WorldWideScience

Sample records for modeling multiple species

  1. Modeling considerations for using expression data from multiple species.

    Science.gov (United States)

    Siewert, Elizabeth; Kechris, Katerina J

    2013-10-15

    Although genome-wide expression data sets from multiple species are now more commonly generated, there have been few studies on how to best integrate this type of correlated data into models. Starting with a single-species, linear regression model that predicts transcription factor binding sites as a case study, we investigated how best to take into account the correlated expression data when extending this model to multiple species. Using a multivariate regression model, we accounted for the phylogenetic relationships among the species in two ways: (i) a repeated-measures model, where the error term is constrained; and (ii) a Bayesian hierarchical model, where the prior distributions of the regression coefficients are constrained. We show that both multiple-species models improve predictive performance over the single-species model. When compared with each other, the repeated-measures model outperformed the Bayesian model. We suggest a possible explanation for the better performance of the model with the constrained error term. Copyright © 2013 John Wiley & Sons, Ltd.

  2. Finding all multiple stable fixpoints of n-species Lotka-Volterra competition models.

    Science.gov (United States)

    Lischke, Heike; Löffler, Thomas J

    2017-06-01

    One way to explore assembly of extant and novel communities from species pools, and by that biodiversity and species ranges, is to study the equilibrium behavior of dynamic competition models such as the Lotka-Volterra competition (LVC) model. We present a novel method (COMMUSTIX) to determine all stable fixpoints of the general LVC model with abundances x from a given pool of n species. To that purpose, we split the species in potentially surviving species (xi>0) and in others going extinct (xi=0). We derived criteria for the stability of xi=0 and for the equilibrium of xi>0 to determine possible combinations of extinct and surviving species by iteratively applying a mixed binary linear optimization algorithm. We tested this new method against (a) the numerical solution at equilibrium of the LVC ordinary differential equations (ODEs) and (b) the fixpoints of all combinations of surviving and extinct species (possible only for small n), tested for stability and non-negativity. The tests revealed that COMMUSTIX is reliable, it detects all multiple stable fixpoints (SFPs), which is not guaranteed by solving the ODEs, and more efficient than the combinations method. With COMMUSTIX, we studied the dependence of the fixpoint behavior on the competition strengths relative to the intra-specific competition. If inter-specific competition was considerably lower than intra-specific competition, only globally SFPs occurred. In contrast, if all inter-specific was higher than intra-specific competition, multiple SFPs consisting of only one species occurred. If competition strengths in the species pool ranged from below to above the intra-specific competition, either global or multiple SFPs strongly differing in species composition occurred. The species richness over all SFPs was high for pools of species with similar, either weak or strong competition, and lower for species with dissimilar or close to intra-specific competition strengths. The new approach is a reliable and

  3. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species.

    Science.gov (United States)

    Dawson, Michael N; Sen Gupta, Alex; England, Matthew H

    2005-08-23

    The anthropogenic introduction of exotic species is one of the greatest modern threats to marine biodiversity. Yet exotic species introductions remain difficult to predict and are easily misunderstood because knowledge of natural dispersal patterns, species diversity, and biogeography is often insufficient to distinguish between a broadly dispersed natural population and an exotic one. Here we compare a global molecular phylogeny of a representative marine meroplanktonic taxon, the moon-jellyfish Aurelia, with natural dispersion patterns predicted by a global biophysical ocean model. Despite assumed high dispersal ability, the phylogeny reveals many cryptic species and predominantly regional structure with one notable exception: the globally distributed Aurelia sp.1, which, molecular data suggest, may occasionally traverse the Pacific unaided. This possibility is refuted by the ocean model, which shows much more limited dispersion and patterns of distribution broadly consistent with modern biogeographic zones, thus identifying multiple introductions worldwide of this cryptogenic species. This approach also supports existing evidence that (i) the occurrence in Hawaii of Aurelia sp. 4 and other native Indo-West Pacific species with similar life histories is most likely due to anthropogenic translocation, and (ii) there may be a route for rare natural colonization of northeast North America by the European marine snail Littorina littorea, whose status as endemic or exotic is unclear.

  4. Predicting aquatic toxicities of chemical pesticides in multiple test species using nonlinear QSTR modeling approaches.

    Science.gov (United States)

    Basant, Nikita; Gupta, Shikha; Singh, Kunwar P

    2015-11-01

    In this study, we established nonlinear quantitative-structure toxicity relationship (QSTR) models for predicting the toxicities of chemical pesticides in multiple aquatic test species following the OECD (Organization for Economic Cooperation and Development) guidelines. The decision tree forest (DTF) and decision tree boost (DTB) based QSTR models were constructed using a pesticides toxicity dataset in Selenastrum capricornutum and a set of six descriptors. Other six toxicity data sets were used for external validation of the constructed QSTRs. Global QSTR models were also constructed using the combined dataset of all the seven species. The diversity in chemical structures and nonlinearity in the data were evaluated. Model validation was performed deriving several statistical coefficients for the test data and the prediction and generalization abilities of the QSTRs were evaluated. Both the QSTR models identified WPSA1 (weighted charged partial positive surface area) as the most influential descriptor. The DTF and DTB QSTRs performed relatively better than the single decision tree (SDT) and support vector machines (SVM) models used as a benchmark here and yielded R(2) of 0.886 and 0.964 between the measured and predicted toxicity values in the complete dataset (S. capricornutum). The QSTR models applied to six other aquatic species toxicity data yielded R(2) of >0.92 (DTF) and >0.97 (DTB), respectively. The prediction accuracies of the global models were comparable with those of the S. capricornutum models. The results suggest for the appropriateness of the developed QSTR models to reliably predict the aquatic toxicity of chemicals and can be used for regulatory purpose.

  5. A Distributed Agent Implementation of Multiple Species Flocking Model for Document Partitioning Clustering

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Xiaohui [ORNL; Potok, Thomas E [ORNL

    2006-01-01

    The Flocking model, first proposed by Craig Reynolds, is one of the first bio-inspired computational collective behavior models that has many popular applications, such as animation. Our early research has resulted in a flock clustering algorithm that can achieve better performance than the Kmeans or the Ant clustering algorithms for data clustering. This algorithm generates a clustering of a given set of data through the embedding of the highdimensional data items on a two-dimensional grid for efficient clustering result retrieval and visualization. In this paper, we propose a bio-inspired clustering model, the Multiple Species Flocking clustering model (MSF), and present a distributed multi-agent MSF approach for document clustering.

  6. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    Energy Technology Data Exchange (ETDEWEB)

    Spill, Fabian, E-mail: fspill@bu.edu [Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Guerrero, Pilar [Department of Mathematics, University College London, Gower Street, London WC1E 6BT (United Kingdom); Alarcon, Tomas [Centre de Recerca Matematica, Campus de Bellaterra, Edifici C, 08193 Bellaterra (Barcelona) (Spain); Departament de Matemàtiques, Universitat Atonòma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Maini, Philip K. [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Byrne, Helen [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Computational Biology Group, Department of Computer Science, University of Oxford, Oxford OX1 3QD (United Kingdom)

    2015-10-15

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.

  7. Forelimb preferences in human beings and other species: multiple models for testing hypotheses on lateralization

    Directory of Open Access Journals (Sweden)

    Elisabetta eVersace

    2015-03-01

    Full Text Available Consistent preferences in the use of right/left forelimbs are not exclusively present in humans. Functional asymmetries in forelimb use have been widely documented in a variety of vertebrate and invertebrate species. A matter of debate is whether non-human species exhibit a degree and consistency of functional forelimb asymmetries comparable to human handedness. The comparison is made difficult by the variability in hand use in humans and the few comparable studies conducted on other species. In spite of this, interesting continuities appear in functions such as feeding, object manipulation and communicative gestures. Studies on invertebrates show how widespread forelimb preferences are among animals, and the importance of experience for the development of forelimb asymmetries. Vertebrate species have been extensively investigated to clarify the origins of forelimb functional asymmetries: comparative evidence shows that selective pressures for different functions have likely driven the evolution of human handedness. Evidence of a complex genetic architecture of human handedness is in line with the idea of multiple evolutionary origins of this trait.

  8. Integrating multiple data sources in species distribution modeling: a framework for data fusion.

    Science.gov (United States)

    Pacifici, Krishna; Reich, Brian J; Miller, David A W; Gardner, Beth; Stauffer, Glenn; Singh, Susheela; McKerrow, Alexa; Collazo, Jaime A

    2017-03-01

    The last decade has seen a dramatic increase in the use of species distribution models (SDMs) to characterize patterns of species' occurrence and abundance. Efforts to parameterize SDMs often create a tension between the quality and quantity of data available to fit models. Estimation methods that integrate both standardized and non-standardized data types offer a potential solution to the tradeoff between data quality and quantity. Recently several authors have developed approaches for jointly modeling two sources of data (one of high quality and one of lesser quality). We extend their work by allowing for explicit spatial autocorrelation in occurrence and detection error using a Multivariate Conditional Autoregressive (MVCAR) model and develop three models that share information in a less direct manner resulting in more robust performance when the auxiliary data is of lesser quality. We describe these three new approaches ("Shared," "Correlation," "Covariates") for combining data sources and show their use in a case study of the Brown-headed Nuthatch in the Southeastern U.S. and through simulations. All three of the approaches which used the second data source improved out-of-sample predictions relative to a single data source ("Single"). When information in the second data source is of high quality, the Shared model performs the best, but the Correlation and Covariates model also perform well. When the information quality in the second data source is of lesser quality, the Correlation and Covariates model performed better suggesting they are robust alternatives when little is known about auxiliary data collected opportunistically or through citizen scientists. Methods that allow for both data types to be used will maximize the useful information available for estimating species distributions. © 2016 The Authors. Ecology, published by Wiley Periodicals, Inc., on behalf of the Ecological Society of America.

  9. Hybrid approaches for multiple-species stochastic reaction-diffusion models.

    KAUST Repository

    Spill, Fabian

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  10. Using empirical models of species colonization under multiple threatening processes to identify complementary threat-mitigation strategies.

    Science.gov (United States)

    Tulloch, Ayesha I T; Mortelliti, Alessio; Kay, Geoffrey M; Florance, Daniel; Lindenmayer, David

    2016-08-01

    Approaches to prioritize conservation actions are gaining popularity. However, limited empirical evidence exists on which species might benefit most from threat mitigation and on what combination of threats, if mitigated simultaneously, would result in the best outcomes for biodiversity. We devised a way to prioritize threat mitigation at a regional scale with empirical evidence based on predicted changes to population dynamics-information that is lacking in most threat-management prioritization frameworks that rely on expert elicitation. We used dynamic occupancy models to investigate the effects of multiple threats (tree cover, grazing, and presence of an hyperaggressive competitor, the Noisy Miner (Manorina melanocephala) on bird-population dynamics in an endangered woodland community in southeastern Australia. The 3 threatening processes had different effects on different species. We used predicted patch-colonization probabilities to estimate the benefit to each species of removing one or more threats. We then determined the complementary set of threat-mitigation strategies that maximized colonization of all species while ensuring that redundant actions with little benefit were avoided. The single action that resulted in the highest colonization was increasing tree cover, which increased patch colonization by 5% and 11% on average across all species and for declining species, respectively. Combining Noisy Miner control with increasing tree cover increased species colonization by 10% and 19% on average for all species and for declining species respectively, and was a higher priority than changing grazing regimes. Guidance for prioritizing threat mitigation is critical in the face of cumulative threatening processes. By incorporating population dynamics in prioritization of threat management, our approach helps ensure funding is not wasted on ineffective management programs that target the wrong threats or species.

  11. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species

    OpenAIRE

    Dawson, Michael N; Gupta, Alex Sen; England, Matthew H.

    2005-01-01

    The anthropogenic introduction of exotic species is one of the greatest modern threats to marine biodiversity. Yet exotic species introductions remain difficult to predict and are easily misunderstood because knowledge of natural dispersal patterns, species diversity, and biogeography is often insufficient to distinguish between a broadly dispersed natural population and an exotic one. Here we compare a global molecular phylogeny of a representative marine meroplanktonic taxon, the moon-jelly...

  12. A physiologically based pharmacokinetic (PB/PK) model for multiple exposure routes for soman in multiple species

    NARCIS (Netherlands)

    Sweeney, R.E.; Langenberg, J.P.; Maxwell, D.M.

    2006-01-01

    A physiologically based pharmacokinetic (PB/PK) model has been developed in advanced computer simulation language (ACSL) to describe blood and tissue concentration-time profiles of the C(±)P(-) stereoisomers of soman after inhalation, subcutaneous and intravenous exposures at low (0.8-1.0 × LD50), m

  13. Structural libraries of protein models for multiple species to understand evolution of the renin-angiotensin system.

    Science.gov (United States)

    Prokop, Jeremy W; Petri, Victoria; Shimoyama, Mary E; Watanabe, Ingrid K M; Casarini, Dulce E; Leeper, Thomas C; Bilinovich, Stephanie M; Jacob, Howard J; Santos, Robson A S; Martins, Almir S; Araujo, Fabiano C; Reis, Fernando M; Milsted, Amy

    2015-05-01

    The details of protein pathways at a structural level provides a bridge between genetics/molecular biology and physiology. The renin-angiotensin system is involved in many physiological pathways with informative structural details in multiple components. Few studies have been performed assessing structural knowledge across the system. This assessment allows use of bioinformatics tools to fill in missing structural voids. In this paper we detail known structures of the renin-angiotensin system and use computational approaches to estimate and model components that do not have their protein structures defined. With the subsequent large library of protein structures, we then created a species specific protein library for human, mouse, rat, bovine, zebrafish, and chicken for the system. The rat structural system allowed for rapid screening of genetic variants from 51 commonly used rat strains, identifying amino acid variants in angiotensinogen, ACE2, and AT1b that are in contact positions with other macromolecules. We believe the structural map will be of value for other researchers to understand their experimental data in the context of an environment for multiple proteins, providing pdb files of proteins for the renin-angiotensin system in six species. With detailed structural descriptions of each protein, it is easier to assess a species for use in translating human diseases with animal models. Additionally, as whole genome sequencing continues to decrease in cost, tools such as molecular modeling will gain use as an initial step in designing efficient hypothesis driven research, addressing potential functional outcomes of genetic variants with precompiled protein libraries aiding in rapid characterizations.

  14. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available 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].

  15. Bounding Species Distribution Models

    Science.gov (United States)

    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].

  16. Hybrid approaches for multiple-species stochastic reaction-diffusion models

    CERN Document Server

    Spill, Fabian; Alarcon, Tomas; Maini, Philip K; Byrne, Helen

    2015-01-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains ...

  17. EXISTENCE OF MULTIPLE PERIODIC SOLUTIONS TO THREE-SPECIES DELAYED LOTKA-VOLTERRA MODEL WITH DISPERSION AND HARVESTING

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    The positive periodic solutions to a three-species delayed Lotka-Volterra model with dispersion and harvesting terms are studied in this paper. By the coincidence degree theory, the sufficient conditions for existence of eight positive periodic solutions to the model are obtained.

  18. Bounding species distribution models

    Institute of Scientific and Technical Information of China (English)

    Thomas J. STOHLGREN; Catherine S. JARNEVICH; Wayne E. ESAIAS; Jeffrey T. MORISETTE

    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].

  19. A Quantitative Model of Motility Reveals Low-Dimensional Variation in Exploratory Behavior Across Multiple Nematode Species

    Science.gov (United States)

    Helms, Stephen; Avery, Leon; Stephens, Greg; Shimizu, Tom

    2014-03-01

    Animal behavior emerges from many layers of biological organization--from molecular signaling pathways and neuronal networks to mechanical outputs of muscles. In principle, the large number of interconnected variables at each of these layers could imply dynamics that are complex and hard to control or even tinker with. Yet, for organisms to survive in a competitive, ever-changing environment, behavior must readily adapt. We applied quantitative modeling to identify important aspects of behavior in chromadorean nematodes ranging from the lab strain C. elegans N2 to wild strains and distant species. We revealed subtle yet important features such as speed control and heavy-tailed directional changes. We found that the parameters describing this behavioral model varied among individuals and across species in a correlated way that is consistent with a trade-off between exploratory and exploitative behavior.

  20. Diffusion of multiple species with excluded-volume effects

    CERN Document Server

    Bruna, Maria

    2012-01-01

    Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diff...

  1. Multiple peaks of species abundance distributions induced by sparse interactions

    CERN Document Server

    Obuchi, Tomoyuki; Tokita, Kei

    2016-01-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self interaction $u$, we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of $u$ below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all spe...

  2. Whole genome phylogenies for multiple Drosophila species

    Directory of Open Access Journals (Sweden)

    Seetharam Arun

    2012-12-01

    Full Text Available Abstract Background Reconstructing the evolutionary history of organisms using traditional phylogenetic methods may suffer from inaccurate sequence alignment. An alternative approach, particularly effective when whole genome sequences are available, is to employ methods that don’t use explicit sequence alignments. We extend a novel phylogenetic method based on Singular Value Decomposition (SVD to reconstruct the phylogeny of 12 sequenced Drosophila species. SVD analysis provides accurate comparisons for a high fraction of sequences within whole genomes without the prior identification of orthologs or homologous sites. With this method all protein sequences are converted to peptide frequency vectors within a matrix that is decomposed to provide simplified vector representations for each protein of the genome in a reduced dimensional space. These vectors are summed together to provide a vector representation for each species, and the angle between these vectors provides distance measures that are used to construct species trees. Results An unfiltered whole genome analysis (193,622 predicted proteins strongly supports the currently accepted phylogeny for 12 Drosophila species at higher dimensions except for the generally accepted but difficult to discern sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. Similar results were obtained when just the melanogaster subgroup was analyzed. Conclusions These results indicate that using our novel phylogenetic method, it is possible to consult and interpret all predicted protein sequences within multiple whole genomes to produce accurate phylogenetic estimations of relatedness between

  3. Diffusion of multiple species with excluded-volume effects

    KAUST Repository

    Bruna, Maria

    2012-01-01

    Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results. © 2012 American Institute of Physics.

  4. First-order kinetics-controlled multiple species reactive transport of dissolved organic compounds in groundwater: Development and application of a numerical model

    Energy Technology Data Exchange (ETDEWEB)

    McNab, W.W. Jr.

    1990-05-01

    Reactive chemical transport models developed over the past decade have generally relied on the assumption that local thermodynamic equilibrium is achieved at all times between aqueous species in a given system. Consequently, homogeneous aqueous systems characterized by a number of kinetically slow reactions, particularly problems involving organic species, cannot be satisfactorily modeled. In this study, we present a prototype computer model, KINETRAN, which is designed to handle kinetically-controlled homogeneous reactions in the aqueous phase, along with the transport of the various species involved, through geologic media. 31 refs., 53 figs., 10 tabs.

  5. Mapping habitat for multiple species in the Desert Southwest

    Science.gov (United States)

    Inman, Richard D.; Nussear, Kenneth E.; Esque, Todd C.; Vandergast, Amy G.; Hathaway, Stacie A.; Wood, Dustin A.; Barr, Kelly R.; Fisher, Robert N.

    2014-01-01

    Many utility scale renewable energy projects are currently proposed across the Mojave Ecoregion. Agencies that manage biological resources throughout this region need to understand the potential impacts of these renewable energy projects and their associated infrastructure (for example, transmission corridors, substations, access roads, etc.) on species movement, genetic exchange among populations, and species’ abilities to adapt to changing environmental conditions. Understanding these factors will help managers’ select appropriate project sites and possibly mitigate for anticipated effects of management activities. We used species distribution models to map habitat for 15 species across the Mojave Ecoregion to aid regional land-use management planning. Models were developed using a common 1 × 1 kilometer resolution with maximum entropy and generalized additive models. Occurrence data were compiled from multiple sources, including VertNet (http://vertnet.org/), HerpNET (http://www.herpnet.org), and MaNIS (http://manisnet.org), as well as from internal U.S. Geological Survey databases and other biologists. Background data included 20 environmental covariates representing terrain, vegetation, and climate covariates. This report summarizes these environmental covariates and species distribution models used to predict habitat for the 15 species across the Mojave Ecoregion.

  6. Tri-Monthly Wildlife Information Reports, Multiple Species

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Tri-Monthly Wildlife Information Reports on multiple species of wildlife including reptiles, mammals, and avian species at Morgan Brake NWR.

  7. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny;

    2006-01-01

    species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  8. Multiplicative LSTM for sequence modelling

    OpenAIRE

    Krause, Ben; Lu, Liang; Murray, Iain; Renals, Steve

    2016-01-01

    This paper introduces multiplicative LSTM, a novel hybrid recurrent neural network architecture for sequence modelling that combines the long short-term memory (LSTM) and multiplicative recurrent neural network architectures. Multiplicative LSTM is motivated by its flexibility to have very different recurrent transition functions for each possible input, which we argue helps make it more expressive in autoregressive density estimation. We show empirically that multiplicative LSTM outperforms ...

  9. Optimal design of compact and connected nature reserves for multiple species.

    Science.gov (United States)

    Wang, Yicheng; Önal, Hayri

    2016-04-01

    When designing a conservation reserve system for multiple species, spatial attributes of the reserves must be taken into account at species level. The existing optimal reserve design literature considers either one spatial attribute or when multiple attributes are considered the analysis is restricted only to one species. We built a linear integer programing model that incorporates compactness and connectivity of the landscape reserved for multiple species. The model identifies multiple reserves that each serve a subset of target species with a specified coverage probability threshold to ensure the species' long-term survival in the reserve, and each target species is covered (protected) with another probability threshold at the reserve system level. We modeled compactness by minimizing the total distance between selected sites and central sites, and we modeled connectivity of a selected site to its designated central site by selecting at least one of its adjacent sites that has a nearer distance to the central site. We considered structural distance and functional distances that incorporated site quality between sites. We tested the model using randomly generated data on 2 species, one ground species that required structural connectivity and the other an avian species that required functional connectivity. We applied the model to 10 bird species listed as endangered by the state of Illinois (U.S.A.). Spatial coherence and selection cost of the reserves differed substantially depending on the weights assigned to these 2 criteria. The model can be used to design a reserve system for multiple species, especially species whose habitats are far apart in which case multiple disjunct but compact and connected reserves are advantageous. The model can be modified to increase or decrease the distance between reserves to reduce or promote population connectivity.

  10. Modelling biological invasions: species traits, species interactions, and habitat heterogeneity.

    Science.gov (United States)

    Cannas, Sergio A; Marco, Diana E; Páez, Sergio A

    2003-05-01

    In this paper we explore the integration of different factors to understand, predict and control ecological invasions, through a general cellular automaton model especially developed. The model includes life history traits of several species in a modular structure interacting multiple cellular automata. We performed simulations using field values corresponding to the exotic Gleditsia triacanthos and native co-dominant trees in a montane area. Presence of G. triacanthos juvenile bank was a determinant condition for invasion success. Main parameters influencing invasion velocity were mean seed dispersal distance and minimum reproductive age. Seed production had a small influence on the invasion velocity. Velocities predicted by the model agreed well with estimations from field data. Values of population density predicted matched field values closely. The modular structure of the model, the explicit interaction between the invader and the native species, and the simplicity of parameters and transition rules are novel features of the model.

  11. VORICONAZOLE TOXICITY IN MULTIPLE PENGUIN SPECIES.

    Science.gov (United States)

    Hyatt, Michael W; Georoff, Timothy A; Nollens, Hendrik H; Wells, Rebecca L; Clauss, Tonya M; Ialeggio, Donna M; Harms, Craig A; Wack, Allison N

    2015-12-01

    Aspergillosis is a common respiratory fungal disease in penguins managed under human care. Triazole antifungal drugs, including itraconazole, are most commonly used for treatment; however, itraconazole treatment failures from drug resistance are becoming more common, requiring newer treatment options. Voriconazole, a newer triazole, is being used more often. Until recently, no voriconazole pharmacokinetic studies had been performed in penguins, leading to empiric dosing based on other avian studies. This has led to increased anecdotal reporting of apparent voriconazole toxicity in penguins. This report describes 18 probable and 6 suspected cases of voriconazole toxicity in six penguin species from nine institutions: 12 African penguins (Spheniscus demersus), 5 Humboldt penguins (Spheniscus humboldti), 3 Magellanic penguins (Spheniscus magellanicus), 2 gentoo penguins (Pygoscelis papua papua), 1 macaroni penguin (Eudyptes chrysolophus), and 1 emperor penguin (Aptenodytes forsteri). Observed clinical signs of toxicity included anorexia, lethargy, weakness, ataxia, paresis, apparent vision changes, seizure-like activity, and generalized seizures. Similar signs of toxicity have also been reported in humans, in whom voriconazole therapeutic plasma concentration for Aspergillus spp. infections is 2-6 μg/ml. Plasma voriconazole concentrations were measured in 18 samples from penguins showing clinical signs suggestive of voriconazole toxicity. The concentrations ranged from 8.12 to 64.17 μg/ml, with penguins having plasma concentrations above 30 μg/ml exhibiting moderate to severe neurologic signs, including ataxia, paresis, and seizures. These concentrations were well above those known to result in central nervous system toxicity, including encephalopathy, in humans. This case series highlights the importance of species-specific dosing of voriconazole in penguins and plasma therapeutic drug monitoring. Further investigation, including pharmacokinetic studies, is

  12. Multiple proteinases from two Microsporum species.

    Science.gov (United States)

    Simpanya, M F; Baxter, M

    1996-01-01

    Enzyme expression of 67 isolates of two Microsporum species, M. canis and M. cookei, were compared in both shake and stationary cultures using substrate copolymerized SDS-PAGE. Most M. canis isolates expressed more proteolytic bands in shake culture, while M. cookei isolates expressed more in stationary culture. M. canis isolates expressed up to six proteinases of different relative mobilities (122, 64, 62, 45, 31 and 25 kDa). M. cookei expressed up to seven proteinases in stationary culture (67, 66, 64, 62, 45, 42 and 39 kDa). Those of 67 and 66 kDa were not expressed in shake culture. The proteinases expressed by M. cookei were similar to those expressed by M. canis except for 122 and 25 kDa. With the exception of isolates from non-infected cats, 25 kDa was also commonly expressed by isolates from infected hosts in the shake culture treatment. The differences in enzyme expression obtained may reflect differences in the contrasting ecological roles of the two species.

  13. A single predator multiple prey model with prey mutation

    Science.gov (United States)

    Mullan, Rory; Abernethy, Gavin M.; Glass, David H.; McCartney, Mark

    2016-11-01

    A multiple species predator-prey model is expanded with the introduction of a coupled map lattice for the prey, allowing the prey to mutate discretely into other prey species. The model is examined in its single predator, multiple mutating prey form. Two unimodal maps are used for the underlying dynamics of the prey species, with different predation strategies being used. Conclusions are drawn on how varying the control parameters of the model governs the overall behaviour and survival of the species. It is observed that in such a complex system, with multiple mutating prey, a large range of non-linear dynamics is possible.

  14. Multiplicity description by gluon model

    CERN Document Server

    Kokoulina, E S

    2015-01-01

    Study of high multiplicity events in proton-proton interactions is carried out at the U-70 accelerator (IHEP, Protvino). These events are extremely rare. Usually, Monte Carlo codes underestimate topological cross sections in this region. The gluon dominance model (GDM) was offered to describe them. It is based on QCD and a phenomenological scheme of a hadronization stage. This model indicates a recombination mechanism of hadronization and a gluon fission. Future program of the SVD Collaboration is aimed at studying a long-standing puzzle of excess soft photon yield and its connection with high multiplicity at the U-70 and Nuclotron facility at JINR, Dubna.

  15. On the asymmetric simple exclusion process with multiple species

    CERN Document Server

    Tracy, Craig A

    2011-01-01

    In the asymmetric simple exclusion process on the integers each particle waits exponential time, then with probability p it moves one step to the right if the site is unoccupied, otherwise it stays put; and with probability q=1-p it moves one step to the left if the site is unoccupied, otherwise it stays put. In previous work the authors, using the Bethe Ansatz, found for N-particle ASEP a formula --- a sum of multiple integrals --- for the probability that a system is in a particular configuration at time t given an initial configuration. The present work extends this to the case where particles are of different species, with particles of a higher species having priority over those of a lower species. Here the integrands in the multiple integrals are not given explicitly but are defined by a system of equations whose consistency requires verifying that the Yang-Baxter equations are satisfied.

  16. Multiple Model Approaches to Modelling and Control,

    DEFF Research Database (Denmark)

    Why Multiple Models?This book presents a variety of approaches which produce complex models or controllers by piecing together a number of simpler subsystems. Thisdivide-and-conquer strategy is a long-standing and general way of copingwith complexity in engineering systems, nature and human probl...

  17. CARS Spectral Fitting with Multiple Resonant Species using Sparse Libraries

    Science.gov (United States)

    Cutler, Andrew D.; Magnotti, Gaetano

    2010-01-01

    The dual pump CARS technique is often used in the study of turbulent flames. Fast and accurate algorithms are needed for fitting dual-pump CARS spectra for temperature and multiple chemical species. This paper describes the development of such an algorithm. The algorithm employs sparse libraries, whose size grows much more slowly with number of species than a conventional library. The method was demonstrated by fitting synthetic "experimental" spectra containing 4 resonant species (N2, O2, H2 and CO2), both with noise and without it, and by fitting experimental spectra from a H2-air flame produced by a Hencken burner. In both studies, weighted least squares fitting of signal, as opposed to least squares fitting signal or square-root signal, was shown to produce the least random error and minimize bias error in the fitted parameters.

  18. As multiple fish species in large marine ecosystems are harvested ...

    African Journals Online (AJOL)

    CMPTMAC10

    culling to increase fish available for human harvesting ... species to develop positive surplus production invari- ... Whole-ecosystem foodweb models, specifically the dynamic model ECOSIM, contain specific ... of younger animals, would unrealistically overestimate ..... sidered to have sufficient weight to have reproductive.

  19. Experimental study of a multiplicative model of multiple ionospheric reflections

    Science.gov (United States)

    Mirkotan, S. F.; Zhuravlev, S. V.; Kosovtsov, Iu. N.

    1983-04-01

    An important parameter of a partially scattered ionospheric signal is the signal-noise energy parameter beta. A new method for determining beta sub n (where n is the multiplicity of reflection) has been proposed on the basis of the statistical multiplicative model of Mirkotan et al. (1981, 1982). This paper describes an experimental verification of the proposed method; data on beta sub n obtained by the traditional method and by the new method are compared. In addition, the validity of the multiplicative model is evaluated, and features of the mechanism responsible for the multiple scattering of an ionospheric signal are examined.

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

    Science.gov (United States)

    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.

  1. Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

    Directory of Open Access Journals (Sweden)

    McLeish Michael J

    2012-01-01

    Full Text Available Abstract Background The interaction between insects and plants takes myriad forms in the generation of spectacular diversity. In this association a species host range is fundamental and often measured using an estimate of phylogenetic concordance between species. Pollinating fig wasps display extreme host species specificity, but the intraspecific variation in empirical accounts of host affiliation has previously been underestimated. In this investigation, lineage delimitation and codiversification tests are used to generate and discuss hypotheses elucidating on pollinating fig wasp associations with Ficus. Results Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies. Conclusions The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution.

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

    Science.gov (United States)

    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

  3. Multiple scattering Model in GEANT4

    CERN Document Server

    Urbàn, L

    2002-01-01

    We present a new multiple scattering (MSC) model to simulate the multiple scattering of charged particles in matter. This model does not use the Moliere formalism, it is based on the more complete Lewis theory. The model simulates the scattering of the particle after a given step, computes the path length correction and the lateral displacement as well.

  4. Multiple factors and thresholds explaining fish species distributions in lowland streams

    Directory of Open Access Journals (Sweden)

    Cristina Trigal

    2015-07-01

    Full Text Available Appropriate restoration and conservation measures require a good understanding of the factors limiting the distribution of species, the presence of steep changes in the distribution along environmental gradients and the effect of environmental interactions on species distribution. We used 12 environmental variables describing connectivity, hydrology, climate and stream morphology, to model the distributions of 17 fish species from 2005 Swedish stream sites that were sampled between 2000 and 2011. Modeling was performed using boosted regression trees and random forest, two machine learning techniques to assess the relationship between species distributions and their environment. Temperature, width and connectivity (minimum distance to lake or the sea and water discharge, were the most important variables explaining changes in species distribution at large spatial scales. Response curves of fitted occurrence probabilities along predictors often showed abrupt changes, however, clear threshold effects were difficult to detect. Our results show also differences across species and even in the outcomes of the two algorithms, implying that a simultaneous assessment of multiple species may provide a better signal of ecosystem change than the use of surrogate species.

  5. Incorporating Context Dependency of Species Interactions in Species Distribution Models.

    Science.gov (United States)

    Lany, Nina K; Zarnetske, Phoebe L; Gouhier, Tarik C; Menge, Bruce A

    2017-07-01

    Species distribution models typically use correlative approaches that characterize the species-environment relationship using occurrence or abundance data for a single species. However, species distributions are determined by both abiotic conditions and biotic interactions with other species in the community. Therefore, climate change is expected to impact species through direct effects on their physiology and indirect effects propagated through their resources, predators, competitors, or mutualists. Furthermore, the sign and strength of species interactions can change according to abiotic conditions, resulting in context-dependent species interactions that may change across space or with climate change. Here, we incorporated the context dependency of species interactions into a dynamic species distribution model. We developed a multi-species model that uses a time-series of observational survey data to evaluate how abiotic conditions and species interactions affect the dynamics of three rocky intertidal species. The model further distinguishes between the direct effects of abiotic conditions on abundance and the indirect effects propagated through interactions with other species. We apply the model to keystone predation by the sea star Pisaster ochraceus on the mussel Mytilus californianus and the barnacle Balanus glandula in the rocky intertidal zone of the Pacific coast, USA. Our method indicated that biotic interactions between P. ochraceus and B. glandula affected B. glandula dynamics across >1000 km of coastline. Consistent with patterns from keystone predation, the growth rate of B. glandula varied according to the abundance of P. ochraceus in the previous year. The data and the model did not indicate that the strength of keystone predation by P. ochraceus varied with a mean annual upwelling index. Balanus glandula cover increased following years with high phytoplankton abundance measured as mean annual chlorophyll-a. M. californianus exhibited the same

  6. Modeling Multiple Causes of Carcinogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Jones, T D

    1999-01-24

    An array of epidemiological results and databases on test animal indicate that risk of cancer and atherosclerosis can be up- or down-regulated by diet through a range of 200%. Other factors contribute incrementally and include the natural terrestrial environment and various human activities that jointly produce complex exposures to endotoxin-producing microorganisms, ionizing radiations, and chemicals. Ordinary personal habits and simple physical irritants have been demonstrated to affect the immune response and risk of disease. There tends to be poor statistical correlation of long-term risk with single agent exposures incurred throughout working careers. However, Agency recommendations for control of hazardous exposures to humans has been substance-specific instead of contextually realistic even though there is consistent evidence for common mechanisms of toxicological and carcinogenic action. That behavior seems to be best explained by molecular stresses from cellular oxygen metabolism and phagocytosis of antigenic invasion as well as breakdown of normal metabolic compounds associated with homeostatic- and injury-related renewal of cells. There is continually mounting evidence that marrow stroma, comprised largely of monocyte-macrophages and fibroblasts, is important to phagocytic and cytokinetic response, but the complex action of the immune process is difficult to infer from first-principle logic or biomarkers of toxic injury. The many diverse database studies all seem to implicate two important processes, i.e., the univalent reduction of molecular oxygen and breakdown of aginuine, an amino acid, by hydrolysis or digestion of protein which is attendant to normal antigen-antibody action. This behavior indicates that protection guidelines and risk coefficients should be context dependent to include reference considerations of the composite action of parameters that mediate oxygen metabolism. A logic of this type permits the realistic common-scale modeling of

  7. Multiple Imputation Strategies for Multiple Group Structural Equation Models

    Science.gov (United States)

    Enders, Craig K.; Gottschall, Amanda C.

    2011-01-01

    Although structural equation modeling software packages use maximum likelihood estimation by default, there are situations where one might prefer to use multiple imputation to handle missing data rather than maximum likelihood estimation (e.g., when incorporating auxiliary variables). The selection of variables is one of the nuances associated…

  8. Dynamical modelling of coordinated multiple robot systems

    Science.gov (United States)

    Hayati, Samad

    1987-01-01

    The state of the art in the modeling of the dynamics of coordinated multiple robot manipulators is summarized and various problems related to this subject are discussed. It is recognized that dynamics modeling is a component used in the design of controllers for multiple cooperating robots. As such, the discussion addresses some problems related to the control of multiple robots. The techniques used to date in the modeling of closed kinematic chains are summarized. Various efforts made to date for the control of coordinated multiple manipulators is summarized.

  9. Spatial organization of multiple plant species in arid ecosystems:linking patterns and processes

    Institute of Scientific and Technical Information of China (English)

    Amit; CHAKRABORTY; B.Larry; LI

    2010-01-01

    Spatial organization of multiple plant species that appears as a non-random distribution of vegetative patches is one of the mostly observed spatial patterns in arid ecosystems. Yet understanding of ecological processes allowing this spatial pattern to emerge through interspecific interactions is still lacking. With a proposed conceptual model involving interspecific trade-offs between species competitive ability and colonization ability, we have argued that within patch abundance dynamics regulated by the mechanisms of competition are strongly influenced by the between patches colonization dynamics that are maintained via this trade-offs and it holds a positive, intraspecific occupancy-abundance relationship, in which increased patch occupancy increases species density within inhabiting patches. In a constant environment, while local abundance dynamics approach toward a stable equilibrium point, a fixed spatial arrangement of species can be retained through this coupled dynamics. However, in fluctuating environments where existence of such stable equilibriums is highly uncertain, it may involve continuous transitions from one community state to another as species re-organized themselves over space through the rapid changes in local species abundances. While some of the inhabiting patches are destroyed exogenously or endogenously, or species responses to increasing environmental fluctuations vary increasingly with time, discontinuous transitions into an abrupt, irreversible state of the community dynamics may occur, as with this effect the inherent positive relationship between occupancy and abundance of species is no longer maintained.

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

    Science.gov (United States)

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

    2015-11-01

    Allopatry is commonly used to predict boundaries in species delimitation investigations under the assumption that currently allopatric distributions are indicative of reproductive isolation; however, species ranges are known to change over time. Incorporating a temporal perspective of geographic distributions should improve species delimitation; to explore this, we investigate three species of western Plethodon salamanders that have shifted their ranges since the end of the Pleistocene. We generate species distribution models (SDM) of the current range, hindcast these models onto a climatic model 21 Ka, and use three molecular approaches to delimit species in an integrated fashion. In contrast to expectations based on the current distribution, we detect no independent lineages in species with allopatric and patchy distributions (Plethodon vandykei and Plethodon larselli). The SDMs indicate that probable habitat is more expansive than their current range, especially during the last glacial maximum (LGM) (21 Ka). However, with a contiguous distribution, two independent lineages were detected in Plethodon idahoensis, possibly due to isolation in multiple glacial refugia. Results indicate that historical SDMs are a better predictor of species boundaries than current distributions, and strongly imply that researchers should incorporate SDM and hindcasting into their investigations and the development of species hypotheses. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Multiple models for Rosaceae genomics.

    Science.gov (United States)

    Shulaev, Vladimir; Korban, Schuyler S; Sosinski, Bryon; Abbott, Albert G; Aldwinckle, Herb S; Folta, Kevin M; Iezzoni, Amy; Main, Dorrie; Arús, Pere; Dandekar, Abhaya M; Lewers, Kim; Brown, Susan K; Davis, Thomas M; Gardiner, Susan E; Potter, Daniel; Veilleux, Richard E

    2008-07-01

    The plant family Rosaceae consists of over 100 genera and 3,000 species that include many important fruit, nut, ornamental, and wood crops. Members of this family provide high-value nutritional foods and contribute desirable aesthetic and industrial products. Most rosaceous crops have been enhanced by human intervention through sexual hybridization, asexual propagation, and genetic improvement since ancient times, 4,000 to 5,000 B.C. Modern breeding programs have contributed to the selection and release of numerous cultivars having significant economic impact on the U.S. and world markets. In recent years, the Rosaceae community, both in the United States and internationally, has benefited from newfound organization and collaboration that have hastened progress in developing genetic and genomic resources for representative crops such as apple (Malus spp.), peach (Prunus spp.), and strawberry (Fragaria spp.). These resources, including expressed sequence tags, bacterial artificial chromosome libraries, physical and genetic maps, and molecular markers, combined with genetic transformation protocols and bioinformatics tools, have rendered various rosaceous crops highly amenable to comparative and functional genomics studies. This report serves as a synopsis of the resources and initiatives of the Rosaceae community, recent developments in Rosaceae genomics, and plans to apply newly accumulated knowledge and resources toward breeding and crop improvement.

  12. In vivo models of multiple system atrophy.

    Science.gov (United States)

    Fernagut, Pierre-Olivier; Ghorayeb, Imad; Diguet, Elsa; Tison, François

    2005-08-01

    Multiple system atrophy (MSA) is a sporadic adult-onset neurodegenerative disorder of unknown etiology clinically characterized by a combination of parkinsonian, pyramidal, and cerebellar signs. Levodopa-unresponsive parkinsonism is present in 80% of MSA cases, and this dominant clinical presentation (MSA-P) is associated with a combined degeneration of the substantia nigra pars compacta and the striatum in anatomically related areas. The limited knowledge of the pathophysiology of MSA and the lack of therapeutic strategies prompted the development of lesion models reproducing striatonigral degeneration, the substrate of levodopa-unresponsive parkinsonism in MSA-P. This method was carried out first in rats with two different stereotaxic strategies using either two neurotoxins ("double toxin-double lesion") or a single neurotoxin ("single toxin-double lesion"). Double-lesioned rat models showed severe motor impairment compared to those with a single nigral or striatal lesion and helped to mimic different stages of the disease. Systemic models were also developed in mice and primates using the nigral toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and the striatal toxin 3-nitropropionic (3-NP). In mice, although MPTP reduced the subsequent sensitivity to 3-NP in a sequential lesion, simultaneous nigral and striatal insults were shown to exacerbate striatal damage. MPTP-treated monkeys displayed a significant worsening of parkinsonism and a loss of levodopa-responsiveness after the appearance of hindlimb dystonia and striatal lesion formation induced by subsequent 3-NP intoxication. The different species and intoxication paradigms used will be useful to investigate functional changes in substantia nigra and striatum and to define neuroprotective, neurorestorative, or symptomatic therapeutic strategies.

  13. Integrating multiple evidences in taxonomy: species diversity and phylogeny of mustached bats (Mormoopidae: Pteronotus).

    Science.gov (United States)

    Pavan, Ana Carolina; Marroig, Gabriel

    2016-10-01

    A phylogenetic systematic perspective is instrumental in recovering new species and their evolutionary relationships. The advent of new technologies for molecular and morphological data acquisition and analysis, allied to the integration of knowledge from different areas, such as ecology and population genetics, allows for the emergence of more rigorous, accurate and complete scientific hypothesis on species diversity. Mustached bats (genus Pteronotus) are a good model for the application of this integrative approach. They are a widely distributed and a morphologically homogeneous group, but comprising species with remarkable differences in their echolocation strategy and feeding behavior. The latest systematic review suggested six species with 17 subspecies in Pteronotus. Subsequent studies using discrete morphological characters supported the same arrangement. However, recent papers reported high levels of genetic divergence among conspecific taxa followed by bioacoustic and geographic agreement, suggesting an underestimated diversity in the genus. To date, no study merging genetic evidences and morphometric variation along the entire geographic range of this group has been attempted. Based on a comprehensive sampling including representatives of all current taxonomic units, we attempt to delimit species in Pteronotus through the application of multiple methodologies and hierarchically distinct datasets. The molecular approach includes six molecular markers from three genetic transmission systems; morphological investigations used 41 euclidean distances estimated through three-dimensional landmarks collected from 1628 skulls. The phylogenetic analysis reveals a greater diversity than previously reported, with a high correspondence among the genetic lineages and the currently recognized subspecies in the genus. Discriminant analysis of variables describing size and shape of cranial bones support the rising of the genetic groups to the specific status. Based on

  14. Multiplicity Control in Structural Equation Modeling

    Science.gov (United States)

    Cribbie, Robert A.

    2007-01-01

    Researchers conducting structural equation modeling analyses rarely, if ever, control for the inflated probability of Type I errors when evaluating the statistical significance of multiple parameters in a model. In this study, the Type I error control, power and true model rates of famsilywise and false discovery rate controlling procedures were…

  15. Characteristics of 263K scrapie agent in multiple hamster species.

    Science.gov (United States)

    Meade-White, Kimberly D; Barbian, Kent D; Race, Brent; Favara, Cynthia; Gardner, Don; Taubner, Lara; Porcella, Stephen; Race, Richard

    2009-02-01

    Transmissible spongiform encephalopathy (TSE) diseases are known to cross species barriers, but the pathologic and biochemical changes that occur during transmission are not well understood. To better understand these changes, we infected 6 hamster species with 263K hamster scrapie strain and, after each of 3 successive passages in the new species, analyzed abnormal proteinase K (PK)-resistant prion protein (PrPres) glycoform ratios, PrPres PK sensitivity, incubation periods, and lesion profiles. Unique 263K molecular and biochemical profiles evolved in each of the infected hamster species. Characteristics of 263K in the new hamster species seemed to correlate best with host factors rather than agent strain. Furthermore, 2 polymorphic regions of the prion protein amino acid sequence correlated with profile differences in these TSE-infected hamster species.

  16. Multicolor Electron Microscopy for Simultaneous Visualization of Multiple Molecular Species

    NARCIS (Netherlands)

    Adams, Stephen R; Mackey, Mason R; Ramachandra, Ranjan; Palida Lemieux, Sakina F; Steinbach, Paul; Bushong, Eric A; Butko, Margaret T; Giepmans, Ben N G; Ellisman, Mark H; Tsien, Roger Y

    2016-01-01

    Electron microscopy (EM) remains the primary method for imaging cellular and tissue ultrastructure, although simultaneous localization of multiple specific molecules continues to be a challenge for EM. We present a method for obtaining multicolor EM views of multiple subcellular components. The meth

  17. A Solvable Model of Species Body Mass Evolution

    CERN Document Server

    Clauset, Aaron

    2008-01-01

    We present a quantitative model for the biological evolution of species body masses within large groups of related species, e.g., terrestrial mammals, in which body mass M evolves according to branching (speciating) multiplicative diffusion and an extinction probability that increases logarithmically with mass. We describe this evolution in terms of a convection-diffusion-reaction equation for ln M. The steady-state behavior is in good agreement with empirical data on recent terrestrial mammals, and the time-dependent behavior also agrees with data on extinct mammal species between 95 - 50 million years ago.

  18. Multiple strategies for drought survival among woody plant species

    OpenAIRE

    Pivovaroff, AL; Pasquini, SC; De Guzman, ME; Alstad, KP; Stemke, JS; Santiago, LS

    2015-01-01

    © 2015 British Ecological Society Drought-induced mortality and regional dieback of woody vegetation are reported from numerous locations around the world. Yet within any one site, predicting which species are most likely to survive global change-type drought is a challenge. We studied the diversity of drought survival traits of a community of 15 woody plant species in a desert-chaparral ecotone. The vegetation was a mix of chaparral and desert shrubs, as well as endemic species that only occ...

  19. Pseudoabsence generation strategies for species distribution models.

    Directory of Open Access Journals (Sweden)

    Brice B Hanberry

    Full Text Available 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

  20. PCR-Based Multiple Species Cell Counting for In Vitro Mixed Culture.

    Directory of Open Access Journals (Sweden)

    Ruijie Huang

    Full Text Available Changes of bacterial profiles in microbial communities are strongly associated with human health. There is an increasing need for multiple species research in vitro. To avoid high cost or measurement of a limited number of species, PCR-based multiple species cell counting (PCR-MSCC has been conceived. Species-specific sequence is defined as a unique sequence of one species in a multiple species mixed culture. This sequence is identified by comparing a random 1000 bp genomic sequence of one species with the whole genome sequences of the other species in the same artificial mixed culture. If absent in the other genomes, it is the species-specific sequence. Species-specific primers were designed based on the species-specific sequences. In the present study, ten different oral bacterial species were mixed and grown in Brain Heart Infusion Yeast Extract with 1% sucrose for 24 hours. Biofilm was harvested and processed for DNA extraction and q-PCR amplification with the species-specific primers. By comparing the q-PCR data of each species in the unknown culture with reference cultures, in which the cell number of each species was determined by colony forming units on agar plate, the cell number of that strain in the unknown mixed culture was calculated. This technique is reliable to count microorganism numbers that are less than 100,000 fold different from other species within the same culture. Theoretically, it can be used in detecting a species in a mixed culture of over 200 species. Currently PCR-MSCC is one of the most economic methods for quantifying single species cell numbers, especially for the low abundant species, in a multiple artificial mixed culture in vitro.

  1. PCR-Based Multiple Species Cell Counting for In Vitro Mixed Culture.

    Science.gov (United States)

    Huang, Ruijie; Zhang, Junjie; Yang, X Frank; Gregory, Richard L

    2015-01-01

    Changes of bacterial profiles in microbial communities are strongly associated with human health. There is an increasing need for multiple species research in vitro. To avoid high cost or measurement of a limited number of species, PCR-based multiple species cell counting (PCR-MSCC) has been conceived. Species-specific sequence is defined as a unique sequence of one species in a multiple species mixed culture. This sequence is identified by comparing a random 1000 bp genomic sequence of one species with the whole genome sequences of the other species in the same artificial mixed culture. If absent in the other genomes, it is the species-specific sequence. Species-specific primers were designed based on the species-specific sequences. In the present study, ten different oral bacterial species were mixed and grown in Brain Heart Infusion Yeast Extract with 1% sucrose for 24 hours. Biofilm was harvested and processed for DNA extraction and q-PCR amplification with the species-specific primers. By comparing the q-PCR data of each species in the unknown culture with reference cultures, in which the cell number of each species was determined by colony forming units on agar plate, the cell number of that strain in the unknown mixed culture was calculated. This technique is reliable to count microorganism numbers that are less than 100,000 fold different from other species within the same culture. Theoretically, it can be used in detecting a species in a mixed culture of over 200 species. Currently PCR-MSCC is one of the most economic methods for quantifying single species cell numbers, especially for the low abundant species, in a multiple artificial mixed culture in vitro.

  2. Multiple Model Approaches to Modelling and Control,

    DEFF Research Database (Denmark)

    on the ease with which prior knowledge can be incorporated. It is interesting to note that researchers in Control Theory, Neural Networks,Statistics, Artificial Intelligence and Fuzzy Logic have more or less independently developed very similar modelling methods, calling them Local ModelNetworks, Operating...... of introduction of existing knowledge, as well as the ease of model interpretation. This book attempts to outlinemuch of the common ground between the various approaches, encouraging the transfer of ideas.Recent progress in algorithms and analysis is presented, with constructive algorithms for automated model...

  3. Development of a recombinant antibody towards PAPP-A for immunohistochemical use in multiple animal species

    DEFF Research Database (Denmark)

    Mikkelsen, Jakob H; Steffensen, Lasse B; Oxvig, Claus

    2014-01-01

    normal physiology and under different pathological conditions. However, antibodies for the detection of PAPP-A in non-human tissues have been lacking, although needed for use with several animal models which are currently being developed. To develop a monoclonal antibody suitable...... for the immunohistochemical detection of PAPP-A, we therefore selected a phage-derived scFv antibody, PAC1, specifically recognizing an epitope of PAPP-A, which is highly conserved between multiple animal species. We first converted this antibody into bivalent IgG, and verified its ability to recognize PAPP-A in sections...

  4. Mapping vulnerability of multiple aquifers using multiple models and fuzzy logic to objectively derive model structures.

    Science.gov (United States)

    Nadiri, Ata Allah; Sedghi, Zahra; Khatibi, Rahman; Gharekhani, Maryam

    2017-09-01

    Driven by contamination risks, mapping Vulnerability Indices (VI) of multiple aquifers (both unconfined and confined) is investigated by integrating the basic DRASTIC framework with multiple models overarched by Artificial Neural Networks (ANN). The DRASTIC framework is a proactive tool to assess VI values using the data from the hydrosphere, lithosphere and anthroposphere. However, a research case arises for the application of multiple models on the ground of poor determination coefficients between the VI values and non-point anthropogenic contaminants. The paper formulates SCFL models, which are derived from the multiple model philosophy of Supervised Committee (SC) machines and Fuzzy Logic (FL) and hence SCFL as their integration. The Fuzzy Logic-based (FL) models include: Sugeno Fuzzy Logic (SFL), Mamdani Fuzzy Logic (MFL), Larsen Fuzzy Logic (LFL) models. The basic DRASTIC framework uses prescribed rating and weighting values based on expert judgment but the four FL-based models (SFL, MFL, LFL and SCFL) derive their values as per internal strategy within these models. The paper reports that FL and multiple models improve considerably on the correlation between the modeled vulnerability indices and observed nitrate-N values and as such it provides evidence that the SCFL multiple models can be an alternative to the basic framework even for multiple aquifers. The study area with multiple aquifers is in Varzeqan plain, East Azerbaijan, northwest Iran. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Finessing atlas data for species distribution models

    NARCIS (Netherlands)

    Niamir, A.; Skidmore, A.K.; Toxopeus, A.G.; Munoz, A.R.; Real, R.

    2011-01-01

    Aim The spatial resolution of species atlases and therefore resulting model predictions are often too coarse for local applications. Collecting distribution data at a finer resolution for large numbers of species requires a comprehensive sampling effort, making it impractical and expensive. This stu

  6. Finessing atlas data for species distribution models

    NARCIS (Netherlands)

    Niamir, A.; Skidmore, A.K.; Toxopeus, A.G.; Munoz, A.R.; Real, R.

    2011-01-01

    Aim The spatial resolution of species atlases and therefore resulting model predictions are often too coarse for local applications. Collecting distribution data at a finer resolution for large numbers of species requires a comprehensive sampling effort, making it impractical and expensive. This

  7. Species ages in neutral biodiversity models.

    Science.gov (United States)

    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. Dynamic species distribution models from categorical survey data.

    Science.gov (United States)

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

    2013-11-01

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

  9. Informing species conservation at multiple scales using data collected for marine mammal stock assessments.

    Directory of Open Access Journals (Sweden)

    Alana Grech

    Full Text Available BACKGROUND: Conservation planning and the design of marine protected areas (MPAs requires spatially explicit information on the distribution of ecological features. Most species of marine mammals range over large areas and across multiple planning regions. The spatial distributions of marine mammals are difficult to predict using habitat modelling at ecological scales because of insufficient understanding of their habitat needs, however, relevant information may be available from surveys conducted to inform mandatory stock assessments. METHODOLOGY AND RESULTS: We use a 20-year time series of systematic aerial surveys of dugong (Dugong dugong abundance to create spatially-explicit models of dugong distribution and relative density at the scale of the coastal waters of northeast Australia (∼136,000 km(2. We interpolated the corrected data at the scale of 2 km * 2 km planning units using geostatistics. Planning units were classified as low, medium, high and very high dugong density on the basis of the relative density of dugongs estimated from the models and a frequency analysis. Torres Strait was identified as the most significant dugong habitat in northeast Australia and the most globally significant habitat known for any member of the Order Sirenia. The models are used by local, State and Federal agencies to inform management decisions related to the Indigenous harvest of dugongs, gill-net fisheries and Australia's National Representative System of Marine Protected Areas. CONCLUSION/SIGNIFICANCE: In this paper we demonstrate that spatially-explicit population models add value to data collected for stock assessments, provide a robust alternative to predictive habitat distribution models, and inform species conservation at multiple scales.

  10. Multiplicative earthquake likelihood models incorporating strain rates

    Science.gov (United States)

    Rhoades, D. A.; Christophersen, A.; Gerstenberger, M. C.

    2017-01-01

    SUMMARYWe examine the potential for strain-rate variables to improve long-term earthquake likelihood models. We derive a set of multiplicative hybrid earthquake likelihood models in which cell rates in a spatially uniform baseline model are scaled using combinations of covariates derived from earthquake catalogue data, fault data, and strain-rates for the New Zealand region. Three components of the strain rate estimated from GPS data over the period 1991-2011 are considered: the shear, rotational and dilatational strain rates. The hybrid model parameters are optimised for earthquakes of M 5 and greater over the period 1987-2006 and tested on earthquakes from the period 2012-2015, which is independent of the strain rate estimates. The shear strain rate is overall the most informative individual covariate, as indicated by Molchan error diagrams as well as multiplicative modelling. Most models including strain rates are significantly more informative than the best models excluding strain rates in both the fitting and testing period. A hybrid that combines the shear and dilatational strain rates with a smoothed seismicity covariate is the most informative model in the fitting period, and a simpler model without the dilatational strain rate is the most informative in the testing period. These results have implications for probabilistic seismic hazard analysis and can be used to improve the background model component of medium-term and short-term earthquake forecasting models.

  11. Discrete choice models with multiplicative error terms

    DEFF Research Database (Denmark)

    Fosgerau, Mogens; Bierlaire, Michel

    2009-01-01

    differences. We develop some properties of this type of model and show that in several cases the change from an additive to a multiplicative formulation, maintaining a specification of V, may lead to a large improvement in fit, sometimes larger than that gained from introducing random coefficients in V....

  12. A Multiple Model Approach to Modeling Based on LPF Algorithm

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Input-output data fitting methods are often used for unknown-structure nonlinear system modeling. Based on model-on-demand tactics, a multiple model approach to modeling for nonlinear systems is presented. The basic idea is to find out, from vast historical system input-output data sets, some data sets matching with the current working point, then to develop a local model using Local Polynomial Fitting (LPF) algorithm. With the change of working points, multiple local models are built, which realize the exact modeling for the global system. By comparing to other methods, the simulation results show good performance for its simple, effective and reliable estimation.``

  13. A Single Species Model with Impulsive Diffusion

    Institute of Scientific and Technical Information of China (English)

    Jing Hui; Lan-sun Chen

    2005-01-01

    In most models of population dynamics, diffusion between patches is assumed to be continuous or discrete, but in practice many species diffuse only during a single period. In this paper we propose a single species model with impulsive diffusion between two patches, which provides a more natural description of population dynamics. By using the discrete dynamical system generated by a monotone, concave map for the population,we prove that the map alwayshas a globally stable positive fixed point. This means that a single species system with impulsive diffusion always has a globally stable positive periodic solution. This result is further substantiated by numerical simulation. Under impulsive diffusion the single species survives in the two patches.

  14. Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

    Science.gov (United States)

    Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

    2014-04-01

    Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

  15. Multiple models adaptive feedforward decoupling controller

    Institute of Scientific and Technical Information of China (English)

    Wang Xin; Li Shaoyuan; Wang Zhongjie

    2005-01-01

    When the parameters of the system change abruptly, a new multivariable adaptive feedforward decoupling controller using multiple models is presented to improve the transient response. The system models are composed of multiple fixed models, one free-running adaptive model and one re-initialized adaptive model. The fixed models are used to provide initial control to the process. The re-initialized adaptive model can be reinitialized as the selected model to improve the adaptation speed. The free-running adaptive controller is added to guarantee the overall system stability. At each instant, the best system model is selected according to the switching index and the corresponding controller is designed. During the controller design, the interaction is viewed as the measurable disturbance and eliminated by the choice of the weighting polynomial matrix. It not only eliminates the steady-state error but also decouples the system dynamically. The global convergence is obtained and several simulation examples are presented to illustrate the effectiveness of the proposed controller.

  16. Multiple dispersal vectors drive range expansion in an invasive marine species.

    Science.gov (United States)

    Richardson, Mark F; Sherman, Craig D H; Lee, Randall S; Bott, Nathan J; Hirst, Alastair J

    2016-10-01

    The establishment and subsequent spread of invasive species is widely recognized as one of the most threatening processes contributing to global biodiversity loss. This is especially true for marine and estuarine ecosystems, which have experienced significant increases in the number of invasive species with the increase in global maritime trade. Understanding the rate and mechanisms of range expansion is therefore of significant interest to ecologists and conservation managers alike. Using a combination of population genetic surveys, environmental DNA (eDNA) plankton sampling and hydrodynamic modelling, we examined the patterns of introduction of the predatory Northern Pacific seastar (Asterias amurensis) and pathways of secondary spread within southeast Australia. Genetic surveys across the invasive range reveal some genetic divergence between the two main invasive regions and no evidence of ongoing gene flow, a pattern that is consistent with the establishment of the second invasive region via a human-mediated translocation event. In contrast, hydrodynamic modelling combined with eDNA plankton sampling demonstrated that the establishment of range expansion populations within a region is consistent with natural larval dispersal and recruitment. Our results suggest that both anthropogenic and natural dispersal vectors have played an important role in the range expansion of this species in Australia. The multiple modes of spread combined with high levels of fecundity and a long larval duration in A. amurensis suggests it is likely to continue its range expansion and significantly impact Australian marine ecosystems. © 2016 John Wiley & Sons Ltd.

  17. Spontaneous motor entrainment to music in multiple vocal mimicking species.

    Science.gov (United States)

    Schachner, Adena; Brady, Timothy F; Pepperberg, Irene M; Hauser, Marc D

    2009-05-26

    The human capacity for music consists of certain core phenomena, including the tendency to entrain, or align movement, to an external auditory pulse [1-3]. This ability, fundamental both for music production and for coordinated dance, has been repeatedly highlighted as uniquely human [4-11]. However, it has recently been hypothesized that entrainment evolved as a by-product of vocal mimicry, generating the strong prediction that only vocal mimicking animals may be able to entrain [12, 13]. Here we provide comparative data demonstrating the existence of two proficient vocal mimicking nonhuman animals (parrots) that entrain to music, spontaneously producing synchronized movements resembling human dance. We also provide an extensive comparative data set from a global video database systematically analyzed for evidence of entrainment in hundreds of species both capable and incapable of vocal mimicry. Despite the higher representation of vocal nonmimics in the database and comparable exposure of mimics and nonmimics to humans and music, only vocal mimics showed evidence of entrainment. We conclude that entrainment is not unique to humans and that the distribution of entrainment across species supports the hypothesis that entrainment evolved as a by-product of selection for vocal mimicry.

  18. Realistic face modeling based on multiple deformations

    Institute of Scientific and Technical Information of China (English)

    GONG Xun; WANG Guo-yin

    2007-01-01

    On the basis of the assumption that the human face belongs to a linear class, a multiple-deformation model is proposed to recover face shape from a few points on a single 2D image. Compared to the conventional methods, this study has the following advantages. First, the proposed modified 3D sparse deforming model is a noniterative approach that can compute global translation efficiently and accurately. Subsequently, the overfitting problem can be alleviated based on the proposed multiple deformation model. Finally, by keeping the main features, the texture generated is realistic. The comparison results show that this novel method outperforms the existing methods by using ground truth data and that realistic 3D faces can be recovered efficiently from a single photograph.

  19. Detection of multiple Bartonella species in digestive and reproductive tissues of fleas collected from sympatric mammals.

    Science.gov (United States)

    Brinkerhoff, R Jory; Kabeya, Hidenori; Inoue, Kai; Bai, Ying; Maruyama, Soichi

    2010-07-01

    At least 12 species in the genus Bartonella are zoonotic pathogens that may be transmitted among mammalian hosts by fleas or other arthropods. Apparent host specificity by some Bartonella species to mammalian hosts has been observed, and the detection of multiple Bartonella species in mammalian fleas suggests that fleas take bloodmeals from a variety of host species. However, many flea species are observed to parasitize a narrow host range. Therefore, we suspect that fleas may acquire Bartonella by a mechanism other than ingesting infectious blood. We found that detection of multiple Bartonella genotypes and species is apparently common in fleas and that the majority of fleas tested (5/9) carried Bartonella species atypical of their hosts. We also detected Bartonella DNA in flea reproductive tissues, suggesting that vertical transmission of this organism in vectors is possible, potentially leading to the accumulation of Bartonella diversity over time within fleas.

  20. Model for Dynamic Multiple of CPPI Strategy

    Directory of Open Access Journals (Sweden)

    Guangyuan Xing

    2014-01-01

    Full Text Available Focusing on the parameter “Multiple” of CPPI strategy, this study proposes a dynamic setting model of multiple for gap risk management purpose. First, CPPI gap risk is measured as the probability that the value loss of active asset exceeds its allowed maximum drop determined by a given multiple setting. Moreover, according to the statistical estimation using SV-EVT approach, a dynamic choice of multiple is detailed as a function of time-varying asset volatility, expected loss, and the possibility of occurrence of extreme events in the active asset returns illustrated empirically on Shanghai composite index data. This study not only enriches the literature of dynamic proportion portfolio insurance, but also provides a practical reference for CPPI investors to choose a moderate risky exposure achieving gap risk management, which promotes CPPI’s application in emerging capital market.

  1. Fungal species and multiple mycotoxin contamination of cultivated forage crops

    Directory of Open Access Journals (Sweden)

    Galina Kononenko

    2015-12-01

    Full Text Available The quality of grass samples used for animal feed by combining mycotoxin measures and mycological determination of mycobiota were explored. The samples of the plant material were collected in 2014 in two stages: before the first mowing (May–June and before the second one (July–August from the fields of stock-farms located in northwestern part of the Russia. All samples were divided into three types: grasses, mixture of different grasses and clover, alfalfa mixed with timothy. The occurrence of aflatoxin B1, alternariol, citrinin, cyclopiazonic acid, deoxynivalenol, diacetoxyscirpenol, emodin, ergot alkaloids, fumonisins, mycophenolic acid, ochratoxin A, PR-toxin, roridin A, sterigmatocystin, T-2 toxin, and zearalenone were determined using ELISA. The multiple fungal and mycotoxin contaminations are already formed in plant tissues by the moment of first mowing. The complexes of mycotoxins including up to 14–16 components and the combined character of plant contamination quite correspond to the taxonomic variety of mycobiota.

  2. Species Tree Inference Using a Mixture Model.

    Science.gov (United States)

    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

  3. Benchmarking novel approaches for modelling species range dynamics.

    Science.gov (United States)

    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

  4. In vivo models of multiple myeloma (MM).

    Science.gov (United States)

    Sanchez, Eric; Chen, Haiming; Berenson, James R

    2014-06-01

    The development of the plasma cell tumor (PCT) model was the first widely accepted in vivo model of multiple myeloma (MM). Potter and colleagues used this chemically induced PCT model to study the pathophysiology of malignant plasma cells and also used it to screen anti-MM agents. Two decades later the C57BL/KaLwRij mouse strain was found to spontaneously develop MM. Testing of pamidronate using this endogenously arising MM model revealed significant reductions in MM-associated bone disease, which was subsequently confirmed in human trials in MM patients. Transgenic models have also been developed in which the MM is localized in the bone marrow causing lytic bone lesions. Experiments in a transgenic model showed that a new oral proteasome inhibitor was effective at reducing MM burden. A clinical trial later confirmed this observation and validated the model. The xenograft model has been used to grow human MM in immunocompromised mice. The xenograft models of MM have been very useful in optimizing drug schedules and doses, which have helped in the treatments given to MM patients. However, in vivo models have been criticized for having a low clinical predictive power of new chemical entities (NCEs). Despite this, the knowledge gained from in vivo models of MM has without a doubt benefited MM patients.

  5. Detection of Multiple Pathogenic Species in Saliva Is Associated with Periodontal Infection in Adults▿

    OpenAIRE

    2008-01-01

    We investigated whether certain bacterial species and their combinations in saliva can be used as markers for periodontitis. In 1,198 subjects, the detection of multiple species, rather than the presence of a certain pathogen, in saliva was associated with periodontitis as determined by the number of teeth with deepened periodontal pockets.

  6. Predicting multiple ecotoxicological profiles in agrochemical fungicides: a multi-species chemoinformatic approach.

    Science.gov (United States)

    Speck-Planche, Alejandro; Kleandrova, Valeria V; Luan, Feng; Cordeiro, M Natália D S

    2012-06-01

    Agriculture is needed to deal with crop losses caused by biotic stresses like pests. The use of pesticides has played a vital role, contributing to improve crop production and harvest productivity, providing a better crop quality and supply, and consequently contributing with the improvement of the human health. An important group of these pesticides is fungicides. However, the use of these agrochemical fungicides is an important source of contamination, damaging the ecosystems. Several studies have been realized for the assessment of the toxicity in agrochemical fungicides, but the principal limitation is the use of structurally related compounds against usually one indicator species. In order to overcome this problem, we explore the quantitative structure-toxicity relationships (QSTR) in agrochemical fungicides. Here, we developed the first multi-species (ms) chemoinformatic approach for the prediction multiple ecotoxicological profiles of fungicides against 20 indicators species and their classifications in toxic or nontoxic. The ms-QSTR discriminant model was based on substructural descriptors and a heterogeneous database of compounds. The percentages of correct classification were higher than 90% for both, training and prediction series. Also, substructural alerts responsible for the toxicity/no toxicity in fungicides respect all ecotoxicological profiles, were extracted and analyzed.

  7. True lemurs…true species - species delimitation using multiple data sources in the brown lemur complex

    OpenAIRE

    2013-01-01

    Background Species are the fundamental units in evolutionary biology. However, defining them as evolutionary independent lineages requires integration of several independent sources of information in order to develop robust hypotheses for taxonomic classification. Here, we exemplarily propose an integrative framework for species delimitation in the “brown lemur complex” (BLC) of Madagascar, which consists of seven allopatric populations of the genus Eulemur (Primates: Lemuridae), which were s...

  8. Optimising the application of multiple-capture traps for invasive species management using spatial simulation.

    Science.gov (United States)

    Warburton, Bruce; Gormley, Andrew M

    2015-01-01

    Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums (Trichosurus vulpecula), stoats (Mustela ermine), and ship rats (Rattus rattus) are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities (as is typical of orchestrated pest management programmes) it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha), 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several single

  9. Optimising the application of multiple-capture traps for invasive species management using spatial simulation.

    Directory of Open Access Journals (Sweden)

    Bruce Warburton

    Full Text Available Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums (Trichosurus vulpecula, stoats (Mustela ermine, and ship rats (Rattus rattus are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities (as is typical of orchestrated pest management programmes it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha, 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several

  10. Simplifying biochemical models with intermediate species

    DEFF Research Database (Denmark)

    Feliu, Elisenda; Wiuf, Carsten

    2013-01-01

    canonical model that characterizes crucial dynamical properties, such as mono- and multistationarity and stability of steady states, of all models in the class. We show that if the core model does not have conservation laws, then the introduction of intermediates does not change the steady...... techniques, we study systematically the effects of intermediate, or transient, species in biochemical systems and provide a simple, yet rigorous mathematical classification of all models obtained from a core model by including intermediates. Main examples include enzymatic and post-translational modification...... systems, where intermediates often are considered insignificant and neglected in a model, or they are not included because we are unaware of their existence. All possible models obtained from the core model are classified into a finite number of classes. Each class is defined by a mathematically simple...

  11. Variable bit rate video traffic modeling by multiplicative multifractal model

    Institute of Scientific and Technical Information of China (English)

    Huang Xiaodong; Zhou Yuanhua; Zhang Rongfu

    2006-01-01

    Multiplicative multifractal process could well model video traffic. The multiplier distributions in the multiplicative multifractal model for video traffic are investigated and it is found that Gaussian is not suitable for describing the multipliers on the small time scales. A new statistical distribution-symmetric Pareto distribution is introduced. It is applied instead of Gaussian for the multipliers on those scales. Based on that, the algorithm is updated so that symmetric pareto distribution and Gaussian distribution are used to model video traffic but on different time scales. The simulation results demonstrate that the algorithm could model video traffic more accurately.

  12. Application of Multiple Evaluation Models in Brazil

    Directory of Open Access Journals (Sweden)

    Rafael Victal Saliba

    2008-07-01

    Full Text Available Based on two different samples, this article tests the performance of a number of Value Drivers commonly used for evaluating companies by finance practitioners, through simple regression models of cross-section type which estimate the parameters associated to each Value Driver, denominated Market Multiples. We are able to diagnose the behavior of several multiples in the period 1994-2004, with an outlook also on the particularities of the economic activities performed by the sample companies (and their impacts on the performance through a subsequent analysis with segregation of companies in the sample by sectors. Extrapolating simple multiples evaluation standards from analysts of the main financial institutions in Brazil, we find that adjusting the ratio formulation to allow for an intercept does not provide satisfactory results in terms of pricing errors reduction. Results found, in spite of evidencing certain relative and absolute superiority among the multiples, may not be generically representative, given samples limitation.

  13. Incremental activity modeling in multiple disjoint cameras.

    Science.gov (United States)

    Loy, Chen Change; Xiang, Tao; Gong, Shaogang

    2012-09-01

    Activity modeling and unusual event detection in a network of cameras is challenging, particularly when the camera views are not overlapped. We show that it is possible to detect unusual events in multiple disjoint cameras as context-incoherent patterns through incremental learning of time delayed dependencies between distributed local activities observed within and across camera views. Specifically, we model multicamera activities using a Time Delayed Probabilistic Graphical Model (TD-PGM) with different nodes representing activities in different decomposed regions from different views and the directed links between nodes encoding their time delayed dependencies. To deal with visual context changes, we formulate a novel incremental learning method for modeling time delayed dependencies that change over time. We validate the effectiveness of the proposed approach using a synthetic data set and videos captured from a camera network installed at a busy underground station.

  14. Applications of species distribution modeling to paleobiology

    DEFF Research Database (Denmark)

    Svenning, J.-C.; Fløjgaard, Camilla; A. Marske, Katharine

    2011-01-01

    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...... 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...

  15. BLT-MS (Breach, Leach, and Transport -- Multiple Species) data input guide. A computer model for simulating release of contaminants from a subsurface low-level waste disposal facility

    Energy Technology Data Exchange (ETDEWEB)

    Sullivan, T.M.; Kinsey, R.R.; Aronson, A.; Divadeenam, M. [Brookhaven National Lab., Upton, NY (United States); MacKinnon, R.J. [Brookhaven National Lab., Upton, NY (United States)]|[Ecodynamics Research Associates, Inc., Albuquerque, NM (United States)

    1996-11-01

    The BLT-MS computer code has been developed, implemented, and tested. BLT-MS is a two-dimensional finite element computer code capable of simulating the time evolution of concentration resulting from the time-dependent release and transport of aqueous phase species in a subsurface soil system. BLT-MS contains models to simulate the processes (water flow, container degradation, waste form performance, transport, and radioactive production and decay) most relevant to estimating the release and transport of contaminants from a subsurface disposal system. Water flow is simulated through tabular input or auxiliary files. Container degradation considers localized failure due to pitting corrosion and general failure due to uniform surface degradation processes. Waste form performance considers release to be limited by one of four mechanisms: rinse with partitioning, diffusion, uniform surface degradation, or solubility. Radioactive production and decay in the waste form are simulated. Transport considers the processes of advection, dispersion, diffusion, radioactive production and decay, reversible linear sorption, and sources (waste forms releases). To improve the usefulness of BLT-MS a preprocessor, BLTMSIN, which assists in the creation of input files, and a post-processor, BLTPLOT, which provides a visual display of the data have been developed. This document reviews the models implemented in BLT-MS and serves as a guide to creating input files for BLT-MS.

  16. Does multiple hosts mean multiple parasites? Population genetic structure of Schistosoma japonicum between definitive host species.

    Science.gov (United States)

    Wang, T P; Shrivastava, J; Johansen, M V; Zhang, S Q; Wang, F F; Webster, J P

    2006-10-01

    Multi-host parasites, those capable of infecting more than one species of host, are responsible for the majority of all zoonotic, emerging or persistent human and animal diseases and are considered one of the major challenges for the biomedical sciences in the 21st century. We characterized the population structure of the multi-host parasite Schistosoma japonicum in relation to its definitive host species by genotyping miracidia collected from humans and domestic animals across five villages around the Yangtze River in Anhui Province, mainland China, using microsatellite markers. High levels of polymorphisms were observed and two main genetic clusters were identified which separated water buffalo, cattle and humans from goats, pigs, dogs and cats. We thereby believe that we present the first evidence of definitive host-based genetic variation in Schistosoma japonicum which has important epidemiological, evolutionary, medical and veterinary implications.

  17. Invasive species information networks: Collaboration at multiple scales for prevention, early detection, and rapid response to invasive alien species

    Science.gov (United States)

    Simpson, Annie; Jarnevich, Catherine S.; Madsen, John; Westbrooks, Randy G.; Fournier, Christine; Mehrhoff, Les; Browne, Michael; Graham, Jim; Sellers, Elizabeth A.

    2009-01-01

    Accurate analysis of present distributions and effective modeling of future distributions of invasive alien species (IAS) are both highly dependent on the availability and accessibility of occurrence data and natural history information about the species. Invasive alien species monitoring and detection networks (such as the Invasive Plant Atlas of New England and the Invasive Plant Atlas of the MidSouth) generate occurrence data at local and regional levels within the United States, which are shared through the US National Institute of Invasive Species Science. The Inter-American Biodiversity Information Network's Invasives Information Network (I3N), facilitates cooperation on sharing invasive species occurrence data throughout the Western Hemisphere. The I3N and other national and regional networks expose their data globally via the Global Invasive Species Information Network (GISIN). International and interdisciplinary cooperation on data sharing strengthens cooperation on strategies and responses to invasions. However, limitations to effective collaboration among invasive species networks leading to successful early detection and rapid response to invasive species include: lack of interoperability; data accessibility; funding; and technical expertise. This paper proposes various solutions to these obstacles at different geographic levels and briefly describes success stories from the invasive species information networks mentioned above. Using biological informatics to facilitate global information sharing is especially critical in invasive species science, as research has shown that one of the best indicators of the invasiveness of a species is whether it has been invasive elsewhere. Data must also be shared across disciplines because natural history information (e.g. diet, predators, habitat requirements, etc.) about a species in its native range is vital for effective prevention, detection, and rapid response to an invasion. Finally, it has been our

  18. Asteroid Models from Multiple Data Sources

    CERN Document Server

    Durech, J; Delbo, M; Kaasalainen, M; Viikinkoski, M

    2015-01-01

    In the past decade, hundreds of asteroid shape models have been derived using the lightcurve inversion method. At the same time, a new framework of 3-D shape modeling based on the combined analysis of widely different data sources such as optical lightcurves, disk-resolved images, stellar occultation timings, mid-infrared thermal radiometry, optical interferometry, and radar delay-Doppler data, has been developed. This multi-data approach allows the determination of most of the physical and surface properties of asteroids in a single, coherent inversion, with spectacular results. We review the main results of asteroid lightcurve inversion and also recent advances in multi-data modeling. We show that models based on remote sensing data were confirmed by spacecraft encounters with asteroids, and we discuss how the multiplication of highly detailed 3-D models will help to refine our general knowledge of the asteroid population. The physical and surface properties of asteroids, i.e., their spin, 3-D shape, densit...

  19. Mixtures of multiplicative cascade models in geochemistry

    Directory of Open Access Journals (Sweden)

    F. P. Agterberg

    2007-05-01

    Full Text Available Multifractal modeling of geochemical map data can help to explain the nature of frequency distributions of element concentration values for small rock samples and their spatial covariance structure. Useful frequency distribution models are the lognormal and Pareto distributions which plot as straight lines on logarithmic probability and log-log paper, respectively. The model of de Wijs is a simple multiplicative cascade resulting in discrete logbinomial distribution that closely approximates the lognormal. In this model, smaller blocks resulting from dividing larger blocks into parts have concentration values with constant ratios that are scale-independent. The approach can be modified by adopting random variables for these ratios. Other modifications include a single cascade model with ratio parameters that depend on magnitude of concentration value. The Turcotte model, which is another variant of the model of de Wijs, results in a Pareto distribution. Often a single straight line on logarithmic probability or log-log paper does not provide a good fit to observed data and two or more distributions should be fitted. For example, geochemical background and anomalies (extremely high values have separate frequency distributions for concentration values and for local singularity coefficients. Mixtures of distributions can be simulated by adding the results of separate cascade models. Regardless of properties of background, an unbiased estimate can be obtained of the parameter of the Pareto distribution characterizing anomalies in the upper tail of the element concentration frequency distribution or lower tail of the local singularity distribution. Computer simulation experiments and practical examples are used to illustrate the approach.

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

    Science.gov (United States)

    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.

  1. Instability-Enhanced Collisional Friction Determines the Bohm Criterion in Multiple-Ion-Species Plasmas

    Science.gov (United States)

    Baalrud, S. D.; Hegna, C. C.; Callen, J. D.

    2009-11-01

    Ion-ion streaming instabilities are excited in the presheath region of plasmas with multiple ion species if the ions are much colder than the electrons. Streaming instabilities onset when the relative fluid flow between ion species exceeds a critical speed, δVc, of order the ion thermal speeds. Using a generalized Lenard-Balescu theory that accounts for instability-enhanced collective responses [1], one is able to show the instabilities rapidly enhance the collisional friction between ion species far beyond the contribution from Coulomb collisions alone. This strong frictional force determines the relative fluid speed between species. When this condition is combined with the Bohm criterion generalized for multiple ion species, the fluid speed of each ion species is determined at the sheath edge. For each species, this speed differs from the common ``system'' sound speed by a factor that depends on the species concentrations, masses and δVc.[4pt] [1] S.D. Baalrud, J.D. Callen, and C.C. Hegna, Phys. Plasmas 15, 092111 (2008).

  2. The common marmoset as an indispensable animal model for immunotherapy development in multiple sclerosis

    NARCIS (Netherlands)

    Kap, Yolanda S.; Jagessar, S. Anwar; Dunham, Jordon; 't Hart, Bert A.

    2016-01-01

    New drugs often fail in the translation from the rodent experimental autoimmune encephalomyelitis (EAE) model to human multiple sclerosis (MS). Here, we present the marmoset EAE model as an indispensable model for translational research into MS. The genetic heterogeneity of this species and lifelong

  3. The Species versus Subspecies Conundrum: Quantitative Delimitation from Integrating Multiple Data Types within a Single Bayesian Approach in Hercules Beetles.

    Science.gov (United States)

    Huang, Jen-Pan; Knowles, L Lacey

    2016-07-01

    With the recent attention and focus on quantitative methods for species delimitation, an overlooked but equally important issue regards what has actually been delimited. This study investigates the apparent arbitrariness of some taxonomic distinctions, and in particular how species and subspecies are assigned. Specifically, we use a recently developed Bayesian model-based approach to show that in the Hercules beetles (genus Dynastes) there is no statistical difference in the probability that putative taxa represent different species, irrespective of whether they were given species or subspecies designations. By considering multiple data types, as opposed to relying exclusively on genetic data alone, we also show that both previously recognized species and subspecies represent a variety of points along the speciation spectrum (i.e., previously recognized species are not systematically further along the continuum than subspecies). For example, based on evolutionary models of divergence, some taxa are statistically distinguishable on more than one axis of differentiation (e.g., along both phenotypic and genetic dimensions), whereas other taxa can only be delimited statistically from a single data type. Because both phenotypic and genetic data are analyzed in a common Bayesian framework, our study provides a framework for investigating whether disagreements in species boundaries among data types reflect (i) actual discordance with the actual history of lineage splitting, or instead (ii) differences among data types in the amount of time required for differentiation to become apparent among the delimited taxa. We discuss what the answers to these questions imply about what characters are used to delimit species, as well as the diverse processes involved in the origin and maintenance of species boundaries. With this in mind, we then reflect more generally on how quantitative methods for species delimitation are used to assign taxonomic status. © The Author(s) 2015

  4. Molecular evidence for high frequency of multiple paternity in a freshwater shrimp species Caridina ensifera.

    Directory of Open Access Journals (Sweden)

    Gen Hua Yue

    Full Text Available BACKGROUND: Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers. CONCLUSIONS/SIGNIFICANCE: Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species.

  5. Multiple Temperature Model for Near Continuum Flows

    Energy Technology Data Exchange (ETDEWEB)

    XU, Kun; Liu, Hongwei [Hong Kong University of Science and Technology, Kowloon (Hong Kong); Jiang, Jianzheng [Chinese Academy ofSciences, Beijing (China)

    2007-09-15

    In the near continuum flow regime, the flow may have different translational temperatures in different directions. It is well known that for increasingly rarefied flow fields, the predictions from continuum formulation, such as the Navier-Stokes equations, lose accuracy. These inaccuracies may be partially due to the single temperature assumption in the Navier-Stokes equations. Here, based on the gas-kinetic Bhatnagar-Gross-Krook (BGK) equation, a multitranslational temperature model is proposed and used in the flow calculations. In order to fix all three translational temperatures, two constraints are additionally proposed to model the energy exchange in different directions. Based on the multiple temperature assumption, the Navier-Stokes relation between the stress and strain is replaced by the temperature relaxation term, and the Navier-Stokes assumption is recovered only in the limiting case when the flow is close to the equilibrium with the same temperature in different directions. In order to validate the current model, both the Couette and Poiseuille flows are studied in the transition flow regime.

  6. Compound leaf development in model plant species.

    Science.gov (United States)

    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).

  7. Genetic components to caste allocation in a multiple-queen ant species

    NARCIS (Netherlands)

    Libbrecht, Romain; Schwander, Tanja; Keller, Laurent

    2011-01-01

    Reproductive division of labor and the coexistence of distinct castes are hallmarks of insect societies. In social insect species with multiple queens per colony, the fitness of nestmate queens directly depends on the process of caste allocation (i.e., the relative investment in queen, sterile

  8. Multiple Retrieval Models and Regression Models for Prior Art Search

    CERN Document Server

    Lopez, Patrice

    2009-01-01

    This paper presents the system called PATATRAS (PATent and Article Tracking, Retrieval and AnalysiS) realized for the IP track of CLEF 2009. Our approach presents three main characteristics: 1. The usage of multiple retrieval models (KL, Okapi) and term index definitions (lemma, phrase, concept) for the three languages considered in the present track (English, French, German) producing ten different sets of ranked results. 2. The merging of the different results based on multiple regression models using an additional validation set created from the patent collection. 3. The exploitation of patent metadata and of the citation structures for creating restricted initial working sets of patents and for producing a final re-ranking regression model. As we exploit specific metadata of the patent documents and the citation relations only at the creation of initial working sets and during the final post ranking step, our architecture remains generic and easy to extend.

  9. Multiple cryptic species in the blue-spotted maskray (Myliobatoidei: Dasyatidae: Neotrygon spp.): An update.

    Science.gov (United States)

    Borsa, Philippe; Shen, Kang-Ning; Arlyza, Irma S; Hoareau, Thierry B

    2016-01-01

    Previous investigations have uncovered divergent mitochondrial clades within the blue-spotted maskray, previously Neotrygon kuhlii (Müller and Henle). The hypothesis that the blue-spotted maskray may consist of a complex of multiple cryptic species has been proposed, and four species have been recently described or resurrected. To test the multiple cryptic species hypothesis, we investigated the phylogenetic relationships and coalescence patterns of mitochondrial sequences in a sample of 127 new individuals from the Indian Ocean and the Coral Triangle region, sequenced at both the CO1 and cytochrome b loci. The maximum-likelihood (ML) tree of concatenated CO1+cytochrome b gene sequences, rooted by the New Caledonian maskray N. trigonoides, yielded 9 strongly supported, main clades. Puillandre's ABGD algorithm detected gaps in nucleotide distance consistent with the ML phylogeny. The general mixed Yule-coalescent algorithm partitioned the dataset into putative species generally consistent with the ML phylogeny. Nuclear markers generally confirmed that distinct mitochondrial clades correspond to genetically isolated lineages. The nine main lineages identified by ML analysis were geographically distributed in a parapatric fashion, indicating reproductive isolation. The hypothesis of multiple cryptic species is thus validated.

  10. Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus

    Directory of Open Access Journals (Sweden)

    Rasoloarison Rodin M

    2009-02-01

    Full Text Available Abstract Background Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus and assess the status of the seven described species, based on phylogenetic and population genetic analysis of mtDNA (cytb + cox2 and three nuclear markers (adora3, fiba and vWF. Results This study identified three distinct evolutionary lineages within the genus Cheirogaleus. Population genetic cluster analyses revealed a further layer of population divergence with six distinct genotypic clusters. Conclusion Based on the general metapopulation lineage concept and multiple concordant data sets, we identify three exclusive groups of dwarf lemur populations that correspond to three of the seven named species: C. major, C. medius and C. crossleyi. These three species were found to be genealogically exclusive in both mtDNA and nDNA loci and are morphologically distinguishable. The molecular and morphometric data indicate that C. adipicaudatus and C. ravus are synonymous with C. medius and C. major, respectively. Cheirogaleus sibreei falls into the C. medius mtDNA clade, but in morphological analyses the membership is not clearly resolved. We do not have sufficient data to assess the status of C. minusculus. Although additional patterns of population differentiation are evident, there are no clear subdivisions that would warrant additional specific status. We propose that ecological and more geographic data should be collected to confirm these results.

  11. Native Australian species are effective in extracting multiple heavy metals from biosolids.

    Science.gov (United States)

    Mok, Hoi-Fei; Majumder, Ramaprasad; Laidlaw, W Scott; Gregory, David; Baker, Alan J M; Arndt, Stefan K

    2013-01-01

    Selecting native plant species with characteristics suitable for extraction of heavy metals may have multiple advantages over non-native plants. Six Australian perennial woody plant species and one willow were grown in a pot trial in heavy metal-contaminated biosolids and a potting mix. The plants were harvested after fourteen months and above-ground parts were analysed for heavy metal concentrations and total metal contents. All native species were capable of growing in biosolids and extracted heavy metals to varying degrees. No single species was able to accumulate heavy metals at particularly high levels and metal extraction depended upon the bioavailability of the metal in the substrate. Metal extraction efficiency was driven by biomass accumulation, with the species extracting the most metals also having the greatest biomass yield. The study demonstrated that Grevillea robusta, Acacia mearnsii, Eucalyptus polybractea, and E. cladocalyx have the greatest potential as phytoextractor species in the remediation of heavy metal-contaminated biosolids. Species survival and growth were the main determinants of metal extraction efficiency and these traits will be important for future screening of native species.

  12. Modeling and characterization of multiple coupled lines

    Science.gov (United States)

    Tripathi, Alok

    1999-10-01

    A configuration-oriented circuit model for multiple coupled lines in an inhomogeneous medium is developed and presented in this thesis. This circuit model consists of a network of uncoupled transmission lines and is readily modeled with simulation tools like LIBRA© and SPICE ©. It provides an equivalent circuit representation which is simple and topologically meaningful as compared to the model based on modal decomposition. The configuration-oriented model is derived by decomposing the immittance matrices associated with an n coupled line 2n-port system. Time- and frequency- domain simulations of typical coupled line multiports are included to exemplify the utility of the model. The model is useful for the simulation and design of general single and multilayer coupled line components, such as filters and couplers, and for the investigation of signal integrity issues including crosstalk in interconnects associated with high speed digital and mixed signal electronic modules and packages. It is shown that multiconductor lossless structures in an inhomogeneous medium can be characterized by multiport time-domain reflection (MR) measurements. A synthesis technique of an equivalent lossless (non-dispersive) uniform multiconductor n coupled lines (UMCL) 2n-port system from the measured discrete time-domain reflection response is presented. This procedure is based on the decomposition of the characteristic immittance matrices of the UMCL in terms of partial mode immittance matrices. The decomposition scheme leads to the discrete transition matrix function of a UMCL 2n-port system. This in turn establishes a relationship between the normal-mode parameters of the UMCL and the measured impulse reflection and transmission response. Equivalence between the synthesis procedure presented in this thesis and the solution of a special form of an algebraic Riccati matrix equation whose solution can lead to the normal-mode parameters and a real termination network is illustrated. In

  13. Novel evidence for within-species leaf economics spectrum at multiple spatial scales

    Directory of Open Access Journals (Sweden)

    Yu-Kun eHu

    2015-10-01

    Full Text Available Leaf economics spectrum (LES, characterizing covariation among a suite of leaf traits relevant to carbon and nutrient economics, has been examined largely among species but hardly within species. In addition, very little attempt has been made to examine whether the existence of LES depends on spatial scales. To address these questions, we quantified the variation and covariation of four leaf economic traits (specific leaf area, leaf dry matter content, leaf nitrogen and phosphorus contents in a cosmopolitan wetland species (Phragmites australis at three spatial (inter-regional, regional and site scales across most of the species range in China. The species expressed large intraspecific variation in the leaf economic traits at all of the three spatial scales. It also showed strong covariation among the four leaf economic traits across the species range. The coordination among leaf economic traits resulted in LES at all three scales and the environmental variables determining variation in leaf economic traits were different among the spatial scales. Our results provide novel evidence for within-species LES at multiple spatial scales, indicating that resource trade-off could also constrain intraspecific trait variation mainly driven by climatic and/or edaphic differences.

  14. Improving species distribution models: the value of data on abundance

    National Research Council Canada - National Science Library

    Howard, Christine; Stephens, Philip A; Pearce‐Higgins, James W; Gregory, Richard D; Willis, Stephen G; McPherson, Jana

    2014-01-01

    Species distribution models (SDMs) are important tools for forecasting the potential impacts of future environmental changes but debate remains over the most robust modelling approaches for making projections...

  15. Multiple start codons and phosphorylation result in discrete Rad52 protein species

    DEFF Research Database (Denmark)

    de Mayolo, A.A.; Lisby, M.; Erdeniz, N.

    2006-01-01

    protein species are due to promiscuous choice of start codons as well as post-translational modification. Specifically, Rad52 is phosphorylated both in a cell cycle-independent and in a cell cycle-dependent manner. Furthermore, phosphorylation is dependent on the presence of the Rad52 C terminus......The sequence of the Saccharomyces cerevisiae RAD52 gene contains five potential translation start sites and protein-blot analysis typically detects multiple Rad52 species with different electrophoretic mobilities. Here we define the gene products encoded by RAD52. We show that the multiple Rad52......, but not dependent on its interaction with Rad51. We also show that the Rad52 protein can be translated from the last three start sites and expression from any one of them is sufficient for spontaneous recombination and the repair of gamma-ray-induced double-strand breaks....

  16. Identification of Demand Models of Multiple Purchases

    OpenAIRE

    Itai Sher; Kyoo il Kim

    2012-01-01

    We study the nonparametric identification of distributions of utility functions in a multiple purchase setting with a finite number of consumers. Each utility function takes as arguments subsets or, alternatively, quantities of the multiple goods. We exploit mathematical insights from auction theory to generically identify the distribution of utility functions. We use price variation and aggregate data on the sales of each product, but not on individual level purchases or the total sales of b...

  17. Generative models: Human embryonic stem cells and multiple modeling relations.

    Science.gov (United States)

    Fagan, Melinda Bonnie

    2016-04-01

    Model organisms are at once scientific models and concrete living things. It is widely assumed by philosophers of science that (1) model organisms function much like other kinds of models, and (2) that insofar as their scientific role is distinctive, it is in virtue of representing a wide range of biological species and providing a basis for generalizations about those targets. This paper uses the case of human embryonic stem cells (hESC) to challenge both assumptions. I first argue that hESC can be considered model organisms, analogous to classic examples such as Escherichia coli and Drosophila melanogaster. I then discuss four contrasts between the epistemic role of hESC in practice, and the assumptions about model organisms noted above. These contrasts motivate an alternative view of model organisms as a network of systems related constructively and developmentally to one another. I conclude by relating this result to other accounts of model organisms in recent philosophy of science. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Blending synthetic pheromones of cerambycid beetles to develop trap lures that simultaneously attract multiple species.

    Science.gov (United States)

    Wong, Joseph C H; Mitchell, Robert F; Striman, Becca L; Millar, Jocelyn G; Hanks, Lawrence M

    2012-06-01

    We evaluated attraction of cerambycid beetle species to blends of known cerambycid pheromones to determine whether such blends could be used as effective trap lures for detecting and monitoring multiple species simultaneously. Pheromone-baited traps captured 1,358 cerambycid beetles of which 1,101 (81.1%) belonged to three species in the subfamily Cerambycinae: Neoclytus acuminatus (F.), Neoclytus mucronatus (F.), and Xylotrechus colonus (F.). Beetles of these species were significantly attracted to synthetic blends that contained their pheromone components (isomers of 3-hydroxy-2-hexanone, 2,3-hexanediol, or both), despite the presence of pheromone components of different species, including other isomers of 2,3-hexanediol, (E/Z)-6,10-dimethyl-5,9-undecadien-2-yl acetate, and citral. In some cases, attraction was partially inhibited by the pheromone components of heterospecific species, whereas for N. acuminatus, attraction was completely inhibited when blends contained (2R*,3S*)-hexanediol, the racemic mixture of diastereomers of its pheromone, (2S,3S)-hexanediol. Among the remaining beetles captured were three species in the subfamily Lamiinae: Astyleiopus variegatus (Haldeman), Graphisurus fasciatus (Degeer), and Lepturges angulatus (LeConte). All three lamiine species were previously known to be attracted to (E/Z)-6,10-dimethyl-5,9-undecadien-2-yl acetate and were captured in significant numbers by blends containing that compound. Our results suggest that different types of cerambycid pheromones can be combined to create effective multispecies lures for use in surveillance programs that target exotic cerambycid species.

  19. Identification and characterization of multiple emissive species in aggregated minor antenna complexes.

    Science.gov (United States)

    Wahadoszamen, Md; Belgio, Erica; Rahman, Md Ashiqur; Ara, Anjue Mane; Ruban, Alexander V; van Grondelle, Rienk

    2016-12-01

    Aggregation induced conformational change of light harvesting antenna complexes is believed to constitute one of the pathways through which photosynthetic organisms can safely dissipate the surplus of energy while exposed to saturating light. In this study, Stark fluorescence (SF) spectroscopy is applied to minor antenna complexes (CP24, CP26 and CP29) both in their light-harvesting and energy-dissipating states to trace and characterize different species generated upon energy dissipation through aggregation (in-vitro) induced conformational change. SF spectroscopy could identify three spectral species in the dissipative state of CP24, two in CP26 and only one in CP29. The comprehensive analysis of the SF spectra yielded different sets of molecular parameters for the multiple spectral species identified in CP24 or CP26, indicating the involvement of different pigments in their formation. Interestingly, a species giving emission around the 730nm spectral region is found to form in both CP24 and CP26 following transition to the energy dissipative state, but not in CP29. The SF analyses revealed that the far red species has exceptionally large charge transfer (CT) character in the excited state. Moreover, the far red species was found to be formed invariably in both Zeaxanthin (Z)- and Violaxathin (V)-enriched CP24 and CP26 antennas with identical CT character but with larger emission yield in Z-enriched ones. This suggests that the carotenoid Z is not directly involved but only confers an allosteric effect on the formation of the far red species. Similar far red species with remarkably large CT character were also observed in the dissipative state of the major light harvesting antenna (LHCII) of plants [Wahadoszamen et al. PCCP, 2012], the fucoxanthin-chlorophyll protein (FCP) of brown algae [Wahadoszamen et al. BBA, 2014] and cyanobacterial IsiA [Wahadoszamen et al. BBA, 2015], thus pointing to identical sites and pigments active in the formation of the far red

  20. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Effects of multiple heteroatom species and topographic defects on electrocatalytic and capacitive performances of graphene

    Science.gov (United States)

    Fan, Mengmeng; Huang, Yang; Yuan, Fanshu; Hao, Qingli; Yang, Jiazhi; Sun, Dongping

    2017-10-01

    N-doped graphene has been widely researched as metal-free electrocatalyst and electrode material of energy storage devices but the effect of heteroatom species and topographic defects on these applications was rarely reported. We successfully prepared dual (N, S) or ternary heteroatoms (N, S, P)-doped graphene by simple hydrothermal and then carbonization treatment. Compared to singly N doping, multiple heteroatom species dopant is beneficial to positively move onset potential, approach four electron catalytic pathway in oxygen reduction reaction (ORR) due to the synergistic effect. The emerging topographic defects induced by removing heteroatoms and oxygen at high temperature also act as efficient active sites for positively shifting onset potential. Meanwhile, the porous ternary heteroatoms-doped graphene possesses a good capacitive performance such as high gravimetric capacitance (196.4 Fg-1 at 1 Ag-1), high retained rate (92.7%), 98% retention over 2000 recycling. The excellent capacitive properties derive from large specific surface area (943.5 m2 g-1), mesoporous structure, particularly the important role of abundant dopants of multiple heteroatom species. Therefore, we demonstrated the effect of heteroatom species and topographic defects on electrocatalyzing ORR and capacitive performance.

  2. Seroepidemiological Prevalence of Multiple Species of Filoviruses in Fruit Bats (Eidolon helvum) Migrating in Africa.

    Science.gov (United States)

    Ogawa, Hirohito; Miyamoto, Hiroko; Nakayama, Eri; Yoshida, Reiko; Nakamura, Ichiro; Sawa, Hirofumi; Ishii, Akihiro; Thomas, Yuka; Nakagawa, Emiko; Matsuno, Keita; Kajihara, Masahiro; Maruyama, Junki; Nao, Naganori; Muramatsu, Mieko; Kuroda, Makoto; Simulundu, Edgar; Changula, Katendi; Hang'ombe, Bernard; Namangala, Boniface; Nambota, Andrew; Katampi, Jackson; Igarashi, Manabu; Ito, Kimihito; Feldmann, Heinz; Sugimoto, Chihiro; Moonga, Ladslav; Mweene, Aaron; Takada, Ayato

    2015-10-01

    Fruit bats are suspected to be a natural reservoir of filoviruses, including Ebola and Marburg viruses. Using an enzyme-linked immunosorbent assay based on the viral glycoprotein antigens, we detected filovirus-specific immunoglobulin G antibodies in 71 of 748 serum samples collected from migratory fruit bats (Eidolon helvum) in Zambia during 2006-2013. Although antibodies to African filoviruses (eg, Zaire ebolavirus) were most prevalent, some serum samples showed distinct specificity for Reston ebolavirus, which that has thus far been found only in Asia. Interestingly, the transition of filovirus species causing outbreaks in Central and West Africa during 2005-2014 seemed to be synchronized with the change of the serologically dominant virus species in these bats. These data suggest the introduction of multiple species of filoviruses in the migratory bat population and point to the need for continued surveillance of filovirus infection of wild animals in sub-Saharan Africa, including hitherto nonendemic countries.

  3. Multiple species of scuttle flies (Diptera: Phoridae) as contaminants in forensic entomology laboratory insect colony.

    Science.gov (United States)

    Zuha, R M; Jenarthanan, L X Q; Disney, R H L; Omar, B

    2015-09-01

    In forensic entomology, larval rearing usually includes the presence of biological contaminants including scuttle flies (Diptera: Phoridae). Scuttle flies are recognized as forensically important insects and have been reported causing nuisance and contamination in laboratory environments. This paper reports for the first time the finding of multiple scuttle fly species affecting colonies of third instar larvae of the Oriental latrine blowfly, Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae), reared indoors at the Forensic Science Simulation Site, Universiti Kebangsaan Malaysia. Adult scuttle flies were discovered inside a rearing container after the emergence of adult C. megacephala., The scuttle fly species are Megaselia scalaris (Loew), M. spiracularis Schmitz and Puliciphora borinquenensis (Wheeler). Notes on the life history and biology of these species are discussed herein.

  4. Characters with multiple usages- phenotypic variability analysis at Echinacea purpurea (L. Moench species

    Directory of Open Access Journals (Sweden)

    Mihai Radu POP

    2010-11-01

    Full Text Available Merging aesthetics with utility, some medicinal plants can benefit both of a high production and decoration potential. This calls for diversification of improvement directions of the species. Through this article we suggest one of these species, Echinacea purpurea (L. Moench. This is considered to be important at this time, acquisition of new biological forms - varieties in this species, which show multiple attributes utility based on key biological characteristics, agronomic, physiological, biochemical and agrochemical (medicinal, decorative, culinary etc.. To achieve this goal, studies were undertaken, given in this article, which is the starting point for selecting characters representative for our targets.The results presented in this study reveal a pronounced genetic polymorphism showing the selection operation can use the original material for a quantitative and qualitative differentiation of valuable genotypes that could be approved.

  5. Explaining clinical behaviors using multiple theoretical models.

    Science.gov (United States)

    Eccles, Martin P; Grimshaw, Jeremy M; MacLennan, Graeme; Bonetti, Debbie; Glidewell, Liz; Pitts, Nigel B; Steen, Nick; Thomas, Ruth; Walker, Anne; Johnston, Marie

    2012-10-17

    , the mean construct scores were above the mid-point on the scale with median values across the five behaviors generally being above four out of seven and the range being from 1.53 to 6.01. Across all of the theories, the highest proportion of the variance explained was always for intention and the lowest was for behavior. The Knowledge-Attitudes-Behavior Model performed poorly across all behaviors and dependent variables; CSSRM also performed poorly. For TPB, SCT, II, and LT across the five behaviors, we predicted median R2 of 25% to 42.6% for intention, 6.2% to 16% for behavioral simulation, and 2.4% to 6.3% for behavior. We operationalized multiple theories measuring across five behaviors. Continuing challenges that emerge from our work are: better specification of behaviors, better operationalization of theories; how best to appropriately extend the range of theories; further assessment of the value of theories in different settings and groups; exploring the implications of these methods for the management of chronic diseases; and moving to experimental designs to allow an understanding of behavior change.

  6. Explaining clinical behaviors using multiple theoretical models

    Directory of Open Access Journals (Sweden)

    Eccles Martin P

    2012-10-01

    the five surveys. For the predictor variables, the mean construct scores were above the mid-point on the scale with median values across the five behaviors generally being above four out of seven and the range being from 1.53 to 6.01. Across all of the theories, the highest proportion of the variance explained was always for intention and the lowest was for behavior. The Knowledge-Attitudes-Behavior Model performed poorly across all behaviors and dependent variables; CSSRM also performed poorly. For TPB, SCT, II, and LT across the five behaviors, we predicted median R2 of 25% to 42.6% for intention, 6.2% to 16% for behavioral simulation, and 2.4% to 6.3% for behavior. Conclusions We operationalized multiple theories measuring across five behaviors. Continuing challenges that emerge from our work are: better specification of behaviors, better operationalization of theories; how best to appropriately extend the range of theories; further assessment of the value of theories in different settings and groups; exploring the implications of these methods for the management of chronic diseases; and moving to experimental designs to allow an understanding of behavior change.

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

    Science.gov (United States)

    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.…

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

    Science.gov (United States)

    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.…

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

    Science.gov (United States)

    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

  10. Identification and Management of Multiple Threats to Rare and Endangered Plant Species

    Science.gov (United States)

    2013-07-30

    contract to the Department of Defense Strategic Environmental Research and Development Program (SERDP). The publication of this report does not indicate...30 July 2013 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER W912H08-c-0002 Identification and Management of Multiple Threats to Rare...of Acronyms GLM Generalized Linear Model GLMM Generalized Mixed Linear Model LM Linear Model LTRE Life table response experiment MLM Mixed

  11. San Diego Multiple Species Conservation Program (MSCP) Rare Plant Monitoring Review and Revision

    Science.gov (United States)

    McEachern, Kathryn; Pavlik, Bruce M.; Rebman, Jon; Sutter, Rob

    2007-01-01

    Introduction The San Diego Multiple Species Conservation Program (MSCP) was developed for the conservation of plants and animals in the south part of San Diego County, under the California Natural Community Conservation Planning Act of 1991 (California Department of Fish and Game) and the Federal Endangered Species Act of 1973, as amended (16 U.S. Code 1531-1544.) The Program is on the leading edge of conservation, as it seeks to both guide development and conserve at-risk species with the oversight of both State and Federal agencies. Lands were identified for inclusion in the MSCP based on their value as habitat for at-risk plants or plant communities (Natural Community Conservation Planning, 2005). Since its inception in the mid-1990s the Program has protected over 100,000 acres, involving 15 jurisdictions and the U.S. Fish and Wildlife Service (USFWS) and California Department of Fish and Game (CDFG) in the conservation of 87 taxa. Surveys for covered species have been conducted, and management and monitoring have been implemented at some high priority sites. Each jurisdiction or agency manages and monitors their conservation areas independently, while collaborating regionally for long-term protection. The San Diego MSCP is on the forefront of conservation, in one of the most rapidly growing urban areas of the country. The planning effort that developed the MSCP was state-of-the-art, using expert knowledge, spatial habitat modeling, and principles of preserve design to identify and prioritize areas for protection. Land acquisition and protection are ahead of schedule for most jurisdictions. Surveys have verified the locations of many rare plant populations known from earlier collections, and they provide general information on population size and health useful for further conservation planning. Management plans have been written or are in development for most MSCP parcels under jurisdictional control. Several agencies are developing databases for implementation

  12. Affine LIBOR Models with Multiple Curves

    DEFF Research Database (Denmark)

    Grbac, Zorana; Papapantoleon, Antonis; Schoenmakers, John

    2015-01-01

    We introduce a multiple curve framework that combines tractable dynamics and semianalytic pricing formulas with positive interest rates and basis spreads. Negative rates and positive spreads can also be accommodated in this framework. The dynamics of overnight indexed swap and LIBOR rates...... with dependent LIBOR rates is developed that allows for an efficient and accurate calibration to a system of caplet prices....

  13. DUSTMS-D: DISPOSAL UNIT SOURCE TERM - MULTIPLE SPECIES - DISTRIBUTED FAILURE DATA INPUT GUIDE.

    Energy Technology Data Exchange (ETDEWEB)

    SULLIVAN, T.M.

    2006-01-01

    Performance assessment of a low-level waste (LLW) disposal facility begins with an estimation of the rate at which radionuclides migrate out of the facility (i.e., the source term). The focus of this work is to develop a methodology for calculating the source term. In general, the source term is influenced by the radionuclide inventory, the wasteforms and containers used to dispose of the inventory, and the physical processes that lead to release from the facility (fluid flow, container degradation, wasteform leaching, and radionuclide transport). Many of these physical processes are influenced by the design of the disposal facility (e.g., how the engineered barriers control infiltration of water). The complexity of the problem and the absence of appropriate data prevent development of an entirely mechanistic representation of radionuclide release from a disposal facility. Typically, a number of assumptions, based on knowledge of the disposal system, are used to simplify the problem. This has been done and the resulting models have been incorporated into the computer code DUST-MS (Disposal Unit Source Term-Multiple Species). The DUST-MS computer code is designed to model water flow, container degradation, release of contaminants from the wasteform to the contacting solution and transport through the subsurface media. Water flow through the facility over time is modeled using tabular input. Container degradation models include three types of failure rates: (a) instantaneous (all containers in a control volume fail at once), (b) uniformly distributed failures (containers fail at a linear rate between a specified starting and ending time), and (c) gaussian failure rates (containers fail at a rate determined by a mean failure time, standard deviation and gaussian distribution). Wasteform release models include four release mechanisms: (a) rinse with partitioning (inventory is released instantly upon container failure subject to equilibrium partitioning (sorption) with

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

    Science.gov (United States)

    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.

  15. Multiple vs. single phytoplankton species alter stoichiometry of trophic interaction with zooplankton.

    Science.gov (United States)

    Plum, Christoph; Hüsener, Matthias; Hillebrand, Helmut

    2015-11-01

    Despite the progress made in explaining trophic interactions through the stoichiometric interplay between consumers and resources, it remains unclear how the number of species in a trophic group influences the effects of elemental imbalances in food webs. Therefore, we conducted a laboratory experiment to test the hypothesis that multispecies producer assemblages alter the nutrient dynamics in a pelagic community. Four algal species were reared in mono- and polycultures under a 2 x 2 factorial combination of light and nutrient supply, thereby contrasting the stoichiometry of trophic interactions involving single vs. multiple producer species. After 9 d, these cultures were fed to the calanoid copepod Acartia tonsa, and we monitored biomass, resource use, and C:N:P stoichiometry in both phyto- and zooplankton. According to our expectations, light and N supply resulted in gradients of phytoplankton biomass and nutrient composition (C:N:P). Significant net diversity effects for algal biomass and C:N:P ratios reflected the greater responsiveness of the phytoplankton polyculture to altered resource supply compared to monocultures. These alterations of elemental ratios were common, and were partly triggered by changes in species frequency in the mixtures and partly by diversity-related changes in resource use. Copepod individual biomass increased under high light (HL) and N-reduced (-N) conditions, when food was high in C:N but low in C:P and N:P, whereas copepod growth was obviously P limited, and copepod stoichiometry was not affected by phytoplankton elemental composition. Correspondingly, copepod individual biomass reflected significant net diversity effects: compared to expectations- derived from monocultures, copepod individuals feeding on algal polycultures remained smaller than predicted under HL and N-sufficient (+N) conditions but grew larger than predicted under HL, -N and low light +N conditions. In conclusion, multiple producer species altered the

  16. A Unified Mutual Coupling Model for Multiple Antenna Systems

    Institute of Scientific and Technical Information of China (English)

    WU Yu-jiang; NIE Zai-ping

    2006-01-01

    A unified mutual coupling model for multiple antenna communication systems based on moment methods is proposed. This model combines antenna coupling and RF front-end circuit coupling, thus providing a more accurate and complete analysis of the mutual coupling effect on multiple antenna systems.

  17. New highland distribution records of multiple Anopheles species in the Ecuadorian Andes

    Directory of Open Access Journals (Sweden)

    Hunter Fiona F

    2011-08-01

    Full Text Available Abstract Background Several recent climate change reviews have stressed the possibility of some malaria vectors occupying regions of higher altitudes than previously recorded. Indeed, highland malaria has been observed in several African nations, possibly attributable to changes in land use, vector control and local climate. This study attempts to expand the current knowledge of the distribution of common Anopheles species in Ecuador, with particular attention to highland regions (> 500 m of the Andes. Methods Extensive field collections of larvae were undertaken in 2008, 2009 and 2010 throughout all regions of Ecuador (except the lower-altitude Amazonian plain and compared to historical distribution maps reproduced from the 1940s. Larvae were identified using both a morphological key and sequencing of the 800 bp region of the CO1 mitochondrial gene. In addition, spatial statistics (Getis-Ord Hotspot Analysis: Gi* were used to determine high and low-density clusters of each species in Ecuador. Results Distributions have been updated for five species of Anopheles in Ecuador: Anopheles albimanus, Anopheles pseudopunctipennis, Anopheles punctimacula, Anopheles eiseni and Anopheles oswaldoi s.l.. Historical maps indicate that An. pseudopunctipennis used to be widespread in highland Andean valleys, while other species were completely restricted to lowland areas. By comparison, updated maps for the other four collected species show higher maximum elevations and/or more widespread distributions in highland regions than previously recorded. Gi* analysis determined some highland hot spots for An. albimanus, but only cold spots for all other species. Conclusions This study documents the establishment of multiple anopheline species in high altitude regions of Ecuador, often in areas where malaria eradication programs are not focused.

  18. High prevalence of multiple paternity in the invasive crayfish species, Procambarus clarkii

    Directory of Open Access Journals (Sweden)

    Gen Hua Yue, Jia Le Li, Chun Ming Wang, Jun Hong Xia, Gen Lin Wang, Jian Bing Feng

    2010-01-01

    Full Text Available Reproductive strategy is a central feature of the ecology of invasive species as it determines the potential for population increase and range expansion. The red swamp crayfish, Procambarus clarkii, has invaded many countries and caused serious problems in freshwater ecosystems. However, little is known about the effects of environmental conditions on crayfish paternity and offspring traits in the wild. We studied these reproductive characteristics of P. clarkii in wild populations from two different habitats (ponds and ditches in three locations with different environmental conditions in China. Genotyping of 1,436 offspring and 30 mothers of 30 broods was conducted by using four microsatellites. An analysis of genotyping results revealed that gravid females were the exclusive mother of the progeny they tended. Twenty-nine of 30 mothers had mated with multiple (2-4 males, each of which contributed differently to the number of offspring in a brood. The average number of fathers per brood and the number of offspring per brood were similar (P > 0.05 among six sampling sites, indicating that in P. clarkii multiple paternity and offspring number per brood are independent of environmental conditions studied. Indirect benefits from increasing the genetic diversity of broods, male and sperm competition, and cryptic female choice are a possible explanation for the high level multiple paternity and different contribution of fathers to offspring in this species.

  19. Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

    Directory of Open Access Journals (Sweden)

    Jörger Katharina M

    2012-12-01

    Full Text Available Abstract Background Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic and the success rate has never been explored on mesopsammic Mollusca. Results We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH. In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC, statistical parsimony, Bayesian Species Delineation (BPP and Automatic Barcode Gap Discovery (ABGD. The secondary species hypothesis (SSH is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’, resulting in the discovery of a radiation of (at least 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions. Conclusions Our study confirms extensive, morphologically

  20. Insecticidal potency of novel compounds on multiple insect species of medical and veterinary importance.

    Science.gov (United States)

    Kaufman, Phillip E; Mann, Rajinder S; Butler, Jerry F

    2011-01-01

    Vector-borne diseases continue to present significant threats to human, animal and plant health. Mosquitoes, houseflies, sand flies and stable flies are well-known vectors of several human and animal pathogens. The toxicity of selected semiochemicals with molecular structures indicative of insecticidal activity was determined against these insect species with the aim of developing novel insecticides toxic to multiple insect species. Three semiochemicals, namely beta-damascone, cyclemone A and melafleur, showed remarkable toxicity to three mosquitoes, Aedes aegypti L., Ae. albopictus (Skuse) and Anopheles quadrimaculatus Say, the housefly, Musca domestica L., the stable fly, Stomoxys calcitrans L., and the sand fly, Lutzomyia shannoni (Dyar). The chemicals were equally toxic to several field-collected permethrin-tolerant housefly strains. When formulated as 500 mL L(-1) emulsifiable concentrates, the chemicals demonstrated stability and toxicity on filter paper and camouflage military fabrics, with persistence up to 8 days under laboratory conditions. The chemicals were equally effective under field conditions when evaluated on unpainted plywood panels, although a higher dosage was required under field conditions to achieve similar efficacy. Laboratory quantification of LC(50) values and field efficacy of three semiochemicals as formulated compounds on mosquitoes, houseflies, stable flies and sand flies showed that these semiochemicals could serve as potent insecticides for multiple insect species. Copyright © 2010 Society of Chemical Industry.

  1. State-shared model for multiple-input multiple-output systems

    Institute of Scientific and Technical Information of China (English)

    Zhenhua TIAN; Karlene A. HOO

    2005-01-01

    This work proposes a method to construct a state-shared model for multiple-input multiple-output (MIMO)systems. A state-shared model is defined as a linear time invariant state-space structure that is driven by measurement signals-the plant outputs and the manipulated variables, but shared by different multiple input/output models. The genesis of the state-shared model is based on a particular reduced non-minimal realization. Any such realization necessarily fulfills the requirement that the output of the state-shared model is an asymptotically correct estimate of the output of the plant, if the process model is selected appropriately. The approach is demonstrated on a nonlinear MIMO system- a physiological model of calcium fluxes that controls muscle contraction and relaxation in human cardiac myocytes.

  2. Multiple genes elucidate the evolution of venomous snail-hunting Conus species.

    Science.gov (United States)

    Nam, Hannah H; Corneli, Patrice Showers; Watkins, Maren; Olivera, Baldomero; Bandyopadhyay, Pradip

    2009-12-01

    The species-rich Cone snails (Conus sp.) are predatory, marine gastropods known for small venom peptides that are valuable for pharmacological research applications. Phylogenetic analyses with mitochondrial rRNA sequences have facilitated peptide discovery. However, these relatively conserved genes leave unresolved the closer relationships among many species. We sequenced 26 internal transcribed spacer 2 (ITS2) sequences from genomic ribosomal DNA to elucidate the evolutionary relationships among molluscivorous species and to piscivorous and vermivorous species. We show that ITS2 sequences are well conserved within species but are sufficiently variable among species to resolve recent divergences. Using Bayesian, maximum likelihood and log-determinant methods, we use the ITS sequences to resolve portions of the tree that could not be resolved using the more conventional mt rRNA sequences. When the ITS2 sequences are added to existing COI and to the more conserved rRNA sequences and then properly modeled, support throughout the tree is increased. This enables us to show finer relationships among the molluscivorous species that reveal three well-supported clades (Conus, Cylinder, and Darioconus) and renders the ITS2 sequences an essential component in advancing the discovery and pharmacological characterization of novel peptides from the venoms of these molluscs.

  3. Modeling Multiple Risks: Hidden Domain of Attraction

    CERN Document Server

    Mitra, Abhimanyu

    2011-01-01

    Hidden regular variation is a sub-model of multivariate regular variation and facilitates accurate estimation of joint tail probabilities. We generalize the model of hidden regular variation to what we call hidden domain of attraction. We exhibit examples that illustrate the need for a more general model and discuss detection and estimation techniques.

  4. Multiple-membership multiple-classification models for social network and group dependences

    OpenAIRE

    Tranmer, Mark; Steel, David; Browne, William J

    2014-01-01

    The social network literature on network dependences has largely ignored other sources of dependence, such as the school that a student attends, or the area in which an individual lives. The multilevel modelling literature on school and area dependences has, in turn, largely ignored social networks. To bridge this divide, a multiple-membership multiple-classification modelling approach for jointly investigating social network and group dependences is presented. This allows social network and ...

  5. In vitro establishment and multiplication of Guettarda clarense, a Cuban endemic species in extinction danger

    Directory of Open Access Journals (Sweden)

    Elisa Quiala

    2005-01-01

    Full Text Available The present work was carried out with the objective of achieving the in vitro establishment and multiplication of Guettarda clarense which is an endemic local of Santa Clara city and it is considered in extinction danger. Seeds of mature fruits collected under field conditions were used. The effect of a concentration of NaOCl (2% during 15, 20 and 25 minutes in the disinfection of the seeds was studied. The seeds were sowed in a culture medium of germination compound by 50% of MS salts. During the multiplication phase of the explants, the effect of three concentrations of 6-BAP (0.2, 0.4 and 0.6 mg. l-1 was studied. The culture medium was compound by the MS salts, 1.0 mg. l-1 of thiamine and 3% of sucrose. The bigger number of seeds free of visible microbial pollutants (50% was obtained when the treatment with 2.0% of NaOCl during 25 minutes was used. The 85% of the seeds germinated in the culture medium compound by the 50% of the MS salts without growth regulators. During the multiplication phase of the explants, the multiplication coefficient and the longitude of the plants were increased in the same proportion as the concentration of 6-BAP was increased. The highest values were obtained (6.1 explants and 6.7 cm respectively in the treatment with 0.6 mg. l-1. Key words: cuabal, in vitro culture, micropropagation, threatened species

  6. Hopf bifurcations in a three-species food chain system with multiple delays

    Directory of Open Access Journals (Sweden)

    Xie Xiaoliang

    2017-04-01

    Full Text Available This paper is concerned with a three-species Lotka-Volterra food chain system with multiple delays. By linearizing the system at the positive equilibrium and analyzing the associated characteristic equation, the stability of the positive equilibrium and existence of Hopf bifurcations are investigated. Furthermore, the direction of bifurcations and the stability of bifurcating periodic solutions are determined by the normal form theory and the center manifold theorem for functional differential equations. Finally, some numerical simulations are carried out for illustrating the theoretical results.

  7. An outbreak of Sarcocystis calchasi encephalitis in multiple psittacine species within an enclosed zoological aviary.

    Science.gov (United States)

    Rimoldi, Guillermo; Speer, Brian; Wellehan, James F X; Bradway, Daniel S; Wright, Lewis; Reavill, Drury; Barr, Bradd C; Childress, April; Shivaprasad, H L; Chin, Richard P

    2013-11-01

    A total of 5 psittacine birds in an enclosed zoological exhibit, including 2 princess parrots and 3 cockatoos of 2 different species, developed severe central nervous system clinical signs over a 2-3-month period and died or were euthanized. Histologically, all birds had a lymphoplasmacytic and histiocytic encephalitis with intralesional protozoa consistent with a Sarcocystis species in addition to intramuscular tissue sarcocysts. By immunohistochemical staining, merozoites in brain and tissue cysts in muscle did not react with polyclonal antisera against Sarcocystis falcatula, Sarcocystis neurona, Toxoplasma gondii, and Neospora caninum, or with a monoclonal antibody to S. neurona. Transmission electron microscopy on sarcocyst tissue cyst walls from 2 birds was morphologically consistent with Sarcocystis calchasi. Polymerase chain reaction (PCR) amplification and sequencing of partial 18S ribosomal RNA from muscle tissue cysts and brain schizonts from 3 birds was consistent with a clade containing S. calchasi and Sarcocystis columbae but could not distinguish these closely related Sarcocystis species. However, PCR amplification and sequencing of the internal transcribed spacer 1 RNA segment in the brain from 2 birds and muscle from 2 birds specifically identified the isolates as S. calchasi. The current report documents that multiple psittacine species are susceptible intermediate hosts of S. calchasi, and that infection can cause encephalitis resulting in significant morbidity and mortality in psittacine aviaries.

  8. A Dirty Model for Multiple Sparse Regression

    CERN Document Server

    Jalali, Ali; Sanghavi, Sujay

    2011-01-01

    Sparse linear regression -- finding an unknown vector from linear measurements -- is now known to be possible with fewer samples than variables, via methods like the LASSO. We consider the multiple sparse linear regression problem, where several related vectors -- with partially shared support sets -- have to be recovered. A natural question in this setting is whether one can use the sharing to further decrease the overall number of samples required. A line of recent research has studied the use of \\ell_1/\\ell_q norm block-regularizations with q>1 for such problems; however these could actually perform worse in sample complexity -- vis a vis solving each problem separately ignoring sharing -- depending on the level of sharing. We present a new method for multiple sparse linear regression that can leverage support and parameter overlap when it exists, but not pay a penalty when it does not. A very simple idea: we decompose the parameters into two components and regularize these differently. We show both theore...

  9. Mapping Habitat Connectivity for Multiple Rare, Threatened, and Endangered Species on and Around Military Installations

    Science.gov (United States)

    2011-05-01

    Circuitscape, CONNECT, decision-support system, Dispersal, Eastern Tiger Salamander, Fort Bragg, graph theory, Habitat Management, Individual-based...cockaded woodpecker, St. Francis’ satyr butterfly, Carolina gopher frog, and eastern tiger salamander). Our objectives were to model habitat-mediated...population sizes, reduced flow of individuals and genes between populations, and greater risk of extinction of native species (Fisher and Lindenmayer 2007

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

    Science.gov (United States)

    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.

  11. A simple model for skewed species-lifetime distributions

    KAUST Repository

    Murase, Yohsuke

    2010-06-11

    A simple model of a biological community assembly is studied. Communities are assembled by successive migrations and extinctions of species. In the model, species are interacting with each other. The intensity of the interaction between each pair of species is denoted by an interaction coefficient. At each time step, a new species is introduced to the system with randomly assigned interaction coefficients. If the sum of the coefficients, which we call the fitness of a species, is negative, the species goes extinct. The species-lifetime distribution is found to be well characterized by a stretched exponential function with an exponent close to 1/2. This profile agrees not only with more realistic population dynamics models but also with fossil records. We also find that an age-independent and inversely diversity-dependent mortality, which is confirmed in the simulation, is a key mechanism accounting for the distribution. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

  12. SDG and qualitative trend based model multiple scale validation

    Science.gov (United States)

    Gao, Dong; Xu, Xin; Yin, Jianjin; Zhang, Hongyu; Zhang, Beike

    2017-09-01

    Verification, Validation and Accreditation (VV&A) is key technology of simulation and modelling. For the traditional model validation methods, the completeness is weak; it is carried out in one scale; it depends on human experience. The SDG (Signed Directed Graph) and qualitative trend based multiple scale validation is proposed. First the SDG model is built and qualitative trends are added to the model. And then complete testing scenarios are produced by positive inference. The multiple scale validation is carried out by comparing the testing scenarios with outputs of simulation model in different scales. Finally, the effectiveness is proved by carrying out validation for a reactor model.

  13. Structural model analysis of multiple quantitative traits.

    Directory of Open Access Journals (Sweden)

    Renhua Li

    2006-07-01

    Full Text Available We introduce a method for the analysis of multilocus, multitrait genetic data that provides an intuitive and precise characterization of genetic architecture. We show that it is possible to infer the magnitude and direction of causal relationships among multiple correlated phenotypes and illustrate the technique using body composition and bone density data from mouse intercross populations. Using these techniques we are able to distinguish genetic loci that affect adiposity from those that affect overall body size and thus reveal a shortcoming of standardized measures such as body mass index that are widely used in obesity research. The identification of causal networks sheds light on the nature of genetic heterogeneity and pleiotropy in complex genetic systems.

  14. Multiple View Stereo by Reflectance Modeling

    DEFF Research Database (Denmark)

    Kim, Sujung; Kim, Seong Dae; Dahl, Anders Lindbjerg

    2012-01-01

    we argue that a visual metric based on a surface reflectance model should be founded on more observations than the degrees of freedom (dof) of the reflectance model. If (partly) specular surfaces are to be handled, this implies a model with at least two dof. In this paper, we propose to construct...... visual metrics of more than one dof using the DAISY methodology, which compares favorably to the state of the art in the experiments carried out. These experiments are based on a novel data set of eight scenes with diffuse and specular surfaces and accompanying ground truth. The performance of six...

  15. Statistical selection of multiple-input multiple-output nonlinear dynamic models of spike train transformation.

    Science.gov (United States)

    Song, Dong; Chan, Rosa H M; Marmarelis, Vasilis Z; Hampson, Robert E; Deadwyler, Sam A; Berger, Theodore W

    2007-01-01

    Multiple-input multiple-output nonlinear dynamic model of spike train to spike train transformations was previously formulated for hippocampal-cortical prostheses. This paper further described the statistical methods of selecting significant inputs (self-terms) and interactions between inputs (cross-terms) of this Volterra kernel-based model. In our approach, model structure was determined by progressively adding self-terms and cross-terms using a forward stepwise model selection technique. Model coefficients were then pruned based on Wald test. Results showed that the reduced kernel models, which contained much fewer coefficients than the full Volterra kernel model, gave good fits to the novel data. These models could be used to analyze the functional interactions between neurons during behavior.

  16. Infinite multiple membership relational modeling for complex networks

    DEFF Research Database (Denmark)

    Mørup, Morten; Schmidt, Mikkel Nørgaard; Hansen, Lars Kai

    2011-01-01

    Learning latent structure in complex networks has become an important problem fueled by many types of networked data originating from practically all fields of science. In this paper, we propose a new non-parametric Bayesian multiple-membership latent feature model for networks. Contrary to exist......Learning latent structure in complex networks has become an important problem fueled by many types of networked data originating from practically all fields of science. In this paper, we propose a new non-parametric Bayesian multiple-membership latent feature model for networks. Contrary...... to existing multiplemembership models that scale quadratically in the number of vertices the proposed model scales linearly in the number of links admitting multiple-membership analysis in large scale networks. We demonstrate a connection between the single membership relational model and multiple membership...

  17. Mitochondrial Genome Analyses Suggest Multiple Trichuris Species in Humans, Baboons, and Pigs from Different Geographical Regions.

    Directory of Open Access Journals (Sweden)

    Mohamed B F Hawash

    Full Text Available The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found in primates.We sequenced and annotated complete mitochondrial genomes of Trichuris recovered from a human in Uganda, an olive baboon in the US, a hamadryas baboon in Denmark, and two pigs from Denmark and Uganda. Comparative analyses using other published mitochondrial genomes of Trichuris recovered from a human and a porcine host in China and from a françois' leaf-monkey (China were performed, including phylogenetic analyses and pairwise genetic and amino acid distances. Genetic and protein distances between human Trichuris in Uganda and China were high (~19% and 15%, respectively suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from Trichuris from françois' leaf monkey, suggesting multiple whipworm species circulating among non-human primates. The genetic and protein distances between pig Trichuris from Denmark and other regions were roughly 9% and 6%, respectively, while Chinese and Ugandan whipworms were more closely related.Our results indicate that Trichuris species infecting humans and pigs are phylogenetically distinct across geographical regions, which might have important implications for the implementation of suitable and effective control strategies in different regions. Moreover, we provide support for the hypothesis that Trichuris infecting primates represents a complex of cryptic species with some species being able to infect both humans and non-human primates.

  18. ID Model Construction and Validation: A Multiple Intelligences Case

    Science.gov (United States)

    Tracey, Monica W.; Richey, Rita C.

    2007-01-01

    This is a report of a developmental research study that aimed to construct and validate an instructional design (ID) model that incorporates the theory and practice of multiple intelligences (MI). The study consisted of three phases. In phase one, the theoretical foundations of multiple Intelligences and ID were examined to guide the development…

  19. Multiple Social Networks, Data Models and Measures for

    DEFF Research Database (Denmark)

    Magnani, Matteo; Rossi, Luca

    2017-01-01

    Multiple Social Network Analysis is a discipline defining models, measures, methodologies, and algorithms to study multiple social networks together as a single social system. It is particularly valuable when the networks are interconnected, e.g., the same actors are present in more than one...... network....

  20. Modelling of rate effects at multiple scales

    DEFF Research Database (Denmark)

    Pedersen, R.R.; Simone, A.; Sluys, L. J.

    2008-01-01

    At the macro- and meso-scales a rate dependent constitutive model is used in which visco-elasticity is coupled to visco-plasticity and damage. A viscous length scale effect is introduced to control the size of the fracture process zone. By comparison of the widths of the fracture process zone......, the length scale in the meso-model and the macro-model can be coupled. In this fashion, a bridging of length scales can be established. A computational analysis of  a Split Hopkinson bar test at medium and high impact load is carried out at macro-scale and meso-scale including information from  the micro-scale....

  1. Impacts of Species Misidentification on Species Distribution Modeling with Presence-Only Data

    Directory of Open Access Journals (Sweden)

    Hugo Costa

    2015-11-01

    Full Text Available Spatial records of species are commonly misidentified, which can change the predicted distribution of a species obtained from a species distribution model (SDM. Experiments were undertaken to predict the distribution of real and simulated species using MaxEnt and presence-only data “contaminated” with varying rates of misidentification error. Additionally, the difference between the niche of the target and contaminating species was varied. The results show that species misidentification errors may act to contract or expand the predicted distribution of a species while shifting the predicted distribution towards that of the contaminating species. Furthermore the magnitude of the effects was positively related to the ecological distance between the species’ niches and the size of the error rates. Critically, the magnitude of the effects was substantial even when using small error rates, smaller than common average rates reported in the literature, which may go unnoticed while using a standard evaluation method, such as the area under the receiver operating characteristic curve. Finally, the effects outlined were shown to impact negatively on practical applications that use SDMs to identify priority areas, commonly selected for various purposes such as management. The results highlight that species misidentification should not be neglected in species distribution modeling.

  2. Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species.

    Science.gov (United States)

    Ren, Da Wei; Chen, Wen Feng; Sui, Xin Hua; Wang, En Tao; Chen, Wen Xin

    2011-03-01

    A group of rhizobial strains isolated from nodules of multiple legume species grown in different geographical regions of China had identical 16S rRNA genes. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the novel strains formed a subclade in the genus Rhizobium together with Rhizobium galegae, Rhizobium huautlense and Rhizobium alkalisoli, with 99.8  % gene sequence similarity between the strains. The DNA-DNA relatedness values between the representative strain CCBAU 05176(T) and R. galegae ATCC 43677(T), R. huautlense S02(T) and R. alkalisoli CCBAU 01393(T) were 22.6  %, 8.9  % and 15.9  %, respectively. The novel strains were distinguished from recognized species of the genus Rhizobium by using a polyphasic approach, including PCR-based restriction fragment length polymorphism analysis (RFLP) of the 16S-23S intergenic spacer (IGS), phenotypic and physiological tests, sequence comparisons of housekeeping genes and cellular fatty acid profiles. Therefore, it is suggested that this group of strains represents a novel species for which the name Rhizobium vignae sp. nov. is proposed. The type strain is CCBAU 05176(T) (=HAMBI 3039(T)=LMG 25447(T)).

  3. Missing in action: Species competition is a neglected predictor variable in species distribution modelling.

    Science.gov (United States)

    Mpakairi, Kudzai Shaun; Ndaimani, Henry; Tagwireyi, Paradzayi; Gara, Tawanda Winmore; Zvidzai, Mark; Madhlamoto, Daphine

    2017-01-01

    The central role of species competition in shaping community structure in ecosystems is well appreciated amongst ecologists. However species competition is a consistently missing variable in Species Distribution Modelling (SDM). This study presents results of our attempt to incorporate species competition in SDMs. We used a suit of predictor variables including Soil Adjusted Vegetation Index (SAVI), as well as distance from roads, settlements and water, fire frequency and distance from the nearest herbivore sighting (of selected herbivores) to model individual habitat preferences of five grazer species (buffalo, warthog, waterbuck, wildebeest and zebra) with the Ensemble SDM algorithm for Gonarezhou National Park, Zimbabwe. Our results showed that distance from the nearest animal sighting (a proxy for competition among grazers) was the best predictor of the potential distribution of buffalo, wildebeest and zebra but the second best predictor for warthog and waterbuck. Our findings provide evidence to that competition is an important predictor of grazer species' potential distribution. These findings suggest that species distribution modelling that neglects species competition may be inadequate in explaining the potential distribution of species. Therefore our findings encourage the inclusion of competition in SDM as well as potentially igniting discussions that may lead to improving the predictive power of future SDM efforts.

  4. Control design approaches for nonlinear systems using multiple models

    Institute of Scientific and Technical Information of China (English)

    Junyong ZHAI; Shumin FEI; Feipeng DA

    2007-01-01

    It is difficult to realize control for some complex nonlinear systems operated in different operating regions.Based on developing local models for different operating regions of the process, a novel algorithm using multiple models is proposed. It utilizes dynamic model bank to establish multiple local models, and their membership functions are defined according to respective regions. Then the nonlinear system is approximated to a weighted combination of the local models.The stability of the nonlinear system is proven. Finally, simulations are given to demonstrate the validity of the proposed method.

  5. Animal model of human disease. Multiple myeloma

    NARCIS (Netherlands)

    Radl, J.; Croese, J.W.; Zurcher, C.; Enden-Vieveen, M.H.M. van den; Leeuw, A.M. de

    1988-01-01

    Animal models of spontaneous and induced plasmacytomas in some inbred strains of mice have proven to be useful tools for different studies on tumorigenesis and immunoregulation. Their wide applicability and the fact that after their intravenous transplantation, the recipient mice developed bone

  6. Models of reactive oxygen species in cancer

    OpenAIRE

    Lu, Weiqin; Ogasawara, Marcia A.; Huang, Peng

    2007-01-01

    Increased generation of reactive oxygen species (ROS) has been observed in cancer, degenerative diseases, and other pathological conditions. ROS can stimulate cell proliferation, promote genetic instability, and induce adaptive responses that enable cancer cells to maintain their malignant phenotypes. However, when cellular redox balance is severely disturbed, high levels of ROS may cause various damages leading to cell death. The studies of ROS effects on biological systems, their underlying...

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

    Science.gov (United States)

    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.

  8. Study of Self-Organization Model of Multiple Mobile Robot

    OpenAIRE

    Li Shu-qin; Ceng Xian-yi; Xia De-shen

    2006-01-01

    A good organization model of multiple mobile robot should be able to improve the efficiency of the system, reduce the complication of robot interactions, and detract the difficulty of computation. From the sociology aspect of topology, structure and organization, this paper studies the multiple mobile robot organization formation and running mechanism in the dynamic, complicated and unknown environment. It presents and describes in detail a Hierarchical- Web Recursive Organization Model (HWRO...

  9. Airport choice model in multiple airport regions

    Directory of Open Access Journals (Sweden)

    Claudia Muñoz

    2017-02-01

    Full Text Available Purpose: This study aims to analyze travel choices made by air transportation users in multi airport regions because it is a crucial component when planning passenger redistribution policies. The purpose of this study is to find a utility function which makes it possible to know the variables that influence users’ choice of the airports on routes to the main cities in the Colombian territory. Design/methodology/approach: This research generates a Multinomial Logit Model (MNL, which is based on the theory of maximizing utility, and it is based on the data obtained on revealed and stated preference surveys applied to users who reside in the metropolitan area of Aburrá Valley (Colombia. This zone is the only one in the Colombian territory which has two neighboring airports for domestic flights. The airports included in the modeling process were Enrique Olaya Herrera (EOH Airport and José María Córdova (JMC Airport. Several structure models were tested, and the MNL proved to be the most significant revealing the common variables that affect passenger airport choice include the airfare, the price to travel the airport, and the time to get to the airport. Findings and Originality/value: The airport choice model which was calibrated corresponds to a valid powerful tool used to calculate the probability of each analyzed airport of being chosen for domestic flights in the Colombian territory. This is done bearing in mind specific characteristic of each of the attributes contained in the utility function. In addition, these probabilities will be used to calculate future market shares of the two airports considered in this study, and this will be done generating a support tool for airport and airline marketing policies.

  10. Teaching students to apply multiple physical modeling methods

    NARCIS (Netherlands)

    Wiegers, T.; Verlinden, J.C.; Vergeest, J.S.M.

    2014-01-01

    Design students should be able to explore a variety of shapes before elaborating one particular shape. Current modelling courses don’t address this issue. We developed the course Rapid Modelling, which teaches students to explore multiple shape models in a short time, applying different methods and

  11. A model for multiple scattering in GEANT4

    CERN Document Server

    Urbán, László

    2006-01-01

    We present a model to simulate the multiple scattering of charged particles in matter. The model is based on Lewis theory; it does not use the Moliere formalism. It simulates the scattering of a charged particle after a given step, computes the path length correction and the lateral displacement as well. This model is used in GEANT4.

  12. MULTIPLE IMPUTATION OF MISSING DATA IN SUSTAINABLE DEVELOPMENT MODELLING

    OpenAIRE

    Roberto Benedetti; Rita Lima; Alessandro Pandimiglio

    2006-01-01

    A multiple imputation technique is proposed to measure sustainable development using models of structural equations (LISREL) for the treatment of missing data. The reliability of such technique is verified comparing the estimation model with missing data to the estimation model with imputed data. The results show that the missing data problem significantly affect the estimation.

  13. Teaching students to apply multiple physical modeling methods

    NARCIS (Netherlands)

    Wiegers, T.; Verlinden, J.C.; Vergeest, J.S.M.

    2014-01-01

    Design students should be able to explore a variety of shapes before elaborating one particular shape. Current modelling courses don’t address this issue. We developed the course Rapid Modelling, which teaches students to explore multiple shape models in a short time, applying different methods and

  14. Molecular genotyping of human Ureaplasma species based on multiple-banded antigen (MBA) gene sequences.

    Science.gov (United States)

    Kong, F; Ma, Z; James, G; Gordon, S; Gilbert, G L

    2000-09-01

    Ureaplasma urealyticum has been divided into 14 serovars. Recently, subdivision of U. urealyticum into two species has been proposed: U. parvum (previously U. urealyticum parvo biovar), comprising four serovars (1, 3, 6, 14) and U. urealyticum (previously U. urealyticum T-960 biovar), 10 serovars (2, 4, 5, 7-13). The multiple-banded antigen (MBA) genes of these species contain both species and serovar/subtype specific sequences. Based on whole sequences of the 5'-ends of MBA genes of U. parvum serovars and partial sequences of the 5'-ends of MBA genes of U. urealyticum serovars, we previously divided each of these species into three MBA genotypes. To further elucidate the relationships between serovars, we sequenced the whole 5'-ends of MBA genes of all 10 U. urealyticum serovars and partial repetitive regions of these genes from all serovars of U. parvum and U. urealyticum. For the first time, all four serovars of U. parvum were clearly differentiated from each other. In addition, the 10 serovars of U. urealyticum were divided into five MBA genotypes, as follows: MBA genotype A comprises serovars 2, 5, 8; MBA genotype B, serovar 10 only; MBA genotype C, serovars 4, 12, 13; MBA genotype D, serovar 9 only; and MBA genotype E comprises serovars 7 and 11. There were no sequence differences between members within each MBA genotype. Further work is required to identify other genes or other regions of the MBA genes that may be used to differentiate U. urealyticum serovars within MBA genotypes A, C and E. A better understanding of the molecular basis of serotype differentiation will help to improve subtyping methods for use in studies of the pathogenesis and epidemiology of these organisms.

  15. Green communication: The enabler to multiple business models

    DEFF Research Database (Denmark)

    Lindgren, Peter; Clemmensen, Suberia; Taran, Yariv

    2010-01-01

    Companies stand at the forefront of a new business model reality with new potentials - that will change their basic understanding and practice of running their business models radically. One of the drivers to this change is green communication, its strong relation to green business models and its...... possibility to enable lower energy consumption. This paper shows how green communication enables innovation of green business models and multiple business models running simultaneously in different markets to different customers....

  16. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.

    Directory of Open Access Journals (Sweden)

    Aron J Fazekas

    Full Text Available A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s. We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples. The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA to 59% (trnH-psbA of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci, with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs. Several loci (matK, psbK-psbI, trnH-psbA were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations. This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the

  17. Entrepreneurial intention modeling using hierarchical multiple regression

    Directory of Open Access Journals (Sweden)

    Marina Jeger

    2014-12-01

    Full Text Available The goal of this study is to identify the contribution of effectuation dimensions to the predictive power of the entrepreneurial intention model over and above that which can be accounted for by other predictors selected and confirmed in previous studies. As is often the case in social and behavioral studies, some variables are likely to be highly correlated with each other. Therefore, the relative amount of variance in the criterion variable explained by each of the predictors depends on several factors such as the order of variable entry and sample specifics. The results show the modest predictive power of two dimensions of effectuation prior to the introduction of the theory of planned behavior elements. The article highlights the main advantages of applying hierarchical regression in social sciences as well as in the specific context of entrepreneurial intention formation, and addresses some of the potential pitfalls that this type of analysis entails.

  18. Sequence-specific electrochemical recognition of multiple species using nanoparticle labels

    Energy Technology Data Exchange (ETDEWEB)

    Cai Hong [Department of Chemical Engineering, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Hong Kong (China); Shang, Chii [Department of Civil Engineering, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Hong Kong (China); Hsing, I.-Ming [Department of Chemical Engineering, Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Hong Kong (China)]. E-mail: kehsing@ust.hk

    2004-10-04

    In this work, we report an electrochemical methodology that enables the rapid identification of different DNA sequences on the microfabricated electrodes. Our approach starts with an electropolymerization process on a patterned indium tin oxide (ITO)-coated glass electrode, followed by a selective immobilization of biotin-tagged probes on individually addressable spots via the biotin-streptavidin linkage. An exemplary target mixture containing E. coli and Stachybotrys Chartarum, an airborne pathogen, is then introduced. Recognition of the DNA hybridization event of the immobilized probes with the target pathogen PCR products or synthetic oligonucleotides is achieved by a novel electrochemistry-based technique utilizing the preferential catalytic silver electrodeposition process on the DNA-linked nanogold shells. The ability to selectively immobilize different oligonucleotide probes together with a sensitive electrochemistry-based detection for multiple species, as demonstrated in this study, is an important step forward for the realization of a portable bioanalytical microdevice for the rapid detection of pathogens.

  19. Predicting weed problems in maize cropping by species distribution modelling

    Directory of Open Access Journals (Sweden)

    Bürger, Jana

    2014-02-01

    Full Text Available Increasing maize cultivation and changed cropping practices promote the selection of typical maize weeds that may also profit strongly from climate change. Predicting potential weed problems is of high interest for plant production. Within the project KLIFF, experiments were combined with species distribution modelling for this task in the region of Lower Saxony, Germany. For our study, we modelled ecological and damage niches of nine weed species that are significant and wide spread in maize cropping in a number of European countries. Species distribution models describe the ecological niche of a species, these are the environmental conditions under which a species can maintain a vital population. It is also possible to estimate a damage niche, i.e. the conditions under which a species causes damage in agricultural crops. For this, we combined occurrence data of European national data bases with high resolution climate, soil and land use data. Models were also projected to simulated climate conditions for the time horizon 2070 - 2100 in order to estimate climate change effects. Modelling results indicate favourable conditions for typical maize weed occurrence virtually all over the study region, but only a few species are important in maize cropping. This is in good accordance with the findings of an earlier maize weed monitoring. Reaction to changing climate conditions is species-specific, for some species neutral (E. crus-galli, other species may gain (Polygonum persicaria or loose (Viola arvensis large areas of suitable habitats. All species with damage potential under present conditions will remain important in maize cropping, some more species will gain regional importance (Calystegia sepium, Setara viridis.

  20. Study of three interesting Amanita species from Thailand: Morphology, multiple-gene phylogeny and toxin analysis.

    Science.gov (United States)

    Thongbai, Benjarong; Miller, Steven L; Stadler, Marc; Wittstein, Kathrin; Hyde, Kevin D; Lumyong, Saisamorn; Raspé, Olivier

    2017-01-01

    Amanita ballerina and A. brunneitoxicaria spp. nov. are introduced from Thailand. Amanita fuligineoides is also reported for the first time from Thailand, increasing the known distribution of this taxon. Together, those findings support our view that many taxa are yet to be discovered in the region. While both morphological characters and a multiple-gene phylogeny clearly place A. brunneitoxicaria and A. fuligineoides in sect. Phalloideae (Fr.) Quél., the placement of A. ballerina is problematic. On the one hand, the morphology of A. ballerina shows clear affinities with stirps Limbatula of sect. Lepidella. On the other hand, in a multiple-gene phylogeny including taxa of all sections in subg. Lepidella, A. ballerina and two other species, including A. zangii, form a well-supported clade sister to the Phalloideae sensu Bas 1969, which include the lethal "death caps" and "destroying angels". Together, the A. ballerina-A. zangii clade and the Phalloideae sensu Bas 1969 also form a well-supported clade. We therefore screened for two of the most notorious toxins by HPLC-MS analysis of methanolic extracts from the basidiomata. Interestingly, neither α-amanitin nor phalloidin was found in A. ballerina, whereas Amanita fuligineoides was confirmed to contain both α-amanitin and phalloidin, and A. brunneitoxicaria contained only α-amanitin. Together with unique morphological characteristics, the position in the phylogeny indicates that A. ballerina is either an important link in the evolution of the deadly Amanita sect. Phalloideae species, or a member of a new section also including A. zangii.

  1. Five (or so) challenges for species distribution modelling

    DEFF Research Database (Denmark)

    Bastos Araujo, Miguel; Guisan, Antoine

    2006-01-01

    Species distribution modelling is central to both fundamental and applied research in biogeography. Despite widespread use of models, there are still important conceptual ambiguities as well as biotic and algorithmic uncertainties that need to be investigated in order to increase confidence...... in model results. We identify and discuss five areas of enquiry that are of high importance for species distribution modelling: (1) clarification of the niche concept; (2) improved designs for sampling data for building models; (3) improved parameterization; (4) improved model selection and predictor...

  2. Fit-for-purpose: species distribution model performance depends on evaluation criteria - Dutch Hoverflies as a case study.

    Science.gov (United States)

    Aguirre-Gutiérrez, Jesús; Carvalheiro, Luísa G; Polce, Chiara; van Loon, E Emiel; Raes, Niels; Reemer, Menno; Biesmeijer, Jacobus C

    2013-01-01

    Understanding species distributions and the factors limiting them is an important topic in ecology and conservation, including in nature reserve selection and predicting climate change impacts. While Species Distribution Models (SDM) are the main tool used for these purposes, choosing the best SDM algorithm is not straightforward as these are plentiful and can be applied in many different ways. SDM are used mainly to gain insight in 1) overall species distributions, 2) their past-present-future probability of occurrence and/or 3) to understand their ecological niche limits (also referred to as ecological niche modelling). The fact that these three aims may require different models and outputs is, however, rarely considered and has not been evaluated consistently. Here we use data from a systematically sampled set of species occurrences to specifically test the performance of Species Distribution Models across several commonly used algorithms. Species range in distribution patterns from rare to common and from local to widespread. We compare overall model fit (representing species distribution), the accuracy of the predictions at multiple spatial scales, and the consistency in selection of environmental correlations all across multiple modelling runs. As expected, the choice of modelling algorithm determines model outcome. However, model quality depends not only on the algorithm, but also on the measure of model fit used and the scale at which it is used. Although model fit was higher for the consensus approach and Maxent, Maxent and GAM models were more consistent in estimating local occurrence, while RF and GBM showed higher consistency in environmental variables selection. Model outcomes diverged more for narrowly distributed species than for widespread species. We suggest that matching study aims with modelling approach is essential in Species Distribution Models, and provide suggestions how to do this for different modelling aims and species' data

  3. Reference genes for quantitative gene expression studies in multiple avian species.

    Directory of Open Access Journals (Sweden)

    Philipp Olias

    Full Text Available Quantitative real-time PCR (qPCR rapidly and reliably quantifies gene expression levels across different experimental conditions. Selection of suitable reference genes is essential for meaningful normalization and thus correct interpretation of data. In recent years, an increasing number of avian species other than the chicken has been investigated molecularly, highlighting the need for an experimentally validated pan-avian primer set for reference genes. Here we report testing a set for 14 candidate reference genes (18S, ABL, GAPDH, GUSB, HMBS, HPRT, PGK1, RPL13, RPL19, RPS7, SDHA, TFRC, VIM, YWHAZ on different tissues of the mallard (Anas platyrhynchos, domestic chicken (Gallus gallus domesticus, common crane (Grus grus, white-tailed eagle (Haliaeetus albicilla, domestic turkey (Meleagris gallopavo f. domestica, cockatiel (Nymphicus hollandicus, Humboldt penguin (Sphenicus humboldti, ostrich (Struthio camelus and zebra finch (Taeniopygia guttata, spanning a broad range of the phylogenetic tree of birds. Primer pairs for six to 11 genes were successfully established for each of the nine species. As a proof of principle, we analyzed expression levels of 10 candidate reference genes as well as FOXP2 and the immediate early genes, EGR1 and CFOS, known to be rapidly induced by singing in the avian basal ganglia. We extracted RNA from microbiopsies of the striatal song nucleus Area X of adult male zebra finches after they had sang or remained silent. Using three different statistical algorithms, we identified five genes (18S, PGK1, RPS7, TFRC, YWHAZ that were stably expressed within each group and also between the singing and silent conditions, establishing them as suitable reference genes. In conclusion, the newly developed pan-avian primer set allows accurate normalization and quantification of gene expression levels in multiple avian species.

  4. Enhancement of Innate and Adaptive Immune Functions by Multiple Echinacea Species

    Science.gov (United States)

    Zhai, Zili; Liu, Yi; Wu, Lankun; Senchina, David S.; Wurtele, Eve S.; Murphy, Patricia A.; Kohut, Marian L.; Cunnick, Joan E.

    2008-01-01

    Echinacea preparations are commonly used as nonspecific immunomodulatory agents. Alcohol extracts from three widely used Echinacea species, Echinacea angustifolia, Echinacea pallida, and Echinacea purpurea, were investigated for immunomodulating properties. The three Echinacea species demonstrated a broad difference in concentrations of individual lipophilic amides and hydrophilic caffeic acid derivatives. Mice were gavaged once a day (for 7 days) with one of the Echinacea extracts (130 mg/kg) or vehicle and immunized with sheep red blood cells (sRBC) 4 days prior to collection of immune cells for multiple immunological assays. The three herb extracts induced similar, but differential, changes in the percentage of immune cell populations and their biological functions, including increased percentages of CD49+ and CD19+ lymphocytes in spleen and natural killer cell cytotoxicity. Antibody response to sRBC was significantly increased equally by extracts of all three Echinacea species. Concanavalin A-stimulated splenocytes from E. angustifolia- and E. pallida-treated mice demonstrated significantly higher T cell proliferation. In addition, the Echinacea treatment significantly altered the cytokine production by mitogen-stimulated splenic cells. The three herbal extracts significantly increased interferon-γ production, but inhibited the release of tumor necrosis factor-α and interleukin (IL)-1β. Only E. angustifolia- and E. pallida-treated mice demonstrated significantly higher production of IL-4 and increased IL-10 production. Taken together, these findings demonstrated that Echinacea is a wide-spectrum immunomodulator that modulates both innate and adaptive immune responses. In particular, E. angustifolia or E. pallida may have more anti-inflammatory potential. PMID:17887935

  5. Reference genes for quantitative gene expression studies in multiple avian species.

    Science.gov (United States)

    Olias, Philipp; Adam, Iris; Meyer, Anne; Scharff, Constance; Gruber, Achim D

    2014-01-01

    Quantitative real-time PCR (qPCR) rapidly and reliably quantifies gene expression levels across different experimental conditions. Selection of suitable reference genes is essential for meaningful normalization and thus correct interpretation of data. In recent years, an increasing number of avian species other than the chicken has been investigated molecularly, highlighting the need for an experimentally validated pan-avian primer set for reference genes. Here we report testing a set for 14 candidate reference genes (18S, ABL, GAPDH, GUSB, HMBS, HPRT, PGK1, RPL13, RPL19, RPS7, SDHA, TFRC, VIM, YWHAZ) on different tissues of the mallard (Anas platyrhynchos), domestic chicken (Gallus gallus domesticus), common crane (Grus grus), white-tailed eagle (Haliaeetus albicilla), domestic turkey (Meleagris gallopavo f. domestica), cockatiel (Nymphicus hollandicus), Humboldt penguin (Sphenicus humboldti), ostrich (Struthio camelus) and zebra finch (Taeniopygia guttata), spanning a broad range of the phylogenetic tree of birds. Primer pairs for six to 11 genes were successfully established for each of the nine species. As a proof of principle, we analyzed expression levels of 10 candidate reference genes as well as FOXP2 and the immediate early genes, EGR1 and CFOS, known to be rapidly induced by singing in the avian basal ganglia. We extracted RNA from microbiopsies of the striatal song nucleus Area X of adult male zebra finches after they had sang or remained silent. Using three different statistical algorithms, we identified five genes (18S, PGK1, RPS7, TFRC, YWHAZ) that were stably expressed within each group and also between the singing and silent conditions, establishing them as suitable reference genes. In conclusion, the newly developed pan-avian primer set allows accurate normalization and quantification of gene expression levels in multiple avian species.

  6. An Ant-Based Model for Multiple Sequence Alignment

    CERN Document Server

    Guinand, Frédéric

    2008-01-01

    Multiple sequence alignment is a key process in today's biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple sequence alignment focuses on the building of structures in a new graph model: the factor graph model. This model relies on block-based formulation of the original problem, formulation that seems to be one of the most suitable ways for capturing evolutionary aspects of alignment. The structures are implicitly built by a colony of ants laying down pheromones in the factor graphs, according to relations between blocks belonging to the different sequences.

  7. Evolving Four Part Harmony Using a Multiple Worlds Model

    DEFF Research Database (Denmark)

    Scirea, Marco; Brown, Joseph Alexander

    2015-01-01

    This application of the Multiple Worlds Model examines a collaborative fitness model for generating four part harmonies. In this model we have multiple populations and the fitness of the individuals is based on the ability of a member from each population to work with the members of other...... populations. We present the result of two experiments: the generation of compositions, given a static voice line, both in a constrained and unconstrained harmonic framework. The remaining three voices are evolved using this collaborative fitness function, which looks for a number of classical composition...

  8. Efficient Adoption and Assessment of Multiple Process Improvement Reference Models

    Directory of Open Access Journals (Sweden)

    Simona Jeners

    2013-06-01

    Full Text Available A variety of reference models such as CMMI, COBIT or ITIL support IT organizations to improve their processes. These process improvement reference models (IRMs cover different domains such as IT development, IT Services or IT Governance but also share some similarities. As there are organizations that address multiple domains and need to coordinate their processes in their improvement we present MoSaIC, an approach to support organizations to efficiently adopt and conform to multiple IRMs. Our solution realizes a semantic integration of IRMs based on common meta-models. The resulting IRM integration model enables organizations to efficiently implement and asses multiple IRMs and to benefit from synergy effects.

  9. Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

    Directory of Open Access Journals (Sweden)

    Deng Minghua

    2008-12-01

    Full Text Available Abstract Background Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs. Therefore, revealing the underlying regulatory mechanisms of transcripts becomes imperative. However, for a complete understanding of transcriptional regulatory mechanisms, we need to identify the regions in which they are found. We will call these transcriptional regulation regions, or TRRs, which can be considered functional regions containing a cluster of regulatory elements that cooperatively recruit transcriptional factors for binding and then regulating the expression of transcripts. Results We constructed a hierarchical stochastic language (HSL model for the identification of core TRRs in yeast based on regulatory cooperation among TRR elements. The HSL model trained based on yeast achieved comparable accuracy in predicting TRRs in other species, e.g., fruit fly, human, and rice, thus demonstrating the conservation of TRRs across species. The HSL model was also used to identify the TRRs of genes, such as p53 or OsALYL1, as well as microRNAs. In addition, the ENCODE regions were examined by HSL, and TRRs were found to pervasively locate in the genomes. Conclusion Our findings indicate that 1 the HSL model can be used to accurately predict core TRRs of transcripts across species and 2 identified core TRRs by HSL are proper candidates for the further scrutiny of specific regulatory elements and mechanisms. Meanwhile, the regulatory activity taking place in the abundant numbers of ncRNAs might account for the ubiquitous presence of TRRs across the genome. In addition, we also found that the TRRs of protein coding genes and ncRNAs are similar in structure, with the latter being more conserved than the former.

  10. A methodology to calibrate pedestrian walker models using multiple objectives

    NARCIS (Netherlands)

    Campanella, M.C.; Daamen, W.; Hoogendoorn, S.P.

    2012-01-01

    The application of walker models to simulate real situations require accuracy in several traffic situations. One strategy to obtain a generic model is to calibrate the parameters in several situations using multiple-objective functions in the optimization process. In this paper, we propose a general

  11. Theoretical biology: Comparing models of species abundance - Brief Communications Arising

    NARCIS (Netherlands)

    Chave, J.; Alonso, D.; Etienne, R.S.

    2006-01-01

    Ecologists are struggling to explain how so many tropical tree species can coexist in tropical forests, and several empirical studies have demonstrated that negative density dependence is an important mechanism of tree-species coexistence1, 2. Volkov et al.3 compare a model incorporating negative de

  12. Comparing the performance of species distribution models of

    NARCIS (Netherlands)

    Valle , M.; van Katwijk, M.M.; de Jong, D.J.; Bouma, T.; Schipper, A.M.; Chust, G.; Benito, B.M.; Garmendia, J.M.; Borja, A.

    2013-01-01

    Intertidal seagrasses show high variability in their extent and location, with local extinctions and (re-)colonizations being inherent in their population dynamics. Suitable habitats are identified usually using Species Distribution Models (SDM), based upon the overall distribution of the species;

  13. Immersed boundary lattice Boltzmann model based on multiple relaxation times.

    Science.gov (United States)

    Lu, Jianhua; Han, Haifeng; Shi, Baochang; Guo, Zhaoli

    2012-01-01

    As an alterative version of the lattice Boltzmann models, the multiple relaxation time (MRT) lattice Boltzmann model introduces much less numerical boundary slip than the single relaxation time (SRT) lattice Boltzmann model if some special relationship between the relaxation time parameters is chosen. On the other hand, most current versions of the immersed boundary lattice Boltzmann method, which was first introduced by Feng and improved by many other authors, suffer from numerical boundary slip as has been investigated by Le and Zhang. To reduce such a numerical boundary slip, an immerse boundary lattice Boltzmann model based on multiple relaxation times is proposed in this paper. A special formula is given between two relaxation time parameters in the model. A rigorous analysis and the numerical experiments carried out show that the numerical boundary slip reduces dramatically by using the present model compared to the single-relaxation-time-based model.

  14. Incorporating spatial autocorrelation into species distribution models alters forecasts of climate-mediated range shifts.

    Science.gov (United States)

    Crase, Beth; Liedloff, Adam; Vesk, Peter A; Fukuda, Yusuke; Wintle, Brendan A

    2014-08-01

    Species distribution models (SDMs) are widely used to forecast changes in the spatial distributions of species and communities in response to climate change. However, spatial autocorrelation (SA) is rarely accounted for in these models, despite its ubiquity in broad-scale ecological data. While spatial autocorrelation in model residuals is known to result in biased parameter estimates and the inflation of type I errors, the influence of unmodeled SA on species' range forecasts is poorly understood. Here we quantify how accounting for SA in SDMs influences the magnitude of range shift forecasts produced by SDMs for multiple climate change scenarios. SDMs were fitted to simulated data with a known autocorrelation structure, and to field observations of three mangrove communities from northern Australia displaying strong spatial autocorrelation. Three modeling approaches were implemented: environment-only models (most frequently applied in species' range forecasts), and two approaches that incorporate SA; autologistic models and residuals autocovariate (RAC) models. Differences in forecasts among modeling approaches and climate scenarios were quantified. While all model predictions at the current time closely matched that of the actual current distribution of the mangrove communities, under the climate change scenarios environment-only models forecast substantially greater range shifts than models incorporating SA. Furthermore, the magnitude of these differences intensified with increasing increments of climate change across the scenarios. When models do not account for SA, forecasts of species' range shifts indicate more extreme impacts of climate change, compared to models that explicitly account for SA. Therefore, where biological or population processes induce substantial autocorrelation in the distribution of organisms, and this is not modeled, model predictions will be inaccurate. These results have global importance for conservation efforts as inaccurate

  15. Multiple QoS modeling and algorithm in computational grid

    Institute of Scientific and Technical Information of China (English)

    Li Chunlin; Feng Meilai; Li Layuan

    2007-01-01

    Multiple QoS modeling and algorithm in grid system is considered.Grid QoS requirements can be formulated as a utility function for each task as a weighted sum of its each dimensional QoS utility functions.Multiple QoS constraint resource scheduling optimization in computational grid is distributed to two subproblems: optimization of grid user and grid resource provider.Grid QoS scheduling can be achieved by solving sub problems via an iterative algorithm.

  16. GLOBAL ATTRACTIVITY IN A PERIODIC DELAY SINGLE SPECIES MODEL

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    In this paper, we establish the existence of a positive periodic solution for a periodic delay single species population growth model, and obtain sufficient conditions for the periodic solution to be globally attractive.

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

    Directory of Open Access Journals (Sweden)

    Thibaud Rougier

    Full Text Available 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

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

    Science.gov (United States)

    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

  19. AgMIP Training in Multiple Crop Models and Tools

    Science.gov (United States)

    Boote, Kenneth J.; Porter, Cheryl H.; Hargreaves, John; Hoogenboom, Gerrit; Thornburn, Peter; Mutter, Carolyn

    2015-01-01

    The Agricultural Model Intercomparison and Improvement Project (AgMIP) has the goal of using multiple crop models to evaluate climate impacts on agricultural production and food security in developed and developing countries. There are several major limitations that must be overcome to achieve this goal, including the need to train AgMIP regional research team (RRT) crop modelers to use models other than the ones they are currently familiar with, plus the need to harmonize and interconvert the disparate input file formats used for the various models. Two activities were followed to address these shortcomings among AgMIP RRTs to enable them to use multiple models to evaluate climate impacts on crop production and food security. We designed and conducted courses in which participants trained on two different sets of crop models, with emphasis on the model of least experience. In a second activity, the AgMIP IT group created templates for inputting data on soils, management, weather, and crops into AgMIP harmonized databases, and developed translation tools for converting the harmonized data into files that are ready for multiple crop model simulations. The strategies for creating and conducting the multi-model course and developing entry and translation tools are reviewed in this chapter.

  20. The occurrence of mtDNA heteroplasmy in multiple cetacean species.

    Science.gov (United States)

    Vollmer, Nicole L; Viricel, Amélia; Wilcox, Lynsey; Katherine Moore, M; Rosel, Patricia E

    2011-04-01

    In population genetics and phylogenetic studies, mitochondrial DNA (mtDNA) is commonly used for examining differences both between and within groups of individuals. For these studies, correct interpretation of every nucleotide position is crucial but can be complicated by the presence of ambiguous bases resulting from heteroplasmy. Particularly for non-model taxa, the presence of heteroplasmy in mtDNA is rarely reported, therefore, it is unclear how commonly it occurs and how it can affect phylogenetic relationships among taxa and the overall understanding of evolutionary processes. We examined the occurrence of both site and length heteroplasmy within the mtDNA of ten marine mammal species, for most of which mtDNA heteroplasmy has never been reported. After sequencing a portion of the mtDNA control region for 5,062 individuals, we found heteroplasmy in at least 2% of individuals from seven species, including Stenella frontalis where 58.9% were heteroplasmic. We verified the presence of true heteroplasmy, ruling out artifacts from amplification and sequencing methods and the presence of nuclear copies of mitochondrial genes. We found no evidence that mtDNA heteroplasmy influenced phylogenetic relationships, however, its occurrence does have the potential to increase the genetic diversity for all species in which it is found. This study stresses the importance of both detecting and reporting the occurrence of heteroplasmy in wild populations in order to enhance the knowledge of both the introduction and the persistence of mutant mitochondrial haplotypes in the evolutionary process.

  1. Modeling microstructural evolution of multiple texture components during recrystallization

    DEFF Research Database (Denmark)

    Vandermeer, R.A.; Juul Jensen, D.

    1994-01-01

    using stereological point and lineal measurements of microstructural properties in combination with EBSP analysis for orientation determinations. The potential of the models to describe the observed recrystallization behavior of heavily cold-rolled commercial aluminum was demonstrated. A successful MPM......Models were formulated in an effort to characterize recrystallization in materials with multiple texture components. The models are based on a microstructural path methodology (MPM). Experimentally the microstructural evolution of conmmercial aluminum during recrystallization was characterized...

  2. Multiple comparisons in genetic association studies: a hierarchical modeling approach.

    Science.gov (United States)

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

    2014-02-01

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

  3. Manifold learning for object tracking with multiple nonlinear models.

    Science.gov (United States)

    Nascimento, Jacinto C; Silva, Jorge G; Marques, Jorge S; Lemos, Joao M

    2014-04-01

    This paper presents a novel manifold learning algorithm for high-dimensional data sets. The scope of the application focuses on the problem of motion tracking in video sequences. The framework presented is twofold. First, it is assumed that the samples are time ordered, providing valuable information that is not presented in the current methodologies. Second, the manifold topology comprises multiple charts, which contrasts to the most current methods that assume one single chart, being overly restrictive. The proposed algorithm, Gaussian process multiple local models (GP-MLM), can deal with arbitrary manifold topology by decomposing the manifold into multiple local models that are probabilistic combined using Gaussian process regression. In addition, the paper presents a multiple filter architecture where standard filtering techniques are integrated within the GP-MLM. The proposed approach exhibits comparable performance of state-of-the-art trackers, namely multiple model data association and deep belief networks, and compares favorably with Gaussian process latent variable models. Extensive experiments are presented using real video data, including a publicly available database of lip sequences and left ventricle ultrasound images, in which the GP-MLM achieves state of the art results.

  4. A Bayesian Hierarchical Model for Relating Multiple SNPs within Multiple Genes to Disease Risk

    Directory of Open Access Journals (Sweden)

    Lewei Duan

    2013-01-01

    Full Text Available A variety of methods have been proposed for studying the association of multiple genes thought to be involved in a common pathway for a particular disease. Here, we present an extension of a Bayesian hierarchical modeling strategy that allows for multiple SNPs within each gene, with external prior information at either the SNP or gene level. The model involves variable selection at the SNP level through latent indicator variables and Bayesian shrinkage at the gene level towards a prior mean vector and covariance matrix that depend on external information. The entire model is fitted using Markov chain Monte Carlo methods. Simulation studies show that the approach is capable of recovering many of the truly causal SNPs and genes, depending upon their frequency and size of their effects. The method is applied to data on 504 SNPs in 38 candidate genes involved in DNA damage response in the WECARE study of second breast cancers in relation to radiotherapy exposure.

  5. Species clustering in competitive Lotka-Volterra models.

    Science.gov (United States)

    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.

  6. Biomass models to estimate carbon stocks for hardwood tree species

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz-Peinado, R.; Montero, G.; Rio, M. del

    2012-11-01

    To estimate forest carbon pools from forest inventories it is necessary to have biomass models or biomass expansion factors. In this study, tree biomass models were developed for the main hardwood forest species in Spain: Alnus glutinosa, Castanea sativa, Ceratonia siliqua, Eucalyptus globulus, Fagus sylvatica, Fraxinus angustifolia, Olea europaea var. sylvestris, Populus x euramericana, Quercus canariensis, Quercus faginea, Quercus ilex, Quercus pyrenaica and Quercus suber. Different tree biomass components were considered: stem with bark, branches of different sizes, above and belowground biomass. For each species, a system of equations was fitted using seemingly unrelated regression, fulfilling the additivity property between biomass components. Diameter and total height were explored as independent variables. All models included tree diameter whereas for the majority of species, total height was only considered in the stem biomass models and in some of the branch models. The comparison of the new biomass models with previous models fitted separately for each tree component indicated an improvement in the accuracy of the models. A mean reduction of 20% in the root mean square error and a mean increase in the model efficiency of 7% in comparison with recently published models. So, the fitted models allow estimating more accurately the biomass stock in hardwood species from the Spanish National Forest Inventory data. (Author) 45 refs.

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

    Science.gov (United States)

    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.

  8. Comparison of multiplicative heterogeneous variance adjustment models for genetic evaluations.

    Science.gov (United States)

    Márkus, Sz; Mäntysaari, E A; Strandén, I; Eriksson, J-Å; Lidauer, M H

    2014-06-01

    Two heterogeneous variance adjustment methods and two variance models were compared in a simulation study. The method used for heterogeneous variance adjustment in the Nordic test-day model, which is a multiplicative method based on Meuwissen (J. Dairy Sci., 79, 1996, 310), was compared with a restricted multiplicative method where the fixed effects were not scaled. Both methods were tested with two different variance models, one with a herd-year and the other with a herd-year-month random effect. The simulation study was built on two field data sets from Swedish Red dairy cattle herds. For both data sets, 200 herds with test-day observations over a 12-year period were sampled. For one data set, herds were sampled randomly, while for the other, each herd was required to have at least 10 first-calving cows per year. The simulations supported the applicability of both methods and models, but the multiplicative mixed model was more sensitive in the case of small strata sizes. Estimation of variance components for the variance models resulted in different parameter estimates, depending on the applied heterogeneous variance adjustment method and variance model combination. Our analyses showed that the assumption of a first-order autoregressive correlation structure between random-effect levels is reasonable when within-herd heterogeneity is modelled by year classes, but less appropriate for within-herd heterogeneity by month classes. Of the studied alternatives, the multiplicative method and a variance model with a random herd-year effect were found most suitable for the Nordic test-day model for dairy cattle evaluation.

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

    Science.gov (United States)

    Gonzalez, Sergio C; Soto-Centeno, J Angel; Reed, David L

    2011-09-19

    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. 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. 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.

  10. Collisonal Friction Enhanced by Two-Stream Instabilities Determines the Bohm Criterion in Plasmas With Multiple Ion Species

    Science.gov (United States)

    Baalrud, S. D.; Hegna, C. C.; Callen, J. D.

    2009-10-01

    Ion-ion streaming instabilities are excited in the presheath region of plasmas with multiple ion species if the ions are much colder than the electrons. Streaming instabilities onset when the relative fluid flow between ion species exceeds a critical speed, δVc, of order the ion thermal speeds. Using a generalized Lenard-Balescu theory that accounts for instability-enhanced collective responses [1], one is able to show the instabilities rapidly (within a few Debye lengths) enhance the collisional friction between ion species far beyond the contribution from Coulomb collisions alone. This strong frictional force determines the relative fluid speed between species. When this condition is combined with the Bohm criterion generalized for multiple ion species, the fluid speed of each ion species is determined at the sheath edge. For each species, this speed differs from the common ``system'' sound speed by a factor that depends on the species concentration and δVc.[4pt] [1] S.D. Baalrud, J.D. Callen, and C.C. Hegna, Phys. Plasmas 15, 092111 (2008).

  11. Image-based red blood cell counter for multiple species of wild and domestic animals

    Directory of Open Access Journals (Sweden)

    C.R.M. Mauricio

    Full Text Available ABSTRACT RBC count plays an important role in animal diagnosis. Despite the many technologies available in different automated hematology analyzers, when it comes to the blood of wild animals it is still difficult to find an easy and affordable solution for multiple species. This study aims to evaluate the proposed automatic red blood cell counter. Blood samples (1 ocelot - Leopardus pardalis, 1 monkey - Cebus apella, 1 coati - Nasua nasua, 62 dogs - Canis familiaris, and 5 horses - Equus caballus were analyzed using three methods: 1-manual count, 2-automatic count by image, and 3-semi-automatic count by image; blood from dogs and horses were also analyzed by a fourth method: 4-automatic count by impedance. The counts in methods 2 and 3 were produced by the proposed red blood cell counter. Results were compared using Pearson's correlation and plots with different methods as the criterion standard. RBC counts in methods 1, 2, and 3 correlated very well with those in the method 4 (r ≥ 0.94. RBC counts produced by method 2 were highly correlated with method 3 (r = 0.998. The results indicate that the proposed method can be used as an automatic or semi-automatic counting method in clinics that are currently using the manual method for RBC assessment.

  12. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.

    Science.gov (United States)

    Chen, Wen; Djama, Zeinab Robleh; Coffey, Michael D; Martin, Frank N; Bilodeau, Guillaume J; Radmer, Lorien; Denton, Geoff; Lévesque, C André

    2013-01-01

    Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

  13. Development of an Immunochromatography Assay (QuickNavi-Ebola) to Detect Multiple Species of Ebolaviruses.

    Science.gov (United States)

    Yoshida, Reiko; Muramatsu, Shino; Akita, Hiroshi; Saito, Yuji; Kuwahara, Miwa; Kato, Daisuke; Changula, Katendi; Miyamoto, Hiroko; Kajihara, Masahiro; Manzoor, Rashid; Furuyama, Wakako; Marzi, Andrea; Feldmann, Heinz; Mweene, Aaron; Masumu, Justin; Kapeteshi, Jimmy; Muyembe-Tamfum, Jean-Jacques; Takada, Ayato

    2016-10-15

    The latest outbreak of Ebola virus disease (EVD) in West Africa has highlighted the urgent need for the development of rapid and reliable diagnostic assays. We used monoclonal antibodies specific to the ebolavirus nucleoprotein to develop an immunochromatography (IC) assay (QuickNavi-Ebola) for rapid diagnosis of EVD. The IC assay was first evaluated with tissue culture supernatants of infected Vero E6 cells and found to be capable of detecting 10(3)-10(4) focus-forming units/mL of ebolaviruses. Using serum samples from experimentally infected nonhuman primates, we confirmed that the assay could detect the viral antigen shortly after disease onset. It was also noted that multiple species of ebolaviruses could be detected by the IC assay. Owing to the simplicity of the assay procedure and absence of requirements for special equipment and training, QuickNavi-Ebola is expected to be a useful tool for rapid diagnosis of EVD. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

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

    Science.gov (United States)

    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

  15. A Collaborative Scheduling Model for the Supply-Hub with Multiple Suppliers and Multiple Manufacturers

    Directory of Open Access Journals (Sweden)

    Guo Li

    2014-01-01

    Full Text Available This paper investigates a collaborative scheduling model in the assembly system, wherein multiple suppliers have to deliver their components to the multiple manufacturers under the operation of Supply-Hub. We first develop two different scenarios to examine the impact of Supply-Hub. One is that suppliers and manufacturers make their decisions separately, and the other is that the Supply-Hub makes joint decisions with collaborative scheduling. The results show that our scheduling model with the Supply-Hub is a NP-complete problem, therefore, we propose an auto-adapted differential evolution algorithm to solve this problem. Moreover, we illustrate that the performance of collaborative scheduling by the Supply-Hub is superior to separate decision made by each manufacturer and supplier. Furthermore, we also show that the algorithm proposed has good convergence and reliability, which can be applicable to more complicated supply chain environment.

  16. Analytically tractable model for community ecology with many species

    Science.gov (United States)

    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.

  17. Multiple commodities in statistical microeconomics: Model and market

    Science.gov (United States)

    Baaquie, Belal E.; Yu, Miao; Du, Xin

    2016-11-01

    A statistical generalization of microeconomics has been made in Baaquie (2013). In Baaquie et al. (2015), the market behavior of single commodities was analyzed and it was shown that market data provides strong support for the statistical microeconomic description of commodity prices. The case of multiple commodities is studied and a parsimonious generalization of the single commodity model is made for the multiple commodities case. Market data shows that the generalization can accurately model the simultaneous correlation functions of up to four commodities. To accurately model five or more commodities, further terms have to be included in the model. This study shows that the statistical microeconomics approach is a comprehensive and complete formulation of microeconomics, and which is independent to the mainstream formulation of microeconomics.

  18. 3D scene modeling from multiple range views

    Science.gov (United States)

    Sequeira, Vitor; Goncalves, Joao G. M.; Ribeiro, M. Isabel

    1995-09-01

    This paper presents a new 3D scene analysis system that automatically reconstructs the 3D geometric model of real-world scenes from multiple range images acquired by a laser range finder on board of a mobile robot. The reconstruction is achieved through an integrated procedure including range data acquisition, geometrical feature extraction, registration, and integration of multiple views. Different descriptions of the final 3D scene model are obtained: a polygonal triangular mesh, a surface description in terms of planar and biquadratics surfaces, and a 3D boundary representation. Relevant experimental results from the complete 3D scene modeling are presented. Direct applications of this technique include 3D reconstruction and/or update of architectual or industrial plans into a CAD model, design verification of buildings, navigation of autonomous robots, and input to virtual reality systems.

  19. Particle multiplicities and particle ratios in excluded volume model

    CERN Document Server

    Mishra, M

    2008-01-01

    One of the most surprising results is to find that a consistent description of all the experimental results on particle multiplicities and particle ratios obtained from the lowest AGS to the highest RHIC energies is possible within the framework of a thermal statistical model. We propose here a thermodynamically consistent excluded-volume model involving an interacting multi-component hadron gas. We find that the energy dependence of the total multiplicities of strange and non-strange hadrons obtained in this model agrees closely with the experimental results. It indicates that the freeze out volume of the fireball is uniformly the same for all the particles. We have also compared the variation of the particle ratios such as $/, /, K^{-}/K^{+}, \\bar{p}/p, \\bar{\\Lambda}/\\Lambda, \\bar{\\Xi}/\\Xi, \\bar{\\Omega}/\\Omega, /, /, /$ and $/$ with respect to the center-of-mass energy as predicted by our model with the recent experimental data.

  20. A Survey of Health Care Models that Encompass Multiple Departments

    NARCIS (Netherlands)

    Vanberkel, Peter T.; Boucherie, Richardus J.; Hans, Elias W.; Hurink, Johann L.; Litvak, Nelli

    2009-01-01

    In this survey we review quantitative health care models to illustrate the extent to which they encompass multiple hospital departments. The paper provides general overviews of the relationships that exists between major hospital departments and describes how these relationships are accounted for by

  1. A survey of health care models that encompass multiple departments

    NARCIS (Netherlands)

    Vanberkel, P.T.; Boucherie, Richardus J.; Hans, Elias W.; Hurink, Johann L.; Litvak, Nelli

    2009-01-01

    In this survey we review quantitative health care models to illustrate the extent to which they encompass multiple hospital departments. The paper provides general overviews of the relationships that exists between major hospital departments and describes how these relationships are accounted for by

  2. EAE : imperfect but useful models of multiple sclerosis

    NARCIS (Netherlands)

    't Hart, Bert A.; Gran, Bruno; Weissert, Robert

    2011-01-01

    The high failure rate of immunotherapies in multiple sclerosis (MS) clinical trials demonstrates problems in translating new treatment concepts from animal models to the patient. One main reason for this 'immunotherapy gap' is the usage of immunologically immature, microbiologically clean and geneti

  3. Multiple-Model Adaptive Switching Control for Uncertain Multivariable Systems

    NARCIS (Netherlands)

    Baldi, Simone; Battistelli, Giorgio; Mari, Daniele; Mosca, Edoardo; Tesi, Pietro

    2011-01-01

    This paper addresses the problem of controlling an uncertain multi-input multi-output (MIMO) system by means of adaptive switching control schemes. In particular, the paper aims at extending the approach of multiple-model unfalsified adaptive switched control, so far restricted to single-input singl

  4. Geant4 models for simulation of multiple scattering

    CERN Document Server

    Ivanchenko, V N; Maire, M; Urban, L

    2010-01-01

    Recent progress in development of single and multiple scattering models within the Geant4 toolkit is presented. Different options available to users are discussed. The comparisons with the data are shown. The trade of precision versus CPU performance is discussed with the focus on LHC detectors simulation

  5. Fraction Multiplication and Division Models: A Practitioner Reference Paper

    Science.gov (United States)

    Ervin, Heather K.

    2017-01-01

    It is well documented in literature that rational number is an important area of understanding in mathematics. Therefore, it follows that teachers and students need to have an understanding of rational number and related concepts such as fraction multiplication and division. This practitioner reference paper examines models that are important to…

  6. Multiple Imputation of Predictor Variables Using Generalized Additive Models

    NARCIS (Netherlands)

    de Jong, Roel; van Buuren, Stef; Spiess, Martin

    2016-01-01

    The sensitivity of multiple imputation methods to deviations from their distributional assumptions is investigated using simulations, where the parameters of scientific interest are the coefficients of a linear regression model, and values in predictor variables are missing at random. The performanc

  7. Modeling symbiosis by interactions through species carrying capacities

    Science.gov (United States)

    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.

  8. Modelling bioaccumulation of oil constituents in aquatic species

    NARCIS (Netherlands)

    Hoop, de L.; Huijbregts, M.A.J.; Schipper, A.M.; Veltman, K.; Laender, de F.; Viaene, K.P.J.; Klok, C.; Hendriks, A.J.

    2013-01-01

    Crude oil poses a risk to marine ecosystems due to its toxicity and tendency to accumulate in biota. The present study evaluated the applicability of the OMEGA model for estimating oil accumulation in aquatic species by comparing model predictions of kinetic rates (absorption and elimination) and bi

  9. Modelling the effect of climate change on species ranges

    NARCIS (Netherlands)

    Nagelkerke, C.J.; Alkemade, J.R.M.

    2003-01-01

    Three main types of models can be used to understand and predict climate-related range shifts. Equilibrium models predict potential future distributions from the current climate envelope of a species, but do not take migration constraints into account. They show that future range changes can be

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

    Science.gov (United States)

    Fordyce, James A.

    2017-01-01

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

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

    Science.gov (United States)

    Robinson, Jason L; Fordyce, James A

    2017-01-01

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

  12. Multiple-relaxation-time model for the correct thermohydrodynamic equations.

    Science.gov (United States)

    Zheng, Lin; Shi, Baochang; Guo, Zhaoli

    2008-08-01

    A coupling lattice Boltzmann equation (LBE) model with multiple relaxation times is proposed for thermal flows with viscous heat dissipation and compression work. In this model the fixed Prandtl number and the viscous dissipation problems in the energy equation, which exist in most of the LBE models, are successfully overcome. The model is validated by simulating the two-dimensional Couette flow, thermal Poiseuille flow, and the natural convection flow in a square cavity. It is found that the numerical results agree well with the analytical solutions and/or other numerical results.

  13. Infinite Multiple Membership Relational Modeling for Complex Networks

    DEFF Research Database (Denmark)

    Mørup, Morten; Schmidt, Mikkel Nørgaard; Hansen, Lars Kai

    Learning latent structure in complex networks has become an important problem fueled by many types of networked data originating from practically all fields of science. In this paper, we propose a new non-parametric Bayesian multiplemembership latent feature model for networks. Contrary to existing...... multiplemembership models that scale quadratically in the number of vertices the proposedmodel scales linearly in the number of links admittingmultiple-membership analysis in large scale networks. We demonstrate a connection between the single membership relational model and multiple membership models and show...

  14. Niche variability and its consequences for species distribution modeling.

    Directory of Open Access Journals (Sweden)

    Matt J Michel

    Full Text Available When species distribution models (SDMs are used to predict how a species will respond to environmental change, an important assumption is that the environmental niche of the species is conserved over evolutionary time-scales. Empirical studies conducted at ecological time-scales, however, demonstrate that the niche of some species can vary in response to environmental change. We use habitat and locality data of five species of stream fishes collected across seasons to examine the effects of niche variability on the accuracy of projections from Maxent, a popular SDM. We then compare these predictions to those from an alternate method of creating SDM projections in which a transformation of the environmental data to similar scales is applied. The niche of each species varied to some degree in response to seasonal variation in environmental variables, with most species shifting habitat use in response to changes in canopy cover or flow rate. SDMs constructed from the original environmental data accurately predicted the occurrences of one species across all seasons and a subset of seasons for two other species. A similar result was found for SDMs constructed from the transformed environmental data. However, the transformed SDMs produced better models in ten of the 14 total SDMs, as judged by ratios of mean probability values at known presences to mean probability values at all other locations. Niche variability should be an important consideration when using SDMs to predict future distributions of species because of its prevalence among natural populations. The framework we present here may potentially improve these predictions by accounting for such variability.

  15. Incorporating Student Mobility in Achievement Growth Modeling: A Cross-Classified Multiple Membership Growth Curve Model

    Science.gov (United States)

    Grady, Matthew W.; Beretvas, S. Natasha

    2010-01-01

    Multiple membership random effects models (MMREMs) have been developed for use in situations where individuals are members of multiple higher level organizational units. Despite their availability and the frequency with which multiple membership structures are encountered, no studies have extended the MMREM approach to hierarchical growth curve…

  16. Multiple ontologies in action: composite annotations for biosimulation models.

    Science.gov (United States)

    Gennari, John H; Neal, Maxwell L; Galdzicki, Michal; Cook, Daniel L

    2011-02-01

    There now exists a rich set of ontologies that provide detailed semantics for biological entities of interest. However, there is not (nor should there be) a single source ontology that provides all the necessary semantics for describing biological phenomena. In the domain of physiological biosimulation models, researchers use annotations to convey semantics, and many of these annotations require the use of multiple reference ontologies. Therefore, we have developed the idea of composite annotations that access multiple ontologies to capture the physics-based meaning of model variables. These composite annotations provide the semantic expressivity needed to disambiguate the often-complex features of biosimulation models, and can be used to assist with model merging and interoperability. In this paper, we demonstrate the utility of composite annotations for model merging by describing their use within SemGen, our semantics-based model composition software. More broadly, if orthogonal reference ontologies are to meet their full potential, users need tools and methods to connect and link these ontologies. Our composite annotations and the SemGen tool provide one mechanism for leveraging multiple reference ontologies.

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

    Science.gov (United States)

    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.

  18. Can fire atlas data improve species distribution model projections?

    Science.gov (United States)

    Crimmins, Shawn M; Dobrowski, Solomon Z; Mynsberge, Alison R; Safford, Hugh D

    2014-07-01

    Correlative species distribution models (SDMs) are widely used in studies of climate change impacts, yet are often criticized for failing to incorporate disturbance processes that can influence species distributions. Here we use two temporally independent data sets of vascular plant distributions, climate data, and fire atlas data to examine the influence of disturbance history on SDM projection accuracy through time in the mountain ranges of California, USA. We used hierarchical partitioning to examine the influence of fire occurrence on the distribution of 144 vascular plant species and built a suite of SDMs to examine how the inclusion of fire-related predictors (fire occurrence and departure from historical fire return intervals) affects SDM projection accuracy. Fire occurrence provided the least explanatory power among predictor variables for predicting species' distributions, but provided improved explanatory power for species whose regeneration is tied closely to fire. A measure of the departure from historic fire return interval had greater explanatory power for calibrating modern SDMs than fire occurrence. This variable did not improve internal model accuracy for most species, although it did provide marginal improvement to models for species adapted to high-frequency fire regimes. Fire occurrence and fire return interval departure were strongly related to the climatic covariates used in SDM development, suggesting that improvements in model accuracy may not be expected due to limited additional explanatory power. Our results suggest that the inclusion of coarse-scale measures of disturbance in SDMs may not be necessary to predict species distributions under climate change, particularly for disturbance processes that are largely mediated by climate.

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

    Science.gov (United States)

    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

    2016-07-06

    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.

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

    Science.gov (United States)

    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.

  1. Considerations for building climate-based species distribution models

    Science.gov (United States)

    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.

  2. Weibull model of multiplicity distribution in hadron-hadron collisions

    Science.gov (United States)

    Dash, Sadhana; Nandi, Basanta K.; Sett, Priyanka

    2016-06-01

    We introduce the use of the Weibull distribution as a simple parametrization of charged particle multiplicities in hadron-hadron collisions at all available energies, ranging from ISR energies to the most recent LHC energies. In statistics, the Weibull distribution has wide applicability in natural processes that involve fragmentation processes. This provides a natural connection to the available state-of-the-art models for multiparticle production in hadron-hadron collisions, which involve QCD parton fragmentation and hadronization. The Weibull distribution describes the multiplicity data at the most recent LHC energies better than the single negative binomial distribution.

  3. Dynamic force spectroscopy on multiple bonds: experiments and model

    CERN Document Server

    Erdmann, T; Nassoy, P; Schwarz, U S

    2007-01-01

    We probe the dynamic strength of multiple biotin-streptavidin adhesion bonds under linear loading using the biomembrane force probe setup for dynamic force spectroscopy. Measured rupture force histograms are compared to results from a master equation model for the stochastic dynamics of bond rupture under load. This allows us to extract the distribution of the number of initially closed bonds. We also extract the molecular parameters of the adhesion bonds, in good agreement with earlier results from single bond experiments. Our analysis shows that the peaks in the measured histograms are not simple multiples of the single bond values, but follow from a superposition procedure which generates different peak positions.

  4. Using occupancy estimation to assess the effectiveness of a regional multiple-species conservation plan: bats in the Pacific Northwest

    Science.gov (United States)

    Theodore Weller

    2008-01-01

    Regional conservation plans are increasingly used to plan for and protect biodiversity at large spatial scales however the means of quantitatively evaluating their effectiveness are rarely specified. Multiple-species approaches, particular those which employ site-occupancy estimation, have been proposed as robust and efficient alternatives for assessing the status of...

  5. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization

    CSIR Research Space (South Africa)

    Gcebe, N

    2017-04-01

    Full Text Available Journal of Systematic and Evolutionary Microbiology: DOI 10.1099/ijsem.0.001678 Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization Gcebe N Rutten V Gey...

  6. Heterogeneity in DNA multiple alignments: modeling, inference, and applications in motif finding.

    Science.gov (United States)

    Chen, Gong; Zhou, Qing

    2010-09-01

    Transcription factors bind sequence-specific sites in DNA to regulate gene transcription. Identifying transcription factor binding sites (TFBSs) is an important step for understanding gene regulation. Although sophisticated in modeling TFBSs and their combinatorial patterns, computational methods for TFBS detection and motif finding often make oversimplified homogeneous model assumptions for background sequences. Since nucleotide base composition varies across genomic regions, it is expected to be helpful for motif finding to incorporate the heterogeneity into background modeling. When sequences from multiple species are utilized, variation in evolutionary conservation violates the common assumption of an identical conservation level in multiple alignments. To handle both types of heterogeneity, we propose a generative model in which a segmented Markov chain is used to partition a multiple alignment into regions of homogeneous nucleotide base composition and a hidden Markov model (HMM) is employed to account for different conservation levels. Bayesian inference on the model is developed via Gibbs sampling with dynamic programming recursions. Simulation studies and empirical evidence from biological data sets reveal the dramatic effect of background modeling on motif finding, and demonstrate that the proposed approach is able to achieve substantial improvements over commonly used background models.

  7. Neuroprotection in a novel mouse model of multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    Katie Lidster

    Full Text Available Multiple sclerosis is an immune-mediated, demyelinating and neurodegenerative disease that currently lacks any neuroprotective treatments. Innovative neuroprotective trial designs are required to hasten the translational process of drug development. An ideal target to monitor the efficacy of strategies aimed at treating multiple sclerosis is the visual system, which is the most accessible part of the human central nervous system. A novel C57BL/6 mouse line was generated that expressed transgenes for a myelin oligodendrocyte glycoprotein-specific T cell receptor and a retinal ganglion cell restricted-Thy1 promoter-controlled cyan fluorescent protein. This model develops spontaneous or induced optic neuritis, in the absence of paralytic disease normally associated with most rodent autoimmune models of multiple sclerosis. Demyelination and neurodegeneration could be monitored longitudinally in the living animal using electrophysiology, visual sensitivity, confocal scanning laser ophthalmoscopy and optical coherence tomography all of which are relevant to human trials. This model offers many advantages, from a 3Rs, economic and scientific perspective, over classical experimental autoimmune encephalomyelitis models that are associated with substantial suffering of animals. Optic neuritis in this model led to inflammatory damage of axons in the optic nerve and subsequent loss of retinal ganglion cells in the retina. This was inhibited by the systemic administration of a sodium channel blocker (oxcarbazepine or intraocular treatment with siRNA targeting caspase-2. These novel approaches have relevance to the future treatment of neurodegeneration of MS, which has so far evaded treatment.

  8. INHIBITION OF HSV-1 MULTIPLICATION BY FIVE SPECIES OF MEDICINAL PLANTS

    Directory of Open Access Journals (Sweden)

    Maliheh Farahani

    2013-08-01

    Full Text Available Medicinal plants have been traditionally used for different kinds of ailments including infectious diseases. As viral resistance to available chemical drugs causes problems in the treatment of herpes simplex virus type 1 infection, there is an evolving need for new antiherpes drugs. Therefore in the present study 5 species of medicinal plants with ethno-medical background were screened for antiherpes effect against HSV-1in Hep-2(Human epithelial type 2 cells. Different parts of the plants were collected and aqueous extract of them were prepared. These extracts were screened for their cytotoxicity against Hep-2 cell line by cytopathic effect (CPE assay at concentrations 50-1000 μg/ml. Antiherpes properties of the extracts were determined by cytopathic effect inhibition assay. Four plants extract; Thymus kotschyanus, Echinacea purpurea, Camellia sinensis and Echium amoenum L exhibited significant antiherpes effect against HSV-1 at nontoxic concentrations to the cell lines used. The extracts of Thymus kotschyanus and Camellia sinensis showed highest antiherpes activity against HSV-1 at most concentrations. Our findings indicated that Camellia sinensis extract has inhibit HSV-1 multiplication at concentrations 50-1000 μg/ml while this figure for Thymus kotschyanus is 100-800 μg/ml and for Echinacea purpurea and Echium amoenum L are >400 μg/ml. Four plants extract of assay exhibited significant antiherpes activity at a concentration nontoxic to the cell line used. EC50 of Camellia sinensis extract was best sample and findings showed Camellia sinensis has most selectivity indices. Further research is needed to elucidate the active constituents of these plants which may be useful in the development of new antiviral drugs.

  9. Genetic complexity and multiple infections with more Parvovirus species in naturally infected cats

    Directory of Open Access Journals (Sweden)

    Battilani Mara

    2011-03-01

    Full Text Available Abstract Parvoviruses of carnivores include three closely related autonomous parvoviruses: canine parvovirus (CPV, feline panleukopenia virus (FPV and mink enteritis virus (MEV. These viruses cause a variety of serious diseases, especially in young patients, since they have a remarkable predilection for replication in rapidly dividing cells. FPV is not the only parvovirus species which infects cats; in addition to MEV, the new variants of canine parvovirus, CPV-2a, 2b and 2c have also penetrated the feline host-range, and they are able to infect and replicate in cats, causing diseases indistinguishable from feline panleukopenia. Furthermore, as cats are susceptible to both CPV-2 and FPV viruses, superinfection and co-infection with multiple parvovirus strains may occur, potentially facilitating recombination and high genetic heterogeneity. In the light of the importance of cats as a potential source of genetic diversity for parvoviruses and, since feline panleukopenia virus has re-emerged as a major cause of mortality in felines, the present study has explored the molecular characteristics of parvovirus strains circulating in cat populations. The most significant findings reported in this study were (a the detection of mixed infection FPV/CPV with the presence of one parvovirus variant which is a true intermediate between FPV/CPV and (b the quasispecies cloud size of one CPV sample variant 2c. In conclusion, this study provides new important results about the evolutionary dynamics of CPV infections in cats, showing that CPV has presumably started a new process of readaptation in feline hosts.

  10. The role of advection in a two-species competition model

    CERN Document Server

    Averill, Isabel; Lou, Yuan

    2017-01-01

    The effects of weak and strong advection on the dynamics of reaction-diffusion models have long been studied. In contrast, the role of intermediate advection remains poorly understood. For example, concentration phenomena can occur when advection is strong, providing a mechanism for the coexistence of multiple populations, in contrast with the situation of weak advection where coexistence may not be possible. The transition of the dynamics from weak to strong advection is generally difficult to determine. In this work the authors consider a mathematical model of two competing populations in a spatially varying but temporally constant environment, where both species have the same population dynamics but different dispersal strategies: one species adopts random dispersal, while the dispersal strategy for the other species is a combination of random dispersal and advection upward along the resource gradient. For any given diffusion rates the authors consider the bifurcation diagram of positive steady states by u...

  11. Tools and Models for Integrating Multiple Cellular Networks

    Energy Technology Data Exchange (ETDEWEB)

    Gerstein, Mark [Yale Univ., New Haven, CT (United States). Gerstein Lab.

    2015-11-06

    In this grant, we have systematically investigated the integrated networks, which are responsible for the coordination of activity between metabolic pathways in prokaryotes. We have developed several computational tools to analyze the topology of the integrated networks consisting of metabolic, regulatory, and physical interaction networks. The tools are all open-source, and they are available to download from Github, and can be incorporated in the Knowledgebase. Here, we summarize our work as follow. Understanding the topology of the integrated networks is the first step toward understanding its dynamics and evolution. For Aim 1 of this grant, we have developed a novel algorithm to determine and measure the hierarchical structure of transcriptional regulatory networks [1]. The hierarchy captures the direction of information flow in the network. The algorithm is generally applicable to regulatory networks in prokaryotes, yeast and higher organisms. Integrated datasets are extremely beneficial in understanding the biology of a system in a compact manner due to the conflation of multiple layers of information. Therefore for Aim 2 of this grant, we have developed several tools and carried out analysis for integrating system-wide genomic information. To make use of the structural data, we have developed DynaSIN for protein-protein interactions networks with various dynamical interfaces [2]. We then examined the association between network topology with phenotypic effects such as gene essentiality. In particular, we have organized E. coli and S. cerevisiae transcriptional regulatory networks into hierarchies. We then correlated gene phenotypic effects by tinkering with different layers to elucidate which layers were more tolerant to perturbations [3]. In the context of evolution, we also developed a workflow to guide the comparison between different types of biological networks across various species using the concept of rewiring [4], and Furthermore, we have developed

  12. Multiplicative models for survival percentiles: estimating percentile ratios and multiplicative interaction in the metric of time

    Directory of Open Access Journals (Sweden)

    Andrea Bellavia

    2016-09-01

    Full Text Available Evaluating percentiles of survival was proposed as a possible method to analyze time-to-event outcomes. This approach sets the cumulative risk of the event of interest to a specific proportion and evaluates the time by which this proportion is attainedIn this context, exposure-outcome associations can be expressed in terms of differences in survival percentiles, expressing the difference in survival time by which different subgroups of the study population experience the same proportion of events, or in terms of percentile ratios, expressing the strength of the exposure in accelerating the time to the event. Additive models for conditional survival percentiles have been introduced, and their use to estimate multivariable-adjusted percentile differences, and additive interaction on the metric of time has been described. On the other hand, the percentile ratio has never been fully described, neither statistical methods have been presented for its models-based estimation. To bridge this gap, we provide a detailed presentation of the percentile ratio as a relative measure to assess exposure-outcome associations in the context of time-to-event analysis, discussing its interpretation and advantages. We then introduce multiplicative statistical models for conditional survival percentiles, and present their use in estimating percentile ratios and multiplicative interactions in the metric of time. The introduction of multiplicative models for survival percentiles allows researchers to apply this approach in a large variety of context where multivariable adjustment is required, enriching the potentials of the percentile approach as a flexible and valuable tool to evaluate time-to-event outcomes in medical research.

  13. Linking turbine collision risks with population models to assess cumulative impacts of multiple wind farms on threatened birds

    Energy Technology Data Exchange (ETDEWEB)

    Smales, Ian; Muir, Stuart; Meredith, Charles; Baird, Robert

    2011-07-01

    Full text: Assessment of the effects on birds of wind turbine collisions has generally been focussed on the number of individuals that might be killed at a particular facility. However, this measure, of itself, may have little relevance to evaluating the potential or real effects on conservation status of threatened species. Determination of the overall effect any such mortality may have on the functioning of these populations will provide a better basis for decisions that have a strong foundation in ecology. For species with sufficient demographic information, we have developed and applied an approach combining collision risk modelling for all wind farms within the range of a threatened species with population modelling. This permits population-level evaluation of potential cumulative impacts of multiple wind farms. In Australia, regulatory authorities are increasingly interested in the cumulative risk to threatened species that may be posed by multiple wind energy facilities within a species. range. The approach outlined here has been applied in the pre-construction approval stage using collision risk modelling, and can be applied to operational facilities using data on actual mortalities. Cumulative modelling of risk posed by multiple wind farms requires different approaches for sedentary and migratory species. For sedentary species the cumulative effect will be the sum of the impact experienced by those parts of the population whose range intersects with wind farms. Cumulative impact is derived for migratory species by assessing the probability of birds surviving encounters with one wind farm after another on the migratory route and is thus the product of their survivorship rates for the relevant wind farms. The collision risk modelling used will be outlined along with the method in which it is integrated with a population model. Case studies for a crane (Brolga Grus rubicundus) and a parrot (orange- bellied parrot Neophema chrysogaster) species will be

  14. Forecasting relativistic electron flux using dynamic multiple regression models

    Directory of Open Access Journals (Sweden)

    H.-L. Wei

    2011-02-01

    Full Text Available The forecast of high energy electron fluxes in the radiation belts is important because the exposure of modern spacecraft to high energy particles can result in significant damage to onboard systems. A comprehensive physical model of processes related to electron energisation that can be used for such a forecast has not yet been developed. In the present paper a systems identification approach is exploited to deduce a dynamic multiple regression model that can be used to predict the daily maximum of high energy electron fluxes at geosynchronous orbit from data. It is shown that the model developed provides reliable predictions.

  15. Modeling transcriptional networks in Drosophila development at multiple scales.

    Science.gov (United States)

    Wunderlich, Zeba; DePace, Angela H

    2011-12-01

    Quantitative models of developmental processes can provide insights at multiple scales. Ultimately, models may be particularly informative for key questions about network level behavior during development such as how does the system respond to environmental perturbation, or operate reliably in different genetic backgrounds? The transcriptional networks that pattern the Drosophila embryo have been the subject of numerous quantitative experimental studies coupled to modeling frameworks in recent years. In this review, we describe three studies that consider these networks at different levels of molecular detail and therefore result in different types of insights. We also discuss other developmental transcriptional networks operating in Drosophila, with the goal of highlighting what additional insights they may provide.

  16. Determinants of species richness patterns in the Netherlands across multiple taxonomic groups

    NARCIS (Netherlands)

    Schouten, M.A.; Verweij, P.A.; Barendrecht, A.; Kleukers, R.

    2009-01-01

    We examined the species richness patterns of five different species groups (mosses, reptiles and amphibians, grasshoppers and crickets, dragonflies, and hoverflies) in the Netherlands (41,500 km2) using sampling units of 5 × 5 km. We compared the spatial patterns of species richness of the five grou

  17. S-UTD-CH model in multiple diffractions

    Science.gov (United States)

    Baris Tabakcioglu, Mehmet

    2016-05-01

    The propagation of electromagnetic waves in empty space is an extremely simplified case. Thus, the significant question is how an electromagnetic wave propagates in an environment with obstacles such as buildings, trees or hills. Electromagnetic waves are partially reflected and partially diffracted from these obstacles. To predict the relative path loss of electromagnetic waves at the receiving position, many electromagnetic-wave propagation models have been proposed. These propagation models can be classified into models based on numerical integration and those based on ray tracing. Uniform theory of diffraction (UTD) and slope-UTD (S-UTD) models are ray-tracing-based propagation models and are briefly explained in this paper. In addition, detailed information is provided about the improved slope UTD model, which is called the S-UTD with Convex Hull (S-UTD-CH) model. The fundamentals of the S-UTD-CH model are the S-UTD, convex hull and Fresnel zone concept. In particular, the S-UTD-CH model can be applied to multiple diffraction scenarios in the transition region. Moreover, the S-UTD-CH model is considered an optimum model in terms of its accuracy and calculation or computation time. Widespread simulation results are provided to compare the models based on theoretical rays in terms of prediction accuracy and computation time. To compare these models, different operation frequencies and transmitting antenna heights are considered by using a high-performance computing technique.

  18. Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches

    Science.gov (United States)

    Fournier, Bertrand; Mouly, Arnaud; Gillet, François

    2016-01-01

    Understanding the factors underlying the co-occurrence of multiple species remains a challenge in ecology. Biotic interactions, environmental filtering and neutral processes are among the main mechanisms evoked to explain species co-occurrence. However, they are most often studied separately or even considered as mutually exclusive. This likely hampers a more global understanding of species assembly. Here, we investigate the general hypothesis that the structure of co-occurrence networks results from multiple assembly rules and its potential implications for grassland ecosystems. We surveyed orthopteran and plant communities in 48 permanent grasslands of the French Jura Mountains and gathered functional and phylogenetic data for all species. We constructed a network of plant and orthopteran species co-occurrences and verified whether its structure was modular or nested. We investigated the role of all species in the structure of the network (modularity and nestedness). We also investigated the assembly rules driving the structure of the plant-orthopteran co-occurrence network by using null models on species functional traits, phylogenetic relatedness and environmental conditions. We finally compared our results to abundance-based approaches. We found that the plant-orthopteran co-occurrence network had a modular organization. Community assembly rules differed among modules for plants while interactions with plants best explained the distribution of orthopterans into modules. Few species had a disproportionately high positive contribution to this modular organization and are likely to have a key importance to modulate future changes. The impact of agricultural practices was restricted to some modules (3 out of 5) suggesting that shifts in agricultural practices might not impact the entire plant-orthopteran co-occurrence network. These findings support our hypothesis that multiple assembly rules drive the modular structure of the plant-orthopteran network. This

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

    Science.gov (United States)

    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. A PDP model of the simultaneous perception of multiple objects

    Science.gov (United States)

    Henderson, Cynthia M.; McClelland, James L.

    2011-06-01

    Illusory conjunctions in normal and simultanagnosic subjects are two instances where the visual features of multiple objects are incorrectly 'bound' together. A connectionist model explores how multiple objects could be perceived correctly in normal subjects given sufficient time, but could give rise to illusory conjunctions with damage or time pressure. In this model, perception of two objects benefits from lateral connections between hidden layers modelling aspects of the ventral and dorsal visual pathways. As with simultanagnosia, simulations of dorsal lesions impair multi-object recognition. In contrast, a large ventral lesion has minimal effect on dorsal functioning, akin to dissociations between simple object manipulation (retained in visual form agnosia and semantic dementia) and object discrimination (impaired in these disorders) [Hodges, J.R., Bozeat, S., Lambon Ralph, M.A., Patterson, K., and Spatt, J. (2000), 'The Role of Conceptual Knowledge: Evidence from Semantic Dementia', Brain, 123, 1913-1925; Milner, A.D., and Goodale, M.A. (2006), The Visual Brain in Action (2nd ed.), New York: Oxford]. It is hoped that the functioning of this model might suggest potential processes underlying dorsal and ventral contributions to the correct perception of multiple objects.

  1. A Multiple Reaction Modelling Framework for Microbial Electrochemical Technologies

    Science.gov (United States)

    Oyetunde, Tolutola; Sarma, Priyangshu M.; Ahmad, Farrukh; Rodríguez, Jorge

    2017-01-01

    A mathematical model for the theoretical evaluation of microbial electrochemical technologies (METs) is presented that incorporates a detailed physico-chemical framework, includes multiple reactions (both at the electrodes and in the bulk phase) and involves a variety of microbial functional groups. The model is applied to two theoretical case studies: (i) A microbial electrolysis cell (MEC) for continuous anodic volatile fatty acids (VFA) oxidation and cathodic VFA reduction to alcohols, for which the theoretical system response to changes in applied voltage and VFA feed ratio (anode-to-cathode) as well as membrane type are investigated. This case involves multiple parallel electrode reactions in both anode and cathode compartments; (ii) A microbial fuel cell (MFC) for cathodic perchlorate reduction, in which the theoretical impact of feed flow rates and concentrations on the overall system performance are investigated. This case involves multiple electrode reactions in series in the cathode compartment. The model structure captures interactions between important system variables based on first principles and provides a platform for the dynamic description of METs involving electrode reactions both in parallel and in series and in both MFC and MEC configurations. Such a theoretical modelling approach, largely based on first principles, appears promising in the development and testing of MET control and optimization strategies. PMID:28054959

  2. Modeling of Alkane Oxidation Using Constituents and Species

    Science.gov (United States)

    Bellan, Jasette; Harstad, Kenneth G.

    2010-01-01

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

  3. Plasticity in above- and belowground resource acquisition traits in response to single and multiple environmental factors in three tree species.

    Science.gov (United States)

    Freschet, Grégoire T; Bellingham, Peter J; Lyver, Philip O'B; Bonner, Karen I; Wardle, David A

    2013-04-01

    Functional trait plasticity is a major component of plant adjustment to environmental stresses. Here, we explore how multiple local environmental gradients in resources required by plants (light, water, and nutrients) and soil disturbance together influence the direction and amplitude of intraspecific changes in leaf and fine root traits that facilitate capture of these resources. We measured population-level analogous above- and belowground traits related to resource acquisition, i.e. "specific leaf area"-"specific root length" (SLA-SRL), and leaf and root N, P, and dry matter content (DMC), on three dominant understory tree species with contrasting carbon and nutrient economics across 15 plots in a temperate forest influenced by burrowing seabirds. We observed similar responses of the three species to the same single environmental influences, but partially species-specific responses to combinations of influences. The strength of intraspecific above- and belowground trait responses appeared unrelated to species resource acquisition strategy. Finally, most analogous leaf and root traits (SLA vs. SRL, and leaf versus root P and DMC) were controlled by contrasting environmental influences. The decoupled responses of above- and belowground traits to these multiple environmental factors together with partially species-specific adjustments suggest complex responses of plant communities to environmental changes, and potentially contrasting feedbacks of plant traits with ecosystem properties. We demonstrate that despite the growing evidence for broadly consistent resource-acquisition strategies at the whole plant level among species, plants also show partially decoupled, finely tuned strategies between above- and belowground parts at the intraspecific level in response to their environment. This decoupling within species suggests a need for many species-centred ecological theories on how plants respond to their environments (e.g. competitive/stress-tolerant/ruderal and

  4. An integrated modelling framework for neural circuits with multiple neuromodulators

    Science.gov (United States)

    Vemana, Vinith

    2017-01-01

    Neuromodulators are endogenous neurochemicals that regulate biophysical and biochemical processes, which control brain function and behaviour, and are often the targets of neuropharmacological drugs. Neuromodulator effects are generally complex partly owing to the involvement of broad innervation, co-release of neuromodulators, complex intra- and extrasynaptic mechanism, existence of multiple receptor subtypes and high interconnectivity within the brain. In this work, we propose an efficient yet sufficiently realistic computational neural modelling framework to study some of these complex behaviours. Specifically, we propose a novel dynamical neural circuit model that integrates the effective neuromodulator-induced currents based on various experimental data (e.g. electrophysiology, neuropharmacology and voltammetry). The model can incorporate multiple interacting brain regions, including neuromodulator sources, simulate efficiently and easily extendable to large-scale brain models, e.g. for neuroimaging purposes. As an example, we model a network of mutually interacting neural populations in the lateral hypothalamus, dorsal raphe nucleus and locus coeruleus, which are major sources of neuromodulator orexin/hypocretin, serotonin and norepinephrine/noradrenaline, respectively, and which play significant roles in regulating many physiological functions. We demonstrate that such a model can provide predictions of systemic drug effects of the popular antidepressants (e.g. reuptake inhibitors), neuromodulator antagonists or their combinations. Finally, we developed user-friendly graphical user interface software for model simulation and visualization for both fundamental sciences and pharmacological studies. PMID:28100828

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

    Directory of Open Access Journals (Sweden)

    Manfred Schartl

    2014-02-01

    Full Text Available 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.

  6. A Multiple Model Approach to Modeling Based on Fuzzy Support Vector Machines

    Institute of Scientific and Technical Information of China (English)

    冯瑞; 张艳珠; 宋春林; 邵惠鹤

    2003-01-01

    A new multiple models(MM) approach was proposed to model complex industrial process by using Fuzzy Support Vector Machines (F SVMs). By applying the proposed approach to a pH neutralization titration experi-ment, F_SVMs MM not only provides satisfactory approximation and generalization property, but also achieves superior performance to USOCPN multiple modeling method and single modeling method based on standard SVMs.

  7. The common marmoset as an indispensable animal model for immunotherapy development in multiple sclerosis.

    Science.gov (United States)

    Kap, Yolanda S; Jagessar, S Anwar; Dunham, Jordon; 't Hart, Bert A

    2016-08-01

    New drugs often fail in the translation from the rodent experimental autoimmune encephalomyelitis (EAE) model to human multiple sclerosis (MS). Here, we present the marmoset EAE model as an indispensable model for translational research into MS. The genetic heterogeneity of this species and lifelong exposure to chronic latent infections and environmental pathogens create a human-like immune system. Unique to this model is the presence of the pathological hallmark of progressive MS, in particular cortical grey matter lesions. Another great possibility of this model is systemic and longitudinal immune profiling, whereas in humans and mice immune profiling is usually performed in a single compartment (i.e. blood or spleen, respectively). Overall, the marmoset model provides unique opportunities for systemic drug-effect profiling.

  8. Multiple flux difference effect in the lattice hydrodynamic model

    Institute of Scientific and Technical Information of China (English)

    Wang Tao; Gao Zi-You; Zhao Xiao-Mei

    2012-01-01

    Considering the effect of multiple flux difference,an extended lattice model is proposed to improve the stability of traffic flow.The stability condition of the new model is obtained by using linear stability theory.The theoretical analysis result shows that considering the flux difference effect ahead can stabilize traffic flow.The nonlinear analysis is also conducted by using a reductive perturbation method.The modified KdV (mKdV) equation near the critical point is derived and the kink-antikink solution is obtained from the mKdV equation.Numerical simulation results show that the multiple flux difference effect can suppress the traffic jam considerably,which is in line with the analytical result.

  9. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus in China with multiple gene markers.

    Directory of Open Access Journals (Sweden)

    Qing-Yan Dai

    Full Text Available Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI gene and two alternative internal transcribed spacer (ITS genes (ITS1 and ITS2. Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML/Neighbor-joining (NJ, "best close match" (BCM, Minimum distance (MD, and BP-based method (BP, representing commonly used methodology (tree-based and non-tree based in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In

  10. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    Science.gov (United States)

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  11. Model for Predicting Passage of Invasive Fish Species Through Culverts

    Science.gov (United States)

    Neary, V.

    2010-12-01

    Conservation efforts to promote or inhibit fish passage include the application of simple fish passage models to determine whether an open channel flow allows passage of a given fish species. Derivations of simple fish passage models for uniform and nonuniform flow conditions are presented. For uniform flow conditions, a model equation is developed that predicts the mean-current velocity threshold in a fishway, or velocity barrier, which causes exhaustion at a given maximum distance of ascent. The derivation of a simple expression for this exhaustion-threshold (ET) passage model is presented using kinematic principles coupled with fatigue curves for threatened and endangered fish species. Mean current velocities at or above the threshold predict failure to pass. Mean current velocities below the threshold predict successful passage. The model is therefore intuitive and easily applied to predict passage or exclusion. The ET model’s simplicity comes with limitations, however, including its application only to uniform flow, which is rarely found in the field. This limitation is addressed by deriving a model that accounts for nonuniform conditions, including backwater profiles and drawdown curves. Comparison of these models with experimental data from volitional swimming studies of fish indicates reasonable performance, but limitations are still present due to the difficulty in predicting fish behavior and passage strategies that can vary among individuals and different fish species.

  12. Weibull model of Multiplicity Distribution in hadron-hadron collisions

    CERN Document Server

    Dash, Sadhana

    2014-01-01

    We introduce the Weibull distribution as a simple parametrization of charged particle multiplicities in hadron-hadron collisions at all available energies, ranging from ISR energies to the most recent LHC energies. In statistics, the Weibull distribution has wide applicability in natural processes involving fragmentation processes. This gives a natural connection to the available state-of-the-art models for multi-particle production in hadron hadron collisions involving QCD parton fragmentation and hadronization.

  13. Impact of festival factor on electric quantity multiplication forecast model

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    This research aims to improve the forecasting precision of electric quantity. It is discovered that the total electricity consumption considerably increased during the Spring Festival by the analysis of the electric quantity time series from 2002 to 2007 in Shandong province. The festival factor is ascertained to be one of the important seasonal factors affecting the electric quantity fluctuations, and the multiplication model for forecasting is improved by introducing corresponding variables and parameters...

  14. Multiple Potts Models Coupled to Two-Dimensional Quantum Gravity

    CERN Document Server

    Baillie, C F

    1992-01-01

    We perform Monte Carlo simulations using the Wolff cluster algorithm of {\\it multiple} $q=2,3,4$ state Potts models on dynamical phi-cubed graphs of spherical topology in order to investigate the $c>1$ region of two-dimensional quantum gravity. Contrary to naive expectation we find no obvious signs of pathological behaviour for $c>1$. We discuss the results in the light of suggestions that have been made for a modified DDK ansatz for $c>1$.

  15. Multiple Potts models coupled to two-dimensional quantum gravity

    Science.gov (United States)

    Baillie, C. F.; Johnston, D. A.

    1992-07-01

    We perform Monte Carlo simulations using the Wolff cluster algorithm of multiple q=2, 3, 4 state Potts models on dynamical phi-cubed graphs of spherical topology in order to investigate the c>1 region of two-dimensional quantum gravity. Contrary to naive expectation we find no obvious signs of pathological behaviour for c>1. We discuss the results in the light of suggestions that have been made for a modified DDK ansatz for c>1.

  16. A galaxy-halo model for multiple cosmological tracers

    Science.gov (United States)

    Bull, Philip

    2017-10-01

    The information extracted from large galaxy surveys with the likes of DES, DESI, Euclid, LSST, SKA, and WFIRST will be greatly enhanced if the resultant galaxy catalogues can be cross-correlated with one another. Predicting the nature of the information gain, and developing the tools to realize it, depends on establishing a consistent model of how the galaxies detected by each survey trace the same underlying matter distribution. Existing analytic methods, such as halo occupation distribution modelling, are not well suited for this task, and can suffer from ambiguities and tuning issues when applied to multiple tracers. In this paper, we take the first step towards constructing an alternative that provides a common model for the connection between galaxies and dark matter haloes across a wide range of wavelengths (and thus tracer populations). This is based on a chain of parametrized statistical distributions that model the connection between (i) halo mass and bulk physical properties of galaxies, such as star formation rate; and (ii) those same physical properties and a variety of emission processes. The result is a flexible parametric model that allows analytic halo model calculations of one-point functions to be carried out for multiple tracers, as well as providing semi realistic galaxy properties for fast mock catalogue generation.

  17. INTERACTING MULTIPLE MODEL ALGORITHM BASED ON JOINT LIKELIHOOD ESTIMATION

    Institute of Scientific and Technical Information of China (English)

    Sun Jie; Jiang Chaoshu; Chen Zhuming; Zhang Wei

    2011-01-01

    A novel approach is proposed for the estimation of likelihood on Interacting Multiple-Model (IMM) filter.In this approach,the actual innovation,based on a mismatched model,can be formulated as sum of the theoretical innovation based on a matched model and the distance between matched and mismatched models,whose probability distributions are known.The joint likelihood of innovation sequence can be estimated by convolution of the two known probability density functions.The likelihood of tracking models can be calculated by conditional probability formula.Compared with the conventional likelihood estimation method,the proposed method improves the estimation accuracy of likelihood and robustness of IMM,especially when maneuver occurs.

  18. Probability-summation model of multiple laser-exposure effects.

    Science.gov (United States)

    Menendez, A R; Cheney, F E; Zuclich, J A; Crump, P

    1993-11-01

    A probability-summation model is introduced to provide quantitative criteria for discriminating independent from interactive effects of multiple laser exposures on biological tissue. Data that differ statistically from predictions of the probability-summation model indicate the action of sensitizing (synergistic/positive) or desensitizing (hardening/negative) biophysical interactions. Interactions are indicated when response probabilities vary with changes in the spatial or temporal separation of exposures. In the absence of interactions, probability-summation parsimoniously accounts for "cumulative" effects. Data analyzed using the probability-summation model show instances of both sensitization and desensitization of retinal tissue by laser exposures. Other results are shown to be consistent with probability-summation. The relevance of the probability-summation model to previous laser-bioeffects studies, models, and safety standards is discussed and an appeal is made for improved empirical estimates of response probabilities for single exposures.

  19. Joint modeling of longitudinal data in multiple behavioral change.

    Science.gov (United States)

    Charnigo, Richard; Kryscio, Richard; Bardo, Michael T; Lynam, Donald; Zimmerman, Rick S

    2011-06-01

    Multiple behavioral change is an exciting and evolving research area, albeit one that presents analytic challenges to investigators. This manuscript considers the problem of modeling jointly trajectories for two or more possibly non-normally distributed dependent variables, such as marijuana smoking and risky sexual activity, collected longitudinally. Of particular scientific interest is applying such modeling to elucidate the nature of the interaction, if any, between an intervention and personal characteristics, such as sensation seeking and impulsivity. The authors describe three analytic approaches: generalized linear mixed modeling, group-based trajectory modeling, and latent growth curve modeling. In particular, the authors identify identify the strengths and weaknesses of these analytic approaches and assess their impact (or lack thereof) on the psychological and behavioral science literature. The authors also compare what investigators have been doing analytically versus what they might want to be doing in the future and discuss the implications for basic and translational research.

  20. Predictions for an invaded world: A strategy to predict the distribution of native and non-indigenous species at multiple scales

    Science.gov (United States)

    Reusser, D.A.; Lee, H.

    2008-01-01

    Habitat models can be used to predict the distributions of marine and estuarine non-indigenous species (NIS) over several spatial scales. At an estuary scale, our goal is to predict the estuaries most likely to be invaded, but at a habitat scale, the goal is to predict the specific locations within an estuary that are most vulnerable to invasion. As an initial step in evaluating several habitat models, model performance for a suite of benthic species with reasonably well-known distributions on the Pacific coast of the US needs to be compared. We discuss the utility of non-parametric multiplicative regression (NPMR) for predicting habitat- and estuary-scale distributions of native and NIS. NPMR incorporates interactions among variables, allows qualitative and categorical variables, and utilizes data on absence as well as presence. Preliminary results indicate that NPMR generally performs well at both spatial scales and that distributions of NIS are predicted as well as those of native species. For most species, latitude was the single best predictor, although similar model performance could be obtained at both spatial scales with combinations of other habitat variables. Errors of commission were more frequent at a habitat scale, with omission and commission errors approximately equal at an estuary scale. ?? 2008 International Council for the Exploration of the Sea. Published by Oxford Journals. All rights reserved.

  1. Dealing with Multiple Solutions in Structural Vector Autoregressive Models.

    Science.gov (United States)

    Beltz, Adriene M; Molenaar, Peter C M

    2016-01-01

    Structural vector autoregressive models (VARs) hold great potential for psychological science, particularly for time series data analysis. They capture the magnitude, direction of influence, and temporal (lagged and contemporaneous) nature of relations among variables. Unified structural equation modeling (uSEM) is an optimal structural VAR instantiation, according to large-scale simulation studies, and it is implemented within an SEM framework. However, little is known about the uniqueness of uSEM results. Thus, the goal of this study was to investigate whether multiple solutions result from uSEM analysis and, if so, to demonstrate ways to select an optimal solution. This was accomplished with two simulated data sets, an empirical data set concerning children's dyadic play, and modifications to the group iterative multiple model estimation (GIMME) program, which implements uSEMs with group- and individual-level relations in a data-driven manner. Results revealed multiple solutions when there were large contemporaneous relations among variables. Results also verified several ways to select the correct solution when the complete solution set was generated, such as the use of cross-validation, maximum standardized residuals, and information criteria. This work has immediate and direct implications for the analysis of time series data and for the inferences drawn from those data concerning human behavior.

  2. Models to relate species to environment: a hierarchical statistical approac

    NARCIS (Netherlands)

    Jamil, T.

    2012-01-01

    In the last two decades, the interest of community ecologists in trait-based approaches has grown dramatically and these approaches have been increasingly applied to explain and predict response of species to environmental conditions. A variety of modelling techniques are available. The dominant

  3. Models to relate species to environment: a hierarchical statistical approac

    NARCIS (Netherlands)

    Jamil, T.

    2012-01-01

    In the last two decades, the interest of community ecologists in trait-based approaches has grown dramatically and these approaches have been increasingly applied to explain and predict response of species to environmental conditions. A variety of modelling techniques are available. The dominant tec

  4. Coexistence of two species in a strongly coupled cooperating model

    DEFF Research Database (Denmark)

    Pedersen, Michael

    In this paper, the cooperating two-species Lotka-Volterra model is discussed. We study the existence of solutions to a elliptic system with homogeneous Dirichlet boundary conditions. Our results show that this problem possesses at least one coexistence state if the birth rates are big and self...

  5. Coexistence of two species in a strongly coupled cooperating model

    DEFF Research Database (Denmark)

    Pedersen, Michael

    In this paper, the cooperating two-species Lotka-Volterra model is discussed. We study the existence of solutions to a elliptic system with homogeneous Dirichlet boundary conditions. Our results show that this problem possesses at least one coexistence state if the birth rates are big and self...

  6. A tactical supply chain planning model with multiple flexibility options

    DEFF Research Database (Denmark)

    Esmaeilikia, Masoud; Fahimnia, Behnam; Sarkis, Joeseph

    2016-01-01

    Supply chain flexibility is widely recognized as an approach to manage uncertainty. Uncertainty in the supply chain may arise from a number of sources such as demand and supply interruptions and lead time variability. A tactical supply chain planning model with multiple flexibility options...... incorporated in sourcing, manufacturing and logistics functions can be used for the analysis of flexibility adjustment in an existing supply chain. This paper develops such a tactical supply chain planning model incorporating a realistic range of flexibility options. A novel solution method is designed...

  7. Automatic Generation of 3D Building Models with Multiple Roofs

    Institute of Scientific and Technical Information of China (English)

    Kenichi Sugihara; Yoshitugu Hayashi

    2008-01-01

    Based on building footprints (building polygons) on digital maps, we are proposing the GIS and CG integrated system that automatically generates 3D building models with multiple roofs. Most building polygons' edges meet at right angles (orthogonal polygon). The integrated system partitions orthogonal building polygons into a set of rectangles and places rectangular roofs and box-shaped building bodies on these rectangles. In order to partition an orthogonal polygon, we proposed a useful polygon expression in deciding from which vertex a dividing line is drawn. In this paper, we propose a new scheme for partitioning building polygons and show the process of creating 3D roof models.

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

    Directory of Open Access Journals (Sweden)

    Anna Hubackova

    2014-01-01

    Full Text Available 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.

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

    Science.gov (United States)

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

    2014-01-01

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

  10. TIME SERIES FORECASTING WITH MULTIPLE CANDIDATE MODELS: SELECTING OR COMBINING?

    Institute of Scientific and Technical Information of China (English)

    YU Lean; WANG Shouyang; K. K. Lai; Y.Nakamori

    2005-01-01

    Various mathematical models have been commonly used in time series analysis and forecasting. In these processes, academic researchers and business practitioners often come up against two important problems. One is whether to select an appropriate modeling approach for prediction purposes or to combine these different individual approaches into a single forecast for the different/dissimilar modeling approaches. Another is whether to select the best candidate model for forecasting or to mix the various candidate models with different parameters into a new forecast for the same/similar modeling approaches. In this study, we propose a set of computational procedures to solve the above two issues via two judgmental criteria. Meanwhile, in view of the problems presented in the literature, a novel modeling technique is also proposed to overcome the drawbacks of existing combined forecasting methods. To verify the efficiency and reliability of the proposed procedure and modeling technique, the simulations and real data examples are conducted in this study.The results obtained reveal that the proposed procedure and modeling technique can be used as a feasible solution for time series forecasting with multiple candidate models.

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

    Science.gov (United States)

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

    2017-06-01

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

  12. Functional traits drive the contribution of solar radiation to leaf litter decomposition among multiple arid-zone species.

    Science.gov (United States)

    Pan, Xu; Song, Yao-Bin; Liu, Guo-Fang; Hu, Yu-Kun; Ye, Xue-Hua; Cornwell, William K; Prinzing, Andreas; Dong, Ming; Cornelissen, Johannes H C

    2015-08-18

    In arid zones, strong solar radiation has important consequences for ecosystem processes. To better understand carbon and nutrient dynamics, it is important to know the contribution of solar radiation to leaf litter decomposition of different arid-zone species. Here we investigated: (1) whether such contribution varies among plant species at given irradiance regime, (2) whether interspecific variation in such contribution correlates with interspecific variation in the decomposition rate under shade; and (3) whether this correlation can be explained by leaf traits. We conducted a factorial experiment to determine the effects of solar radiation and environmental moisture for the mass loss and the decomposition constant k-values of 13 species litters collected in Northern China. The contribution of solar radiation to leaf litter decomposition varied significantly among species. Solar radiation accelerated decomposition in particular in the species that already decompose quickly under shade. Functional traits, notably specific leaf area, might predict the interspecific variation in that contribution. Our results provide the first empirical evidence for how the effect of solar radiation on decomposition varies among multiple species. Thus, the effect of solar radiation on the carbon flux between biosphere and atmosphere may depend on the species composition of the vegetation.

  13. Modelling bioaccumulation of oil constituents in aquatic species.

    Science.gov (United States)

    De Hoop, Lisette; Huijbregts, Mark A J; Schipper, Aafke M; Veltman, Karin; De Laender, Frederik; Viaene, Karel P J; Klok, Chris; Hendriks, A Jan

    2013-11-15

    Crude oil poses a risk to marine ecosystems due to its toxicity and tendency to accumulate in biota. The present study evaluated the applicability of the OMEGA model for estimating oil accumulation in aquatic species by comparing model predictions of kinetic rates (absorption and elimination) and bioconcentration factors (BCF) with measured values. The model was a better predictor than the means of the measurements for absorption and elimination rate constants, but did not outperform the mean measured BCF. Model estimates and measurements differed less than one order of magnitude for 91%, 80% and 61% of the absorption and elimination rates and BCFs of all oil constituents, respectively. Of the "potentially modifying" factors: exposure duration, biotransformation, molecular mass, and water temperature, the last two tended to influence the performance of the model. Inclusion of more explanatory variables in the bioaccumulation model, like the molecular mass, is expected to improve model performance.

  14. A Galaxy-Halo Model for Multiple Cosmological Tracers

    CERN Document Server

    Bull, Philip

    2016-01-01

    The information extracted from large galaxy surveys with the likes of DES, DESI, Euclid, LSST, SKA, and WFIRST will be greatly enhanced if the resultant galaxy catalogues can be cross-correlated with one another. Predicting the nature of the information gain, and developing the tools to realise it, depends on establishing a consistent model of how the galaxies detected by each survey trace the same underlying matter distribution. Existing analytic methods, such as halo occupation distribution (HOD) modelling, are not well-suited for this task, and can suffer from ambiguities and tuning issues when applied to multiple tracers. We construct a simple alternative that provides a common model for the connection between galaxies and dark matter halos across a wide range of wavelengths (and thus tracer populations). This is based on a chain of parametrised statistical distributions that model the connection between (a) halo mass and bulk physical properties of galaxies, such as star-formation rate; and (b) those sam...

  15. Characterization of Blue Mold Penicillium Species Isolated from Stored Fruits Using Multiple Highly Conserved Loci

    Directory of Open Access Journals (Sweden)

    Guohua Yin

    2017-03-01

    Full Text Available Penicillium is a large genus of common molds with over 400 described species; however, identification of individual species is difficult, including for those species that cause postharvest rots. In this study, blue rot fungi from stored apples and pears were isolated from a variety of hosts, locations, and years. Based on morphological and cultural characteristics and partial amplification of the β-tubulin locus, the isolates were provisionally identified as several different species of Penicillium. These isolates were investigated further using a suite of molecular DNA markers and compared to sequences of the ex-type for cognate species in GenBank, and were identified as P. expansum (3 isolates, P. solitum (3 isolates, P. carneum (1 isolate, and P. paneum (1 isolate. Three of the markers we used (ITS, internal transcribed spacer rDNA sequence; benA, β-tubulin; CaM, calmodulin were suitable for distinguishing most of our isolates from one another at the species level. In contrast, we were unable to amplify RPB2 sequences from four of the isolates. Comparison of our sequences with cognate sequences in GenBank from isolates with the same species names did not always give coherent data, reinforcing earlier studies that have shown large intraspecific variability in many Penicillium species, as well as possible errors in some sequence data deposited in GenBank.

  16. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia

    Directory of Open Access Journals (Sweden)

    Bacon Christine D

    2012-02-01

    Full Text Available Abstract Background Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages. Results Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups. Conclusions Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation.

  17. Production of sophorolipids biosurfactants by multiple species of the Starmerella (Candida) bombicola yeast clade

    Science.gov (United States)

    Sophorolipid production was tested for 26 strains representing 19 species of the Starmerella yeast clade, including S. bombicola and Candida apicola, which were previously reported to produce sophorolipids. Five of the 19 species tested showed significant production of sophorolipids: S. bombicola, ...

  18. SESAM – a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages

    DEFF Research Database (Denmark)

    Guisan, Antoine; Rahbek, Carsten

    2011-01-01

    , and ecological assembly rules to constrain predictions of the richness and composition of species assemblages obtained by stacking predictions of individual species distributions. We believe that such a framework could prove useful in many theoretical and applied disciplines of ecology and evolution, both......Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realized properties of species assemblages, whereas the second approach (stacked species distribution modelling, S-SDM) starts...... with constituent species to approximate the properties of assemblages. Here, we propose to unify the two approaches in a single ‘spatially explicit species assemblage modelling’ (SESAM) framework. This framework uses relevant designations of initial species source pools for modelling, macroecological variables...

  19. Oscillations and multiple steady states in active membrane transport models.

    Science.gov (United States)

    Vieira, F M; Bisch, P M

    1994-01-01

    The dynamic behavior of some non-linear extensions of the six-state alternating access model for active membrane transport is investigated. We use stoichio-metric network analysis to study the stability of steady states. The bifurcation analysis has been done through standard numerical methods. For the usual six-state model we have proved that there is only one steady state, which is globally asymptotically stable. When we added an autocatalytic step we found self-oscillations. For the competition between a monomer cycle and a dimer cycle, with steps of dimer formation, we have also found self-oscillations. We have also studied models involving the formation of a complex with other molecules. The addition of two steps for formation of a complex of the monomer with another molecule does not alter either the number or the stability of steady states of the basic six-state model. The model which combines the formation of a complex with an autocatalytic step shows both self-oscillations and multiple steady states. The results lead us to conclude that oscillations could be produced by active membrane transport systems if the transport cycle contains a sufficiently large number of steps (six in the present case) and is coupled to at least one autocatalytic reaction,. Oscillations are also predicted when the monomer cycle is coupled to a dimer cycle. In fact, the autocatalytic reaction can be seen as a simplification of the model involving competition between monomer and dimer cycles, which seems to be a more realistic description of biological systems. A self-regulation mechanism of the pumps, related to the multiple stationary states, is expected only for a combined effect of autocatalysis and formation of complexes with other molecules. Within the six-state model this model also leads to oscillation.

  20. Establishing endangered species recovery criteria using predictive simulation modeling

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Céline Gomez

    Full Text Available 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

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

    Directory of Open Access Journals (Sweden)

    Genoveva Rodríguez-Castañeda

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

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

    Science.gov (United States)

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

    2012-01-01

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

  4. Multiplicative ARMA models to generate hourly series of global irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Mora-Lopez, L. [Universidad de Malaga (Spain). Dpto. Lenguajes y C. Computacion; Sidrach-de-Cardona, M. [Universidad de Malaga (Spain). Dpto. Fisica Aplicada

    1998-11-01

    A methodology to generate hourly series of global irradiation is proposed. The only input parameter which is required is the monthly mean value of daily global irradiation, which is available for most locations. The procedure to obtain new series is based on the use of a multiplicative autoregressive moving-average statistical model for time series with regular and seasonal components. The multiplicative nature of these models enables capture of the two types of relationships observed in recorded hourly series of global irradiation: on the one hand, the relationship between the value at one hour and the value at the previous hour; and on the other hand, the relationship between the value at one hour in one day and the value at the same hour in the previous day. In this paper the main drawback which arises when using these models to generate new series is solved: namely, the need for available recorded series in order to obtain the three parameters contained in the statistical ARMA model which is proposed (autoregressive coefficient, moving-average coefficient and variance of the error term). Specifically, expressions which enable estimation of these parameters using only monthly mean values of daily global irradiation are proposed in this paper. (author)

  5. Adaptive mixture observation models for multiple object tracking

    Institute of Scientific and Technical Information of China (English)

    CUI Peng; SUN LiFeng; YANG ShiQiang

    2009-01-01

    Multiple object tracking (MOT) poses many difficulties to conventional well-studied single object track-ing (SOT) algorithms, such as severe expansion of configuration space, high complexity of motion con-ditions, and visual ambiguities among nearby targets, among which the visual ambiguity problem is the central challenge. In this paper, we address this problem by embedding adaptive mixture observation models (AMOM) into a mixture tracker which is implemented in Particle Filter framework. In AMOM, the extracted multiple features for appearance description are combined according to their discriminative power between ambiguity prone objects, where the discriminability of features are evaluated by online entropy-based feature selection techniques. The induction of AMOM can help to surmount the Incapa-bility of conventional mixture tracker in handling object occlusions, and meanwhile retain its merits of flexibility and high efficiency. The final experiments show significant improvement in MOT scenarios compared with other methods.

  6. The relationship between psoriasis and depression: A multiple mediation model.

    Science.gov (United States)

    Łakuta, Patryk; Marcinkiewicz, Kamil; Bergler-Czop, Beata; Brzezińska-Wcisło, Ligia

    2016-12-01

    This study examined the relationship between psoriasis and depression, proposing a multiple mediation model to analyse the relationship. A total of 193 patients with psoriasis aged 20-67 years completed the Beck Depression Inventory, the Stigmatization Scale, the Appearance Schemas Inventory-Revised, and the Body Emotions Scale. The Body Surface Area index was used to assess severity of psoriasis. Serial multiple mediation analysis revealed that experiences of stigmatization, maladaptive beliefs about appearance and its salience to one's self-evaluation, and negative emotional attitudes towards the body, jointly, sequentially mediated the relationship between the presence of skin lesions of psoriasis and depressive symptoms. These results highlight the importance of the associations between stigmatization and cognitive and affective aspects of body image in relation to depression in patients with psoriasis. We suggest that prevention and intervention programs for psoriasis patients that target body image enhancement would be worthy of further research.

  7. Development of aquarium fish models for environmental carcinogenesis: tumor induction in seven species

    Energy Technology Data Exchange (ETDEWEB)

    Hawkins, W.E.; Overstreet, R.M.; Fournie, J.W.; Walker, W.W.

    1985-08-01

    For small fish species to be utilized as models for carcinogenicity testing they should be capable of developing neoplasms, preferably in multiple tissues, when exposed to known carcinogens. Seven species of small fish were exposed to methylazoxymethanol acetate (MAM-Ac) and tumor development was monitored. Specimens 6-10 days old were exposed to nominal concentrations of MAM-Ac up to 100 mg 1( ) for 2 h, then transferred to carcinogen-free water. Hepatic neoplasms developed in the Japanese medaka, guppy, and sheepshead minnow. All tumors were diagnosed in specimens within 1 year post-exposure. Early signs of liver tumors appeared in medaka and guppy at about 1 month post-exposure. These studies show that both medaka and guppy would be good models because they appear sensitive to carcinogens, develop tumors in multiple tissues and are easy to breed and maintain. Certain other small fish species also may prove to be good models because of habitat preferences, breeding strategies, or genetic attributes.

  8. Is braiding an endangered river species? Converging morphological trajectories from multiple geographic contexts.

    Science.gov (United States)

    Stecca, Guglielmo; Zolezzi, Guido; Surian, Nicola; Hicks, Murray

    2017-04-01

    Observations of morphological change in braided rivers, comprising narrowing of the total and active braidplain, degradation (at least in some reaches), increase in vegetation cover, and reduction of braiding complexity towards a transitional style, have been increasingly reported worldwide in the last decades. Most of the available literature concerns rivers in Europe, with particular reference to the Alpine and pre-Alpine region (e.g., Italy, France, Austria, Switzerland). This abundance reflects the magnitude of changes in Europe, where most of braided reaches have been heavily impacted. However, contributions from other regions of Europe (e.g., the Polish Carpathians, Spain, Scotland, Corsica) and of the Earth (e.g., the South Island of New Zealand) document similar stories. These morphodynamic changes have been related to the alteration of the fundamental physical processes in braided rivers driven by the flow and sediment supply regimes, due to anthropogenic changes in constraints and controls. Multiple and context-specific sources of impact on these controls have been identified, including damming, landuse change, gravel mining, torrent control works, channelisation, introduction of alien vegetation. Here, we focus on a comparative analysis of the relatively recent (multi-decadal) evolution of braided rivers located in different geographic regions on the Earth, with particular reference to the Waitaki (New Zealand), Piave (Italy) and Dunajec (Poland) rivers. These rivers display similar morphological trajectories, which nonetheless result from very different paths of causation, i.e., from different management causes and different alteration of physical processes. We focus on the role of different physical and human geographic contexts as drivers of the river evolution, highlighting the relations between the observed trajectories and the local conditions and characteristics. We discuss the relative role of dam construction and operation in contributing to the

  9. On the dynamical behavior of three species food web model

    Energy Technology Data Exchange (ETDEWEB)

    Naji, R.K. [Department of Mathematics, College of Science, University of Baghdad (Iraq)]. E-mail: rknaji@yahoo.com; Balasim, A.T. [Department of Mathematics, College of Science, University of Baghdad (Iraq)]. E-mail: alkhazrejy@yahoo.com

    2007-12-15

    In this paper, a mathematical model consisting of two preys one predator with Beddington-DeAngelis functional response is proposed and analyzed. The local stability analysis of the system is carried out. The necessary and sufficient conditions for the persistence of three species food web model are obtained. For the biologically reasonable range of parameter values, the global dynamics of the system has been investigated numerically. Number of bifurcation diagrams has been obtained; Lyapunov exponents have been computed for different attractor sets. It is observed that the model has different types of attractors including chaos.

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

    Science.gov (United States)

    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

  11. Design and modeling of small scale multiple fracturing experiments

    Energy Technology Data Exchange (ETDEWEB)

    Cuderman, J F

    1981-12-01

    Recent experiments at the Nevada Test Site (NTS) have demonstrated the existence of three distinct fracture regimes. Depending on the pressure rise time in a borehole, one can obtain hydraulic, multiple, or explosive fracturing behavior. The use of propellants rather than explosives in tamped boreholes permits tailoring of the pressure risetime over a wide range since propellants having a wide range of burn rates are available. This technique of using the combustion gases from a full bore propellant charge to produce controlled borehole pressurization is termed High Energy Gas Fracturing (HEGF). Several series of HEGF, in 0.15 m and 0.2 m diameter boreholes at 12 m depths, have been completed in a tunnel complex at NTS where mineback permitted direct observation of fracturing obtained. Because such large experiments are costly and time consuming, smaller scale experiments are desirable, provided results from small experiments can be used to predict fracture behavior in larger boreholes. In order to design small scale gas fracture experiments, the available data from previous HEGF experiments were carefully reviewed, analytical elastic wave modeling was initiated, and semi-empirical modeling was conducted which combined predictions for statically pressurized boreholes with experimental data. The results of these efforts include (1) the definition of what constitutes small scale experiments for emplacement in a tunnel complex at the Nevada Test Site, (2) prediction of average crack radius, in ash fall tuff, as a function of borehole size and energy input per unit length, (3) definition of multiple-hydraulic and multiple-explosive fracture boundaries as a function of boreholes size and surface wave velocity, (4) semi-empirical criteria for estimating stress and acceleration, and (5) a proposal that multiple fracture orientations may be governed by in situ stresses.

  12. Confronting different models of community structure to species-abundance data: a Bayesian model comparison

    NARCIS (Netherlands)

    Etienne, R.S.; Olff, H.

    2005-01-01

    Species abundances are undoubtedly the most widely available macroecological data, but can we use them to distinguish among several models of community structure? Here we present a Bayesian analysis of species-abundance data that yields a full joint probability distribution of each model's

  13. Confronting different models of community structure to species-abundance data : a Bayesian model comparison

    NARCIS (Netherlands)

    Etienne, RS; Olff, H

    Species abundances are undoubtedly the most widely available macroecological data, but can we use them to distinguish among several models of community structure? Here we present a Bayesian analysis of species-abundance data that yields a full joint probability distribution of each model's

  14. Using genetic data to improve species distribution models.

    Science.gov (United States)

    Bouyer, Jérémy; Lancelot, Renaud

    2017-03-23

    Tsetse flies (Diptera, Glossinidae) transmit human and animal trypanosomoses in Africa, respectively a neglected human disease (sleeping sickness) and the most important constraint to cattle production in infested countries (nagana). We recently developed a methodology to map landscape friction (i.e. resistance to movement) for tsetse in West Africa. The goal was to identify natural barriers to tsetse dispersal, and potentially isolated tsetse populations for targeting elimination programmes. Most species distribution models neglect landscape functional connectivity whereas environmental factors affecting suitability or abundance are not necessarily the same as those influencing gene flows. Geographic distributions of a given species can be seen as the intersection between biotic (B), abiotic (A) and movement (M) factors (BAM diagram). Here we show that the suitable habitat for Glossina palpalis gambiensis as modelled by Maxent can be corrected by landscape functional connectivity (M) extracted from our friction analysis. This procedure did not degrade the specificity of the distribution model (P=0.751) whereas the predicted distribution area was reduced. The added value of this approach is that it reveals unconnected habitat patches. The approach we developed on tsetse to inform landscape connectivity (M) is reproducible and does not rely on expert knowledge. It can be applied to any species: we call for a generalization of the use of M to improve distribution models. Copyright © 2017. Published by Elsevier B.V.

  15. Tree demography suggests multiple directions and drivers for species range shifts in mountains of Northeastern United States.

    Science.gov (United States)

    Wason, Jay W; Dovciak, Martin

    2016-12-09

    Climate change is expected to lead to upslope shifts in tree species distributions, but the evidence is mixed partly due to land-use effects and individualistic species responses to climate. We examined how individual tree species demography varies along elevational climatic gradients across four states in the northeastern United States to determine whether species elevational distributions and their potential upslope (or downslope) shifts were controlled by climate, land-use legacies (past logging), or soils. We characterized tree demography, microclimate, land-use legacies, and soils at 83 sites stratified by elevation (~500 to ~1200 m above sea level) across 12 mountains containing the transition from northern hardwood to spruce-fir forests. We modeled elevational distributions of tree species saplings and adults using logistic regression to test whether sapling distributions suggest ongoing species range expansion upslope (or contraction downslope) relative to adults, and we used linear mixed models to determine the extent to which climate, land use, and soil variables explain these distributions. Tree demography varied with elevation by species, suggesting a potential upslope shift only for American beech, downslope shifts for red spruce (more so in cool regions) and sugar maple, and no change with elevation for balsam fir. While soils had relatively minor effects, climate was the dominant predictor for most species and more so for saplings than adults of red spruce, sugar maple, yellow birch, cordate birch, and striped maple. On the other hand, logging legacies were positively associated with American beech, sugar maple, and yellow birch, and negatively with red spruce and balsam fir - generally more so for adults than saplings. All species exhibited individualistic rather than synchronous demographic responses to climate and land use, and the return of red spruce to lower elevations where past logging originally benefited northern hardwood species indicates

  16. Modeling of a Multiple Digital Automatic Gain Control System

    Institute of Scientific and Technical Information of China (English)

    WANG Jingdian; LU Xiuhong; ZHANG Li

    2008-01-01

    Automatic gain control (AGC) has been used in many applications. The key features of AGC, including a steady state output and static/dynamic timing response, depend mainly on key parameters such as the reference and the filter coefficients. A simple model developed to describe AGC systems based on several simple assumptions shows that AGC always converges to the reference and that the timing constant depends on the filter coefficients. Measures are given to prevent oscillations and limit cycle effects. The simple AGC system is adapted to a multiple AGC system for a TV tuner in a much more efficient model. Simulations using the C language are 16 times faster than those with MATLAB, and 10 times faster than those with a mixed register transfer level (RTL)-simulation program with integrated circuit emphasis (SPICE) model.

  17. Carbon-Chain Species in Warm-up Models

    CERN Document Server

    Hassel, George E; Herbst, Eric

    2011-01-01

    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 $T\\approx 30$ 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$_{\\rm n}$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$_2$H, C$_4$H, CH$_3$CCH, and CH$_3$OH toward hot corinos (especially IRAS 16293-2422) as well as towards L1527, with lower abundances for the carbon chain radicals and higher abundances for the other two species toward the hot corinos. In addition, the {\\it Her...

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

    Science.gov (United States)

    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. 77 FR 5564 - Tehachapi Uplands Multiple Species Habitat Conservation Plan; Kern County, CA

    Science.gov (United States)

    2012-02-03

    ... species that may be taken or otherwise affected by on-going ranch activities and future low density... woolly sunflower (Eriophyllum lanatum var. hallii), Kusche's sandwort (Arenaria macradenia var....

  20. Multiple sclerosis animal models: a clinical and histopathological perspective.

    Science.gov (United States)

    Kipp, Markus; Nyamoya, Stella; Hochstrasser, Tanja; Amor, Sandra

    2017-03-01

    There is a broad consensus that multiple sclerosis (MS) represents more than an inflammatory disease: it harbors several characteristic aspects of a classical neurodegenerative disorder, that is, damage to axons, synapses and nerve cell bodies. While we are equipped with appropriate therapeutic options to prevent immune-cell driven relapses, effective therapeutic options to prevent the progressing neurodegeneration are still missing. In this review article, we will discuss to what extent pathology of the progressive disease stage can be modeled in MS animal models. While acute and relapsing-remitting forms of experimental autoimmune encephalomyelitis (EAE), which are T cell dependent, are aptly suited to model relapsing-remitting phases of MS, other EAE models, especially the secondary progressive EAE stage in Biozzi ABH mice is better representing the secondary progressive phase of MS, which is refractory to many immune therapies. Besides EAE, the cuprizone model is rapidly gaining popularity to study the formation and progression of demyelinating CNS lesions without T cell involvement. Here, we discuss these two non-popular MS models. It is our aim to point out the pathological hallmarks of MS, and discuss which pathological aspects of the disease can be best studied in the various animal models available.

  1. Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales.

    Science.gov (United States)

    Young, Hillary S; McCauley, Douglas J; Guevara, Roger; Dirzo, Rodolfo

    2013-07-01

    Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems.

  2. Multiple phenological responses to climate change among 42 plant species in Xi'an, China

    Science.gov (United States)

    Dai, Junhu; Wang, Huanjiong; Ge, Quansheng

    2013-09-01

    Phenological data of 42 woody plants in a temperate deciduous forest from the Chinese Phenological Observation Network (CPON) and the corresponding meteorological data from 1963 to 2011 in Xi'an, Shaanxi Province, China were collected and analyzed. The first leaf date (FLD), leaf coloring date (LCD) and first flower date (FFD) are revealed as strong biological signals of climatic change. The FLD, LCD and FFD of most species are sensitive to average temperature during a certain period before phenophase onset. Regional precipitation also has a significant impact on phenophases of about half of the species investigated. Affected by climate change, the FLD and FFD of these species have advanced by 5.54 days and 10.20 days on average during 2003-2011 compared with the period 1963-1996, respectively. Meanwhile, the LCD has delayed by 10.59 days, and growing season length has extended 16.13 days. Diverse responses of phenology commonly exist among different species and functional groups during the study period. Especially for FFD, the deviations between the above two periods ranged from -20.68 to -2.79 days; biotic pollination species showed a significantly greater advance than abiotic pollination species. These results were conducive to the understanding of possible changes in both the structure of plant communities and interspecific relationships in the context of climate change.

  3. Trust Evaluation Model based on Multiple Service Attributes

    Directory of Open Access Journals (Sweden)

    Xiaoxue Ma

    2011-06-01

    Full Text Available when the most trusted models evaluate level of trust about service entities at present, the credibility of the service attributes whether the two sides trading result is credible is rather ambiguous, which makes the evaluation model lack of persuasion, and not very good depict the complexity and uncertainty of trust relationship between the two sides. In view of the above questions, learning trust relationship from human society, according to the service of the node itself, abstracting representative multiple service attributes from the trusted relationship of the node service, service requester comprehensive evaluates multiple service attributes provided by service provider based on personal interest, and combines with the trust value, decide whether to trade finally; after the transaction, service request calculates QoS(quality of service difference degree according to actual QoS and service provider’own QoS claimed to judge the credibility of service provider, then gives corresponding rewards and punishment and trust update. Simulation results show that the model can evaluative accurately the node’s trust degree and effectively control of malicious nodes attack, when the malicious nodes have a higher proportion in the system ,it can still keep high success rate.

  4. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

    KAUST Repository

    Najibi, Seyed Morteza

    2017-02-08

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  5. Modelling genetic susceptibility to multiple sclerosis with family data.

    Science.gov (United States)

    O'Gorman, Cullen; Lin, Rui; Stankovich, James; Broadley, Simon A

    2013-01-01

    A genetic contribution to susceptibility is well established in multiple sclerosis (MS) and 57 associated genetic loci have been identified. We have undertaken a meta-analysis of familial risk studies with the aims of providing definitive figures for risks to relatives, performing a segregation analysis and estimating the proportion of the overall genetic risk that currently identified genes represent. We have used standard methods of meta-analysis combined with novel approaches to age adjustment to provide directly comparable estimates of lifetime risk. The overall recurrence risk for monozygotic twins was 18.2% and for siblings 2.7%. The recurrence risk for dizygotic twins was significantly higher than for siblings. The overall estimate of sibling relative risk (λ(S)) was 16.8. Risks for older relatives (parents, siblings, aunts, uncles and cousins) show a latitudinal gradient, in line with population risk. No latitudinal gradient for λ(S) was seen. Segregation analysis supports a multiplicative model of one locus of moderate effect with many loci of small effect. The estimated contribution of the 57 known MS loci is 18-24% of λ(S). This meta-analysis supports the notion of MS being in part the result of multiple genetic susceptibility factors and environmental factors.

  6. Modelling the interplay of multiple cues in prosodic focus marking

    Directory of Open Access Journals (Sweden)

    Anja Arnhold

    2017-03-01

    Full Text Available Focus marking is an important function of prosody in many languages. While many phonological accounts concentrate on fundamental frequency (F0, studies have established several additional cues to information structure. However, the relationship between these cues is rarely investigated. We simultaneously analyzed five prosodic cues to focus—F0 range, word duration, intensity, voice quality, the location of the F0 maximum, and the occurrence of pauses—in a set of 947 simple Subject Verb Object (SVO sentences uttered by 17 native speakers of Finnish. Using random forest and generalized additive mixed modelling, we investigated the systematicity of prosodic focus marking, the importance of each cue as a predictor, and their functional shape. Results indicated a highly consistent differentiation between narrow focus and givenness, marked by at least F0 range, word duration, intensity, and the location of the F0 maximum, with F0 range being the most important predictor. No cue had a linear relationship with focus condition. To account for the simultaneous significance of several predictors, we argue that these findings support treating multiple prosodic cues to focus in Finnish as correlates of prosodic phrasing. Thus, we suggest that prosodic phrasing, having multiple functions, is also marked with multiple cues to enhance communicative efficiency.

  7. In vitro and in vivo models of multiple sclerosis.

    Science.gov (United States)

    van der Star, Baukje J; Vogel, Daphne Y S; Kipp, Markus; Puentes, Fabiola; Baker, David; Amor, Sandra

    2012-08-01

    Multiple sclerosis (MS) is widely considered to be the result of an aggressive autoreactive T cell attack on myelin. How these autoimmune responses arise in MS is unclear, but they could result from virus infections. Thus, viral and autoimmune diseases in animals have been used to investigate the possible pathogenic mechanisms operating in MS. The autoimmune model, experimental autoimmune encephalomyelitis, is the most widely-used animal model and has greatly influenced therapeutic approaches targeting autoimmune responses. To investigate demyelination and remyelination in the absence of the adaptive immune response, toxin-induced demyelination models are used. These include using cuprizone, ethidium bromide and lysolecithin to induce myelin damage, which rapidly lead to remyelination when the toxins are withdrawn. The virus models include natural and experimental infections such as canine distemper, visna infection of sheep, and infection of non-human primates. The most commonly used viral models in rodents are Semliki Forest virus and Theiler's murine encephalomyelitis virus. The viral and experimental autoimmune encephalomyelitis models have been instrumental in the understanding of how viruses trigger inflammation, demyelination and neurodegeneration in the central nervous system. However, due to complexity of the animal models, pathological mechanisms are also examined in central nervous system cell culture systems including co-cultures, aggregate cultures and brain slice cultures. Here we critically review in vitro and in vivo models used to investigate MS. Since knowledge gained from these models forms the basis for the development of new therapeutic approaches for MS, we address the applicability of the models. Finally, we provide guidance for using and reporting animal studies with the aim of improving translational studies to the clinic.

  8. Bifurcation analysis in single-species population model with delay

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A single-species population model is investigated in this paper.Firstly,we study the existence of Hopf bifurcation at the positive equilibrium.Furthermore,an explicit algorithm for determining the direction of the Hopf bifurcation and stability of the bifurcation periodic solutions are derived by using the normal form and the center manifold theory.At last,numerical simulations to support the analytical conclusions are carried out.

  9. Strength in numbers? Effects of multiple natural enemy species on plant performance.

    Science.gov (United States)

    Stephens, Andrea E A; Srivastava, Diane S; Myers, Judith H

    2013-06-01

    While plants are invariably attacked by numerous insects and pathogens, the consequences of multiple enemies for plant performance are poorly understood. In particular, a predictive framework is lacking for when to expect enemies to have independent versus non-independent effects on their host plant. This is problematic for weed biological control programmes where multiple enemies are frequently released with the possibility of antagonistic interactions that may reduce control. Here, we conduct an analysis of 74 unique plant-enemy-enemy combinations from 51 studies to determine the frequency of non-independent effects of natural enemies on host plant performance, and test a number of a priori predictions for determinants of independent and antagonistic effects of multiple enemies. For three-quarters of plant response measurements, enemies had independent effects on plant performance. In most of the remainder, multiple enemies led to less reduction in performance than that predicted from each enemy alone. Antagonistic effects occurred when enemies attacked the same plant part concurrently or attacked plant reproductive structures. These two predictors explained why antagonistic effects were particularly prevalent for weeds, plants in the family Asteraceae and enemies in the order Diptera. Our results suggest that a few simple rules about avoiding particular combinations of multiple enemies could improve biological control success.

  10. Multiple filarial species microfilaraemia: a comparative study of areas with endemic and sporadic onchocerciasis

    Directory of Open Access Journals (Sweden)

    Emmanuel Uttah & Dominic C. Ibeh

    2011-12-01

    Full Text Available Background & objectives: The study was aimed at determining the pattern of co-occurrence of species ofmicrofilaraemia between onchocerciasis endemic and sporadic populations.Methods: From every consenting person of one year and above, 50 μl of day and night blood samples werecollected and processed respectively with Haemotoxylin and Giemsa as vital stains. Two skin snips (one eachfrom the waist and the shoulder were also taken from these individuals and processed.Results: Results showed single species microfilaraemia (86.4 and 82.3%, double species microfilaraemia (12.2and 16.9% and triple species microfilaraemia (1.4 and 0.7% for endemic and sporadic populations respectively.All the species had single species microfilaraemia mostly, but Mansonella perstans and Loa loa showed greatestt endency towa rds doubl e and t r ipl e spe c i e s mi c rof i l a r a emi a . The pr eva l enc e of Wuche re r ia banc rof t imicrofilaraemia among those positive for Onchocerca volvulus was significantly lower than the overall prevalenceof Wuchereria bancrofti. Wuchereria bancrofti microfilaraemia was most common among those who had L. loamicrofilaraemia. Wuchereria bancrofti microfilarial intensity was higher among those with M. perstansmicrofilaraemia than among those positive for any of the other filarial species. Similarly, the intensity of M.perstans microfilaraemia among those positive for W. bancrofti exceeded the overall intensity of M. perstans.Conclusion: It is concluded that there was no definite pattern in mf densities discernible from co-occurrenceinfections either in the onchocerciasis endemic or sporadic population. There could be varied outcomes ofonchocerciasis infection attributable to positive or negative regulatory effects of other pathogens harbored bythe victims.

  11. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

    Science.gov (United States)

    Fowlkes, Charless C; Eckenrode, Kelly B; Bragdon, Meghan D; Meyer, Miriah; Wunderlich, Zeba; Simirenko, Lisa; Luengo Hendriks, Cris L; Keränen, Soile V E; Henriquez, Clara; Knowles, David W; Biggin, Mark D; Eisen, Michael B; DePace, Angela H

    2011-10-01

    Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3-4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of

  12. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila.

    Directory of Open Access Journals (Sweden)

    Charless C Fowlkes

    2011-10-01

    Full Text Available Differences in the level, timing, or location of gene expression can contribute to alternative phenotypes at the molecular and organismal level. Understanding the origins of expression differences is complicated by the fact that organismal morphology and gene regulatory networks could potentially vary even between closely related species. To assess the scope of such changes, we used high-resolution imaging methods to measure mRNA expression in blastoderm embryos of Drosophila yakuba and Drosophila pseudoobscura and assembled these data into cellular resolution atlases, where expression levels for 13 genes in the segmentation network are averaged into species-specific, cellular resolution morphological frameworks. We demonstrate that the blastoderm embryos of these species differ in their morphology in terms of size, shape, and number of nuclei. We present an approach to compare cellular gene expression patterns between species, while accounting for varying embryo morphology, and apply it to our data and an equivalent dataset for Drosophila melanogaster. Our analysis reveals that all individual genes differ quantitatively in their spatio-temporal expression patterns between these species, primarily in terms of their relative position and dynamics. Despite many small quantitative differences, cellular gene expression profiles for the whole set of genes examined are largely similar. This suggests that cell types at this stage of development are conserved, though they can differ in their relative position by up to 3-4 cell widths and in their relative proportion between species by as much as 5-fold. Quantitative differences in the dynamics and relative level of a subset of genes between corresponding cell types may reflect altered regulatory functions between species. Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and

  13. Generalized multiplicative error models: Asymptotic inference and empirical analysis

    Science.gov (United States)

    Li, Qian

    This dissertation consists of two parts. The first part focuses on extended Multiplicative Error Models (MEM) that include two extreme cases for nonnegative series. These extreme cases are common phenomena in high-frequency financial time series. The Location MEM(p,q) model incorporates a location parameter so that the series are required to have positive lower bounds. The estimator for the location parameter turns out to be the minimum of all the observations and is shown to be consistent. The second case captures the nontrivial fraction of zero outcomes feature in a series and combines a so-called Zero-Augmented general F distribution with linear MEM(p,q). Under certain strict stationary and moment conditions, we establish a consistency and asymptotic normality of the semiparametric estimation for these two new models. The second part of this dissertation examines the differences and similarities between trades in the home market and trades in the foreign market of cross-listed stocks. We exploit the multiplicative framework to model trading duration, volume per trade and price volatility for Canadian shares that are cross-listed in the New York Stock Exchange (NYSE) and the Toronto Stock Exchange (TSX). We explore the clustering effect, interaction between trading variables, and the time needed for price equilibrium after a perturbation for each market. The clustering effect is studied through the use of univariate MEM(1,1) on each variable, while the interactions among duration, volume and price volatility are captured by a multivariate system of MEM(p,q). After estimating these models by a standard QMLE procedure, we exploit the Impulse Response function to compute the calendar time for a perturbation in these variables to be absorbed into price variance, and use common statistical tests to identify the difference between the two markets in each aspect. These differences are of considerable interest to traders, stock exchanges and policy makers.

  14. Multiplicative point process as a model of trading activity

    Science.gov (United States)

    Gontis, V.; Kaulakys, B.

    2004-11-01

    Signals consisting of a sequence of pulses show that inherent origin of the 1/ f noise is a Brownian fluctuation of the average interevent time between subsequent pulses of the pulse sequence. In this paper, we generalize the model of interevent time to reproduce a variety of self-affine time series exhibiting power spectral density S( f) scaling as a power of the frequency f. Furthermore, we analyze the relation between the power-law correlations and the origin of the power-law probability distribution of the signal intensity. We introduce a stochastic multiplicative model for the time intervals between point events and analyze the statistical properties of the signal analytically and numerically. Such model system exhibits power-law spectral density S( f)∼1/ fβ for various values of β, including β= {1}/{2}, 1 and {3}/{2}. Explicit expressions for the power spectra in the low-frequency limit and for the distribution density of the interevent time are obtained. The counting statistics of the events is analyzed analytically and numerically, as well. The specific interest of our analysis is related with the financial markets, where long-range correlations of price fluctuations largely depend on the number of transactions. We analyze the spectral density and counting statistics of the number of transactions. The model reproduces spectral properties of the real markets and explains the mechanism of power-law distribution of trading activity. The study provides evidence that the statistical properties of the financial markets are enclosed in the statistics of the time interval between trades. A multiplicative point process serves as a consistent model generating this statistics.

  15. Rank-based model selection for multiple ions quantum tomography

    Science.gov (United States)

    Guţă, Mădălin; Kypraios, Theodore; Dryden, Ian

    2012-10-01

    The statistical analysis of measurement data has become a key component of many quantum engineering experiments. As standard full state tomography becomes unfeasible for large dimensional quantum systems, one needs to exploit prior information and the ‘sparsity’ properties of the experimental state in order to reduce the dimensionality of the estimation problem. In this paper we propose model selection as a general principle for finding the simplest, or most parsimonious explanation of the data, by fitting different models and choosing the estimator with the best trade-off between likelihood fit and model complexity. We apply two well established model selection methods—the Akaike information criterion (AIC) and the Bayesian information criterion (BIC)—two models consisting of states of fixed rank and datasets such as are currently produced in multiple ions experiments. We test the performance of AIC and BIC on randomly chosen low rank states of four ions, and study the dependence of the selected rank with the number of measurement repetitions for one ion states. We then apply the methods to real data from a four ions experiment aimed at creating a Smolin state of rank 4. By applying the two methods together with the Pearson χ2 test we conclude that the data can be suitably described with a model whose rank is between 7 and 9. Additionally we find that the mean square error of the maximum likelihood estimator for pure states is close to that of the optimal over all possible measurements.

  16. The multilevel p2 model : A random effects model for the analysis of multiple social networks

    NARCIS (Netherlands)

    Zijlstra, B.J.H.; van Duijn, M.A.J.; Snijders, T.A.B.

    2006-01-01

    The p2 model is a random effects model with covariates for the analysis of binary directed social network data coming from a single observation of a social network. Here, a multilevel variant of the p2 model is proposed for the case of multiple observations of social networks, for example, in a samp

  17. Population dynamics of species-rich ecosystems: the mixture of matrix population models approach

    DEFF Research Database (Denmark)

    Mortier, Frédéric; Rossi, Vivien; Guillot, Gilles;

    2013-01-01

    Matrix population models are widely used to predict population dynamics, but when applied to species-rich ecosystems with many rare species, the small population sample sizes hinder a good fit of species-specific models. This issue can be overcome by assigning species to groups to increase the size...... species with similar population dynamics....

  18. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    Directory of Open Access Journals (Sweden)

    Gareth D Westrop

    Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  19. Linear Modeling of Multiple Sclerosis and Its Subgroubs

    Directory of Open Access Journals (Sweden)

    Yeliz Karaca

    2015-03-01

    Full Text Available OBJECTIVE: In this study,120 patients diagnosed with clinical multiple sclerosis (MS of relapsing remitting type (RRMS, secondary progressive type (SPMS and primary progressive type (PPMS were examined, as well as 19 healthy subjects. All subjects were between the ages of 20 and 55. Disability levels of MS symptoms were determined using Expanded Disability Status Scale (EDSS. We focused on three regions in the brain, brain stem, periventricular corpus callosum, and upper cervical regions EDSS scores and number of lesions in these three regions are considered as the parameters of the linear mathematical model to determine the subgroups of the disease. METHODS: Initially, the distinction between healthy subjects and patients was made. Then, if the subject was determined to have MS, the distinction of type, i.e. RRMS, SPMS/PPMS, and later, RRMS/SPMS distinction was made. In all determinations linear models were used and number of lesions in the specified three regions and EDSS scores were assumed as the parameters of the model. The coefficients of the models were obtained by least squares method. RESULTS: In the linear model attached to MR parameters, there was 100% success for distinction of patients and healthy subjects. Success for distinction of RRMS and SPMS/PPMS patients and RRMS/SPMS patients was 94% and 78.94%, respectively is attained. Based on EDSS scores, linear model provides 99% success in the distinction between patients and healthy subjects. In the models created for the distinction between groups, success rate was 94% was for RRMS-SPMS/PPMS and 64% for RRMS/SPMS. CONCLUSION: The correlation of MS diagnosis using various features obtained from MR images and EDSS scores with subgroups of the disease and the possibility of developing a linear model were determined. Using the features having the highest correlation rate, various linear models were developed and high success was achieved.

  20. Federated or cached searches: Providing expected performance from multiple invasive species databases

    Science.gov (United States)

    Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

    2011-06-01

    Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  1. The Homogeneity of Optimal Sensor Placement Across Multiple Winged Insect Species

    Science.gov (United States)

    Jenkins, Abigail L.

    Taking inspiration from biology, control algorithms can be implemented to imitate the naturally occurring control systems present in nature. This research is primarily concerned with insect flight and optimal wing sensor placement. Many winged insects with halteres are equipped with mechanoreceptors termed campaniform sensilla. Although the exact information these receptors provide to the insect's nervous system is unknown, it is thought to have the capability of measuring inertial rotation forces. During flight, when the wing bends, the information measured by the campaniform sensilla is received by the central nervous system, and provides the insect necessary data to control flight. This research compares three insect species - the hawkmoth Manduca sexta, the honeybee Apis mellifera, and the fruit fly Drosophila melanogaster. Using an observability-based sensor placement algorithm, the optimal sensor placement for these three species is determined. Simulations resolve if this optimal sensor placement corresponds to the insect's campaniform sensilla, as well as if placement is homogeneous across species.

  2. Federated or cached searches:Providing expected performance from multiple invasive species databases

    Institute of Scientific and Technical Information of China (English)

    Jim GRAHAM; Catherine S.JARNEVICH; Annie SIMPSON; Gregory J.NEWMAN; Thomas J.STOHLGREN

    2011-01-01

    Invasive species are a universal global problem,but the information to identify them,manage them,and prevent invasions is stored around the globe in a variety of formats.The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet.A distributed network of databases can be created using the Intemet and a standard web service protocol.There are two options to provide this integration.First,federated searches are being proposed to allow users to search "deep" web documents such as databases for invasive species.A second method is to create a cache of data from the databases for searching.We compare these two methods,and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  3. No Inbreeding depression for low temperature developmental acclimation across multiple drosophila species

    DEFF Research Database (Denmark)

    Kristensen, Torsten Nygård; Loeschcke, Volker; Bilde, Trine

    2011-01-01

    is highly species specific, and differs among ecotypes (e.g., tropical and widespread species). Apart from being exposed to thermal stress many small and fragmented populations face genetic challenges due to, for example, inbreeding. Inbreeding has been shown to reduce inherent resistance levels toward......Populations are from time to time exposed to stressful temperatures. Their thermal resistance levels are determined by inherent and plastic mechanisms, which are both likely to be under selection in natural populations. Previous studies on Drosophila species have shown that inherent resistance...... stressful temperatures, but whether adaptation to thermal stress through plastic responses also is affected by inbreeding is so far not clear. In this study, we test inherent cold resistance and the ability to respond plastically to temperature changes through developmental cold acclimation in inbred...

  4. The product of microbial uranium reduction includes multiple species with U(IV)-phosphate coordination

    Science.gov (United States)

    Alessi, Daniel S.; Lezama-Pacheco, Juan S.; Stubbs, Joanne E.; Janousch, Markus; Bargar, John R.; Persson, Per; Bernier-Latmani, Rizlan

    2014-04-01

    Until recently, the reduction of U(VI) to U(IV) during bioremediation was assumed to produce solely the sparingly soluble mineral uraninite, UO2(s). However, results from several laboratories reveal other species of U(IV) characterized by the absence of an EXAFS U-U pair correlation (referred to here as noncrystalline U(IV)). Because it lacks the crystalline structure of uraninite, this species is likely to be more labile and susceptible to reoxidation. In the case of single species cultures, analyses of U extended X-ray fine structure (EXAFS) spectra have previously suggested U(IV) coordination to carboxyl, phosphoryl or carbonate groups. In spite of this evidence, little is understood about the species that make up noncrystalline U(IV), their structural chemistry and the nature of the U(IV)-ligand interactions. Here, we use infrared spectroscopy (IR), uranium LIII-edge X-ray absorption spectroscopy (XAS), and phosphorus K-edge XAS analyses to constrain the binding environments of phosphate and uranium associated with Shewanella oneidensis MR-1 bacterial cells. Systems tested as a function of pH included: cells under metal-reducing conditions without uranium, cells under reducing conditions that produced primarily uraninite, and cells under reducing conditions that produced primarily biomass-associated noncrystalline U(IV). P X-ray absorption near-edge structure (XANES) results provided clear and direct evidence of U(IV) coordination to phosphate. Infrared (IR) spectroscopy revealed a pronounced perturbation of phosphate functional groups in the presence of uranium. Analysis of these data provides evidence that U(IV) is coordinated to a range of phosphate species, including monomers and polymerized networks. U EXAFS analyses and a chemical extraction measurements support these conclusions. The results of this study provide new insights into the binding mechanisms of biomass-associated U(IV) species which in turn sheds light on the mechanisms of biological U

  5. Social conflict exacerbates an animal model of multiple sclerosis.

    Science.gov (United States)

    Meagher, Mary W; Johnson, Robin R; Vichaya, Elisabeth Good; Young, Erin E; Lunt, Shannon; Welsh, C Jane

    2007-07-01

    A growing body of evidence suggests that social conflict is associated with inflammatory disease onset and exacerbations in multiple sclerosis (MS) patients and in animal models of MS. This review illustrates how animal research can be used to elucidate the biobehavioral mechanisms underlying the adverse health effects of social conflict. The authors review studies indicating that social conflict exacerbates a virally initiated animal model of MS. This research suggests that the deleterious effects of social conflict may be partially mediated by stress-induced increases in pro-inflammatory cytokine levels in the central nervous system. In addition, they provide evidence that the adverse health effects of social conflict can be prevented by blocking the stress-induced increases in cytokine activity. This suggests that interventions designed to prevent or reverse the stress-induced increases in cytokine activity may be able to prevent or reverse some of the negative health effects of social conflict in humans.

  6. Finite element modelling of internal and multiple localized cracks

    Science.gov (United States)

    Saloustros, Savvas; Pelà, Luca; Cervera, Miguel; Roca, Pere

    2017-02-01

    Tracking algorithms constitute an efficient numerical technique for modelling fracture in quasi-brittle materials. They succeed in representing localized cracks in the numerical model without mesh-induced directional bias. Currently available tracking algorithms have an important limitation: cracking originates either from the boundary of the discretized domain or from predefined "crack-root" elements and then propagates along one orientation. This paper aims to circumvent this drawback by proposing a novel tracking algorithm that can simulate cracking starting at any point of the mesh and propagating along one or two orientations. This enhancement allows the simulation of structural case-studies experiencing multiple cracking. The proposed approach is validated through the simulation of a benchmark example and an experimentally tested structural frame under in-plane loading. Mesh-bias independency of the numerical solution, computational cost and predicted collapse mechanisms with and without the tracking algorithm are discussed.

  7. Modelling and validation of multiple reflections for enhanced laser welding

    Science.gov (United States)

    Milewski, J.; Sklar, E.

    1996-05-01

    The effects of multiple internal reflections within a laser weld joint as functions of joint geometry and processing conditions have been characterized. A computer-based ray tracing model is used to predict the reflective propagation of laser beam energy focused into the narrow gap of a metal joint for the purpose of predicting the location of melting and coalescence to form a weld. Quantitative comparisons are made between simulation cases. Experimental results are provided for qualitative model validation. This method is proposed as a way to enhance process efficiency and design laser welds which display deep penetration and high depth-to-width aspect ratios without high powered systems or keyhole mode melting.

  8. Research and application of hierarchical model for multiple fault diagnosis

    Institute of Scientific and Technical Information of China (English)

    An Ruoming; Jiang Xingwei; Song Zhengji

    2005-01-01

    Computational complexity of complex system multiple fault diagnosis is a puzzle at all times. Based on the well-known Mozetic's approach, a novel hierarchical model-based diagnosis methodology is put forward for improving efficiency of multi-fault recognition and localization. Structural abstraction and weighted fault propagation graphs are combined to build diagnosis model. The graphs have weighted arcs with fault propagation probabilities and propagation strength. For solving the problem of coupled faults, two diagnosis strategies are used: one is the Lagrangian relaxation and the primal heuristic algorithms; another is the method of propagation strength. Finally, an applied example shows the applicability of the approach and experimental results are given to show the superiority of the presented technique.

  9. A Hybrid Multiple Criteria Decision Making Model for Supplier Selection

    Directory of Open Access Journals (Sweden)

    Chung-Min Wu

    2013-01-01

    Full Text Available The sustainable supplier selection would be the vital part in the management of a sustainable supply chain. In this study, a hybrid multiple criteria decision making (MCDM model is applied to select optimal supplier. The fuzzy Delphi method, which can lead to better criteria selection, is used to modify criteria. Considering the interdependence among the selection criteria, analytic network process (ANP is then used to obtain their weights. To avoid calculation and additional pairwise comparisons of ANP, a technique for order preference by similarity to ideal solution (TOPSIS is used to rank the alternatives. The use of a combination of the fuzzy Delphi method, ANP, and TOPSIS, proposing an MCDM model for supplier selection, and applying these to a real case are the unique features of this study.

  10. Multiple Scattering Model for Optical Coherence Tomography with Rytov Approximation

    KAUST Repository

    Li, Muxingzi

    2017-04-24

    Optical Coherence Tomography (OCT) is a coherence-gated, micrometer-resolution imaging technique that focuses a broadband near-infrared laser beam to penetrate into optical scattering media, e.g. biological tissues. The OCT resolution is split into two parts, with the axial resolution defined by half the coherence length, and the depth-dependent lateral resolution determined by the beam geometry, which is well described by a Gaussian beam model. The depth dependence of lateral resolution directly results in the defocusing effect outside the confocal region and restricts current OCT probes to small numerical aperture (NA) at the expense of lateral resolution near the focus. Another limitation on OCT development is the presence of a mixture of speckles due to multiple scatterers within the coherence length, and other random noise. Motivated by the above two challenges, a multiple scattering model based on Rytov approximation and Gaussian beam optics is proposed for the OCT setup. Some previous papers have adopted the first Born approximation with the assumption of small perturbation of the incident field in inhomogeneous media. The Rytov method of the same order with smooth phase perturbation assumption benefits from a wider spatial range of validity. A deconvolution method for solving the inverse problem associated with the first Rytov approximation is developed, significantly reducing the defocusing effect through depth and therefore extending the feasible range of NA.

  11. Detection of multiple species of human Paragonimus from Mexico using morphological data and molecular barcodes.

    Science.gov (United States)

    López-Caballero, J; Oceguera-Figueroa, A; León-Règagnon, V

    2013-11-01

    Paragonimus mexicanus is the causal agent of human paragonimiasis in several countries of the Americas. It is considered to be the only species of the genus present in Mexico, where it is responsible for human infection. Through the investigation of P. mexicanus specimens from several places throughout Mexico, we provide morphological, molecular and geographical evidence that strongly suggests the presence of at least three species from this genus in Mexico. These results raise questions regarding the diagnosis, treatment, prophylaxis and control of human paragonimiasis in Mexico. We also provide a brief discussion regarding biodiversity inventories and the convenience of providing molecular and morphological information in biodiversity studies.

  12. Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning

    DEFF Research Database (Denmark)

    Ejsing, Christer S.; Duchoslav, Eva; Sampaio, Julio

    2006-01-01

    We report a method for the identification and quantification of glycerophospholipid molecular species that is based on the simultaneous automated acquisition and processing of 41 precursor ion spectra, specific for acyl anions of common fatty acids moieties and several lipid class-specific fragment...... ions. Absolute quantification of identified species was linear within a concentration range of 10 nM-100 microM and was achieved by spiking into total lipid extracts a set of synthetic lipid standards with diheptadecanoyl (17:0/17:0) fatty acid moieties, representing six common classes...

  13. Metals and organotins in multiple bivalve species in a one-off global survey

    DEFF Research Database (Denmark)

    Larsen, Martin Mørk; Strand, Jakob; Christensen, Jan H.

    2011-01-01

    classified according to human impact using principal component analysis. High relative concentrations of Hg, Pb and P were source indicators for industrial activity and land use; Zn, organotins, Cd and Cu for shipping activities, and V for oil spills. Generally the concentration levels at reference sites...... contamination levels on a global scale. Metal concentrations in nine bivalve species were normalised to the Mytilidae family using conversion factors based on cosampled species and literature bioconcentration factors. The lowest metal and tributyltin concentrations were below background assessment...

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

    Science.gov (United States)

    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

  15. Metabolite profiling of the multiple tyrosine kinase inhibitor lenvatinib : a cross-species comparison

    NARCIS (Netherlands)

    Dubbelman, Anne Charlotte; Nijenhuis, Cynthia M.; Jansen, Robert S; Rosing, Hilde; Mizuo, Hitoshi; Kawaguchi, Shinki; Critchley, David; Shumaker, Robert; Schellens, Jan H M; Beijnen, Jos H.

    2016-01-01

    Lenvatinib is an oral, multiple receptor tyrosine kinase inhibitor. Preclinical drug metabolism studies showed unique metabolic pathways for lenvatinib in monkeys and rats. A human mass balance study demonstrated that lenvatinib related material is mainly excreted via feces with a small fraction as

  16. The multiple process model of goal-directed reaching revisited.

    Science.gov (United States)

    Elliott, Digby; Lyons, James; Hayes, Spencer J; Burkitt, James J; Roberts, James W; Grierson, Lawrence E M; Hansen, Steve; Bennett, Simon J

    2017-01-01

    Recently our group forwarded a model of speed-accuracy relations in goal-directed reaching. A fundamental feature of our multiple process model was the distinction between two types of online regulation: impulse control and limb-target control. Impulse control begins during the initial stages of the movement trajectory and involves a comparison of actual limb velocity and direction to an internal representation of expectations about the limb trajectory. Limb-target control involves discrete error-reduction based on the relative positions of the limb and the target late in the movement. Our model also considers the role of eye movements, practice, energy optimization and strategic behavior in limb control. Here, we review recent work conducted to test specific aspects of our model. As well, we consider research not fully incorporated into our earlier contribution. We conclude that a slightly modified and expanded version of our model, that includes crosstalk between the two forms of online regulation, does an excellent job of explaining speed, accuracy, and energy optimization in goal-directed reaching.

  17. Modelling marine community responses to climate-driven species redistribution to guide monitoring and adaptive ecosystem-based management.

    Science.gov (United States)

    Marzloff, Martin Pierre; Melbourne-Thomas, Jessica; Hamon, Katell G; Hoshino, Eriko; Jennings, Sarah; van Putten, Ingrid E; Pecl, Gretta T

    2016-07-01

    As a consequence of global climate-driven changes, marine ecosystems are experiencing polewards redistributions of species - or range shifts - across taxa and throughout latitudes worldwide. Research on these range shifts largely focuses on understanding and predicting changes in the distribution of individual species. The ecological effects of marine range shifts on ecosystem structure and functioning, as well as human coastal communities, can be large, yet remain difficult to anticipate and manage. Here, we use qualitative modelling of system feedback to understand the cumulative impacts of multiple species shifts in south-eastern Australia, a global hotspot for ocean warming. We identify range-shifting species that can induce trophic cascades and affect ecosystem dynamics and productivity, and evaluate the potential effectiveness of alternative management interventions to mitigate these impacts. Our results suggest that the negative ecological impacts of multiple simultaneous range shifts generally add up. Thus, implementing whole-of-ecosystem management strategies and regular monitoring of range-shifting species of ecological concern are necessary to effectively intervene against undesirable consequences of marine range shifts at the regional scale. Our study illustrates how modelling system feedback with only limited qualitative information about ecosystem structure and range-shifting species can predict ecological consequences of multiple co-occurring range shifts, guide ecosystem-based adaptation to climate change and help prioritise future research and monitoring. © 2016 John Wiley & Sons Ltd.

  18. Model-based uncertainty in species range prediction

    DEFF Research Database (Denmark)

    Pearson, R. G.; Thuiller, Wilfried; Bastos Araujo, Miguel;

    2006-01-01

    Aim Many attempts to predict the potential range of species rely on environmental niche (or 'bioclimate envelope') modelling, yet the effects of using different niche-based methodologies require further investigation. Here we investigate the impact that the choice of model can have on predictions...... day (using the area under the receiver operating characteristic curve (AUC) and kappa statistics) and by assessing consistency in predictions of range size changes under future climate (using cluster analysis). Results Our analyses show significant differences between predictions from different models......, with predicted changes in range size by 2030 differing in both magnitude and direction (e.g. from 92% loss to 322% gain). We explain differences with reference to two characteristics of the modelling techniques: data input requirements (presence/absence vs. presence-only approaches) and assumptions made by each...

  19. Multiplication of an ancestral gene encoding secreted fungalysin preceded species differentiation in the dermatophytes Trichophyton and Microsporum.

    Science.gov (United States)

    Jousson, Olivier; Léchenne, Barbara; Bontems, Olympia; Capoccia, Sabrina; Mignon, Bernard; Barblan, Jachen; Quadroni, Manfredo; Monod, Michel

    2004-02-01

    Dermatophytes are human and animal pathogenic fungi which cause cutaneous infections and grow exclusively in the stratum corneum, nails and hair. In a culture medium containing soy proteins as sole nitrogen source a substantial proteolytic activity was secreted by Trichophyton rubrum, Trichophyton mentagrophytes and Microsporum canis. This proteolytic activity was 55-75 % inhibited by o-phenanthroline, attesting that metalloproteases were secreted by all three species. Using a consensus probe constructed on previously characterized genes encoding metalloproteases (MEP) of the M36 fungalysin family in Aspergillus fumigatus, Aspergillus oryzae and M. canis, a five-member MEP family was isolated from genomic libraries of T. rubrum, T. mentagrophytes and M. canis. A phylogenetic analysis of genomic and protein sequences revealed a robust tree consisting of five main clades, each of them including a MEP sequence type from each dermatophyte species. Each MEP type was remarkably conserved across species (72-97 % amino acid sequence identity). The tree topology clearly indicated that the multiplication of MEP genes in dermatophytes occurred prior to species divergence. In culture medium containing soy proteins as a sole nitrogen source secreted Meps accounted for 19-36 % of total secreted protein extracts; characterization of protein bands by proteolysis and mass spectrometry revealed that the three dermatophyte species secreted two Meps (Mep3 and Mep4) encoded by orthologous genes.

  20. Multiple Genome Sequences of the Important Beer-Spoiling Species Lactobacillus backii

    OpenAIRE

    Geissler, Andreas J.; Behr, Jürgen; Vogel, Rudi F.

    2016-01-01

    Lactobacillus backii is an important beer-spoiling species. Five strains isolated from four different breweries were sequenced using single-molecule real-time sequencing. Five complete genomes were generated, which will help to understand niche adaptation to beer and provide the basis for consecutive analyses.

  1. Sarmentine, a natural herbicide from Piper species with multiple herbicide mechanisms of action

    Science.gov (United States)

    Sarmentine, 1-(1-pyrrolidinyl)-(2E,4E)-2,4-decadien-1-one, is a natural amide isolated from the fruits of Piper species. The compound has a number of interesting biological properties, including its broad-spectrum activity on weeds as a contact herbicide. Initial studies highlighted a similarity in ...

  2. Multiple Phytophthora species associated with a single riparian ecosystem in South Africa.

    Science.gov (United States)

    Nagel, Jan H; Slippers, Bernard; Wingfield, Michael J; Gryzenhout, Marieka

    2015-01-01

    The diversity of Phytophthora spp. in rivers and riparian ecosystems has received considerable international attention, although little such research has been conducted in South Africa. This study determined the diversity of Phytophthora spp. within a single river in Gauteng province of South Africa. Samples were collected over 1 y including biweekly river baiting with Rhododendron indicum leaves. Phytophthora isolates were identified with phylogenetic analyses of sequences for the internal transcribed spacer (ITS) region of the ribosomal DNA and the mitochondrial cytochrome oxidase c subunit I (coxI) gene. Eight Phytophthora spp. were identified, including a new taxon, P. taxon Sisulu-river, and two hybrid species from Cooke's ITS clade 6. Of these, species from Clade 6 were the most abundant, including P. chlamydospora and P. lacustris. Species residing in Clade 2 also were encountered, including P. multivora, P. plurivora and P. citrophthora. The detection of eight species in this investigation of Phytophthora diversity in a single riparian river ecosystem in northern South Africa adds to the known diversity of this genus in South Africa and globally.

  3. Importance of resolving fungal nomenclature: the case of multiple pathogenic species in the Cryptococcus genus

    Science.gov (United States)

    Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoform...

  4. One health, multiple challenges: The inter-species transmission of influenza A virus

    NARCIS (Netherlands)

    K.R. Short (Kirsty); M. Richard (Mathilde); J.H. Verhagen (Josanne); D.A.J. van Riel (Debby); E.J.A. Schrauwen (Eefje); J.M.A. van den Brand (Judith); B. Mänz (Benjamin); R. Bodewes (Rogier); S. Herfst (Sander)

    2015-01-01

    textabstractInfluenza A viruses are amongst the most challenging viruses that threaten both human and animal health. Influenza A viruses are unique in many ways. Firstly, they are unique in the diversity of host species that they infect. This includes waterfowl (the original reservoir), terrestrial

  5. One health, multiple challenges : The inter-species transmission of influenza A virus

    NARCIS (Netherlands)

    Short, Kirsty R; Richard, Mathilde; Verhagen, Josanne H; van Riel, Debby; Schrauwen, Eefje J A; van den Brand, Judith M A; Mänz, Benjamin; Bodewes, Rogier; Herfst, Sander

    2015-01-01

    Influenza A viruses are amongst the most challenging viruses that threaten both human and animal health. Influenza A viruses are unique in many ways. Firstly, they are unique in the diversity of host species that they infect. This includes waterfowl (the original reservoir), terrestrial and aquatic

  6. Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.

    Directory of Open Access Journals (Sweden)

    Derrick E Fouts

    2005-01-01

    Full Text Available Sequencing and comparative genome analysis of four strains of Campylobacter including C. lari RM2100, C. upsaliensis RM3195, and C. coli RM2228 has revealed major structural differences that are associated with the insertion of phage- and plasmid-like genomic islands, as well as major variations in the lipooligosaccharide complex. Poly G tracts are longer, are greater in number, and show greater variability in C. upsaliensis than in the other species. Many genes involved in host colonization, including racR/S, cadF, cdt, ciaB, and flagellin genes, are conserved across the species, but variations that appear to be species specific are evident for a lipooligosaccharide locus, a capsular (extracellular polysaccharide locus, and a novel Campylobacter putative licABCD virulence locus. The strains also vary in their metabolic profiles, as well as their resistance profiles to a range of antibiotics. It is evident that the newly identified hypothetical and conserved hypothetical proteins, as well as uncharacterized two-component regulatory systems and membrane proteins, may hold additional significant information on the major differences in virulence among the species, as well as the specificity of the strains for particular hosts.

  7. Multiple rearrangements in cryptic species of electric knifefish, Gymnotus carapo (Gymnotidae, Gymnotiformes revealed by chromosome painting

    Directory of Open Access Journals (Sweden)

    O'Brien Patricia CM

    2010-04-01

    Full Text Available Abstract Background Gymnotus (Gymnotidae, Gymnotiformes is the Neotropical electric fish genus with the largest geographic distribution and the largest number of species, 33 of which have been validated. The diploid number varies from 2n = 39-40 to 2n = 54. Recently we studied the karyotype of morphologically indistinguishable samples from five populations of G. carapo sensu stricto from the Eastern Amazon of Brazil. We found two cytotypes, 2n = 42 (30 M/SM + 12 ST/A and 2n = 40 (34 M/SM + 6 ST/A and we concluded that the differences between the two cryptic species are due to pericentric inversions and one tandem fusion. Results In this study we use for the first time, whole chromosome probes prepared by FACS of the Gymnotus carapo sensu strictu species, cytotype with 2n = 42. Using two color hybridizations we were able to distinguish pairs 1, 2, 3, 7, 9, 14, 16, 18, 19, 20 and 21. It was not possible to separate by FACS and distinguish each of the following chromosome pairs even with dual color FISH: {4,8}; {10,11}; {5,6,17}; {12,13,15}. The FISH probes were then used in chromosome painting experiments on metaphases of the 2n = 40 cytotype. While some chromosomes show conserved synteny, others are rearranged in different chromosomes. Eight syntenic associations were found. Conclusions These results show that the karyotype differences between these cryptic species are greater than assumed by classical cytogenetics. These data reinforce the previous supposition that these two cytotypes are different species, despite the absence of morphological differences. Additionally, the homology of repetitive DNA between the two provides evidence of recent speciation.

  8. Earlier migration timing, decreasing phenotypic variation, and biocomplexity in multiple salmonid species.

    Directory of Open Access Journals (Sweden)

    Ryan P Kovach

    Full Text Available Climate-induced phenological shifts can influence population, evolutionary, and ecological dynamics, but our understanding of these phenomena is hampered by a lack of long-term demographic data. We use a multi-decade census of 5 salmonid species representing 14 life histories in a warming Alaskan stream to address the following key questions about climate change and phenology: How consistent are temporal patterns and drivers of phenology for similar species and alternative life histories? Are shifts in phenology associated with changes in phenotypic variation? How do phenological changes influence the availability of resource subsidies? For most salmonid species, life stages, and life histories, freshwater temperature influences migration timing--migration events are occurring earlier in time (mean = 1.7 days earlier per decade over the 3-5 decades, and the number of days over which migration events occur is decreasing (mean = 1.5 days per decade. Temporal trends in migration timing were not correlated with changes in intra-annual phenotypic variation, suggesting that these components of the phenotypic distribution have responded to environmental change independently. Despite commonalities across species and life histories, there was important biocomplexity in the form of disparate shifts in migration timing and variation in the environmental factors influencing migration timing for alternative life history strategies in the same population. Overall, adult populations have been stable during these phenotypic and environmental changes (λ ≈ 1.0, but the temporal availability of salmon as a resource in freshwater has decreased by nearly 30 days since 1971 due to changes in the median date of migration timing and decreases in intra-annual variation in migration timing. These novel observations advance our understanding of phenological change in response to climate warming, and indicate that climate change has influenced the ecology of

  9. A population genetic model to infer allotetraploid speciation and long-term evolution applied to two yarrow species.

    Science.gov (United States)

    Guo, Yan-Ping; Tong, Xiao-Yuan; Wang, Lan-Wei; Vogl, Claus

    2013-07-01

    Allotetraploid speciation, that is, the generation of a hybrid tetraploid species from two diploid species, and the long-term evolution of tetraploid populations and species are important in plants. We developed a population genetic model to infer population genetic parameters of tetraploid populations from data of the progenitor and descendant species. Two yarrow species, Achillea alpina-4x and A. wilsoniana-4x, arose by allotetraploidization from the diploid progenitors, A. acuminata-2x and A. asiatica-2x. Yet, the population genetic process has not been studied in detail. We applied the model to sequences of three nuclear genes in populations of the four yarrow species and compared their pattern of variability with that in four plastid regions. The plastid data indicated that the two tetraploid species probably originated from multiple independent allopolyploidization events and have accumulated many mutations since. With the nuclear data, we found a low rate of homeologous recombination or gene conversion and a reduction in diversity relative to the level of both diploid species combined. The present analysis with a novel probabilistic model suggests a genetic bottleneck during tetraploid speciation, that the two tetraploid species have a long evolutionary history, and that they have a small amount of genetic exchange between the homeologous genomes.

  10. Ecological risk assessment conceptual model formulation for nonindigenous species.

    Science.gov (United States)

    Landis, Wayne G

    2004-08-01

    This article addresses the application of ecological risk assessment at the regional scale to the prediction of impacts due to invasive or nonindigenous species (NIS). The first section describes risk assessment, the decision-making process, and introduces regional risk assessment. A general conceptual model for the risk assessment of NIS is then presented based upon the regional risk assessment approach. Two diverse examples of the application of this approach are presented. The first example is based upon the dynamics of introduced plasmids into bacteria populations. The second example is the application risk assessment approach to the invasion of a coastal marine site of Cherry Point, Washington, USA by the European green crab. The lessons learned from the two examples demonstrate that assessment of the risks of invasion of NIS will have to incorporate not only the characteristics of the invasive species, but also the other stresses and impacts affecting the region of interest.

  11. Patterns and causes of species richness: a general simulation model for macroecology

    DEFF Research Database (Denmark)

    Gotelli, Nicholas J; Anderson, Marti J; Arita, Hector T

    2009-01-01

    in macroecology do not make quantitative predictions, and they do not incorporate interactions among multiple forces. As an alternative, we propose a mechanistic modelling approach. We describe computer simulation models of the stochastic origin, spread, and extinction of species' geographical ranges......' for a GSM that specify simple rules for dispersal, evolutionary origins and environmental gradients. Binary combinations of different knob settings correspond to eight distinct simulation models, five of which are already represented in the literature of macroecology. The output from such a GSM will include...... to a mechanistic understanding of the patterns. During the past two decades, macroecologists have successfully addressed technical problems posed by spatial autocorrelation, intercorrelation of predictor variables and non-linearity. However, curve-fitting approaches are problematic because most theoretical models...

  12. The predictive performance and stability of six species distribution models.

    Science.gov (United States)

    Duan, Ren-Yan; Kong, Xiao-Quan; Huang, Min-Yi; Fan, Wei-Yi; Wang, Zhi-Gao

    2014-01-01

    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. 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. 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 (pMAXENT, 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). 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 part of the modeling process.

  13. The predictive performance and stability of six species distribution models.

    Directory of Open Access Journals (Sweden)

    Ren-Yan Duan

    Full Text Available 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.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.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.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 part of the modeling process.

  14. Abundance modelling of invasive and indigenous Culicoides species in Spain

    Directory of Open Access Journals (Sweden)

    Els Ducheyne

    2013-11-01

    Full Text Available In this paper we present a novel methodology applied in Spain to model spatial abundance patterns of potential vectors of disease at a medium spatial resolution of 5 x 5 km using a countrywide database with abundance data for five Culicoides species, random regression Forest modelling and a spatial dataset of ground measured and remotely sensed eco-climatic and environmental predictor variables. First the probability of occurrence was computed. In a second step a direct regression between the probability of occurrence and trap abundance was established to verify the linearity of the relationship. Finally the probability of occurrence was used in combination with the set of predictor variables to model abundance. In each case the variable importance of the predictors was used to biologically interpret results and to compare both model outputs, and model performance was assessed using four different accuracy measures. Results are shown for C. imicola, C. newsteadii, C. pulicaris group, C. punctatus and C. obsoletus group. In each case the probability of occurrence is a good predictor of abundance at the used spatial resolution of 5 x 5 km. In addition, the C. imicola and C. obsoletus group are highly driven by summer rainfall. The spatial pattern is inverse between the two species, indicating that the lower and upper thresholds are different. C. pulicaris group is mainly driven by temperature. The patterns for C. newsteadii and C. punctatus are less clear. It is concluded that the proposed methodology can be used as an input to transmission-infection-recovery (TIR models and R0 models. The methodology will become available to the general public as part of the VECMAPTM software.

  15. Modeling multiple resource limitation in tropical dry forests

    Science.gov (United States)

    Medvigy, D.; Xu, X.; Zarakas, C.

    2015-12-01

    Tropical dry forests (TDFs) are characterized by a long dry season when little rain falls. At the same time, many neotropical soils are highly weathered and relatively nutrient poor. Because TDFs are often subject to both water and nutrient constraints, the question of how they will respond to environmental perturbations is both complex and highly interesting. Models, our basic tools for projecting ecosystem responses to global change, can be used to address this question. However, few models have been specifically parameterized for TDFs. Here, we present a new version of the Ecosystem Demography 2 (ED2) model that includes a new parameterization of TDFs. In particular, we focus on the model's framework for representing limitation by multiple resources (carbon, water, nitrogen, and phosphorus). Plant functional types are represented in terms of a dichotomy between "acquisitive" and "conservative" resource acquisition strategies. Depending on their resource acquisition strategy and basic stoichiometry, plants can dynamically adjust their allocation to organs (leaves, stem, roots), symbionts (e.g. N2-fixing bacteria), and mycorrhizal fungi. Several case studies are used to investigate how resource acquisition strategies affect ecosystem responses to environmental perturbations. Results are described in terms of the basic setting (e.g., rich vs. poor soils; longer vs. shorter dry season), and well as the type and magnitude of environmental perturbation (e.g., changes in precipitation or temperature; changes in nitrogen deposition). Implications for ecosystem structure and functioning are discussed.

  16. Modeling healthcare data using multiple-channel latent Dirichlet allocation.

    Science.gov (United States)

    Lu, Hsin-Min; Wei, Chih-Ping; Hsiao, Fei-Yuan

    2016-04-01

    Information and communications technologies have enabled healthcare institutions to accumulate large amounts of healthcare data that include diagnoses, medications, and additional contextual information such as patient demographics. To gain a better understanding of big healthcare data and to develop better data-driven clinical decision support systems, we propose a novel multiple-channel latent Dirichlet allocation (MCLDA) approach for modeling diagnoses, medications, and contextual information in healthcare data. The proposed MCLDA model assumes that a latent health status group structure is responsible for the observed co-occurrences among diagnoses, medications, and contextual information. Using a real-world research testbed that includes one million healthcare insurance claim records, we investigate the utility of MCLDA. Our empirical evaluation results suggest that MCLDA is capable of capturing the comorbidity structures and linking them with the distribution of medications. Moreover, MCLDA is able to identify the pairing between diagnoses and medications in a record based on the assigned latent groups. MCLDA can also be employed to predict missing medications or diagnoses given partial records. Our evaluation results also show that, in most cases, MCLDA outperforms alternative methods such as logistic regressions and the k-nearest-neighbor (KNN) model for two prediction tasks, i.e., medication and diagnosis prediction. Thus, MCLDA represents a promising approach to modeling healthcare data for clinical decision support.

  17. Analysis and application of opinion model with multiple topic interactions

    Science.gov (United States)

    Xiong, Fei; Liu, Yun; Wang, Liang; Wang, Ximeng

    2017-08-01

    To reveal heterogeneous behaviors of opinion evolution in different scenarios, we propose an opinion model with topic interactions. Individual opinions and topic features are represented by a multidimensional vector. We measure an agent's action towards a specific topic by the product of opinion and topic feature. When pairs of agents interact for a topic, their actions are introduced to opinion updates with bounded confidence. Simulation results show that a transition from a disordered state to a consensus state occurs at a critical point of the tolerance threshold, which depends on the opinion dimension. The critical point increases as the dimension of opinions increases. Multiple topics promote opinion interactions and lead to the formation of macroscopic opinion clusters. In addition, more topics accelerate the evolutionary process and weaken the effect of network topology. We use two sets of large-scale real data to evaluate the model, and the results prove its effectiveness in characterizing a real evolutionary process. Our model achieves high performance in individual action prediction and even outperforms state-of-the-art methods. Meanwhile, our model has much smaller computational complexity. This paper provides a demonstration for possible practical applications of theoretical opinion dynamics.

  18. The effects of model and data complexity on predictions from species distributions models

    DEFF Research Database (Denmark)

    García-Callejas, David; Bastos, Miguel

    2016-01-01

    study contradicts the widely held view that the complexity of species distributions models has significant effects in their predictive ability while findings support for previous observations that the properties of species distributions data and their relationship with the environment are strong...

  19. Integrating remote sensing with species distribution models; Mapping tamarisk invasions using the Software for Assisted Habitat Modeling (SAHM)

    Science.gov (United States)

    West, Amanda M.; Evangelista, Paul H.; Jarnevich, Catherine S.; Young, Nicholas E.; Stohlgren, Thomas J.; Talbert, Colin; Talbert, Marian K.; Morisette, Jeffrey; Anderson, Ryan

    2016-01-01

    Early detection of invasive plant species is vital for the management of natural resources and protection of ecosystem processes. The use of satellite remote sensing for mapping the distribution of invasive plants is becoming more common, however conventional imaging software and classification methods have been shown to be unreliable. In this study, we test and evaluate the use of five species distribution model techniques fit with satellite remote sensing data to map invasive tamarisk (Tamarix spp.) along the Arkansas River in Southeastern Colorado. The models tested included boosted regression trees (BRT), Random Forest (RF), multivariate adaptive regression splines (MARS), generalized linear model (GLM), and Maxent. These analyses were conducted using a newly developed software package called the Software for Assisted Habitat Modeling (SAHM). All models were trained with 499 presence points, 10,000 pseudo-absence points, and predictor variables acquired from the Landsat 5 Thematic Mapper (TM) sensor over an eight-month period to distinguish tamarisk from native riparian vegetation using detection of phenological differences. From the Landsat scenes, we used individual bands and calculated Normalized Difference Vegetation Index (NDVI), Soil-Adjusted Vegetation Index (SAVI), and tasseled capped transformations. All five models identified current tamarisk distribution on the landscape successfully based on threshold independent and threshold dependent evaluation metrics with independent location data. To account for model specific differences, we produced an ensemble of all five models with map output highlighting areas of agreement and areas of uncertainty. Our results demonstrate the usefulness of species distribution models in analyzing remotely sensed data and the utility of ensemble mapping, and showcase the capability of SAHM in pre-processing and executing multiple complex models.

  20. Integrating Remote Sensing with Species Distribution Models; Mapping Tamarisk Invasions Using the Software for Assisted Habitat Modeling (SAHM).

    Science.gov (United States)

    West, Amanda M; Evangelista, Paul H; Jarnevich, Catherine S; Young, Nicholas E; Stohlgren, Thomas J; Talbert, Colin; Talbert, Marian; Morisette, Jeffrey; Anderson, Ryan

    2016-10-11

    Early detection of invasive plant species is vital for the management of natural resources and protection of ecosystem processes. The use of satellite remote sensing for mapping the distribution of invasive plants is becoming more common, however conventional imaging software and classification methods have been shown to be unreliable. In this study, we test and evaluate the use of five species distribution model techniques fit with satellite remote sensing data to map invasive tamarisk (Tamarix spp.) along the Arkansas River in Southeastern Colorado. The models tested included boosted regression trees (BRT), Random Forest (RF), multivariate adaptive regression splines (MARS), generalized linear model (GLM), and Maxent. These analyses were conducted using a newly developed software package called the Software for Assisted Habitat Modeling (SAHM). All models were trained with 499 presence points, 10,000 pseudo-absence points, and predictor variables acquired from the Landsat 5 Thematic Mapper (TM) sensor over an eight-month period to distinguish tamarisk from native riparian vegetation using detection of phenological differences. From the Landsat scenes, we used individual bands and calculated Normalized Difference Vegetation Index (NDVI), Soil-Adjusted Vegetation Index (SAVI), and tasseled capped transformations. All five models identified current tamarisk distribution on the landscape successfully based on threshold independent and threshold dependent evaluation metrics with independent location data. To account for model specific differences, we produced an ensemble of all five models with map output highlighting areas of agreement and areas of uncertainty. Our results demonstrate the usefulness of species distribution models in analyzing remotely sensed data and the utility of ensemble mapping, and showcase the capability of SAHM in pre-processing and executing multiple complex models.

  1. Cryptosporidium rubeyi n. sp. (Apicomplexa: Cryptosporidiidae in multiple Spermophilus ground squirrel species

    Directory of Open Access Journals (Sweden)

    Xunde Li

    2015-12-01

    Full Text Available Previously we reported the unique Cryptosporidium sp. “c” genotype (e.g., Sbey03c, Sbey05c, Sbld05c, Sltl05c from three species of Spermophilus ground squirrel (Spermophilus beecheyi, Spermophilus beldingi, Spermophilus lateralis located throughout California, USA. This follow-up work characterizes the morphology and animal infectivity of this novel genotype as the final step in proposing it as a new species of Cryptosporidium. Analysis of sequences of 18S rRNA, actin, and HSP70 genes of additional Cryptosporidium isolates from recently sampled California ground squirrels (S. beecheyi confirms the presence of the unique Sbey-c genotype in S. beecheyi. Phylogenetic and BLAST analysis indicates that the c-genotype in Spermophilus ground squirrels is distinct from Cryptosporidium species/genotypes from other host species currently available in GenBank. We propose to name this c-genotype found in Spermophilus ground squirrels as Cryptosporidium rubeyi n. sp. The mean size of C. rubeyi n. sp. oocysts is 4.67 (4.4–5.0 μm × 4.34 (4.0–5.0 μm, with a length/width index of 1.08 (n = 220. Oocysts of C. rubeyi n. sp. are not infectious to neonatal BALB/c mice and Holstein calves. GenBank accession numbers for C. rubeyi n. sp. are DQ295012, AY462233, and KM010224 for the 18S rRNA gene, KM010227 for the actin gene, and KM010229 for the HSP70 gene.

  2. Multiple endmember spectral-angle-mapper (SAM) analysis improves discrimination of Savanna tree species

    CSIR Research Space (South Africa)

    Cho, Moses A

    2009-08-01

    Full Text Available architecture. Several mapping methods are applied in remote sensing to quantify species or vegetation community distribution at the local to regional scale. The most commonly used methods include maximum likelihood, spectral mixture analysis (SMA)[1...] and spectral angle mapper (SAM)[2]. The application of some of these methods including SAM and SMA has become popular with the advent of hyperspectral remote sensing. SAM determines the degree of similarity between two spectra by treating the spectra...

  3. Multiple antioxidant proteins protect Chlorobaculum tepidum against oxygen and reactive oxygen species

    DEFF Research Database (Denmark)

    Li, Hui; Jubelirer, Sara; Garcia Costas, Amaya M

    2009-01-01

    The genome of the green sulfur bacterium Chlorobaculum (Cba.) tepidum, a strictly anaerobic photolithoautotroph, is predicted to encode more than ten genes whose products are potentially involved in protection from reactive oxygen species and an oxidative stress response. The encoded proteins...... include cytochrome bd quinol oxidase, NADH oxidase, rubredoxin oxygen oxidoreductase, several thiol peroxidases, alkyl hydroperoxide reductase, superoxide dismutase, methionine sulfoxide reductase, and rubrerythrin. To test the physiological functions of some of these proteins, ten genes were...

  4. Species Coexistence in Nitrifying Chemostats: A Model of Microbial Interactions

    Directory of Open Access Journals (Sweden)

    Maxime Dumont

    2016-12-01

    Full Text Available In a previous study, the two nitrifying functions (ammonia oxidizing bacteria (AOB or nitrite-oxidizing bacteria (NOB of a nitrification reactor—operated continuously over 525 days with varying inputs—were assigned using a mathematical modeling approach together with the monitoring of bacterial phylotypes. Based on these theoretical identifications, we develop here a chemostat model that does not explicitly include only the resources’ dynamics (different forms of soluble nitrogen but also explicitly takes into account microbial inter- and intra-species interactions for the four dominant phylotypes detected in the chemostat. A comparison of the models obtained with and without interactions has shown that such interactions permit the coexistence of two competing ammonium-oxidizing bacteria and two competing nitrite-oxidizing bacteria in competition for ammonium and nitrite, respectively. These interactions are analyzed and discussed.

  5. Nanog1 in NTERA-2 and recombinant NanogP8 from somatic cancer cells adopt multiple protein conformations and migrate at multiple M.W species.

    Directory of Open Access Journals (Sweden)

    Bigang Liu

    Full Text Available Human Nanog1 is a 305-amino acid (aa homeodomain-containing transcription factor critical for the pluripotency of embryonic stem (ES and embryonal carcinoma (EC cells. Somatic cancer cells predominantly express a retrogene homolog of Nanog1 called NanogP8, which is ~99% similar to Nanog at the aa level. Although the predicted M.W of Nanog1/NanogP8 is ∼35 kD, both have been reported to migrate, on Western blotting (WB, at apparent molecular masses of 29-80 kD. Whether all these reported protein bands represent authentic Nanog proteins is unclear. Furthermore, detailed biochemical studies on Nanog1/NanogpP8 have been lacking. By combining WB using 8 anti-Nanog1 antibodies, immunoprecipitation, mass spectrometry, and studies using recombinant proteins, here we provide direct evidence that the Nanog1 protein in NTERA-2 EC cells exists as multiple M.W species from ~22 kD to 100 kD with a major 42 kD band detectable on WB. We then demonstrate that recombinant NanogP8 (rNanogP8 proteins made in bacteria using cDNAs from multiple cancer cells also migrate, on denaturing SDS-PAGE, at ~28 kD to 180 kD. Interestingly, different anti-Nanog1 antibodies exhibit differential reactivity towards rNanogP8 proteins, which can spontaneously form high M.W protein species. Finally, we show that most long-term cultured cancer cell lines seem to express very low levels of or different endogenous NanogP8 protein that cannot be readily detected by immunoprecipitation. Altogether, the current study reveals unique biochemical properties of Nanog1 in EC cells and NanogP8 in somatic cancer cells.

  6. Direction of Effects in Multiple Linear Regression Models.

    Science.gov (United States)

    Wiedermann, Wolfgang; von Eye, Alexander

    2015-01-01

    Previous studies analyzed asymmetric properties of the Pearson correlation coefficient using higher than second order moments. These asymmetric properties can be used to determine the direction of dependence in a linear regression setting (i.e., establish which of two variables is more likely to be on the outcome side) within the framework of cross-sectional observational data. Extant approaches are restricted to the bivariate regression case. The present contribution extends the direction of dependence methodology to a multiple linear regression setting by analyzing distributional properties of residuals of competing multiple regression models. It is shown that, under certain conditions, the third central moments of estimated regression residuals can be used to decide upon direction of effects. In addition, three different approaches for statistical inference are discussed: a combined D'Agostino normality test, a skewness difference test, and a bootstrap difference test. Type I error and power of the procedures are assessed using Monte Carlo simulations, and an empirical example is provided for illustrative purposes. In the discussion, issues concerning the quality of psychological data, possible extensions of the proposed methods to the fourth central moment of regression residuals, and potential applications are addressed.

  7. Investigating multiple solutions in the constrained minimal supersymmetric standard model

    Energy Technology Data Exchange (ETDEWEB)

    Allanach, B.C. [DAMTP, CMS, University of Cambridge,Wilberforce Road, Cambridge, CB3 0HA (United Kingdom); George, Damien P. [DAMTP, CMS, University of Cambridge,Wilberforce Road, Cambridge, CB3 0HA (United Kingdom); Cavendish Laboratory, University of Cambridge,JJ Thomson Avenue, Cambridge, CB3 0HE (United Kingdom); Nachman, Benjamin [SLAC, Stanford University,2575 Sand Hill Rd, Menlo Park, CA 94025 (United States)

    2014-02-07

    Recent work has shown that the Constrained Minimal Supersymmetric Standard Model (CMSSM) can possess several distinct solutions for certain values of its parameters. The extra solutions were not previously found by public supersymmetric spectrum generators because fixed point iteration (the algorithm used by the generators) is unstable in the neighbourhood of these solutions. The existence of the additional solutions calls into question the robustness of exclusion limits derived from collider experiments and cosmological observations upon the CMSSM, because limits were only placed on one of the solutions. Here, we map the CMSSM by exploring its multi-dimensional parameter space using the shooting method, which is not subject to the stability issues which can plague fixed point iteration. We are able to find multiple solutions where in all previous literature only one was found. The multiple solutions are of two distinct classes. One class, close to the border of bad electroweak symmetry breaking, is disfavoured by LEP2 searches for neutralinos and charginos. The other class has sparticles that are heavy enough to evade the LEP2 bounds. Chargino masses may differ by up to around 10% between the different solutions, whereas other sparticle masses differ at the sub-percent level. The prediction for the dark matter relic density can vary by a hundred percent or more between the different solutions, so analyses employing the dark matter constraint are incomplete without their inclusion.

  8. Tackling Biocomplexity with Meta-models for Species Risk Assessment

    Directory of Open Access Journals (Sweden)

    Philip J. Nyhus

    2007-06-01

    Full Text Available We describe results of a multi-year effort to strengthen consideration of the human dimension into endangered species risk assessments and to strengthen research capacity to understand biodiversity risk assessment in the context of coupled human-natural systems. A core group of social and biological scientists have worked with a network of more than 50 individuals from four countries to develop a conceptual framework illustrating how human-mediated processes influence biological systems and to develop tools to gather, translate, and incorporate these data into existing simulation models. A central theme of our research focused on (1 the difficulties often encountered in identifying and securing diverse bodies of expertise and information that is necessary to adequately address complex species conservation issues; and (2 the development of quantitative simulation modeling tools that could explicitly link these datasets as a way to gain deeper insight into these issues. To address these important challenges, we promote a "meta-modeling" approach where computational links are constructed between discipline-specific models already in existence. In this approach, each model can function as a powerful stand-alone program, but interaction between applications is achieved by passing data structures describing the state of the system between programs. As one example of this concept, an integrated meta-model of wildlife disease and population biology is described. A goal of this effort is to improve science-based capabilities for decision making by scientists, natural resource managers, and policy makers addressing environmental problems in general, and focusing on biodiversity risk assessment in particular.

  9. Multiple kinship in two Spanish regions: new model relating multiple and simple consanguinity.

    Science.gov (United States)

    Calderón, R; Peña, J A; Delgado, J; Morales, B

    1998-06-01

    The structure of the different categories of multiple consanguineous marriages (MCMs) and their historical variation patterns are analyzed in the Spanish dioceses of Alava (Basque Country) and Sigüenza-Guadalajara (Castile). Consanguineous marriages, up to third cousins, were taken from ecclesiastical dispensations, and the periods studied were 1831-1980 for Alava and 1861-1980 for Sigüenza-Guadalajara. Significant differences exist in the MCM rates in the two Spanish areas. In this study a model is proposed to prove that in a general population there may be dependence between MCM rates for specific relationships and the frequencies of those types of relationships in the form of simple consanguineous marriages (SCMs). The effects of avoidance and preferentiality and of underreporting are discussed to explain the deviations between observed and expected consanguineous marriage frequencies. A limit to the weight of remote consanguinity on the population inbreeding coefficient F is determined. The relationship between FT/FS and ms values from our two Spanish populations are fitted to curvilinear regressions. FT is the total population inbreeding coefficient, FS is the contribution to FT from SCMs, and ms is the relative observed frequency of SCMs in the general population.

  10. Modeling species’ realized climatic niche space and predicting their response to global warming for several western forest species with small geographic distributions

    Science.gov (United States)

    Marcus V. Warwell; Gerald E. Rehfeldt; Nicholas L. Crookston

    2010-01-01

    The Random Forests multiple regression tree was used to develop an empirically based bioclimatic model of the presence-absence of species occupying small geographic distributions in western North America. The species assessed were subalpine larch (Larix lyallii), smooth Arizona cypress (Cupressus arizonica ssp. glabra...

  11. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A; Lane, Charles R; Thon, Michael R; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  12. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Directory of Open Access Journals (Sweden)

    Riccardo Baroncelli

    Full Text Available Fragaria × ananassa (common name: strawberry is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l. is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  13. Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

    Science.gov (United States)

    Beauparlant, Marc A; Drouin, Guy

    2014-02-01

    Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

  14. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A.; Lane, Charles R.; Thon, Michael R.; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production. PMID:26086351

  15. Periodicity and blowup in a two-species cooperating model

    DEFF Research Database (Denmark)

    Lin, Zhigui; Liu, Jiahong; Pedersen, Michael

    2011-01-01

    In this paper, the cooperating two-species Lotka–Volterra model is discussed. The existence and asymptotic behavior of T -periodic solutions for the periodic reaction diffusion system under homogeneous Dirichlet boundary conditions are first investigated. The blowup properties of solutions...... for the same system are then given. It is shown that periodic solutions exist if the intra-specific competitions are strong whereas blowup solutions exist under certain conditions if the intra-specific competitions are weak. Numerical simulations and a brief discussion are also presented in the last section....

  16. The intergenerational multiple deficit model and the case of dyslexia

    Directory of Open Access Journals (Sweden)

    Elsje evan Bergen

    2014-06-01

    Full Text Available Which children go on to develop dyslexia? Since dyslexia has a multifactorial aetiology, this question can be restated as: What are the factors that put children at high risk for developing dyslexia? It is argued that a useful theoretical framework to address this question is Pennington’s (2006 multiple deficit model (MDM. This model replaces models that attribute dyslexia to a single underlying cause. Subsequently, the generalist genes hypothesis for learning (disabilities (Plomin & Kovas, 2005 is described and integrated with the MDM. Finally, findings are presented from a longitudinal study with children at family risk for dyslexia. Such studies can contribute to testing and specifying the MDM. In this study, risk factors at both the child and family level were investigated. This led to the proposed intergenerational MDM, in which both parents confer liability via intertwined genetic and environmental pathways. Future scientific directions are discussed to investigate parent-offspring resemblance and transmission patterns, which will shed new light on disorder aetiology.

  17. The intergenerational multiple deficit model and the case of dyslexia

    Science.gov (United States)

    van Bergen, Elsje; van der Leij, Aryan; de Jong, Peter F.

    2014-01-01

    Which children go on to develop dyslexia? Since dyslexia has a multifactorial etiology, this question can be restated as: what are the factors that put children at high risk for developing dyslexia? It is argued that a useful theoretical framework to address this question is Pennington’s (2006) multiple deficit model (MDM). This model replaces models that attribute dyslexia to a single underlying cause. Subsequently, the generalist genes hypothesis for learning (dis)abilities (Plomin and Kovas, 2005) is described and integrated with the MDM. Next, findings are presented from a longitudinal study with children at family risk for dyslexia. Such studies can contribute to testing and specifying the MDM. In this study, risk factors at both the child and family level were investigated. This led to the proposed intergenerational MDM, in which both parents confer liability via intertwined genetic and environmental pathways. Future scientific directions are discussed to investigate parent-offspring resemblance and transmission patterns, which will shed new light on disorder etiology. PMID:24920944

  18. Modeling Pan Evaporation for Kuwait by Multiple Linear Regression

    Directory of Open Access Journals (Sweden)

    Jaber Almedeij

    2012-01-01

    Full Text Available Evaporation is an important parameter for many projects related to hydrology and water resources systems. This paper constitutes the first study conducted in Kuwait to obtain empirical relations for the estimation of daily and monthly pan evaporation as functions of available meteorological data of temperature, relative humidity, and wind speed. The data used here for the modeling are daily measurements of substantial continuity coverage, within a period of 17 years between January 1993 and December 2009, which can be considered representative of the desert climate of the urban zone of the country. Multiple linear regression technique is used with a procedure of variable selection for fitting the best model forms. The correlations of evaporation with temperature and relative humidity are also transformed in order to linearize the existing curvilinear patterns of the data by using power and exponential functions, respectively. The evaporation models suggested with the best variable combinations were shown to produce results that are in a reasonable agreement with observation values.

  19. In vitro establishment and multiplication of Guettarda clarense, a Cuban endemic species in extinction danger

    OpenAIRE

    Elisa Quiala; Grecia Montalvo; Jesús Matos; Maité Chávez; Manuel de Feria; Reinaldo Mederos

    2005-01-01

    The present work was carried out with the objective of achieving the in vitro establishment and multiplication of Guettarda clarense which is an endemic local of Santa Clara city and it is considered in extinction danger. Seeds of mature fruits collected under field conditions were used. The effect of a concentration of NaOCl (2%) during 15, 20 and 25 minutes in the disinfection of the seeds was studied. The seeds were sowed in a culture medium of germination compound by 50% of MS salts. Duri...

  20. Multiple-relaxation-time lattice Boltzmann kinetic model for combustion.

    Science.gov (United States)

    Xu, Aiguo; Lin, Chuandong; Zhang, Guangcai; Li, Yingjun

    2015-04-01

    To probe both the hydrodynamic nonequilibrium (HNE) and thermodynamic nonequilibrium (TNE) in the combustion process, a two-dimensional multiple-relaxation-time (MRT) version of lattice Boltzmann kinetic model (LBKM) for combustion phenomena is presented. The chemical energy released in the progress of combustion is dynamically coupled into the system by adding a chemical term to the LB kinetic equation. Aside from describing the evolutions of the conserved quantities, the density, momentum, and energy, which are what the Navier-Stokes model describes, the MRT-LBKM presents also a coarse-grained description on the evolutions of some nonconserved quantities. The current model works for both subsonic and supersonic flows with or without chemical reaction. In this model, both the specific-heat ratio and the Prandtl number are flexible, the TNE effects are naturally presented in each simulation step. The model is verified and validated via well-known benchmark tests. As an initial application, various nonequilibrium behaviors, including the complex interplays between various HNEs, between various TNEs, and between the HNE and TNE, around the detonation wave in the unsteady and steady one-dimensional detonation processes are preliminarily probed. It is found that the system viscosity (or heat conductivity) decreases the local TNE, but increases the global TNE around the detonation wave, that even locally, the system viscosity (or heat conductivity) results in two kinds of competing trends, to increase and to decrease the TNE effects. The physical reason is that the viscosity (or heat conductivity) takes part in both the thermodynamic and hydrodynamic responses.

  1. Multiple Species of Trichosporon Produce Biofilms Highly Resistant to Triazoles and Amphotericin B

    Science.gov (United States)

    Iturrieta-González, Isabel Antonieta; Padovan, Ana Carolina Barbosa; Bizerra, Fernando César; Hahn, Rosane Christine; Colombo, Arnaldo Lopes

    2014-01-01

    Invasive infections caused by Trichosporon spp. have increased considerably in recent years, especially in neutropenic and critically ill patients using catheters and antibiotics. The genus presents limited sensitivity to different antifungal agents, but triazoles are the first choice for treatment. Here, we investigated the biofilm production and antifungal susceptibility to triazoles and amphotericin B of 54 Trichosporon spp. isolates obtained from blood samples (19), urine (20) and superficial mycosis (15). All isolates and 7 reference strains were identified by sequence analysis and phylogenetic inferences of the IGS1 region of the rDNA. Biofilms were grown on 96-well plates and quantitation was performed using crystal violet staining, complemented with Scanning Electron Microscopy (SEM). Susceptibility tests for fluconazole, itraconazole, voriconazole and amphotericin B were processed using the microdilution broth method (CLSI) for planktonic cells and XTT reduction assay for biofilm-forming cells. Our results showed that T. asahii was the most frequent species identified (66.7%), followed by T. faecale (11.1%), T. asteroides (9.3%), T. inkin (7.4%), T. dermatis (3.7%) and one T. coremiiforme (1.8%). We identified 4 genotypes within T. asahii isolates (G1, G3, G4 and G5) and 2 genotypes within T. faecale (G1 and G3). All species exhibited high adhesion and biofilm formation capabilities, mainly T. inkin, T. asteroides and T. faecale. Microscopy images of high biofilm-producing isolates showed that T. asahii presented mainly hyphae and arthroconidia, whereas T. asteroides exhibited mainly short arthroconidia and few filaments. Voriconazole exhibited the best in vitro activity against all species tested. Biofilm-forming cells of isolates and reference strains were highly resistant to all antifungals tested. We concluded that levels of biofilm formation by Trichosporon spp. were similar or even greater than those described for the Candida genus. Biofilm

  2. a Plugin to Interface Openmodeller from Qgis for SPECIES' Potential Distribution Modelling

    Science.gov (United States)

    Becker, Daniel; Willmes, Christian; Bareth, Georg; Weniger, Gerd-Christian

    2016-06-01

    This contribution describes the development of a plugin for the geographic information system QGIS to interface the openModeller software package. The aim is to use openModeller to generate species' potential distribution models for various archaeological applications (site catchment analysis, for example). Since the usage of openModeller's command-line interface and configuration files can be a bit inconvenient, an extension of the QGIS user interface to handle these tasks, in combination with the management of the geographic data, was required. The implementation was realized in Python using PyQGIS and PyQT. The plugin, in combination with QGIS, handles the tasks of managing geographical data, data conversion, generation of configuration files required by openModeller and compilation of a project folder. The plugin proved to be very helpful with the task of compiling project datasets and configuration files for multiple instances of species occurrence datasets and the overall handling of openModeller. In addition, the plugin is easily extensible to take potential new requirements into account in the future.

  3. Influence of coupling on thermal forces and dynamic friction in plasmas with multiple ion species

    CERN Document Server

    Kagan, Grigory; Daligault, Jerome

    2016-01-01

    The recently proposed effective potential theory [Phys. Rev. Lett. 110, 235001 (2013)] is used to investigate the influence of coupling on inter-ion-species diffusion and momentum exchange in multi-component plasmas. Thermo-diffusion and the thermal force are found to diminish rapidly as strong coupling onsets. For the same coupling parameters, the dynamic friction coefficient is found to tend to unity. These results provide an impetus for addressing the role of coupling on diffusive processes in inertial confinement fusion experiments.

  4. A noninvasive, direct real-time PCR method for sex determination in multiple avian species

    Science.gov (United States)

    Brubaker, Jessica L.; Karouna-Renier, Natalie K.; Chen, Yu; Jenko, Kathryn; Sprague, Daniel T.; Henry, Paula F.P.

    2011-01-01

    Polymerase chain reaction (PCR)-based methods to determine the sex of birds are well established and have seen few modifications since they were first introduced in the 1990s. Although these methods allowed for sex determination in species that were previously difficult to analyse, they were not conducive to high-throughput analysis because of the laboriousness of DNA extraction and gel electrophoresis. We developed a high-throughput real-time PCR-based method for analysis of sex in birds, which uses noninvasive sample collection and avoids DNA extraction and gel electrophoresis.

  5. A noninvasive, direct real-time PCR method for sex determination in multiple avian species.

    Science.gov (United States)

    Brubaker, Jessica L; Karouna-Renier, Natalie K; Chen, Yu; Jenko, Kathryn; Sprague, Daniel T; Henry, Paula F P

    2011-03-01

    Polymerase chain reaction (PCR)-based methods to determine the sex of birds are well established and have seen few modifications since they were first introduced in the 1990s. Although these methods allowed for sex determination in species that were previously difficult to analyse, they were not conducive to high-throughput analysis because of the laboriousness of DNA extraction and gel electrophoresis. We developed a high-throughput real-time PCR-based method for analysis of sex in birds, which uses noninvasive sample collection and avoids DNA extraction and gel electrophoresis.

  6. Decreasing Multicollinearity: A Method for Models with Multiplicative Functions.

    Science.gov (United States)

    Smith, Kent W.; Sasaki, M. S.

    1979-01-01

    A method is proposed for overcoming the problem of multicollinearity in multiple regression equations where multiplicative independent terms are entered. The method is not a ridge regression solution. (JKS)

  7. The importance of data quality for generating reliable distribution models for rare, elusive, and cryptic species.

    Science.gov (United States)

    Aubry, Keith B; Raley, Catherine M; McKelvey, Kevin S

    2017-01-01

    The availability of spatially referenced environmental data and species occurrence records in online databases enable practitioners to easily generate species distribution models (SDMs) for a broad array of taxa. Such databases often include occurrence records of unknown reliability, yet little information is available on the influence of data quality on SDMs generated for rare, elusive, and cryptic species that are prone to misidentification in the field. We investigated this question for the fisher (Pekania pennanti), a forest carnivore of conservation concern in the Pacific States that is often confused with the more common Pacific marten (Martes caurina). Fisher occurrence records supported by physical evidence (verifiable records) were available from a limited area, whereas occurrence records of unknown quality (unscreened records) were available from throughout the fisher's historical range. We reserved 20% of the verifiable records to use as a test sample for both models and generated SDMs with each dataset using Maxent. The verifiable model performed substantially better than the unscreened model based on multiple metrics including AUCtest values (0.78 and 0.62, respectively), evaluation of training and test gains, and statistical tests of how well each model predicted test localities. In addition, the verifiable model was consistent with our knowledge of the fisher's habitat relations and potential distribution, whereas the unscreened model indicated a much broader area of high-quality habitat (indices > 0.5) that included large expanses of high-elevation habitat that fishers do not occupy. Because Pacific martens remain relatively common in upper elevation habitats in the Cascade Range and Sierra Nevada, the SDM based on unscreened records likely reflects primarily a conflation of marten and fisher habitat. Consequently, accurate identifications are far more important than the spatial extent of occurrence records for generating reliable SDMs for the

  8. Evidence for Retrovirus and Paramyxovirus Infection of Multiple Bat Species in China

    Directory of Open Access Journals (Sweden)

    Lihong Yuan

    2014-05-01

    Full Text Available Bats are recognized reservoirs for many emerging zoonotic viruses of public health importance. Identifying and cataloguing the viruses of bats is a logical approach to evaluate the range of potential zoonoses of bat origin. We characterized the fecal pathogen microbiome of both insectivorous and frugivorous bats, incorporating 281 individual bats comprising 20 common species, which were sampled in three locations of Yunnan province, by combining reverse transcription polymerase chain reaction (RT-PCR assays and next-generation sequencing. Seven individual bats were paramyxovirus-positive by RT-PCR using degenerate primers, and these paramyxoviruses were mainly classified into three genera (Rubulavirus, Henipavirus and Jeilongvirus. Various additional novel pathogens were detected in the paramyxovirus-positive bats using Illumina sequencing. A total of 7066 assembled contigs (≥200 bp were constructed, and 105 contigs matched eukaryotic viruses (of them 103 belong to 2 vertebrate virus families, 1 insect virus, and 1 mycovirus, 17 were parasites, and 4913 were homologous to prokaryotic microorganisms. Among the 103 vertebrate viral contigs, 79 displayed low identity (<70% to known viruses including human viruses at the amino acid level, suggesting that these belong to novel and genetically divergent viruses. Overall, the most frequently identified viruses, particularly in bats from the family Hipposideridae, were retroviruses. The present study expands our understanding of the bat virome in species commonly found in Yunnan, China, and provides insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into humans.

  9. Evidence from Multiple Species that Spider Silk Glue Component ASG2 is a Spidroin.

    Science.gov (United States)

    Collin, Matthew A; Clarke, Thomas H; Ayoub, Nadia A; Hayashi, Cheryl Y

    2016-02-15

    Spiders in the superfamily Araneoidea produce viscous glue from aggregate silk glands. Aggregate glue coats prey-capture threads and hampers the escape of prey from webs, thereby increasing the foraging success of spiders. cDNAs for Aggregate Spider Glue 1 (ASG1) and 2 (ASG2) have been previously described from the golden orb-weaver, Nephila clavipes, and Western black widow, Latrodectus hesperus. To further investigate aggregate glues, we assembled ASG1 and ASG2 from genomic target capture libraries constructed from three species of cob-web weavers and three species of orb-web weavers, all araneoids. We show that ASG1 is unlikely to be a glue, but rather is part of a widespread arthropod gene family, the peritrophic matrix proteins. For ASG2, we demonstrate its remarkable architectural and sequence similarities to spider silk fibroins, indicating that ASG2 is a member of the spidroin gene family. Thus, spidroins have diversified into glues in addition to task-specific, high performance fibers.

  10. Evidence from Multiple Species that Spider Silk Glue Component ASG2 is a Spidroin

    Science.gov (United States)

    Collin, Matthew A.; Clarke, Thomas H.; Ayoub, Nadia A.; Hayashi, Cheryl Y.

    2016-01-01

    Spiders in the superfamily Araneoidea produce viscous glue from aggregate silk glands. Aggregate glue coats prey-capture threads and hampers the escape of prey from webs, thereby increasing the foraging success of spiders. cDNAs for Aggregate Spider Glue 1 (ASG1) and 2 (ASG2) have been previously described from the golden orb-weaver, Nephila clavipes, and Western black widow, Latrodectus hesperus. To further investigate aggregate glues, we assembled ASG1 and ASG2 from genomic target capture libraries constructed from three species of cob-web weavers and three species of orb-web weavers, all araneoids. We show that ASG1 is unlikely to be a glue, but rather is part of a widespread arthropod gene family, the peritrophic matrix proteins. For ASG2, we demonstrate its remarkable architectural and sequence similarities to spider silk fibroins, indicating that ASG2 is a member of the spidroin gene family. Thus, spidroins have diversified into glues in addition to task-specific, high performance fibers. PMID:26875681

  11. Cancer genomics object model: an object model for multiple functional genomics data for cancer research.

    Science.gov (United States)

    Park, Yu Rang; Lee, Hye Won; Cho, Sung Bum; Kim, Ju Han

    2007-01-01

    The development of functional genomics including transcriptomics, proteomics and metabolomics allow us to monitor a large number of key cellular pathways simultaneously. Several technology-specific data models have been introduced for the representation of functional genomics experimental data, including the MicroArray Gene Expression-Object Model (MAGE-OM), the Proteomics Experiment Data Repository (PEDRo), and the Tissue MicroArray-Object Model (TMA-OM). Despite the increasing number of cancer studies using multiple functional genomics technologies, there is still no integrated data model for multiple functional genomics experimental and clinical data. We propose an object-oriented data model for cancer genomics research, Cancer Genomics Object Model (CaGe-OM). We reference four data models: Functional Genomic-Object Model, MAGE-OM, TMAOM and PEDRo. The clinical and histopathological information models are created by analyzing cancer management workflow and referencing the College of American Pathology Cancer Protocols and National Cancer Institute Common Data Elements. The CaGe-OM provides a comprehensive data model for integrated storage and analysis of clinical and multiple functional genomics data.

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

    Science.gov (United States)

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

    2015-01-01

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

  13. Shared mental models of integrated care: aligning multiple stakeholder perspectives.

    Science.gov (United States)

    Evans, Jenna M; Baker, G Ross

    2012-01-01

    Health service organizations and professionals are under increasing pressure to work together to deliver integrated patient care. A common understanding of integration strategies may facilitate the delivery of integrated care across inter-organizational and inter-professional boundaries. This paper aims to build a framework for exploring and potentially aligning multiple stakeholder perspectives of systems integration. The authors draw from the literature on shared mental models, strategic management and change, framing, stakeholder management, and systems theory to develop a new construct, Mental Models of Integrated Care (MMIC), which consists of three types of mental models, i.e. integration-task, system-role, and integration-belief. The MMIC construct encompasses many of the known barriers and enablers to integrating care while also providing a comprehensive, theory-based framework of psychological factors that may influence inter-organizational and inter-professional relations. While the existing literature on integration focuses on optimizing structures and processes, the MMIC construct emphasizes the convergence and divergence of stakeholders' knowledge and beliefs, and how these underlying cognitions influence interactions (or lack thereof) across the continuum of care. MMIC may help to: explain what differentiates effective from ineffective integration initiatives; determine system readiness to integrate; diagnose integration problems; and develop interventions for enhancing integrative processes and ultimately the delivery of integrated care. Global interest and ongoing challenges in integrating care underline the need for research on the mental models that characterize the behaviors of actors within health systems; the proposed framework offers a starting point for applying a cognitive perspective to health systems integration.

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

    Science.gov (United States)

    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. Copyright © 2014 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

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

    Science.gov (United States)

    Jankovic, Masha; Petrovskii, Sergei; Banerjee, Malay

    2016-08-01

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

  16. Multiple periodic solutions for a discrete time model of plankton allelopathy

    OpenAIRE

    Zhang Jianbao; Fang Hui

    2006-01-01

    We study a discrete time model of the growth of two species of plankton with competitive and allelopathic effects on each other N1(k+1) = N1(k)exp{r1(k)-a11(k)N1(k)-a12(k)N2(k)-b1(k)N1(k)N2(k)}, N2(k+1) = N2(k)exp{r2(k)-a21(k)N2(k)-b2(k)N1(k)N1(k)N2(k)}. A set of sufficient conditions is obtained for the existence of multiple positive periodic solutions for this model. The approach is based on Mawhin's continuation theorem of coincidence degree theory as well as some a priori estimates. Some...

  17. Multiple periodic solutions for a discrete time model of plankton allelopathy

    OpenAIRE

    Zhang Jianbao; Fang Hui

    2006-01-01

    We study a discrete time model of the growth of two species of plankton with competitive and allelopathic effects on each other N1(k+1) = N1(k)exp{r1(k)-a11(k)N1(k)-a12(k)N2(k)-b1(k)N1(k)N2(k)}, N2(k+1) = N2(k)exp{r2(k)-a21(k)N2(k)-b2(k)N1(k)N1(k)N2(k)}. A set of sufficient conditions is obtained for the existence of multiple positive periodic solutions for this model. The approach is based on Mawhin's continuation theorem of coincidence degree theory as well as some a priori estimates. Some...

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

    Directory of Open Access Journals (Sweden)

    Amanda J Chunco

    Full Text Available 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.

  19. A model of interacting multiple choices of continuous opinions

    CERN Document Server

    Chou, C -I

    2016-01-01

    We present a model of interacting multiple choices of opinions. At each step of the process, a listener is persuaded by his/her neighbour, the lobbyist, to modify his/her opinion on two different choices of event. Whether or not the listener will be convinced by the lobbyist depends on the difference between his/her opinion with that of the lobbyist, and with that of the revealed social opinion (the social pressure). If the listener is convinced, he/she will modify his/her opinion and update his/her revealed preference, and proceed to persuade his/her next neighbour. If the listener is not convinced by the lobbyist, he/she will retain his/her revealed preference, and try to persuade the lobbyist to change his/her opinion. In this case, the direction of opinion propagation is reversed. A consensus is reached when all the revealed preference is the same. Our numerical results show that consensus can always be attained in this model. However, the time needed to achieve consensus, or the so-called convergence tim...

  20. Closed-Head TBI Model of Multiple Morbidity.

    Science.gov (United States)

    Thompson, Floyd J; Hou, Jiamei; Bose, Prodip K

    2016-01-01

    brain (Morales et al., Neuroscience 136:971-989, 2005; Foda and Marmarou, J Neurosurg 80:301-313, 1994; Kallakuri et al., Exp Brain Res 148:419-424, 2003). Accordingly, use of this preclinical model offers an opportunity for (a) gaining a greater understanding of the relationships of TBI induced diffuse axonal injuries and associated long term disabilities, and (b) to provide a platform for quantitative assessment of treatment interactions upon the trajectories of TBI-induced disabilities. Using the impact acceleration closed head TBI model to induce mild/moderate injuries in the rat, we have observed and quantitated multiple morbidities commonly observed following TBI in humans (Bose et al., J Neurotrauma 30:1177-1191, 2013). This chapter describes methods and protocols used for TBI-induced multiple morbidity involving cognitive dysfunction, balance instability, spasticity and gait, and anxiety-like disorder.

  1. An rpoB gene-based PCR-DGGE method for simultaneous detection of multiple Vibrio species

    Institute of Scientific and Technical Information of China (English)

    Luo Peng; Hu Chaoqun; Ren Chunhua; Zhang Lvping

    2008-01-01

    Using PCR-denaturing gradient gel electrophoresis (DGGE) targeting the RNA polymerase beta subunit (rpoB) gene, a simultaneous detection method for Vibrio species was established. rpoB gene-based PCR-DGGE was carried out with eight Vibrio Reference strains (each from different species), mixed sample (including these Vibrio Reference strains),two non Vibrio strains, four environmental Vibrio strains, and three unidentified environmental strains. For comparison, 16S rRNA gene-based PCR-DGGE of the eight Vibrio Reference strains was performed with universal primers. In addition, three unidentified strains were identified by 16S rRNA and gyrB gene sequencing and API20E system in order to confirm the accuracy of rpoB gene-based PCR-DGGE detection. Results revealed that rpoB-based PCR-DGGE could well discriminate eight Vibrio Reference strains and could not discriminate different strains within the same species. The bands derived from two non Vibrio strains could not match with any bands in Reference marker. Meanwhile, 16S rRNA gene-based DGGE failed to distinguish these Reference strains. Furthermore, four out of eight Vibrio species exhibited heterogenous bands in 16S rRNA gene-based DGGE. Sequencing and API 20E identification of unidentified strains coincided with the detection by rpoB gene-based PCR-DGGE. The results demonstrated that rpoB-based PCR-DGGE provided a rapid and efficient method for simultaneous detection of multiple Vibrio species, which can avoid the limitations inherent in 16S rRNA gene-based PCR-DGGE.

  2. Studies of acid resistance characteristics in multiple drug resistant Salmonella species isolated from tomatoes.

    Science.gov (United States)

    Naushad, Z; Mishra, S H; Musaddiq, M; Ali, Y A

    2013-04-01

    Salmonella species found to have a great potential of causing a variety of diseases ranging from gastroenteritis to enteric fever. Salmonella have been isolated from all food, animals and also found in the vegetables such as tomatoes, spinach etc. Several out breaks of Salmonellosis have been associated with the consumption of raw tomatoes. This is because of the fact that Salmonella attaches to the surface of tomatoes and also present in the interior part due to geotropic transmission via contaminated soil irrigated with contaminated water. .During the life cycle, Salmonella encounters the various environments such as acidic environment (low pH). To overcome such factors, Salmonella has certain adaptable mechanisms. In present 'study total 200 samples of tomatoes were analyzed out of which 10 samples were found to contain Salmonella. All the 10 isolates were then subjected to the antibiotic susceptibility testing and were found to be resistant against several antibiotics. These were subjected to acid resistant tolerance study.

  3. Reference genes for quantitative gene expression studies in multiple avian species

    DEFF Research Database (Denmark)

    Olias, Philipp; Adam, Iris; Meyer, Anne S.

    2014-01-01

    reference genes as well as FOXP2 and the immediate early genes, EGR1 and CFOS, known to be rapidly induced by singing in the avian basal ganglia. We extracted RNA from microbiopsies of the striatal song nucleus Area X of adult male zebra finches after they had sang or remained silent. Using three different......Quantitative real-time PCR (qPCR) rapidly and reliably quantifies gene expression levels across different experimental conditions. Selection of suitable reference genes is essential for meaningful normalization and thus correct interpretation of data. In recent years, an increasing number of avian...... species other than the chicken has been investigated molecularly, highlighting the need for an experimentally validated pan-avian primer set for reference genes. Here we report testing a set for 14 candidate reference genes (18S, ABL, GAPDH, GUSB, HMBS, HPRT, PGK1, RPL13, RPL19, RPS7, SDHA, TFRC, VIM...

  4. Evaluation of discrepancy between measured and modelled oxidized mercury species

    Directory of Open Access Journals (Sweden)

    G. Kos

    2013-05-01

    Full Text Available L. Zhang et al. (2012, in a recent report, compared model estimates with new observations of oxidized and particulate mercury species (Hg2+ and Hgp in the Great Lakes region and found that the sum of Hg2+ and Hgp varied between a factor of 2 to 10 between measurements and model. They suggested too high emission inputs as Hg2+ and too fast oxidative conversion of Hg0 to Hg2+ and Hgp as possible causes. This study quantitatively explores measurement uncertainties in detail. These include sampling efficiency, composition of sample, interfering species and calibration errors. Model (Global/Regional Atmospheric Heavy Metals Model – GRAHM sensitivity experiments are used to examine the consistency between various Hg measurements and speciation of Hg near emission sources to better understand the discrepancies between modelled and measured concentrations of Hg2+ and Hgp. We find that the ratio of Hg0, Hg2+ and Hgp in the emission inventories, measurements of surface air concentrations of oxidized Hg and measurements of wet deposition are currently inconsistent with each other in the vicinity of emission sources. Current speciation of Hg emissions suggests higher concentrations of Hg2+ in air and in precipitation near emission sources; however, measured air concentrations of Hg2+ and measured concentrations of Hg in precipitation are not found to be significantly elevated near emission sources compared to the remote regions. The averaged unbiased root mean square error (RMSE between simulated and observed concentrations of Hg2+ is found to be reduced by 42% and for Hgp reduced by 40% for 21 North American sites investigated, when a ratio for Hg0 : Hg2+ : Hgp in the emissions is changed from 50 : 40 : 10 (as specified in the original inventories to 90 : 8 : 2. Unbiased RMSE reductions near emissions sources in the eastern United States and Canada are found to be reduced by up to 58% for Hg2+. Significant improvement in the model simulated spatial

  5. Molecular Code Division Multiple Access: Gaussian Mixture Modeling

    Science.gov (United States)

    Zamiri-Jafarian, Yeganeh

    Communications between nano-devices is an emerging research field in nanotechnology. Molecular Communication (MC), which is a bio-inspired paradigm, is a promising technique for communication in nano-network. In MC, molecules are administered to exchange information among nano-devices. Due to the nature of molecular signals, traditional communication methods can't be directly applied to the MC framework. The objective of this thesis is to present novel diffusion-based MC methods when multi nano-devices communicate with each other in the same environment. A new channel model and detection technique, along with a molecular-based access method, are proposed in here for communication between asynchronous users. In this work, the received molecular signal is modeled as a Gaussian mixture distribution when the MC system undergoes Brownian noise and inter-symbol interference (ISI). This novel approach demonstrates a suitable modeling for diffusion-based MC system. Using the proposed Gaussian mixture model, a simple receiver is designed by minimizing the error probability. To determine an optimum detection threshold, an iterative algorithm is derived which minimizes a linear approximation of the error probability function. Also, a memory-based receiver is proposed to improve the performance of the MC system by considering previously detected symbols in obtaining the threshold value. Numerical evaluations reveal that theoretical analysis of the bit error rate (BER) performance based on the Gaussian mixture model match simulation results very closely. Furthermore, in this thesis, molecular code division multiple access (MCDMA) is proposed to overcome the inter-user interference (IUI) caused by asynchronous users communicating in a shared propagation environment. Based on the selected molecular codes, a chip detection scheme with an adaptable threshold value is developed for the MCDMA system when the proposed Gaussian mixture model is considered. Results indicate that the

  6. Equivalence of MAXENT and Poisson point process models for species distribution modeling in ecology.

    Science.gov (United States)

    Renner, Ian W; Warton, David I

    2013-03-01

    Modeling the spatial distribution of a species is a fundamental problem in ecology. A number of modeling methods have been developed, an extremely popular one being MAXENT, a maximum entropy modeling approach. In this article, we show that MAXENT is equivalent to a Poisson regression model and hence is related to a Poisson point process model, differing only in the intercept term, which is scale-dependent in MAXENT. We illustrate a number of improvements to MAXENT that follow from these relations. In particular, a point process model approach facilitates methods for choosing the appropriate spatial resolution, assessing model adequacy, and choosing the LASSO penalty parameter, all currently unavailable to MAXENT. The equivalence result represents a significant step in the unification of the species distribution modeling literature. Copyright © 2013, The International Biometric Society.

  7. Assessment of Serum Nitrogen Species and Inflammatory Parameters in Relapsing-Remitting Multiple Sclerosis Patients Treated with Different Therapeutic Approaches

    Directory of Open Access Journals (Sweden)

    Natalia Niedziela

    2016-01-01

    Full Text Available The role of nitric oxide and its reactive derivatives (NOx is well known in the pathogenesis of multiple sclerosis, which is an inflammatory disease while NOx seems to be important in coordinating inflammatory response. The purpose of the present study was to assess serum NOx as one of the nitrogen species and inflammatory parameters in relapsing-remitting multiple sclerosis patients and to compare the effectiveness of various types of disease-modifying therapies that reduce nitric oxide and inflammatory biomarkers. Elevated NOx level was observed in patients who received the first-line disease-modifying therapy (interferons beta-1a and beta-1b in comparison with the subjects treated with the second-line disease-modifying therapy (natalizumab; fingolimod and healthy controls without significant differences in C-reactive protein and interleukin-1 beta. A negative correlation was observed between serum NOx level and the duration of multiple sclerosis confirmed in the whole study population and in subjects treated with the first-line agents. Only serum NOx, concentration could reveal a potential efficacy of disease-modifying therapy with a better reduction in NOx level due to the second-line agents of disease-modifying therapy.

  8. Acute Toxicity Prediction in Multiple Species by Leveraging Mechanistic ToxCast Mitochondrial Inhibition Data and Simulation of Oral Bioavailability.

    Science.gov (United States)

    Bhhatarai, Barun; Wilson, Daniel M; Bartels, Michael J; Chaudhuri, Shubhra; Price, Paul S; Carney, Edward W

    2015-10-01

    There is great interest in assessing the in vivo toxicity of chemicals using nonanimal alternatives. However, acute mammalian toxicity is not adequately predicted by current in silico or in vitro approaches. Mechanisms of acute toxicity are likely conserved across invertebrate, aquatic, and mammalian species, suggesting that dose-response concordance would be high and in vitro mechanistic data could predict responses in multiple species under conditions of similar bioavailability. We tested this hypothesis by comparing acute toxicity between rat, daphnia, and fish and by comparing their respective acute data to inhibition of mitochondria membrane potential (MMP) using U.S. Environmental Protection Agency ToxCast in vitro high-throughput screening data. Logarithmic scatter plots of acute toxicity data showed a clear relationship between fish, daphnia, and intravenous rat but not oral rat data. Similar plots versus MMP showed a well-delineated upper boundary for fish, daphnia, and intravenous data but were scattered without an upper boundary for rat oral data. Adjustments of acute oral rat toxicity values by simulating fractional absorption and CYP-based metabolism as well as removing compounds with hydrolyzable linkages or flagged as substrates for glucuronidation delineated an upper boundary for rat oral toxicity versus MMP. Mitochondrial inhibition at low concentrations predicted highly acutely toxic chemicals for fish and daphnia but not the rat where toxicity was often attenuated. This use of a single high-throughput screening assay to predict acute toxicity in multiple species represents a milestone and highlights the promise of such approaches but also the need for refined tools to address systemic bioavailability and the impact of limited absorption and first pass metabolism.

  9. pthG from Pantoea agglomerans pv. gypsophilae encodes an avirulence effector that determines incompatibility in multiple beet species.

    Science.gov (United States)

    Ezra, David; Barash, Isaac; Weinthal, Dan M; Gaba, Victor; Manulis, Shulamit

    2004-03-01

    SUMMARY Pantoea agglomerans pv. gypsophilae (Pag) causes root and crown gall disease on gypsophila, whereas P. agglomerans pv. betae (Pab) induces the disease on beet as well as gypsophila. Both pathovars harbour a pathogenicity plasmid (pPATH(Pag) or pPATH(Pab)) that determines disease development. We have previously isolated and partially characterized a pleiotropic gene from the pPATH(Pag), designated as pthG, that encodes a virulence factor in gypsophila and an elicitor of a hypersensitive-like response in beet roots. The present study was undertaken to characterize pthG further as an avr gene. The infiltration of beet leaves with strains expressing PthG (i.e. Pag or Pab containing pthG in trans) caused an hypersensitive reaction (HR) response within 48 h, whereas strains lacking intact pthG (i.e. Pab or Pag mutated in pthG) resulted in gall formation after 5 days. A hypersensitive reaction was elicited by PthG on multiple beet species, whereas a marker exchange mutant of Pag in pthG extended its host range on these beet species. A marker exchange mutant of Pag in hrpJ, encoding a component of the Type III secretion system, prevented HR elicitation. Mutations in each of the hrp regulatory genes (hrpY, hrpS and hrpL) substantially reduced the transcriptional activity of pthG in gypsophila cuttings. PthG could only be detected inside Pag cells during over-expression of hrpS or hrpL. Particle bombardment of GFP-PthG fusion caused cell death in beet, but not in non-host (melon) leaves. Present and previous results have established pthG as a broad-host-range avr gene that functions in multiple host plant species and the first functional avr gene in Pantoea spp.

  10. Mathematical Modeling of Loop Heat Pipes with Multiple Capillary Pumps and Multiple Condensers. Part 1; Stead State Stimulations

    Science.gov (United States)

    Hoang, Triem T.; OConnell, Tamara; Ku, Jentung

    2004-01-01

    Loop Heat Pipes (LHPs) have proven themselves as reliable and robust heat transport devices for spacecraft thermal control systems. So far, the LHPs in earth-orbit satellites perform very well as expected. Conventional LHPs usually consist of a single capillary pump for heat acquisition and a single condenser for heat rejection. Multiple pump/multiple condenser LHPs have shown to function very well in ground testing. Nevertheless, the test results of a dual pump/condenser LHP also revealed that the dual LHP behaved in a complicated manner due to the interaction between the pumps and condensers. Thus it is redundant to say that more research is needed before they are ready for 0-g deployment. One research area that perhaps compels immediate attention is the analytical modeling of LHPs, particularly the transient phenomena. Modeling a single pump/single condenser LHP is difficult enough. Only a handful of computer codes are available for both steady state and transient simulations of conventional LHPs. No previous effort was made to develop an analytical model (or even a complete theory) to predict the operational behavior of the multiple pump/multiple condenser LHP systems. The current research project offered a basic theory of the multiple pump/multiple condenser LHP operation. From it, a computer code was developed to predict the LHP saturation temperature in accordance with the system operating and environmental conditions.

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

    Science.gov (United States)

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

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

    Science.gov (United States)

    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 ...

  13. Role of multiple hosts in the cross-species transmission and emergence of a pandemic parvovirus.

    Science.gov (United States)

    Allison, Andrew B; Harbison, Carole E; Pagan, Israel; Stucker, Karla M; Kaelber, Jason T; Brown, Justin D; Ruder, Mark G; Keel, M Kevin; Dubovi, Edward J; Holmes, Edward C; Parrish, Colin R

    2012-01-01

    Understanding the mechanisms of cross-species virus transmission is critical to anticipating emerging infectious diseases. Canine parvovirus type 2 (CPV-2) emerged as a variant of a feline parvovirus when it acquired mutations that allowed binding to the canine transferrin receptor type 1 (TfR). However, CPV-2 was soon replaced by a variant virus (CPV-2a) that differed in antigenicity and receptor binding. Here we show that the emergence of CPV involved an additional host range variant virus that has circulated undetected in raccoons for at least 24 years, with transfers to and from dogs. Raccoon virus capsids showed little binding to the canine TfR, showed little infection of canine cells, and had altered antigenic structures. Remarkably, in capsid protein (VP2) phylogenies, most raccoon viruses fell as evolutionary intermediates between the CPV-2 and CPV-2a strains, suggesting that passage through raccoons assisted in the evolution of CPV-2a. This highlights the potential role of alternative hosts in viral emergence.

  14. Large-Scale Orthology Predictions for Inferring Gene Functions Across Multiple Species

    Science.gov (United States)

    2010-06-01

    mutations associated with cancer by studying their corresponding orthologous genes in mice (Denny, 2000). Moreover, the identification of orthologous...taxonomic profiling of eukaryotic model organisms: a comparison of orthologous proteins encoded by the human, fly, nematode , and yeast genomes.” Genome

  15. Balancing precision and risk: should multiple detection methods be analyzed separately in N-mixture models?

    Directory of Open Access Journals (Sweden)

    Tabitha A Graves

    Full Text Available Using multiple detection methods can increase the number, kind, and distribution of individuals sampled, which may increase accuracy and precision and reduce cost of population abundance estimates. However, when variables influencing abundance are of interest, if individuals detected via different methods are influenced by the landscape differently, separate analysis of multiple detection methods may be more appropriate. We evaluated the effects of combining two detection methods on the identification of variables important to local abundance using detections of grizzly bears with hair traps (systematic and bear rubs (opportunistic. We used hierarchical abundance models (N-mixture models with separate model components for each detection method. If both methods sample the same population, the use of either data set alone should (1 lead to the selection of the same variables as important and (2 provide similar estimates of relative local abundance. We hypothesized that the inclusion of 2 detection methods versus either method alone should (3 yield more support for variables identified in single method analyses (i.e. fewer variables and models with greater weight, and (4 improve precision of covariate estimates for variables selected in both separate and combined analyses because sample size is larger. As expected, joint analysis of both methods increased precision as well as certainty in variable and model selection. However, the single-method analyses identified different variables and the resulting predicted abundances had different spatial distributions. We recommend comparing single-method and jointly modeled results to identify the presence of individual heterogeneity between detection methods in N-mixture models, along with consideration of detection probabilities, correlations among variables, and tolerance to risk of failing to identify variables important to a subset of the population. The benefits of increased precision should be weighed

  16. Enchytraeus crypticus as model species in soil ecotoxicology.

    Science.gov (United States)

    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, ecotoxicology, with advantages such as good control performance and speed, leading to a reliable and faster ERT.

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

    Science.gov (United States)

    Thomas C. Edwards; D. Richard Cutler; Niklaus E. Zimmermann; Linda Geiser; Gretchen G. Moisen

    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...

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

    Science.gov (United States)

    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.

  19. The Answering Process for Multiple-Choice Questions in Collaborative Learning: A Mathematical Learning Model Analysis

    Science.gov (United States)

    Nakamura, Yasuyuki; Nishi, Shinnosuke; Muramatsu, Yuta; Yasutake, Koichi; Yamakawa, Osamu; Tagawa, Takahiro

    2014-01-01

    In this paper, we introduce a mathematical model for collaborative learning and the answering process for multiple-choice questions. The collaborative learning model is inspired by the Ising spin model and the model for answering multiple-choice questions is based on their difficulty level. An intensive simulation study predicts the possibility of…

  20. Sarmentine, a natural herbicide from Piper species with multiple herbicide mechanisms of action

    Directory of Open Access Journals (Sweden)

    Franck Emmanuel Dayan

    2015-04-01

    Full Text Available Sarmentine, 1-(1-pyrrolidinyl-(2E,4E-2,4-decadien-1-one, is a natural amide isolated from the fruits of Piper species. The compound has a number of interesting biological properties, including its broad-spectrum activity on weeds as a contact herbicide. Initial studies highlighted a similarity in response between plants treated with sarmentine and herbicidal soaps such as pelargonic acid (nonanoic acid. However, little was known about the mechanism of action leading to the rapid desiccation of foliage treated by sarmentine. In cucumber cotyledon disc-assays, sarmentine induced rapid light-independent loss of membrane integrity at 100 µM or higher concentration, whereas 3 mM pelargonic acid was required for a similar effect. Sarmentine was between 10 and 30 times more active than pelargonic acid on wild mustard, velvetleaf, redroot pigweed and crabgrass. Additionally, the potency of 30 µM sarmentine was greatly stimulated by light, suggesting that this natural product may also interfere with photosynthetic processes. This was confirmed by observing a complete inhibition of photosynthetic electron transport at that concentration. Sarmentine also acted as an inhibitor of photosystem II on isolated thylakoid membranes by competing for the binding site of plastoquinone. This can be attributed in part to structural similarities between herbicides like sarmentine and diuron. While this mechanism of action accounts for the light stimulation of the activity of sarmentine, it does not account for its ability to destabilize membranes in darkness. In this respect, sarmentine has some structural similarity to crotonoyl-CoA, the substrate of enoyl-ACP reductase, a key enzyme in the early steps of fatty acid synthesis. Inhibitors of this enzyme, such as triclosan, cause rapid loss of membrane integrity in the dark. Sarmentine inhibited the activity of enoyl-ACP reductase, with an I50app of 18.3 µM. Therefore, the herbicidal activity of sarmentine appears to

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

    Science.gov (United States)

    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. A Fuzzy Logic Framework for Integrating Multiple Learned Models

    Energy Technology Data Exchange (ETDEWEB)

    Hartog, Bobi Kai Den [Univ. of Nebraska, Lincoln, NE (United States)

    1999-03-01

    The Artificial Intelligence field of Integrating Multiple Learned Models (IMLM) explores ways to combine results from sets of trained programs. Aroclor Interpretation is an ill-conditioned problem in which trained programs must operate in scenarios outside their training ranges because it is intractable to train them completely. Consequently, they fail in ways related to the scenarios. We developed a general-purpose IMLM solution, the Combiner, and applied it to Aroclor Interpretation. The Combiner's first step, Scenario Identification (M), learns rules from very sparse, synthetic training data consisting of results from a suite of trained programs called Methods. S1 produces fuzzy belief weights for each scenario by approximately matching the rules. The Combiner's second step, Aroclor Presence Detection (AP), classifies each of three Aroclors as present or absent in a sample. The third step, Aroclor Quantification (AQ), produces quantitative values for the concentration of each Aroclor in a sample. AP and AQ use automatically learned empirical biases for each of the Methods in each scenario. Through fuzzy logic, AP and AQ combine scenario weights, automatically learned biases for each of the Methods in each scenario, and Methods' results to determine results for a sample.

  3. Populus euphratica, a Tolerant Model but Endangered Arborescent Species

    Institute of Scientific and Technical Information of China (English)

    Gu Ruisheng; Pei Dong

    2005-01-01

    @@ Populus euphratica is a most tolerant arborescent species to abiotic stress. It can adapt to extreme conditions, ranging from flood to atmosphere extremely dry, hot from + 54 ℃ to - 45 ℃, and from normal soil to the soil with very high salt concentration ( to 2 ~5%) although being a non-halophyte. However, the natural stands of P. euphratica have been shrinking tremendously for the past decades and some populations are facing the fate of extinction. The preservation of existing resources should be carried out as a burning issue. In parallel, P. euphratica could be taken as a model plant to explore the molecular mechanism of abiotic-stress tolerance and to exploit its tolerant genes due to its smaller genome and easy molecular manipulation. The measures for preservation, germ-plasma exploitation, tolerance mechanism exploration and resource utilization were also discussed in this paper.

  4. A novel multiple species ringdown spectrometer for in situ measurements of methane, carbon dioxide, and carbon isotope

    Science.gov (United States)

    Wang, C.; Srivastava, N.; Jones, B. A.; Reese, R. B.

    2008-08-01

    We have developed a standalone, user-friendly, multi-species ringdown spectrometer for in situ measurements of methane (CH4), carbon dioxide (CO2), and a carbon dioxide isotope (13CO2). The instrument is based on near-infrared continuous-wave cavity ringdown spectroscopy (NIR cw-CRDS) and engineered to be of approximately 16 kg with dimensions of 50 cm × 40 cm × 15 cm. The instrument design, optical configuration, electronic control, and performance are described. CH4, CO2, and 13CO2 are measured at different wavelengths that are obtained through multiplexing two distributed feedback laser diodes with central wavelengths at 1597 and 1650 nm. The spectrometer has low power consumption and runs for 4-6 h when powered by a standard car battery. The instrument is operated either locally by interacting with a 7-inch touch screen or remotely via an Internet connection. The 1-σ detection limits for CH4 and CO2 are 0.2 and 120 ppmv, respectively. The measurement uncertainty is better than ±4% of full-scale reading for CH4 and CO2 and ±1.5‰ for δ13C (part per thousand relative to the Pee Dee Belemnite scale). Measurement of each species is near real-time; switching from measuring one species to another takes less than one minute. This work demonstrates a novel multiple-species CRDS-instrumentation platform, which can be adopted for development of an array of ringdown spectrometers for portable, user-friendly, field analysis of a variety of gases in environmental and industrial applications. Discussion of a future version of the spectrometer with better detection sensitivity, higher accuracy, and a smaller geometry is also presented.

  5. Inflammation modulates anxiety in an animal model of multiple sclerosis.

    Science.gov (United States)

    Peruga, Isabella; Hartwig, Silvia; Thöne, Jan; Hovemann, Bernhard; Gold, Ralf; Juckel, Georg; Linker, Ralf A

    2011-06-20

    Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterized by inflammation, but also degenerative changes. Besides neurological deficits, the rate of affective disorders such as depression and anxiety is at least six fold increased. Many aspects of MS can be mimicked in the animal model of myelin oligodendrocyte glycoprotein experimental autoimmune encephalomyelitis (MOG-EAE). Here we investigate behavioral changes in C57BL/6 mice suffering from mild MOG-EAE. In the later phase of the disease, mice were subjected to behavioral tests including the light-dark-box (LD Box), the acoustic startle response (SR) with a pre-pulse inhibition protocol as well as the learned helplessness (LH) paradigm. Behavioral data were correlated with the motor performance in an open field and rotarod test (RR). In the RR and open field, there was no significant difference in the motor performance between controls and mice suffering from mild MOG-EAE. Yet EAE mice displayed an increased anxiety-like behavior with a 23% reduction of the time spent in the bright compartment of the LD Box as well as an increased SR. In the LH paradigm, mice suffering from MOG-EAE were twice as much prone to depressive-like behavior. These changes correlate with an increase of hippocampal tissue tumor necrosis factor alpha levels and neuronal loss in the hippocampus. Modulation of monoaminergic transmission by chronic application of the antidepressant amitriptyline resulted in a decreased startle reaction and increased hippocampal norepinephrine levels. These data imply that chronic inflammation in the CNS may impact on emotional responses in rodent models of anxiety. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Calcium Intervention Ameliorates Experimental Model of Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Dariush Haghmorad

    2014-05-01

    Full Text Available Objective: Multiple sclerosis (MS is the most common inflammatory disease of the CNS. Experimental autoimmune encephalomyelitis (EAE is a widely used model for MS. In the present research, our aim was to test the therapeutic efficacy of Calcium (Ca in an experimental model of MS. Methods: In this study the experiment was done on C57BL/6 mice. EAE was induced using 200 μg of the MOG35-55 peptide emulsified in CFA and injected subcutaneously on day 0 over two flank areas. In addition, 250 ng of pertussis toxin was injected on days 0 and 2. In the treatment group, 30 mg/kg Ca was administered intraperitoneally four times at regular 48 hour intervals. The mice were sacrificed 21 days after EAE induction and blood samples were taken from their hearts. The brains of mice were removed for histological analysis and their isolated splenocytes were cultured. Results: Our results showed that treatment with Ca caused a significant reduction in the severity of the EAE. Histological analysis indicated that there was no plaque in brain sections of Ca treated group of mice whereas 4 ± 1 plaques were detected in brain sections of controls. The density of mononuclear infiltration in the CNS of Ca treated mice was lower than in controls. The serum level of Nitric Oxide in the treatment group was lower than in the control group but was not significant. Moreover, the levels of IFN-γ in cell culture supernatant of splenocytes in treated mice were significantly lower than in the control group. Conclusion: The data indicates that Ca intervention can effectively attenuate EAE progression.

  7. A general additive-multiplicative rates model for recurrent event data

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this article, we propose a general additive-multiplicative rates model for recurrent event data. The proposed model includes the additive rates and multiplicative rates models as special cases. For the inference on the model parameters, estimating equation approaches are developed, and asymptotic properties of the proposed estimators are established through modern empirical process theory. In addition, an illustration with multiple-infection data from a clinic study on chronic granulomatous disease is provided.

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

    Directory of Open Access Journals (Sweden)

    Hyeyeong Choe

    Full Text Available 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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

    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

  11. Facilitation of intraguild prey by its intraguild predator in a three-species Lotka-Volterra model.

    Science.gov (United States)

    Shchekinova, Elena Y; Löder, Martin G J; Boersma, Maarten; Wiltshire, Karen H

    2014-03-01

    Explaining the coexistence of multiple species in the competition and predation theatre has proven a great challenge. Traditional intraguild predation (IGP) models have only relatively small regions of stable coexistence of all species. Here, we investigate potential additional mechanisms that extend these regions of stable coexistence. We used a 3-species Lotka-Volterra system to which we added an interaction term to model a unidirectional facilitative relationship between the two predators in the IGP. In this modelling study the IG predator was able to precondition a part of the common resource by an instantaneous manipulation, which resulted in the immobilization of the resource species. This mechanism of immobilization facilitated the resource uptake by the IG prey and thus increased its growth rates even in the presence of the common predator. The facilitative relationship of the IG prey by the IG predator produced a stable coexistence of both predators even though the IG prey was an inferior competitor for a common resource, which cannot be attained with the traditional IGP models. Furthermore, our model predicted a 3-species stable coexistence even at high enrichment where no coexistence was found in the basic IGP model. Thus, we showed that diversity of resource traits could significantly alter emergent community patterns via shifts in exploitative competition of IGP-related predators. The described mechanism could potentially lead to a higher efficiency in exploitation of common resources and thus promote higher diversity in a real community. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. Key issues for the development and application of the species sensitivity distribution (SSD) model for ecological risk assessment

    DEFF Research Database (Denmark)

    Xu, Fu-Liu; Li, Yi-Long; Wang, Yin

    2015-01-01

    The species sensitivity distribution (SSD) model is one of the most commonly used methods for ecological risk assessment based on the potentially affected fraction (PAF) of and the combined PAF (msPAF) as quantitative indicators. There are usually four steps for the development of SSD models...... fractions (msPAFs) for the joint ecological risk assessment of multiple pollutants. Among the above mentioned four steps, the first two steps are paramount. In the present study, the following six key issues are discussed: (1) how to select the appropriate species, (2) how to preprocess the toxicity data...... collected from the ecotoxicity database, (3) how to transform the acute toxicity data into chronic data, (4) how to best fit the toxicity data, (5) how to calculate the msPAF of multiple pollutants, and (6) how to determine the uncertainty of the SSD model”. In response to these questions, several...

  13. Assessing future suitability of tree species under climate change by multiple methods: a case study in southern Germany

    Directory of Open Access Journals (Sweden)

    Helge Walentowski

    2017-07-01

    Full Text Available We compared results derived using three different approaches to assess the suitability of common tree species on the Franconian Plateau in southern Germany under projected warmer and drier climate conditions in the period 2061-2080. The study area is currently a relatively warm and dry region of Germany. We calculated species distribution models (SDMs using information on species’ climate envelopes to predict regional species spectra under 63 different climate change scenarios. We complemented this with fine-scale ecological niche analysis using data from 51 vegetation surveys in seven forest reserves in the study area, and tree-ring analysis (TRA from local populations of five tree species to quantify their sensitivity to climatic extreme years. The SDMs showed that predicted future climate change in the region remains within the climate envelope of certain species (e.g. Quercus petraea, whilst for e.g. Fagus sylvatica, future climate conditions in one third of the scenarios are too warm and dry. This was confirmed by the TRA: sensitivity to drought periods is lower for Q. petraea than for F. sylvatica. The niche analysis shows that the local ecological niches of Quercus robur and Fraxinus excelsior are mainly characterized by soils providing favorable water supply than by climate, and Pinus sylvestris (planted is strongly influenced by light availability. The best adapted species for a warmer and potentially drier climate in the study region are Acer campestre, Sorbus torminalis, S. aria, Ulmus minor, and Tilia platyphyllos, which should therefore play a more prominent role in future climate-resilient mixed forest ecosystems.

  14. Effect of phytohormone balance on shoot multiplication and rooting of the species Dianthus serotinus Waldst. and Kit.

    Directory of Open Access Journals (Sweden)

    Marković Marija

    2007-01-01

    Full Text Available The effect of different phytohormone concentrations on shoot multiplication and shoot rooting was researched on the species Dianthus serotinus. All nutritive media contained MS mineral solution, 3% sucrose, 0.8% agar, 100 mg·L-1 mioinositol, 0.05 mg·L-1 thiamin, 0.25 mg·L-1 nicotinic acid and 1 mg·L-1 glycine. For lateral shoot proliferation, the basic medium was supplemented with BAP (6-benzyl-aminopurine in concentrations 0.1-2 mg·L-1 and NAA (α-naphthalene-acetic acid in concentrations 0.1-1 mg·L-1. The best results were achieved on the medium with 0.5 mg·L-1 BAP and NAA. Rooting was most successful (73% on the medium with 0.5 mg·L-1 NAA.

  15. Multiple-trait structured antedependence model to study the relationship between litter size and birth weight in pigs and rabbits.

    Science.gov (United States)

    David, Ingrid; Garreau, Hervé; Balmisse, Elodie; Billon, Yvon; Canario, Laurianne

    2017-01-20

    Some genetic studies need to take into account correlations between traits that are repeatedly measured over time. Multiple-trait random regression models are commonly used to analyze repeated traits but suffer from several major drawbacks. In the present study, we developed a multiple-trait extension of the structured antedependence model (SAD) to overcome this issue and validated its usefulness by modeling the association between litter size (LS) and average birth weight (ABW) over parities in pigs and rabbits. The single-trait SAD model assumes that a random effect at time [Formula: see text] can be explained by the previous values of the random effect (i.e. at previous times). The proposed multiple-trait extension of the SAD model consists in adding a cross-antedependence parameter to the single-trait SAD model. This model can be easily fitted using ASReml and the OWN Fortran program that we have developed. In comparison with the random regression model, we used our multiple-trait SAD model to analyze the LS and ABW of 4345 litters from 1817 Large White sows and 8706 litters from 2286 L-1777 does over a maximum of five successive parities. For both species, the multiple-trait SAD fitted the data better than the random regression model. The difference between AIC of the two models (AIC_random regression-AIC_SAD) were equal to 7 and 227 for pigs and rabbits, respectively. A similar pattern of heritability and correlation estimates was obtained for both species. Heritabilities were lower for LS (ranging from 0.09 to 0.29) than for ABW (ranging from 0.23 to 0.39). The general trend was a decrease of the genetic correlation for a given trait between more distant parities. Estimates of genetic correlations between LS and ABW were negative and ranged from -0.03 to -0.52 across parities. No correlation was observed between the permanent environmental effects, except between the permanent environmental effects of LS and ABW of the same parity, for which the estimate of

  16. Pyrolysis of reinforced polymer composites: Parameterizing a model for multiple compositions

    Science.gov (United States)

    Martin, Geraldine E.

    A single set of material properties was developed to describe the pyrolysis of fiberglass reinforced polyester composites at multiple composition ratios. Milligram-scale testing was performed on the unsaturated polyester (UP) resin using thermogravimetric analysis (TGA) coupled with differential scanning calorimetry (DSC) to establish and characterize an effective semi-global reaction mechanism, of three consecutive first-order reactions. Radiation-driven gasification experiments were conducted on UP resin and the fiberglass composites at compositions ranging from 41 to 54 wt% resin at external heat fluxes from 30 to 70 kW m -2. The back surface temperature was recorded with an infrared camera and used as the target for inverse analysis to determine the thermal conductivity of the systematically isolated constituent species. Manual iterations were performed in a comprehensive pyrolysis model, ThermaKin. The complete set of properties was validated for the ability to reproduce the mass loss rate during gasification testing.

  17. Sensitivity analyses of spatial population viability analysis models for species at risk and habitat conservation planning.

    Science.gov (United States)

    Naujokaitis-Lewis, Ilona R; Curtis, Janelle M R; Arcese, Peter; Rosenfeld, Jordan

    2009-02-01

    Population viability analysis (PVA) is an effective framework for modeling species- and habitat-recovery efforts, but uncertainty in parameter estimates and model structure can lead to unreliable predictions. Integrating complex and often uncertain information into spatial PVA models requires that comprehensive sensitivity analyses be applied to explore the influence of spatial and nonspatial parameters on model predictions. We reviewed 87 analyses of spatial demographic PVA models of plants and animals to identify common approaches to sensitivity analysis in recent publications. In contrast to best practices recommended in the broader modeling community, sensitivity analyses of spatial PVAs were typically ad hoc, inconsistent, and difficult to compare. Most studies applied local approaches to sensitivity analyses, but few varied multiple parameters simultaneously. A lack of standards for sensitivity analysis and reporting in spatial PVAs has the potential to compromise the ability to learn collectively from PVA results, accurately interpret results in cases where model relationships include nonlinearities and interactions, prioritize monitoring and management actions, and ensure conservation-planning decisions are robust to uncertainties in spatial and nonspatial parameters. Our review underscores the need to develop tools for global sensitivity analysis and apply these to spatial PVA.

  18. Model Vehicle Routing Problem dengan Karakteristik Rute Majemuk, Multiple Time Windows, Multiple Products dan Heterogeneous Fleet untuk Depot Tunggal

    Directory of Open Access Journals (Sweden)

    Ary Arvianto

    2014-01-01

    Full Text Available In this paper we developed a VRP model for multiple routes, multiple time windows for multiple products and heterogeneous vehicles. The solution were constructed using a heuristic approach, i.e, a sequential insertion algorithm. Additionally, this model is applied to solve fuel distributions for eight customers in East Nusa Tenggara. It needs two tankers with capacity of 4700 kilo liters, so that those distributions can be accomplished with a minimum number of vehicles, total completion time, and range of completion time. The result of this study shows that for a heterogeneous vehicles problem, a vehicle with the largest capacity may not necessarily be the vehicle that provides an optimal solution. Moreover, advance trials should be conducted by providing a limited number of tankers for each tanker capacity, so the description of heterogeneous vehicles becomes more visible. In the future research, the solution will be improved by utilizing relocation techniques.

  19. Hydrostratigraphic modelling using multiple-point statistics and airborne transient electromagnetic methods

    DEFF Research Database (Denmark)

    Barfod, Adrian; Straubhaar, Julien; Høyer, Anne-Sophie

    2017-01-01

    Creating increasingly realistic hydrological models involves the inclusion of additional geological and geophysical data in the hydrostratigraphic modelling procedure. Using Multiple Point Statistics (MPS) for stochastic hydrostratigraphic modelling provides a degree of flexibility that allows th...

  20. Integrating land cover modeling and adaptive management to conserve endangered species and reduce catastrophic fire risk

    Science.gov (United States)

    Breininger, David; Duncan, Brean; Eaton, Mitchell J.; Johnson, Fred; Nichols, James

    2014-01-01

    Land cover modeling is used to inform land management, but most often via a two-step process, where science informs how management alternatives can influence resources, and then, decision makers can use this information to make decisions. A more efficient process is to directly integrate science and decision-making, where science allows us to learn in order to better accomplish management objectives and is developed to address specific decisions. Co-development of management and science is especially productive when decisions are complicated by multiple objectives and impeded by uncertainty. Multiple objectives can be met by the specification of tradeoffs, and relevant uncertainty can be addressed through targeted science (i.e., models and monitoring). We describe how to integrate habitat and fuel monitoring with decision-making focused on the dual objectives of managing for endangered species and minimizing catastrophic fire risk. Under certain conditions, both objectives might be achieved by a similar management policy; other conditions require tradeoffs between objectives. Knowledge about system responses to actions can be informed by developing hypotheses based on ideas about fire behavior and then applying competing management actions to different land units in the same system state. Monitoring and management integration is important to optimize state-specific management decisions and to increase knowledge about system responses. We believe this approach has broad utility and identifies a clear role for land cover modeling programs intended to inform decision-making.

  1. Integrating Land Cover Modeling and Adaptive Management to Conserve Endangered Species and Reduce Catastrophic Fire Risk

    Science.gov (United States)

    Breininger, David; Duncan, Brean; Eaton, Mitchell; Johnson, Fred; Nichols, James

    2014-01-01

    Land cover modeling is used to inform land management, but most often via a two-step process where science informs how management alternatives can influence resources and then decision makers can use this to make decisions. A more efficient process is to directly integrate science and decision making, where science allows us to learn to better accomplish management objectives and is developed to address specific decisions. Co-development of management and science is especially productive when decisions are complicated by multiple objectives and impeded by uncertainty. Multiple objectives can be met by specification of tradeoffs, and relevant uncertainty can be addressed through targeted science (i.e., models and monitoring). We describe how to integrate habitat and fuels monitoring with decision making focused on dual objectives of managing for endangered species and minimizing catastrophic fire risk. Under certain conditions, both objectives might be achieved by a similar management policy, but habitat trajectories suggest tradeoffs. Knowledge about system responses to actions can be informed by applying competing management actions to different land units in the same system state and by ideas about fire behavior. Monitoring and management integration is important to optimize state-specific management decisions and increase knowledge about system responses. We believe this approach has broad utility for and cover modeling programs intended to inform decision making.

  2. Cross-species extrapolation of prediction model for lead transfer from soil to corn grain under stress of exogenous lead.

    Science.gov (United States)

    Li, Zhaojun; Yang, Hua; Li, Yupeng; Long, Jian; Liang, Yongchao

    2014-01-01

    There has been increasing concern in recent years regarding lead (Pb) transfer in the soil-plant system. In this study the transfer of Pb (exogenous salts) was investigated from a wide range of Chinese soils to corn grain (Zhengdan 958). Prediction models were developed with combination of the Pb bioconcentration factor (BCF) of Zhengdan 958, and soil pH, organic matter (OM) content, and cation exchange capacity (CEC) through multiple stepwise regressions. Moreover, these prediction models from Zhengdan 958 were applied to other non-model corn species through cross-species extrapolation approach. The results showed that the soil pH and OM were the major factors that controlled Pb transfer from soil to corn grain. The lower pH and OM could improve the bioaccumulation of Pb in corn grain. No significant differences were found between two prediction models derived from the different exogenous Pb contents. When the prediction models were applied to other non-model corn species, the ratio ranges between the predicted BCF values and the measured BCF values were within an interval of 2-fold and close to the solid line of 1∶1 relationship. Moreover, the prediction model i.e. Log[BCF] = -0.098 pH-0.150 log[OM] -1.894 at the treatment of high Pb can effectively reduce the measured BCF intra-species variability for all non-model corn species. These suggested that this prediction model derived from the high Pb content was more adaptable to be applied to other non-model corn species to predict the Pb bioconcentration in corn grain and assess the ecological risk of Pb in different agricultural soils.

  3. Species' habitat use inferred from environmental variables at multiple scales: How much we gain from high-resolution vegetation data?

    Science.gov (United States)

    Gastón, Aitor; Ciudad, Carlos; Mateo-Sánchez, María C.; García-Viñas, Juan I.; López-Leiva, César; Fernández-Landa, Alfredo; Marchamalo, Miguel; Cuevas, Jorge; de la Fuente, Begoña; Fortin, Marie-Josée; Saura, Santiago

    2017-03-01

    Spatial resolution of environmental data may influence the results of habitat selection models. As high-resolution data are usually expensive, an assessment of their contribution to the reliability of habitat models is of interest for both researchers and managers. We evaluated how vegetation cover datasets of different spatial resolutions influence the inferences and predictive power of multi-scale habitat selection models for the endangered brown bear populations in the Cantabrian Range (NW Spain). We quantified the relative performance of three types of datasets: (i) coarse resolution data from Corine Land Cover (minimum mapping unit of 25 ha), (ii) medium resolution data from the Forest Map of Spain (minimum mapping unit of 2.25 ha and information on forest canopy cover and tree species present in each polygon), and (iii) high-resolution Lidar data (about 0.5 points/m2) providing a much finer information on forest canopy cover and height. Despite all the models performed well (AUC > 0.80), the predictive ability of multi-scale models significantly increased with spatial resolution, particularly when other predictors of habitat suitability (e.g. human pressure) were not used to indirectly filter out areas with a more degraded vegetation cover. The addition of fine grain information on forest structure (LiDAR) led to a better understanding of landscape use and a more accurate spatial representation of habitat suitability, even for a species with large spatial requirements as the brown bear, which will result in the development of more effective measures to assist endangered species conservation.

  4. Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

    Science.gov (United States)

    Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

    2016-11-01

    It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

  5. Algivore or phototroph? Plakobranchus ocellatus (Gastropoda) continuously acquires kleptoplasts and nutrition from multiple algal species in nature.

    Science.gov (United States)

    Maeda, Taro; Hirose, Euichi; Chikaraishi, Yoshito; Kawato, Masaru; Takishita, Kiyotaka; Yoshida, Takao; Verbruggen, Heroen; Tanaka, Jiro; Shimamura, Shigeru; Takaki, Yoshihiro; Tsuchiya, Masashi; Iwai, Kenji; Maruyama, Tadashi

    2012-01-01

    The sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda) retains photosynthetically active chloroplasts from ingested algae (functional kleptoplasts) in the epithelial cells of its digestive gland for up to 10 months. While its feeding behavior has not been observed in natural habitats, two hypotheses have been proposed: 1) adult P. ocellatus uses kleptoplasts to obtain photosynthates and nutritionally behaves as a photoautotroph without replenishing the kleptoplasts; or 2) it behaves as a mixotroph (photoautotroph and herbivorous consumer) and replenishes kleptoplasts continually or periodically. To address the question of which hypothesis is more likely, we examined the source algae for kleptoplasts and temporal changes in kleptoplast composition and nutritional contribution. By characterizing the temporal diversity of P. ocellatus kleptoplasts using rbcL sequences, we found that P. ocellatus harvests kleptoplasts from at least 8 different siphonous green algal species, that kleptoplasts from more than one species are present in each individual sea slug, and that the kleptoplast composition differs temporally. These results suggest that wild P. ocellatus often feed on multiple species of siphonous algae from which they continually obtain fresh chloroplasts. By estimating the trophic position of wild and starved P. ocellatus using the stable nitrogen isotopic composition of amino acids, we showed that despite the abundance of kleptoplasts, their photosynthates do not contribute greatly to the nutrition of wild P. ocellatus, but that kleptoplast photosynthates form a significant source of nutrition for starved sea slugs. The herbivorous nature of wild P. ocellatus is consistent with insights from molecular analyses indicating that kleptoplasts are frequently replenished from ingested algae, leading to the conclusion that natural populations of P. ocellatus do not rely on photosynthesis but mainly on the digestion of ingested algae.

  6. Algivore or phototroph? Plakobranchus ocellatus (Gastropoda continuously acquires kleptoplasts and nutrition from multiple algal species in nature.

    Directory of Open Access Journals (Sweden)

    Taro Maeda

    Full Text Available The sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda retains photosynthetically active chloroplasts from ingested algae (functional kleptoplasts in the epithelial cells of its digestive gland for up to 10 months. While its feeding behavior has not been observed in natural habitats, two hypotheses have been proposed: 1 adult P. ocellatus uses kleptoplasts to obtain photosynthates and nutritionally behaves as a photoautotroph without replenishing the kleptoplasts; or 2 it behaves as a mixotroph (photoautotroph and herbivorous consumer and replenishes kleptoplasts continually or periodically. To address the question of which hypothesis is more likely, we examined the source algae for kleptoplasts and temporal changes in kleptoplast composition and nutritional contribution. By characterizing the temporal diversity of P. ocellatus kleptoplasts using rbcL sequences, we found that P. ocellatus harvests kleptoplasts from at least 8 different siphonous green algal species, that kleptoplasts from more than one species are present in each individual sea slug, and that the kleptoplast composition differs temporally. These results suggest that wild P. ocellatus often feed on multiple species of siphonous algae from which they continually obtain fresh chloroplasts. By estimating the trophic position of wild and starved P. ocellatus using the stable nitrogen isotopic composition of amino acids, we showed that despite the abundance of kleptoplasts, their photosynthates do not contribute greatly to the nutrition of wild P. ocellatus, but that kleptoplast photosynthates form a significant source of nutrition for starved sea slugs. The herbivorous nature of wild P. ocellatus is consistent with insights from molecular analyses indicating that kleptoplasts are frequently replenished from ingested algae, leading to the conclusion that natural populations of P. ocellatus do not rely on photosynthesis but mainly on the digestion of ingested algae.

  7. Semantics of Temporal Models with Multiple Temporal Dimensions

    DEFF Research Database (Denmark)

    Kraft, Peter; Sørensen, Jens Otto

    Semantics of temporal models with multi temporal dimensions are examined progressing from non-temporal models unto uni-temporal, and further unto bi- and tri-temporal models. An example of a uni-temporal model is the valid time model, an example of a bi-temporal model is the valid time/transactio......Semantics of temporal models with multi temporal dimensions are examined progressing from non-temporal models unto uni-temporal, and further unto bi- and tri-temporal models. An example of a uni-temporal model is the valid time model, an example of a bi-temporal model is the valid time....../transaction time model, and finally an example of a tri-temporal model is a model with valid time, decision time and transaction time dimensions. The semantics are at first specified at the highest conceptual level possible by a graphical notation. Next, the conceptual models are translated into lower level models...

  8. Intraguild interactions implicating invasive species: Harmonia axyridis as a model species

    Directory of Open Access Journals (Sweden)

    Francis, F.

    2010-01-01

    Full Text Available Understanding the mechanisms that result in the success of exotic species will contribute to predicting future invasions and managing invaded systems. Exotic animal species, whether introduced accidentally or deliberately, may impact communities of native species through different intraguild interactions. As an effective generalist predator of aphids and other soft-body pests the harlequin ladybird Harmonia axyridis Pallas has been a successful biological control agent. This species was deliberately introduced into several countries for biological control of different arthropods pests, but it was also introduced accidentally into several other countries. It became an invasive species, affecting the dynamic and composition of several guilds through direct or indirect interactions. In this paper we will specifically review the existing data on mechanisms of intraguild interactions, within exotic guilds, that result in the success of H. axyridis as an invasive alien. We will use these studies to interpret the observed population declines in predator diversity in the field, and predict species at risk in regions not yet invaded. Finally, we will review the available data on the impact of intraguild interactions implicating H. axyridis on pest biocontrol.

  9. Description of light charged particle multiplicities in the framework of dinuclear system model

    Directory of Open Access Journals (Sweden)

    Antonenko N.V.

    2012-12-01

    Full Text Available In the framework of dinuclear system (DNS model we calculate the light charged particle (LCP multiplicities produced in fusion and quasifission reactions and their kinetic energy spectra. Calculations indicate that with increasing bombarding energy the ratio of LCP multiplicity from fragments MFF to corresponding LCP multiplicity from compound nucleus (CN MCN strongly increases.

  10. Seeing the forest and the trees: multilevel models reveal both species and community patterns

    Science.gov (United States)

    Michelle M. Jackson; Monica G. Turner; Scott M. Pearson; Anthony R. Ives

    2012-01-01

    Studies designed to understand species distributions and community assemblages typically use separate analytical approaches (e.g., logistic regression and ordination) to model the distribution of individual species and to relate community composition to environmental variation. Multilevel models (MLMs) offer a promising strategy for integrating species and community-...

  11. On the multiplicity distribution in statistical model: (I) negative binomial distribution

    CERN Document Server

    Xu, Hao-jie

    2016-01-01

    With the distribution of principal thermodynamic variables (e.g.,volume) and the probability condition from reference multiplicity, we develop an improved baseline measure for multiplicity distribution in statistical model to replace the traditional Poisson expectations. We demonstrate the mismatches between experimental measurements and previous theoretical calculations on multiplicity distributions. We derive a general expression for multiplicity distribution, i.e. a conditional probability distribution, in statistical model and calculate its cumulants under Poisson approximation in connection with recent data for multiplicity fluctuations. We find that probability condition from reference multiplicity are crucial to explain the centrality resolution effect in experiment. With the improved baseline measure for multiplicity distribution, we can quantitatively reproduce the cumulants (cumulant products) for multiplicity distribution of total (net) charges measured in experiments.

  12. Variation partitioning of diatom species data matrices: Understanding the influence of multiple factors on benthic diatom communities in tropical streams

    Energy Technology Data Exchange (ETDEWEB)

    Bere, Taurai, E-mail: tbere2015@gmail.com; Mangadze, Tinotenda; Mwedzi, Tongai

    2016-10-01

    Elucidating the confounding influence of multiple environmental factors on benthic diatom communities is important in developing water quality predictive models for better guidance of stream management efforts. The objective of this study was to explore the relative impact of metal pollution and hydromorphological alterations in, addition to nutrient enrichment and organic pollution, on diatom taxonomic composition with the view to improve stream diatom-based water quality inference models. Samples were collected twice at 20 sampling stations in the tropical Manyame Catchment, Zimbabwe. Diatom, macroinvertebrate communities and environmental factors were sampled and analysed. The variations in diatom community composition explained by different categories of environmental factors were analysed using canonical correspondence analysis using variance partitioning (partial CCA). The following variations were explained by the different predictor matrices: nutrient levels and organic pollution - 10.4%, metal pollution - 8.3% and hydromorphological factors - 7.9%. Thus, factors other than nutrient levels and organic pollution explain additional significant variation in these diatom communities. Development of diatom-based stream water quality inference models that incorporate metal pollution and hydromorphological alterations, where these are key issues, is thus deemed necessary. - Highlights: • Confounding influences of multiple environmental factors on diatom communities are elucidated. • Variation explained: nutrients + organic pollution - 10.4%, metals - 8.3% and hydromorphological factors - 7.9%. • Calibration of existing or development of new indices may be necessary.

  13. Model reduction for stochastic chemical systems with abundant species

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Stephen; Cianci, Claudia; Grima, Ramon [School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH93JR, Scotland (United Kingdom)

    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.

  14. Modeling Stratospheric Constituents: Reactive Species That Regulate Ozone

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Remmert, Hermann

    1968-12-01

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

  16. Magnetic field modelling of machine and multiple machine systems using dynamic reluctance mesh modelling

    OpenAIRE

    Yao, Li

    2006-01-01

    This thesis concerns the modified and improved, time-stepping, dynamic reluctance mesh (DRM) modelling technique for machines and its application to multiple machine systems with their control algorithms. Improvements are suggested which enable the stable solution of the resulting complex non-linear equations. The concept of finite element (FE) derived, overlap-curves has been introduced to facilitate the evaluation of the air-gap reluctances linking the teeth on the rotor to those on the sta...

  17. Independent scattering model and velocity dispersion in trabecular bone: comparison with a multiple scattering model.

    Science.gov (United States)

    Haïat, G; Naili, S

    2011-02-01

    Speed of sound measurements are used clinically to assess bone strength. Trabecular bone is an attenuating composite material in which negative values of velocity dispersion have been measured; this behavior remaining poorly explained physically. The aim of this work is to describe the ultrasonic propagation in trabecular bone modeled by infinite cylinders immersed in a saturating matrix and to derive the physical determinants of velocity dispersion. An original homogenization model accounting for the coupling of independent scattering and absorption phenomena allows the computation of phase velocity and of dispersion while varying bone properties. The first step of the model consists in the computation of the attenuation coefficient at all frequencies. The second step of the model corresponds to the application of the general Kramers-Krönig relationship to derive the frequency dependence of phase velocity. The model predicts negative values of velocity dispersion in agreement with experimental results obtained in phantoms mimicking trabecular bone. In trabecular bone, only negative values of velocity dispersion are predicted by the model, which span within the range of values measured experimentally. However, the comparison of the present results with results obtained in Haiat et al. (J Acoust Soc Am 124:4047-4058, 2008) assuming multiple scattering indicates that accounting for multiple scattering phenomena leads to a better prediction of velocity dispersion in trabecular bone.

  18. Multiple regression models of δ13C and δ15N for fish populations in the eastern Gulf of Mexico

    Science.gov (United States)

    Radabaugh, Kara R.; Peebles, Ernst B.

    2014-08-01

    Multiple regression models were created to explain spatial and temporal variation in the δ13C and δ15N values of fish populations on the West Florida Shelf (eastern Gulf of Mexico, USA). Extensive trawl surveys from three time periods were used to acquire muscle samples from seven groundfish species. Isotopic variation (δ13Cvar and δ15Nvar) was calculated as the deviation from the isotopic mean of each fish species. Static spatial data and dynamic water quality parameters were used to create models predicting δ13Cvar and δ15Nvar in three fish species that were caught in the summers of 2009 and 2010. Additional data sets were then used to determine the accuracy of the models for predicting isotopic variation (1) in a different time period (fall 2010) and (2) among four entirely different fish species that were collected during summer 2009. The δ15Nvar model was relatively stable and could be applied to different time periods and species with similar accuracy (mean absolute errors 0.31-0.33‰). The δ13Cvar model had a lower predictive capability and mean absolute errors ranged from 0.42 to 0.48‰. δ15N trends are likely linked to gradients in nitrogen fixation and Mississippi River influence on the West Florida Shelf, while δ13C trends may be linked to changes in algal species, photosynthetic fractionation, and abundance of benthic vs. planktonic basal resources. These models of isotopic variability may be useful for future stable isotope investigations of trophic level, basal resource use, and animal migration on the West Florida Shelf.

  19. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

    Science.gov (United States)

    Zhu, Tianqi; Dos Reis, Mario; Yang, Ziheng

    2015-03-01

    Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way

  20. Place prioritization for biodiversity content using species ecological niche modeling

    Directory of Open Access Journals (Sweden)

    Víctor Sánchez-Cordero

    2005-01-01

    Full Text Available Place prioritization for biodiversity representation is essential for conservation planning, particularly in megadiverse countries where high deforestation threatens biodiversity. Given the collecting biases and uneven sampling of biological inventories, there is a need to develop robust models of species’ distributions. By modeling species’ ecological niches using point occurrence data and digitized environmental feature maps, we can predict potential and extant distributions of species in untransformed landscapes, as well as in those transformed by vegetation change (including deforestation. Such distributional predictions provide a framework for use of species as biodiversity surrogates in place prioritization procedures such as those based on rarity and complementarity. Beyond biodiversity conservation, these predictions can also be used for place prioritization for ecological restoration under current conditions and under future scenarios of habitat change (e.g., deforestation scenarios. To illustrate these points, we (1 predict distributions under current and future deforestation scenarios for the Mexican endemic mammal Dipodomys phillipsii, and show how areas for restoration may be selected; and (2 propose conservation areas by combining nonvolant mammal distributional predictions as biodiversity surrogates with place prioritization procedures, to connect decreed natural protected areas in a region holding exceptional biodiversity: the Transvolcanic Belt in central Mexico. La selección de áreas prioritarias de conservación es fundamental en la planeación sistemática de la conservación, particularmente en países de mega-diversidad, en donde la alta deforestación es una de las amenazas a la biodiversidad. Debido a los sesgos taxonómicos y geográficos de colecta de los inventarios biológicos, es indispensable generar modelos robustos de distribución de especies. Al modelar el nicho ecológico de especies usando localidades de

  1. Biotic modifiers, environmental modulation and species distribution models

    NARCIS (Netherlands)

    Linder, H. Peter; Bykova, Olga; Dyke, James; Etienne, Rampal S.; Hickler, Thomas; Kuehn, Ingolf; Marion, Glenn; Ohlemueller, Ralf; Schymanski, Stanislaus J.; Singer, Alexander

    2012-01-01

    The ability of species to modulate environmental conditions and resources has long been of interest. In the past three decades the impacts of these biotic modifiers have been investigated as ecosystem engineers, niche constructors, facilitators and keystone species. This environmental modulation can

  2. Biotic modifiers, environmental modulation and species distribution models

    NARCIS (Netherlands)

    Linder, H. Peter; Bykova, Olga; Dyke, James; Etienne, Rampal S.; Hickler, Thomas; Kuehn, Ingolf; Marion, Glenn; Ohlemueller, Ralf; Schymanski, Stanislaus J.; Singer, Alexander

    2012-01-01

    The ability of species to modulate environmental conditions and resources has long been of interest. In the past three decades the impacts of these biotic modifiers have been investigated as ecosystem engineers, niche constructors, facilitators and keystone species. This environmental modulation can

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

    Directory of Open Access Journals (Sweden)

    Yu Liang

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  6. A solvable two-species catalysis-driven aggregation model

    CERN Document Server

    Ke Jian Hong

    2003-01-01

    We study the kinetics of a two-species catalysis-driven aggregation system, in which an irreversible aggregation between any two clusters of one species occurs only with the catalytic action of another species. By means of a generalized mean-field rate equation, we obtain the asymptotic solutions of the cluster mass distributions in a simple process with a constant rate kernel. For the case without any consumption of the catalyst, the cluster mass distribution of either species always approaches a conventional scaling law. However, the evolution behaviour of the system in the case with catalyst consumption is complicated and depends crucially on the relative data of the initial concentrations of the two species.

  7. The importance of data quality for generating reliable distribution models for rare, elusive, and cryptic species

    Science.gov (United States)

    Aubry, Keith B.; Raley, Catherine M.; McKelvey, Kevin S.

    2017-01-01

    The availability of spatially referenced environmental data and species occurrence records in online databases enable practitioners to easily generate species distribution models (SDMs) for a broad array of taxa. Such databases often include occurrence records of unknown reliability, yet little information is available on the influence of data quality on SDMs generated for rare, elusive, and cryptic species that are prone to misidentification in the field. We investigated this question for the fisher (Pekania pennanti), a forest carnivore of conservation concern in the Pacific States that is often confused with the more common Pacific marten (Martes caurina). Fisher occurrence records supported by physical evidence (verifiable records) were available from a limited area, whereas occurrence records of unknown quality (unscreened records) were available from throughout the fisher’s historical range. We reserved 20% of the verifiable records to use as a test sample for both models and generated SDMs with each dataset using Maxent. The verifiable model performed substantially better than the unscreened model based on multiple metrics including AUCtest values (0.78 and 0.62, respectively), evaluation of training and test gains, and statistical tests of how well each model predicted test localities. In addition, the verifiable model was consistent with our knowledge of the fisher’s habitat relations and potential distribution, whereas the unscreened model indicated a much broader area of high-quality habitat (indices > 0.5) that included large expanses of high-elevation habitat that fishers do not occupy. Because Pacific martens remain relatively common in upper elevation habitats in the Cascade Range and Sierra Nevada, the SDM based on unscreened records likely reflects primarily a conflation of marten and fisher habitat. Consequently, accurate identifications are far more important than the spatial extent of occurrence records for generating reliable SDMs for the

  8. Modelling and Verification of Multiple UAV Mission Using SMV

    CERN Document Server

    Sirigineedi, Gopinadh; White, Brian A; Zbikowski, Rafal

    2010-01-01

    Model checking has been used to verify the correctness of digital circuits, security protocols, communication protocols, as they can be modelled by means of finite state transition model. However, modelling the behaviour of hybrid systems like UAVs in a Kripke model is challenging. This work is aimed at capturing the behaviour of an UAV performing cooperative search mission into a Kripke model, so as to verify it against the temporal properties expressed in Computation Tree Logic (CTL). SMV model checker is used for the purpose of model checking.

  9. Modelling and Verification of Multiple UAV Mission Using SMV

    Directory of Open Access Journals (Sweden)

    Gopinadh Sirigineedi

    2010-03-01

    Full Text Available Model checking has been used to verify the correctness of digital circuits, security protocols, communication protocols, as they can be modelled by means of finite state transition model. However, modelling the behaviour of hybrid systems like UAVs in a Kripke model is challenging. This work is aimed at capturing the behaviour of an UAV performing cooperative search mission into a Kripke model, so as to verify it against the temporal properties expressed in Computational Tree Logic (CTL. SMV model checker is used for the purpose of model checking.

  10. EBV Infection and Multiple Sclerosis : Lessons from a Marmoset Mode