances changed and whether tree species with different ecological traits (e.g., seed dispersal distance, competitive capacity) had different responses to varying thematic and spatial resolutions. We used the LANDIS forest landscape model to predict tree species distribution at the landscape scale and designed a series of scenarios with different thematic (different numbers of land types) and spatial resolutions combinations, and then statistically examined the differences of species abundance among these scenarios. Results showed that both thematic and spatial resolutions affected model-based predictions of species distribution, but thematic resolution had a greater effect. Species ecological traits affected the predictions. For species with moderate dispersal distance and relatively abundant seed sources, predicted abundance increased as thematic resolution increased. However, for species with long seeding distance or high shade tolerance, thematic resolution had an inverse effect on predicted abundance. When seed sources and dispersal distance were not limiting, the predicted species abundance increased with spatial resolution and vice versa. Results from this study may provide insights into the choice of thematic and spatial resolutions for model-based predictions of tree species distribution.

  11. 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.

  12. 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.

  13. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches

    PubMed Central

    Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. PMID:26644988

  14. Temporal comparison and predictors of fish species abundance and richness on undisturbed coral reef patches.

    PubMed

    Wagner, Elena L E S; Roche, Dominique G; Binning, Sandra A; Wismer, Sharon; Bshary, Redouan

    2015-01-01

    Large disturbances can cause rapid degradation of coral reef communities, but what baseline changes in species assemblages occur on undisturbed reefs through time? We surveyed live coral cover, reef fish abundance and fish species richness in 1997 and again in 2007 on 47 fringing patch reefs of varying size and depth at Mersa Bareika, Ras Mohammed National Park, Egypt. No major human or natural disturbance event occurred between these two survey periods in this remote protected area. In the absence of large disturbances, we found that live coral cover, reef fish abundance and fish species richness did not differ in 1997 compared to 2007. Fish abundance and species richness on patches was largely related to the presence of shelters (caves and/or holes), live coral cover and patch size (volume). The presence of the ectoparasite-eating cleaner wrasse, Labroides dimidiatus, was also positively related to fish species richness. Our results underscore the importance of physical reef characteristics, such as patch size and shelter availability, in addition to biotic characteristics, such as live coral cover and cleaner wrasse abundance, in supporting reef fish species richness and abundance through time in a relatively undisturbed and understudied region. PMID:26644988

  15. Comparison of Enterococcus species diversity in marine water and wastewater using Enterolert and EPA Method 1600.

    PubMed

    Ferguson, Donna M; Griffith, John F; McGee, Charles D; Weisberg, Stephen B; Hagedorn, Charles

    2013-01-01

    EPA Method 1600 and Enterolert are used interchangeably to measure Enterococcus for fecal contamination of public beaches, but the methods occasionally produce different results. Here we assess whether these differences are attributable to the selectivity for certain species within the Enterococcus group. Both methods were used to obtain 1279 isolates from 17 environmental samples, including influent and effluent of four wastewater treatment plants, ambient marine water from seven different beaches, and freshwater urban runoff from two stream systems. The isolates were identified to species level. Detection of non-Enterococcus species was slightly higher using Enterolert (8.4%) than for EPA Method 1600 (5.1%). E. faecalis and E. faecium, commonly associated with human fecal waste, were predominant in wastewater; however, Enterolert had greater selectivity for E. faecalis, which was also shown using a laboratory-created sample. The same species selectivity was not observed for most beach water and urban runoff samples. These samples had relatively higher proportions of plant associated species, E. casseliflavus (18.5%) and E. mundtii (5.7%), compared to wastewater, suggesting environmental inputs to beaches and runoff. The potential for species selectivity among water testing methods should be considered when assessing the sanitary quality of beaches so that public health warnings are based on indicators representative of fecal sources.

  16. 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

  17. 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

  18. Species distribution models as a tool to estimate reproductive parameters: a case study with a passerine bird species.

    PubMed

    Brambilla, Mattia; Ficetola, Gentile F

    2012-07-01

    1. Correlative species distribution models (SDMs) assess relationships between species distribution data and environmental features, to evaluate the environmental suitability (ES) of a given area for a species, by providing a measure of the probability of presence. If the output of SDMs represents the relationships between habitat features and species performance well, SDM results can be related also to other key parameters of populations, including reproductive parameters. To test this hypothesis, we evaluated whether SDM results can be used as a proxy of reproductive parameters (breeding output, territory size) in red-backed shrikes (Lanius collurio). 2. The distribution of 726 shrike territories in Northern Italy was obtained through multiple focused surveys; for a subset of pairs, we also measured territory area and number of fledged juveniles. We used Maximum Entropy modelling to build a SDM on the basis of territory distribution. We used generalized least squares and spatial generalized mixed models to relate territory size and number of fledged juveniles to SDM suitability, while controlling for spatial autocorrelation. 3. Species distribution models predicted shrike distribution very well. Territory size was negatively related to suitability estimated through SDM, while the number of fledglings significantly increased with the suitability of the territory. This was true also when SDM was built using only spatially and temporally independent data. 4. Results show a clear relationship between ES estimated through presence-only SDMs and two key parameters related to species' reproduction, suggesting that suitability estimated by SDM, and habitat quality determining reproduction parameters in our model system, are correlated. Our study shows the potential use of SDMs to infer important fitness parameters; this information can have great importance in management and conservation.

  19. A generalized approach to the modeling of the species-area relationship.

    PubMed

    Conceição, Katiane Silva; Ulrich, Werner; Diniz, Carlos Alberto Ribeiro; Rodrigues, Francisco Aparecido; de Andrade, Marinho Gomes

    2014-01-01

    This paper proposes a statistical generalized species-area model (GSAM) to represent various patterns of species-area relationship (SAR), which is one of the fundamental patterns in ecology. The approach enables the generalization of many preliminary models, as power-curve model, which is commonly used to mathematically describe the SAR. The GSAM is applied to simulated data set of species diversity in areas of different sizes and a real-world data of insects of Hymenoptera order has been modeled. We show that the GSAM enables the identification of the best statistical model and estimates the number of species according to the area. PMID:25171161

  20. A comparison of arcjet plume properties to model predictions

    NASA Technical Reports Server (NTRS)

    Cappelli, M. A.; Liebeskind, J. G.; Hanson, R. K.; Butler, G. W.; King, D. Q.

    1993-01-01

    This paper describes an experimental study of the plasma plume properties of a 1 kW class hydrogen arcjet thruster and the comparison of measured temperature and velocity field to model predictions. The experiments are based on laser-induced fluorescence excitation of the Balmer-alpha transition. The model is based on a single-fluid magnetohydrodynamic description of the flow originally developed to predict arcjet thruster performance. Excellent agreement between model predictions and experimental velocity is found, despite the complex nature of the flow. Measured and predicted exit plane temperatures are in disagreement by as much as 2000K over a range of operating conditions. The possible sources for this discrepancy are discussed.

  1. 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.

  2. Comparison of optical modeling and neural networks for robot guidance

    NASA Astrophysics Data System (ADS)

    Parasnis, Sameer; Velidandla, Sasanka; Hall, Ernest L.; Anand, Sam

    1998-10-01

    A truly autonomous robot must sense its environment and react appropriately. These issues attain greater importance in an outdoor, variable environment. Previous mobile robot perception systems have relied on hand-coded algorithms for processing sensor information. Recent techniques involve the use of artificial neural networks to process sensor data for mobile robot guidance. A comparison of a fuzzy logic control for an AGV and a neural network perception is described in this work. A mobile robot test bed has been constructed using a golf cart base. The test bed has a fuzzy logic controller which uses both vision and obstacle information and provides the steering and speed controls to the robot. A feed-forward neural network is described to guide the robot using vision and range data. Suitable criteria for comparison will be formulated and the hand-coded system compared with a connectionist model. A comparison of the two systems, with performance, efficiency and reliability as the criteria, will be achieved. The significance of this work is that it provides comparative tradeoffs on two important robot guidance methods.

  3. Comparisons of fish species traits from small streams to large rivers

    USGS Publications Warehouse

    Goldstein, R.M.; Meador, M.R.

    2004-01-01

    To examine the relations between fish community function and stream size, we classified 429 lotic freshwater fish species based on multiple categories within six species traits: (1) substrate preference, (2) geomorphic preference, (3) trophic ecology, (4) locomotion morphology, (5) reproductive strategy, and (6) stream size preference. Stream size categories included small streams, small, medium, and large rivers, and no size preference. The frequencies of each species trait category were determined for each stream size category based on life history information from the literature. Cluster analysis revealed the presence of covarying groups of species trait categories. One cluster (RUN) included the traits of planktivore and herbivore feeding ecology, migratory reproductive behavior and broadcast spawning, preferences for main-channel habitats, and a lack of preferences for substrate type. The frequencies of classifications for the RUN cluster varied significantly across stream size categories (P = 0.009), being greater for large rivers than for small streams and rivers. Another cluster (RIFFLE) included the traits of invertivore feeding ecology, simple nester reproductive behavior, a preference for riffles, and a preference for bedrock, boulder, and cobble-rubble substrate. No significant differences in the frequency of classifications among stream size categories were detected for the RIFFLE cluster (P = 0.328). Our results suggest that fish community function is structured by large-scale differences in habitat and is different for large rivers than for small streams and rivers. Our findings support theoretical predictions of variation in species traits among stream reaches based on ecological frameworks such as landscape filters, habitat templates, and the river continuum concept. We believe that the species trait classifications presented here provide an opportunity for further examination of fish species' relations to physical, chemical, and biological factors

  4. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements. 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

  5. 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

  6. Investigation of the DSMC Approach for Ion/neutral Species in Modeling Low Pressure Plasma Reactor

    NASA Astrophysics Data System (ADS)

    Deng, Hao; Li, Z.; Levin, D.; Gochberg, L.

    2011-05-01

    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

  7. 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

  8. 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

  9. 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

  10. Multiresolution comparison of precipitation datasets for large-scale models

    NASA Astrophysics Data System (ADS)

    Chun, K. P.; Sapriza Azuri, G.; Davison, B.; DeBeer, C. M.; Wheater, H. S.

    2014-12-01

    Gridded precipitation datasets are crucial for driving large-scale models which are related to weather forecast and climate research. However, the quality of precipitation products is usually validated individually. Comparisons between gridded precipitation products along with ground observations provide another avenue for investigating how the precipitation uncertainty would affect the performance of large-scale models. In this study, using data from a set of precipitation gauges over British Columbia and Alberta, we evaluate several widely used North America gridded products including the Canadian Gridded Precipitation Anomalies (CANGRD), the National Center for Environmental Prediction (NCEP) reanalysis, the Water and Global Change (WATCH) project, the thin plate spline smoothing algorithms (ANUSPLIN) and Canadian Precipitation Analysis (CaPA). Based on verification criteria for various temporal and spatial scales, results provide an assessment of possible applications for various precipitation datasets. For long-term climate variation studies (~100 years), CANGRD, NCEP, WATCH and ANUSPLIN have different comparative advantages in terms of their resolution and accuracy. For synoptic and mesoscale precipitation patterns, CaPA provides appealing performance of spatial coherence. In addition to the products comparison, various downscaling methods are also surveyed to explore new verification and bias-reduction methods for improving gridded precipitation outputs for large-scale models.

  11. 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.

  12. 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

  13. 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

  14. BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression.

    PubMed

    Ogasawara, Osamu; Otsuji, Makiko; Watanabe, Kouji; Iizuka, Takayasu; Tamura, Takuro; Hishiki, Teruyoshi; Kawamoto, Shoko; Okubo, Kousaku

    2006-01-01

    BodyMap-Xs (http://bodymap.jp) is a database for cross-species gene expression comparison. It was created by the anatomical breakdown of 17 million animal expressed sequence tag (EST) records in DDBJ using a sorting program tailored for this purpose. In BodyMap-Xs, users are allowed to compare the expression patterns of orthologous and paralogous genes in a coherent manner. This will provide valuable insights for the evolutionary study of gene expression and identification of a responsive motif for a particular expression pattern. In addition, starting from a concise overview of the taxonomical and anatomical breakdown of all animal ESTs, users can navigate to obtain gene expression ranking of a particular tissue in a particular animal. This method may lead to the understanding of the similarities and differences between the homologous tissues across animal species. BodyMap-Xs will be automatically updated in synchronization with the major update in DDBJ, which occurs periodically.

  15. 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.

  16. Toward a Better Approach to Data-Model Comparison

    NASA Astrophysics Data System (ADS)

    Dowsett, H. J.; Robinson, M. M.; Salzmann, U.

    2015-12-01

    The quantitative census of a typical faunal assemblage recovered from a deep-sea core sample is the result of an integration of many different factors including but not limited to environmental (e.g., temperature, salinity, dissolved oxygen, nutrient availability, etc.), temporal (e.g., cycle of annual productivity), and pre- and post-depositional processes (e.g., dissolution, preservation potential, bioturbation, etc.). Extraction of a single environmental variable (e.g., temperature) requires poorly supported assumptions that introduce additional error and results in loss of valuable information contained within the assemblage. Conversely, temperatures generated by a numerical climate model for a given locale do not have any associated error. Thus, comparison of faunal assemblage-based temperature estimates with simulated temperatures from GCMs is an oversimplification of a complex system. It is critical that like data sets are compared. For example, proxies for temperature may estimate conditions at the surface or at various depths or during particular seasons. These estimates are not directly comparable, and pooling Mg/Ca, alkenone and assemblage-based estimates of ocean temperature is inherently wrong. A more appropriate data-model comparison would involve comparing the faunal assemblage found in a core sample to one estimated by a paleoecological model driven by a GCM. An ideal comparison would score a suite of environmental factors gleaned from a faunal assemblage with those simulated by a GCM. Quantification of these factors, however, is not practical in some cases. A paradigm shift in marine paleoclimate reconstruction is overdue, and comparison of paleoenvironments to model simulations requires a revised approach. The PRISM4 reconstruction presents a holistic and nuanced interpretation of multidimensional oceanographic processes and responses that is lost when reduced to a single variable such as temperature. Beyond the global approach, we incorporate

  17. An atmospheric tritium release database for model comparisons

    SciTech Connect

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

    1991-12-19

    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 is 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.

  18. 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.

    ...

  19. 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.

  20. Outcomes comparison of solo-practitioner and group practice models.

    PubMed

    Cameron, C A; Phillips, S L; Chasteen, J E

    1998-02-01

    A solo-practitioner care delivery model is utilized in the predoctoral teaching clinics at the University of Washington School of Dentistry. This model requires students to independently manage their practices using central resources. The model is perceived as cumbersome for patients and students and as failing to achieve optimum educational and productivity outcomes. During the 1995-96 academic year, a group practice model of patient care delivery was pilot tested to assess whether productivity, educational, and care delivery outcomes could be enhanced in comparison to the solo-practitioner model. This group practice model combined third- and fourth-year students for purposes of sharing resources and collaborating in patient care delivery. Resources dedicated to each group practice included a practice advisor, shared patient care coordinator, dental assistant, and shared clinic receptionist. Two group practices and twenty-five student solo practitioners participated in the study. Based upon an analysis of productivity, participant, and patient data, the group practice participants had greater billing volume, better attendance, enhanced satisfaction with the staff/faculty support and their ability to fill appointments, and generally comparable patient satisfaction ratings. These results suggest that the group practice model, through the dedication of resources and collaboration of providers, could enhance the outcomes of the clinical education program. PMID:9487303

  1. 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.

  2. Comparison of species composition and richness of fish assemblages in altered and unaltered littoral habitats

    USGS Publications Warehouse

    Poe, T.P.; Hatcher, C.O.; Brown, C.L.; Schloesser, D.W.

    1986-01-01

    Species composition and richness of fish assemblages in altered and unaltered littoral habitats in Lake St. Clair, Michigan, differed between areas. A percid-cyprinid-cyprinodontid assemblage dominated in the unaltered area, Muscamoot Bay, which has a natural shoreline (with almost no alteration due to dredging or bulkheading), high water quality, and high species richness of aquatic macrophytes. A centrarchid assemblage dominated in the altered area, Belvidere Bay, which has a bulkheaded shoreline, many dredged areas, reduced water quality due to inputs of nutrients from a nearby river, and relatively low species richness of aquatic macrophytes. Habitat factors, species richness and abundance of aquatic macrophytes, had the most influence on fish community structure in both areas. The percid-cyprinid-cyprinodontid assemblage was significantly correlated with six species of macrophytes whereas the centrarchid assemblage was significantly correlated with only four. These patterns suggest that preference for diverse habitats was higher, and tolerance to habitat alteration lower, in percid-cyprinid-cyprinodontid assemblages than in centrarchid assemblages.

  3. Comparison of eye morphology and retinal topography in two species of New World vultures (Aves: Cathartidae).

    PubMed

    Lisney, Thomas J; Stecyk, Karyn; Kolominsky, Jeffrey; Graves, Gary R; Wylie, Douglas R; Iwaniuk, Andrew N

    2013-12-01

    Vultures are highly reliant on their sensory systems for the rapid detection and localization of carrion before other scavengers can exploit the resource. In this study, we compared eye morphology and retinal topography in two species of New World vultures (Cathartidae), turkey vultures (Cathartes aura), with a highly developed olfactory sense, and black vultures (Coragyps atratus), with a less developed sense of olfaction. We found that eye size relative to body mass was the same in both species, but that black vultures have larger corneas relative to eye size than turkey vultures. However, the overall retinal topography, the total number of cells in the retinal ganglion cell layer, peak and average cell densities, cell soma area frequency distributions, and the theoretical peak anatomical spatial resolving power were the same in both species. This suggests that the visual systems of these two species are similar and that vision plays an equally important role in the biology of both species, despite the apparently greater reliance on olfaction for finding carrion in turkey vultures. PMID:24249399

  4. Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species.

    PubMed

    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

  5. 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.

  6. Perfluoroalkyl contaminants in plasma of five sea turtle species: comparisons in concentration and potential health risks.

    PubMed

    Keller, Jennifer M; Ngai, Lily; Braun McNeill, Joanne; Wood, Lawrence D; Stewart, Kelly R; O'Connell, Steven G; Kucklick, John R

    2012-06-01

    The authors compared blood plasma concentrations of 13 perfluoroalkyl contaminants (PFCs) in five sea turtle species with differing trophic levels. Wild sea turtles were blood sampled from the southeastern region of the United States, and plasma was analyzed using liquid chromatography tandem mass spectrometry. Mean concentrations of perfluorooctane sulfonate (PFOS), the predominant PFC, increased with trophic level from herbivorous greens (2.41 ng/g), jellyfish-eating leatherbacks (3.95 ng/g), omnivorous loggerheads (6.47 ng/g), to crab-eating Kemp's ridleys (15.7 ng/g). However, spongivorous hawksbills had surprisingly high concentrations of PFOS (11.9 ng/g) and other PFCs based on their trophic level. These baseline concentrations of biomagnifying PFCs demonstrate interesting species and geographical differences. The measured PFOS concentrations were compared with concentrations known to cause toxic effects in laboratory animals, and estimated margins of safety (EMOS) were calculated. Small EMOS (<100), suggestive of potential risk of adverse health effects, were observed for all five sea turtle species for immunosuppression. Estimated margins of safety less than 100 were also observed for liver, thyroid, and neurobehavorial effects for the more highly exposed species. These baseline concentrations and the preliminary EMOS exercise provide a better understanding of the potential health risks of PFCs for conservation managers to protect these threatened and endangered species.

  7. 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

  8. 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.

  9. 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.

  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. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.

    PubMed

    Hezroni, Hadas; Koppstein, David; Schwartz, Matthew G; Avrutin, Alexandra; Bartel, David P; Ulitsky, Igor

    2015-05-19

    The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousands of previously unannotated genes, most of which produce long intervening noncoding RNAs (lincRNAs). Although in each species, >70% of lincRNAs cannot be traced to homologs in species that diverged >50 million years ago, thousands of human lincRNAs have homologs with similar expression patterns in other species. These homologs share short, 5'-biased patches of sequence conservation nested in exonic architectures that have been extensively rewired, in part by transposable element exonization. Thus, over a thousand human lincRNAs are likely to have conserved functions in mammals, and hundreds beyond mammals, but those functions require only short patches of specific sequences and can tolerate major changes in gene architecture.

  12. 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.

  13. Hepatic phase I and phase II biotransformations in quail and trout: comparison to other species commonly used in toxicity testing.

    PubMed

    Gregus, Z; Watkins, J B; Thompson, T N; Harvey, M J; Rozman, K; Klaassen, C D

    1983-03-15

    The ability of quail and trout to perform a number of representative phase I and phase II biotransformations was examined. To facilitate interspecies comparisons, metabolism of the same substrates was examined simultaneously under uniform conditions for rat, mouse, rabbit, guinea pig, cat, and dog. Both nonmammalian species can metabolize four representative substrates of phase I mixed-function oxidases and one substrate of epoxide hydrolase, though activity tended to be lower than that of the mammals. Important differences in the conjugative pathways were also noted. Among these differences were the quail's relative deficiency in glutathione conjugation and the trout's low ability to conjugate sulfate compounds. Trout liver UDP-glucuronosyltransferase activity was remarkably high toward testosterone and bilirubin, while quail liver formed glucuronides of naphthol, p-nitrophenol, and digitoxigenin-monodigitoxoside. Also noteworthy was the high N-acetyltransferase activity of both quail and trout toward isoniazid, beta-naphthylamine, and 2-aminofluorene. Differences in substrate specificity for a given enzymatic pathway may be an indication that multiple forms of drug metabolizing systems also occur in these nonmammalian species. Observation of several hundred- or even thousand-fold differences between species in their enzyme activities for certain substrates under uniform conditions re-emphasizes the need for caution in extrapolation of xenobiotic metabolism from one species to another.

  14. 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

  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. 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

  17. Comparison of selected species of Bipolaris, Drechslera and Exserohilum by random amplification of polymorphic DNA.

    PubMed

    Bakonyi, J; Pomázi, A; Fischl, G; Hornok, L

    1995-01-01

    Forty-six strains representing 15 species of Drechslera, five of Bipolaris and four of Exserohilum, as well as two formae of Drechslera teres were compared by RAPD analysis. Drechslera formed a large, heterologous group, while species of Bipolaris and Exserohilum were more closely related. Strong pair-wise affinities were observed between D. graminea and D. teres, D. tritici-repentis and D. bromi, D. siccans and D. biseptata, D. fugax and D. poae, B. sorghicola and B. zeicola, as well as between E. rostratum and E. turcicum.

  18. The comparison of immobility time in experimental rat swimming models.

    PubMed

    Calil, Caroline Morini; Marcondes, Fernanda Klein

    2006-09-27

    Rat swimming models have been used in studies about stress and depression. However, there is no consensus about interpreting immobility (helplessness or adaptation) in the literature. In the present study, immobility time, glucose and glycogen mobilization, corticosterone and the effect of desipramine and diazepam were investigated in two different models: swimming stress and the forced swimming test. Immobility time was lower in swimming stress than in the forced swimming test. Both swimming models increased corticosterone levels in comparison with control animal levels. Moreover, swimming stress induced higher corticosterone levels than the forced swimming test did [F(2,14)=59.52; p<0.001]. Liver glycogen content values differed from one another (swimming stresscomparison with the forced swimming test and control. The immobility time was recorded and measured in another group treated with desipramine and diazepam in two protocols: a single session of forced swimming test or swimming stress and two sessions (pre- and retest) of forced swimming model or swimming stress. Desipramine decreased the immobility time in the forced swimming test in both the single [F(2,25)=20.63; p<0.0001] and retest [F(2,37)=7.28; p=0.002] swimming session, without changes in the swimming stress model. Diazepam increased the immobility time in the swimming stress but not in the forced swimming test during the single [F(2,26)=11.24; p=0.0003] and retest sessions [F(2,38)=4.17; p=0.02]. It was concluded that swimming stress and the forced swimming test induced different behavior, hormonal and metabolic responses and represented different situations to the animal.

  19. Comparison of the rhamnomannans from the human pathogen Sporothrix schenckii with those from the Ceratocystis species.

    PubMed

    Travassos, L R; Gorin, P A; Lloyd, K O

    1973-11-01

    Rhamnomannans from several isolates of Sporothrix schenckii and Ceratocystis species were compared. No major differences emerged in the analysis of the carbohydrate composition of polysaccharides from either species. Methylation analysis for the identification of the glycosidic linkages present in the polysaccharides showed that they all were very similar with minor differences being observed among strains and between polysaccharides obtained at 25 and 37 C. Partially methylated derivatives were identified by gas-liquid chromatography and mass spectrometry. Their proportions suggest that polysaccharides from S. schenckii and C. stenoceras have a general structure similar to that of C. ulmi: a (1 --> 6)-linked alpha-d-mannopyranosyl main chain substituted in the 3-positions by alpha-l-rhamnopyranosyl and in many cases by alpha-l-rhamnopyranosyl (1-->2)-l-rhamnopyranosyl side chains. Differences among polysaccharides resided in the proportions of the dirhamnosyl side chains and of 4-O-substituted and 2, 4-di-O-substituted mannose units. Increased proportions of dirhamnosyl side chains were observed in the polysaccharides from S. schenckii strains and from a pathogenic variant of C. stenoceras grown at 25 C. Proton magnetic resonance spectra (H-1 region) of the rhamnomannans showed that S. schenckii strains could be placed in two different groups similar but not identical to any Ceratocystis species. These spectra were very close to those of the polysaccharides from the C. clavata and C. ambrosia groups of Ceratocystis species.

  20. Comparison of the emergence of three Brassicaceae species of different origins grown in Spain and USA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thlaspi arvense, Camelina sativa, C. microcarpa and Neslia paniculata are four Brassicaceae family species that are becoming rare in North-Eastern Spain. Conversely, both T. arvense and C. sativa are being investigated as oilseed crops in North America for industrial/biofuel purposes. C. microcarpa ...

  1. Cross-species comparison of mammalian saliva using an LC-MALDI based proteomic approach.

    PubMed

    de Sousa-Pereira, Patrícia; Cova, Marta; Abrantes, Joana; Ferreira, Rita; Trindade, Fábio; Barros, António; Gomes, Pedro; Colaço, Bruno; Amado, Francisco; Esteves, Pedro J; Vitorino, Rui

    2015-05-01

    Despite the importance of saliva in the regulation of oral cavity homeostasis, few studies have been conducted to quantitatively compare the saliva of different mammal species. Aiming to define a proteome signature of mammals' saliva, an in-depth SDS-PAGE-LC coupled to MS/MS (GeLC-MS/MS) approach was used to characterize the saliva from primates (human), carnivores (dog), glires (rat and rabbit), and ungulates (sheep, cattle, horse). Despite the high variability in the number of distinct proteins identified per species, most protein families were shared by the mammals studied with the exception of cattle and horse. Alpha-amylase is an example that seems to reflect the natural selection related to digestion efficacy and food recognition. Casein protein family was identified in all species but human, suggesting an alternative to statherin in the protection of hard tissues. Overall, data suggest that different proteins might assure a similar role in the regulation of oral cavity homeostasis, potentially explaining the specific mammals' salivary proteome signature. Moreover, some protein families were identified for the first time in the saliva of some species, the presence of proline-rich proteins in rabbit's saliva being a good example.

  2. 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

  3. 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

    2015-03-01

    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

  4. A comparison between the quasi-species evolution and stochastic quantization of fields

    NASA Astrophysics Data System (ADS)

    Bianconi, G.; Rahmede, C.

    2012-06-01

    The quasi-species equation describes the evolution of the probability that a random individual in a population carries a given genome. Here we map the quasi-species equation for individuals of a self-reproducing population to an ensemble of scalar field elementary units undergoing a creation and annihilation process. In this mapping, the individuals of the population are mapped to field units and their genome to the field value. The selective pressure is mapped to an inverse temperature β of the system regulating the evolutionary dynamics of the fields. We show that the quasi-species equation if applied to an ensemble of field units gives in the small β limit can be put in relation with existing stochastic quantization approaches. The ensemble of field units described by the quasi-species equation relaxes to the fundamental state, describing an intrinsically dissipative dynamics. For a quadratic dispersion relation the mean energy ⟨U⟩ of the system changes as a function of the inverse temperature β. For small values of β the average energy ⟨U⟩ takes a relativistic form, for large values of β, the average energy ⟨U⟩ takes a classical form.

  5. Cross-species comparison of mammalian saliva using an LC-MALDI based proteomic approach.

    PubMed

    de Sousa-Pereira, Patrícia; Cova, Marta; Abrantes, Joana; Ferreira, Rita; Trindade, Fábio; Barros, António; Gomes, Pedro; Colaço, Bruno; Amado, Francisco; Esteves, Pedro J; Vitorino, Rui

    2015-05-01

    Despite the importance of saliva in the regulation of oral cavity homeostasis, few studies have been conducted to quantitatively compare the saliva of different mammal species. Aiming to define a proteome signature of mammals' saliva, an in-depth SDS-PAGE-LC coupled to MS/MS (GeLC-MS/MS) approach was used to characterize the saliva from primates (human), carnivores (dog), glires (rat and rabbit), and ungulates (sheep, cattle, horse). Despite the high variability in the number of distinct proteins identified per species, most protein families were shared by the mammals studied with the exception of cattle and horse. Alpha-amylase is an example that seems to reflect the natural selection related to digestion efficacy and food recognition. Casein protein family was identified in all species but human, suggesting an alternative to statherin in the protection of hard tissues. Overall, data suggest that different proteins might assure a similar role in the regulation of oral cavity homeostasis, potentially explaining the specific mammals' salivary proteome signature. Moreover, some protein families were identified for the first time in the saliva of some species, the presence of proline-rich proteins in rabbit's saliva being a good example. PMID:25641928

  6. Comparison of the chemical compositions and nutritive values of various pumpkin (Cucurbitaceae) species and parts

    PubMed Central

    Kim, Mi Young; Kim, Eun Jin; Kim, Young-Nam; Choi, Changsun

    2012-01-01

    Pumpkins have considerable variation in nutrient contents depending on the cultivation environment, species, or part. In this study, the general chemical compositions and some bioactive components, such as tocopherols, carotenoids, and β-sitosterol, were analyzed in three major species of pumpkin (Cucurbitaceae pepo, C. moschata, and C. maxima) grown in Korea and also in three parts (peel, flesh, and seed) of each pumpkin species. C. maxima had significantly more carbohydrate, protein, fat, and fiber than C. pepo or C. moschata (P < 0.05). The moisture content as well as the amino acid and arginine contents in all parts of the pumpkin was highest in C. pepo. The major fatty acids in the seeds were palmitic, stearic, oleic, and linoleic acids. C. pepo and C. moschata seeds had significantly more γ-tocopherol than C. maxima, whose seeds had the highest β-carotene content. C. pepo seeds had significantly more β-sitosterol than the others. Nutrient compositions differed considerably among the pumpkin species and parts. These results will be useful in updating the nutrient compositions of pumpkin in the Korean food composition database. Additional analyses of various pumpkins grown in different years and in different areas of Korea are needed. PMID:22413037

  7. Comparison of seed bank estimation techniques using six weed species in two soil types

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tests of three different seed bank estimation techniques were performed on six different weed species. Petri plate germination was compared to two emergence methods, each on two different soil types (stony loam vs. silt loam). Soil types produced equal emergence proportions, however both emergence...

  8. 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

  9. 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.

  10. Identification of Pathogenic Rare Yeast Species in Clinical Samples: Comparison between Phenotypical and Molecular Methods▿

    PubMed Central

    Cendejas-Bueno, Emilio; Gomez-Lopez, Alicia; Mellado, Emilia; Rodriguez-Tudela, Juan L.; Cuenca-Estrella, Manuel

    2010-01-01

    Species identification using both phenotypic and molecular methods and antifungal susceptibility tests was carried out with 60 uncommon clinical yeasts. Our data show that phenotypic methods were insufficient for correct identification (only 25%) and that most of the wrongly identified strains showed a resistant antifungal profile. PMID:20237094

  11. Comparison of the Morphology and Histomorphometry of Spermatogenic Cyst of Three Sharks Species With Diametric Testes.

    PubMed

    Gomes do Rêgo, Mariana; Fitzpatrick, John L; Hissa V Hazin, Fabio; Araujo, Maria Lucia G; Barros, Maria Edna Gomes; Evêncio Neto, Joaquim

    2016-06-01

    Characterization of the reproductive anatomy of elasmobranchs (sharks, skates, rays, and sawfish) offers unique insights into the evolution of reproductive traits in animals due to their phylogenetic position at the base of the vertebrate tree of life. Yet, despite advances in our understanding of male elasmobranch reproductive physiology and testes histology, very little is known about how testes histomorphometrics varies with male maturation. In this study, we characterize and contrast testes morphology and histomorphology of males at different maturation stages in three shark species with diametric testes development: Prionaceglauca, Rhizoprionodon lalandii, and Mustelus canis. All stages of spermatogenesis were observed in P. glauca and R. lalandii, while for M. canis, only males at early stages of maturation were examined and therefore all the spermatogenesis cells lineage were not present. The number of Sertoli cells increased with cell development by six times in R. lalandii and roughly four times in P. glauca, and were statistically different among stages of spermatogenesis cysts in both species. Statistical differences in cyst diameter and Sertoli cell numbers were observed between P. glauca and R. lalandii. The increase of spermatocyte II cell diameter described for R. Lalandii in this study was not usual to elasmobranch species as compared, for example, to P. glauca. This information proves the importance of studying the testicular development and the process of spermatogenesis is necessary for understanding the reproductive biology of the species, including life cycles and history, variation of reproductive morphology. Anat Rec, 299:759-768, 2016. © 2016 Wiley Periodicals, Inc. PMID:26864330

  12. Comparison of fatty acid composition of oil from original and regenerated populations of wild Helianthus species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Monitori