Science.gov

Sample records for comparative model analysis

  1. Wellness Model of Supervision: A Comparative Analysis

    ERIC Educational Resources Information Center

    Lenz, A. Stephen; Sangganjanavanich, Varunee Faii; Balkin, Richard S.; Oliver, Marvarene; Smith, Robert L.

    2012-01-01

    This quasi-experimental study compared the effectiveness of the Wellness Model of Supervision (WELMS; Lenz & Smith, 2010) with alternative supervision models for developing wellness constructs, total personal wellness, and helping skills among counselors-in-training. Participants were 32 master's-level counseling students completing their…

  2. Comparative analysis of Goodwin's business cycle models

    NASA Astrophysics Data System (ADS)

    Antonova, A. O.; Reznik, S.; Todorov, M. D.

    2016-10-01

    We compare the behavior of solutions of Goodwin's business cycle equation in the form of neutral delay differential equation with fixed delay (NDDE model) and in the form of the differential equations of 3rd, 4th and 5th orders (ODE model's). Such ODE model's (Taylor series expansion of NDDE in powers of θ) are proposed in N. Dharmaraj and K. Vela Velupillai [6] for investigation of the short periodic sawthooth oscillations in NDDE. We show that the ODE's of 3rd, 4th and 5th order may approximate the asymptotic behavior of only main Goodwin's mode, but not the sawthooth modes. If the order of the Taylor series expansion exceeds 5, then the approximate ODE becomes unstable independently of time lag θ.

  3. Comparative analysis of condensation models within DSMC

    SciTech Connect

    Bykov, Nikolay Y.; Gorbachev, Yuriy E.

    2014-12-09

    Two condensation process modeling approaches within DSMC methodology are compared. The first is based on the modified nucleation theory which correctly describes small clusters and the second on the kinetic theory and considers not only supercritical clusters, but clusters of all sizes including dimers. The relaxation of the size distribution function is calculated for the spatially homogeneous cases, where the monomer parameters are kept constant. As an example the vapour of Cu atoms is considered and importance of taking into account of the internal energies of clusters is shown. Peculiarities of the classical and kinetic approaches are discussed herein.

  4. A comparative analysis of different approaches for integrated WWTP modelling.

    PubMed

    Grau, P; Copp, J; Vanrolleghem, P A; Takács, I; Ayesa, E

    2009-01-01

    In this paper a comparative analysis of the most important approaches for integrated WWTP modelling is presented. After an introductory presentation of the most important drawbacks and challenges for plant wide modelling, the fundamentals of three different approaches to construct integrated models are presented: "Interfaces" "Standard Supermodel" and "Tailored Supermodel". Afterwards, a comparative analysis of these approaches from different points of view (difficulties for the model end user, characterization of the process in the plant, flexibility or adaptability for each case of study, simulation platform requirements and computational costs) is carried out. From this comparison, some important conclusions about the suitability of each alternative depending on the simulation case study are extracted. PMID:19151496

  5. Comparative dynamic analysis of the full Grossman model.

    PubMed

    Ried, W

    1998-08-01

    The paper applies the method of comparative dynamic analysis to the full Grossman model. For a particular class of solutions, it derives the equations implicitly defining the complete trajectories of the endogenous variables. Relying on the concept of Frisch decision functions, the impact of any parametric change on an endogenous variable can be decomposed into a direct and an indirect effect. The focus of the paper is on marginal changes in the rate of health capital depreciation. It also analyses the impact of either initial financial wealth or the initial stock of health capital. While the direction of most effects remains ambiguous in the full model, the assumption of a zero consumption benefit of health is sufficient to obtain a definite for any direct or indirect effect.

  6. Comparing models for perfluorooctanoic acid pharmacokinetics using Bayesian analysis.

    PubMed

    Wambaugh, John F; Barton, Hugh A; Setzer, R Woodrow

    2008-12-01

    Selecting the appropriate pharmacokinetic (PK) model given the available data is investigated for perfluorooctanoic acid (PFOA), which has been widely analyzed with an empirical, one-compartment model. This research examined the results of experiments [Kemper R. A., DuPont Haskell Laboratories, USEPA Administrative Record AR-226.1499 (2003)] that administered single oral or iv doses of PFOA to adult male and female rats. PFOA concentration was observed over time; in plasma for some animals and in fecal and urinary excretion for others. There were four rats per dose group, for a total of 36 males and 36 females. Assuming that the PK parameters for each individual within a gender were drawn from the same, biologically varying population, plasma and excretion data were jointly analyzed using a hierarchical framework to separate uncertainty due to measurement error from actual biological variability. Bayesian analysis using Markov Chain Monte Carlo (MCMC) provides tools to perform such an analysis as well as quantitative diagnostics to evaluate and discriminate between models. Starting from a one-compartment PK model with separate clearances to urine and feces, the model was incrementally expanded using Bayesian measures to assess if the expansion was supported by the data. PFOA excretion is sexually dimorphic in rats; male rats have bi-phasic elimination that is roughly 40 times slower than that of the females, which appear to have a single elimination phase. The male and female data were analyzed separately, keeping only the parameters describing the measurement process in common. For male rats, including excretion data initially decreased certainty in the one-compartment parameter estimates compared to an analysis using plasma data only. Allowing a third, unspecified clearance improved agreement and increased certainty when all the data was used, however a significant amount of eliminated PFOA was estimated to be missing from the excretion data. Adding an additional

  7. Hidden Markov models for evolution and comparative genomics analysis.

    PubMed

    Bykova, Nadezda A; Favorov, Alexander V; Mironov, Andrey A

    2013-01-01

    The problem of reconstruction of ancestral states given a phylogeny and data from extant species arises in a wide range of biological studies. The continuous-time Markov model for the discrete states evolution is generally used for the reconstruction of ancestral states. We modify this model to account for a case when the states of the extant species are uncertain. This situation appears, for example, if the states for extant species are predicted by some program and thus are known only with some level of reliability; it is common for bioinformatics field. The main idea is formulation of the problem as a hidden Markov model on a tree (tree HMM, tHMM), where the basic continuous-time Markov model is expanded with the introduction of emission probabilities of observed data (e.g. prediction scores) for each underlying discrete state. Our tHMM decoding algorithm allows us to predict states at the ancestral nodes as well as to refine states at the leaves on the basis of quantitative comparative genomics. The test on the simulated data shows that the tHMM approach applied to the continuous variable reflecting the probabilities of the states (i.e. prediction score) appears to be more accurate then the reconstruction from the discrete states assignment defined by the best score threshold. We provide examples of applying our model to the evolutionary analysis of N-terminal signal peptides and transcription factor binding sites in bacteria. The program is freely available at http://bioinf.fbb.msu.ru/~nadya/tHMM and via web-service at http://bioinf.fbb.msu.ru/treehmmweb.

  8. Comparing models for perfluorooctanoic acid pharmacokinetics using Bayesian analysis

    EPA Science Inventory

    Selecting the appropriate pharmacokinetic (PK) model given the available data is investigated for perfluorooctanoic acid (PFOA), which has been widely analyzed with an empirical, one-compartment model. This research examined the results of experiments [Kemper R. A., DuPont Haskel...

  9. Mental Models about Seismic Effects: Students' Profile Based Comparative Analysis

    ERIC Educational Resources Information Center

    Moutinho, Sara; Moura, Rui; Vasconcelos, Clara

    2016-01-01

    Nowadays, meaningful learning takes a central role in science education and is based in mental models that allow the representation of the real world by individuals. Thus, it is essential to analyse the student's mental models by promoting an easier reconstruction of scientific knowledge, by allowing them to become consistent with the curricular…

  10. Comparing Predictors in Multivariate Regression Models: An Extension of Dominance Analysis

    ERIC Educational Resources Information Center

    Azen, Razia; Budescu, David V.

    2006-01-01

    Dominance analysis (DA) is a method used to compare the relative importance of predictors in multiple regression. DA determines the dominance of one predictor over another by comparing their additional R[squared] contributions across all subset models. In this article DA is extended to multivariate models by identifying a minimal set of criteria…

  11. How to Construct More Accurate Student Models: Comparing and Optimizing Knowledge Tracing and Performance Factor Analysis

    ERIC Educational Resources Information Center

    Gong, Yue; Beck, Joseph E.; Heffernan, Neil T.

    2011-01-01

    Student modeling is a fundamental concept applicable to a variety of intelligent tutoring systems (ITS). However, there is not a lot of practical guidance on how to construct and train such models. This paper compares two approaches for student modeling, Knowledge Tracing (KT) and Performance Factors Analysis (PFA), by evaluating their predictive…

  12. An Analysis Technique/Automated Tool for Comparing and Tracking Analysis Modes of Different Finite Element Models

    NASA Technical Reports Server (NTRS)

    Towner, Robert L.; Band, Jonathan L.

    2012-01-01

    An analysis technique was developed to compare and track mode shapes for different Finite Element Models. The technique may be applied to a variety of structural dynamics analyses, including model reduction validation (comparing unreduced and reduced models), mode tracking for various parametric analyses (e.g., launch vehicle model dispersion analysis to identify sensitivities to modal gain for Guidance, Navigation, and Control), comparing models of different mesh fidelity (e.g., a coarse model for a preliminary analysis compared to a higher-fidelity model for a detailed analysis) and mode tracking for a structure with properties that change over time (e.g., a launch vehicle from liftoff through end-of-burn, with propellant being expended during the flight). Mode shapes for different models are compared and tracked using several numerical indicators, including traditional Cross-Orthogonality and Modal Assurance Criteria approaches, as well as numerical indicators obtained by comparing modal strain energy and kinetic energy distributions. This analysis technique has been used to reliably identify correlated mode shapes for complex Finite Element Models that would otherwise be difficult to compare using traditional techniques. This improved approach also utilizes an adaptive mode tracking algorithm that allows for automated tracking when working with complex models and/or comparing a large group of models.

  13. Comparative quality analysis of models of total electron content in the ionosphere

    NASA Astrophysics Data System (ADS)

    Ivanov, V. B.; Gorbachev, O. A.; Kholmogorov, A. A.

    2016-05-01

    We present a brief description and comparative analysis of the Klobuchar, GEMTEC, and NTCM-GL models of total electron content in the ionosphere. The quality of model performance against experimental data on the total electron content is compared. Statistical estimates for the residual positioning error are obtained for each of these models on the basis of the international Global Navigation Satellite Systems (GNSS) Service data. The GEMTEC and NTCM-GL models are shown to have a higher positioning accuracy than the Klobuchar model. The best results of the ionospheric error correction are provided by the GEMTEC model.

  14. A comparative analysis on different nanofluid models for the oscillatory stagnation point flow

    NASA Astrophysics Data System (ADS)

    Nadeem, S.; Khan, A. U.; Saleem, S.

    2016-08-01

    In this study we have presented the comparative analysis of the oscillatory stagnation point flow of nanofluids. Both the phase flow model and Buongiorno model are discussed for oscillatory stagnation point flows and a comparison between experimental model and theoretical model is presented. The resulting partial differential equations for oscillatory two-dimensional flows are simplified in a fixed frame and a moving frame of reference subject to the assumed form of solutions. The homotopy analysis method is used to solve the reduced system of coupled nonlinear ordinary differential equations. The consequences are examined through graphs and tables. It is also found that comparatively both the Boungiorno nanofluid model and phase flow model are of compatible order for a special set of parameters but generally such results do not hold.

  15. BSM2 Plant-Wide Model construction and comparative analysis with other methodologies for integrated modelling.

    PubMed

    Grau, P; Vanrolleghem, P; Ayesa, E

    2007-01-01

    In this paper, a new methodology for integrated modelling of the WWTP has been used for the construction of the Benchmark Simulation Model N degrees 2 (BSM2). The transformations-approach proposed in this methodology does not require the development of specific transformers to interface unit process models and allows the construction of tailored models for a particular WWTP guaranteeing the mass and charge continuity for the whole model. The BSM2 PWM constructed as case study, is evaluated by means of simulations under different scenarios and its validity in reproducing water and sludge lines in WWTP is demonstrated. Furthermore the advantages that this methodology presents compared to other approaches for integrated modelling are verified in terms of flexibility and coherence. PMID:17978433

  16. Multilevel Structural Equation Models for the Analysis of Comparative Data on Educational Performance

    ERIC Educational Resources Information Center

    Goldstein, Harvey; Bonnet, Gerard; Rocher, Thierry

    2007-01-01

    The Programme for International Student Assessment comparative study of reading performance among 15-year-olds is reanalyzed using statistical procedures that allow the full complexity of the data structures to be explored. The article extends existing multilevel factor analysis and structural equation models and shows how this can extract richer…

  17. Comparative Analysis of Behavioral Models for Adaptive Learning in Changing Environments

    PubMed Central

    Marković, Dimitrije; Kiebel, Stefan J.

    2016-01-01

    Probabilistic models of decision making under various forms of uncertainty have been applied in recent years to numerous behavioral and model-based fMRI studies. These studies were highly successful in enabling a better understanding of behavior and delineating the functional properties of brain areas involved in decision making under uncertainty. However, as different studies considered different models of decision making under uncertainty, it is unclear which of these computational models provides the best account of the observed behavioral and neuroimaging data. This is an important issue, as not performing model comparison may tempt researchers to over-interpret results based on a single model. Here we describe how in practice one can compare different behavioral models and test the accuracy of model comparison and parameter estimation of Bayesian and maximum-likelihood based methods. We focus our analysis on two well-established hierarchical probabilistic models that aim at capturing the evolution of beliefs in changing environments: Hierarchical Gaussian Filters and Change Point Models. To our knowledge, these two, well-established models have never been compared on the same data. We demonstrate, using simulated behavioral experiments, that one can accurately disambiguate between these two models, and accurately infer free model parameters and hidden belief trajectories (e.g., posterior expectations, posterior uncertainties, and prediction errors) even when using noisy and highly correlated behavioral measurements. Importantly, we found several advantages of Bayesian inference and Bayesian model comparison compared to often-used Maximum-Likelihood schemes combined with the Bayesian Information Criterion. These results stress the relevance of Bayesian data analysis for model-based neuroimaging studies that investigate human decision making under uncertainty. PMID:27148030

  18. Comparing model-based and model-free analysis methods for QUASAR arterial spin labeling perfusion quantification.

    PubMed

    Chappell, Michael A; Woolrich, Mark W; Petersen, Esben T; Golay, Xavier; Payne, Stephen J

    2013-05-01

    Amongst the various implementations of arterial spin labeling MRI methods for quantifying cerebral perfusion, the QUASAR method is unique. By using a combination of labeling with and without flow suppression gradients, the QUASAR method offers the separation of macrovascular and tissue signals. This permits local arterial input functions to be defined and "model-free" analysis, using numerical deconvolution, to be used. However, it remains unclear whether arterial spin labeling data are best treated using model-free or model-based analysis. This work provides a critical comparison of these two approaches for QUASAR arterial spin labeling in the healthy brain. An existing two-component (arterial and tissue) model was extended to the mixed flow suppression scheme of QUASAR to provide an optimal model-based analysis. The model-based analysis was extended to incorporate dispersion of the labeled bolus, generally regarded as the major source of discrepancy between the two analysis approaches. Model-free and model-based analyses were compared for perfusion quantification including absolute measurements, uncertainty estimation, and spatial variation in cerebral blood flow estimates. Major sources of discrepancies between model-free and model-based analysis were attributed to the effects of dispersion and the degree to which the two methods can separate macrovascular and tissue signal.

  19. Genome-scale metabolic modeling of Mucor circinelloides and comparative analysis with other oleaginous species.

    PubMed

    Vongsangnak, Wanwipa; Klanchui, Amornpan; Tawornsamretkit, Iyarest; Tatiyaborwornchai, Witthawin; Laoteng, Kobkul; Meechai, Asawin

    2016-06-01

    We present a novel genome-scale metabolic model iWV1213 of Mucor circinelloides, which is an oleaginous fungus for industrial applications. The model contains 1213 genes, 1413 metabolites and 1326 metabolic reactions across different compartments. We demonstrate that iWV1213 is able to accurately predict the growth rates of M. circinelloides on various nutrient sources and culture conditions using Flux Balance Analysis and Phenotypic Phase Plane analysis. Comparative analysis of three oleaginous genome-scale models, including M. circinelloides (iWV1213), Mortierella alpina (iCY1106) and Yarrowia lipolytica (iYL619_PCP) revealed that iWV1213 possesses a higher number of genes involved in carbohydrate, amino acid, and lipid metabolisms that might contribute to its versatility in nutrient utilization. Moreover, the identification of unique and common active reactions among the Zygomycetes oleaginous models using Flux Variability Analysis unveiled a set of gene/enzyme candidates as metabolic engineering targets for cellular improvement. Thus, iWV1213 offers a powerful metabolic engineering tool for multi-level omics analysis, enabling strain optimization as a cell factory platform of lipid-based production.

  20. Comparative analysis of numerical models of pipe handling equipment used in offshore drilling applications

    NASA Astrophysics Data System (ADS)

    Pawlus, Witold; Ebbesen, Morten K.; Hansen, Michael R.; Choux, Martin; Hovland, Geir

    2016-06-01

    Design of offshore drilling equipment is a task that involves not only analysis of strict machine specifications and safety requirements but also consideration of changeable weather conditions and harsh environment. These challenges call for a multidisciplinary approach and make the design process complex. Various modeling software products are currently available to aid design engineers in their effort to test and redesign equipment before it is manufactured. However, given the number of available modeling tools and methods, the choice of the proper modeling methodology becomes not obvious and - in some cases - troublesome. Therefore, we present a comparative analysis of two popular approaches used in modeling and simulation of mechanical systems: multibody and analytical modeling. A gripper arm of the offshore vertical pipe handling machine is selected as a case study for which both models are created. In contrast to some other works, the current paper shows verification of both systems by benchmarking their simulation results against each other. Such criteria as modeling effort and results accuracy are evaluated to assess which modeling strategy is the most suitable given its eventual application.

  1. Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling

    PubMed Central

    2013-01-01

    Background Culture-independent phylogenetic analysis of 16S ribosomal RNA (rRNA) gene sequences has emerged as an incisive method of profiling bacteria present in a specimen. Currently, multiple techniques are available to enumerate the abundance of bacterial taxa in specimens, including the Sanger sequencing, the ‘next generation’ pyrosequencing, microarrays, quantitative PCR, and the rapidly emerging, third generation sequencing, and fourth generation sequencing methods. An efficient statistical tool is in urgent need for the followings tasks: (1) to compare the agreement between these measurement platforms, (2) to select the most reliable platform(s), and (3) to combine different platforms of complementary strengths, for a unified analysis. Results We present the latent variable structural equation modeling (SEM) as a novel statistical application for the comparative analysis of measurement platforms. The latent variable SEM model treats the true (unknown) relative frequency of a given bacterial taxon in a specimen as the latent (unobserved) variable and estimates the reliabilities of, and similarities between, different measurement platforms, and subsequently weighs those measurements optimally for a unified analysis of the microbiome composition. The latent variable SEM contains the repeated measures ANOVA (both the univariate and the multivariate models) as special cases and, as a more general and realistic modeling approach, yields superior goodness-of-fit and more reliable analysis results, as demonstrated by a microbiome study of the human inflammatory bowel diseases. Conclusions Given the rapid evolution of modern biotechnologies, the measurement platform comparison, selection and combination tasks are here to stay and to grow – and the latent variable SEM method is readily applicable to any other biological settings, aside from the microbiome study presented here. PMID:23497007

  2. Comparative Analysis of Soft Computing Models in Prediction of Bending Rigidity of Cotton Woven Fabrics

    NASA Astrophysics Data System (ADS)

    Guruprasad, R.; Behera, B. K.

    2015-10-01

    Quantitative prediction of fabric mechanical properties is an essential requirement for design engineering of textile and apparel products. In this work, the possibility of prediction of bending rigidity of cotton woven fabrics has been explored with the application of Artificial Neural Network (ANN) and two hybrid methodologies, namely Neuro-genetic modeling and Adaptive Neuro-Fuzzy Inference System (ANFIS) modeling. For this purpose, a set of cotton woven grey fabrics was desized, scoured and relaxed. The fabrics were then conditioned and tested for bending properties. With the database thus created, a neural network model was first developed using back propagation as the learning algorithm. The second model was developed by applying a hybrid learning strategy, in which genetic algorithm was first used as a learning algorithm to optimize the number of neurons and connection weights of the neural network. The Genetic algorithm optimized network structure was further allowed to learn using back propagation algorithm. In the third model, an ANFIS modeling approach was attempted to map the input-output data. The prediction performances of the models were compared and a sensitivity analysis was reported. The results show that the prediction by neuro-genetic and ANFIS models were better in comparison with that of back propagation neural network model.

  3. Comparative analysis of Bouc-Wen and Jiles-Atherton models under symmetric excitations

    NASA Astrophysics Data System (ADS)

    Laudani, Antonino; Fulginei, Francesco Riganti; Salvini, Alessandro

    2014-02-01

    The aim of the present paper is to validate the Bouc-Wen (BW) hysteresis model when it is applied to predict dynamic ferromagnetic loops. Indeed, although the Bouc-Wen model has had an increasing interest in last few years, it is usually adopted in mechanical and structural systems and very rarely for magnetic applications. Thus, for addressing this goal the Bouc-Wen model is compared with the dynamic Jiles-Atherton model that, instead, was ideated exactly for simulating magnetic hysteresis. The comparative analysis has involved saturated and symmetric hysteresis loops in ferromagnetic materials. In addition in order to identify the Bouc-Wen parameters a very effective recent heuristic, called Metric-Topological and Evolutionary Optimization (MeTEO) has been utilized. It is based on a hybridization of three meta-heuristics: the Flock-of-Starlings Optimization, the Particle Swarm Optimization and the Bacterial Chemotaxis Algorithm. Thanks to the specific properties of these heuristic, MeTEO allow us to achieve effective identification of such kind of models. Several hysteresis loops have been utilized for final validation tests with the aim to investigate if the BW model can follow the different hysteresis behaviors of both static (quasi-static) and dynamic cases.

  4. Measurement error in time-series analysis: a simulation study comparing modelled and monitored data

    PubMed Central

    2013-01-01

    Background Assessing health effects from background exposure to air pollution is often hampered by the sparseness of pollution monitoring networks. However, regional atmospheric chemistry-transport models (CTMs) can provide pollution data with national coverage at fine geographical and temporal resolution. We used statistical simulation to compare the impact on epidemiological time-series analysis of additive measurement error in sparse monitor data as opposed to geographically and temporally complete model data. Methods Statistical simulations were based on a theoretical area of 4 regions each consisting of twenty-five 5 km × 5 km grid-squares. In the context of a 3-year Poisson regression time-series analysis of the association between mortality and a single pollutant, we compared the error impact of using daily grid-specific model data as opposed to daily regional average monitor data. We investigated how this comparison was affected if we changed the number of grids per region containing a monitor. To inform simulations, estimates (e.g. of pollutant means) were obtained from observed monitor data for 2003–2006 for national network sites across the UK and corresponding model data that were generated by the EMEP-WRF CTM. Average within-site correlations between observed monitor and model data were 0.73 and 0.76 for rural and urban daily maximum 8-hour ozone respectively, and 0.67 and 0.61 for rural and urban loge(daily 1-hour maximum NO2). Results When regional averages were based on 5 or 10 monitors per region, health effect estimates exhibited little bias. However, with only 1 monitor per region, the regression coefficient in our time-series analysis was attenuated by an estimated 6% for urban background ozone, 13% for rural ozone, 29% for urban background loge(NO2) and 38% for rural loge(NO2). For grid-specific model data the corresponding figures were 19%, 22%, 54% and 44% respectively, i.e. similar for rural loge(NO2) but more marked for urban loge(NO2

  5. A comparative analysis of terrain stability models for predicting shallow landslides in colluvial soils

    NASA Astrophysics Data System (ADS)

    Meisina, C.; Scarabelli, S.

    2007-06-01

    Most of the slopes of the hilly areas of the Apennines are composed of colluvial soils originating from the weathering of the bedrock and down slope transportation. Shallow slides affect this superficial cover, depend largely on the surface topography and are a recurrent problem. SINMAP and SHALSTAB are terrain stability models that combine steady state hydrology assumptions with the infinite slope stability model to quantify shallow slope stability. They have a similar physical basis but they use different indices to quantify instability. The purposes of this study are to test and compare the approaches of SINMAP and SHALSTAB models for slope stability analysis and to compare the results of these analyses with the locations of the shallow landslides that occurred on November 2002 in an area of the Oltrepo Pavese (Northern Apennines). The territory of S. Giuletta, characterized by clayey-silty colluvial soils, represents the test site. The Digital Elevation Model was constructed from a 1:5000 scale contour map and was used to estimate the slope of the terrain as well as the potential soil moisture conditions. In situ and laboratory tests provided the basis for measuring values for soil hydraulic and geotechnical parameters (moisture content, soil suction, Atterberg limits, methylene blue dye adsorption, hydraulic conductivity). Soil thickness was extracted from a soil database. An inventory of landslide from interpretation of aerial photographs and field surveys was used to document sites of instability (mostly soil slips) and to provide a test of model performance by comparing observed landslide locations with model predictions. The study discusses the practical advantages and limitations of the two models in connection with the geological characteristics of the studied area, which could be representative of similar geological contexts in the Apennines.

  6. Conceptual model of iCAL4LA: Proposing the components using comparative analysis

    NASA Astrophysics Data System (ADS)

    Ahmad, Siti Zulaiha; Mutalib, Ariffin Abdul

    2016-08-01

    This paper discusses an on-going study that initiates an initial process in determining the common components for a conceptual model of interactive computer-assisted learning that is specifically designed for low achieving children. This group of children needs a specific learning support that can be used as an alternative learning material in their learning environment. In order to develop the conceptual model, this study extracts the common components from 15 strongly justified computer assisted learning studies. A comparative analysis has been conducted to determine the most appropriate components by using a set of specific indication classification to prioritize the applicability. The results of the extraction process reveal 17 common components for consideration. Later, based on scientific justifications, 16 of them were selected as the proposed components for the model.

  7. The effectiveness of physical models in teaching anatomy: a meta-analysis of comparative studies.

    PubMed

    Yammine, Kaissar; Violato, Claudio

    2016-10-01

    There are various educational methods used in anatomy teaching. While three dimensional (3D) visualization technologies are gaining ground due to their ever-increasing realism, reports investigating physical models as a low-cost 3D traditional method are still the subject of considerable interest. The aim of this meta-analysis is to quantitatively assess the effectiveness of such models based on comparative studies. Eight studies (7 randomized trials; 1 quasi-experimental) including 16 comparison arms and 820 learners met the inclusion criteria. Primary outcomes were defined as factual, spatial and overall percentage scores. The meta-analytical results are: educational methods using physical models yielded significantly better results when compared to all other educational methods for the overall knowledge outcome (p < 0.001) and for spatial knowledge acquisition (p < 0.001). Significantly better results were also found with regard to the long-retention knowledge outcome (p < 0.01). No significance was found for the factual knowledge acquisition outcome. The evidence in the present systematic review was found to have high internal validity and at least an acceptable strength. In conclusion, physical anatomical models offer a promising tool for teaching gross anatomy in 3D representation due to their easy accessibility and educational effectiveness. Such models could be a practical tool to bring up the learners' level of gross anatomy knowledge at low cost.

  8. A comparative analysis of hazard models for predicting debris flows in Madison County, VA

    USGS Publications Warehouse

    Morrissey, Meghan M.; Wieczorek, Gerald F.; Morgan, Benjamin A.

    2001-01-01

    During the rainstorm of June 27, 1995, roughly 330-750 mm of rain fell within a sixteen-hour period, initiating floods and over 600 debris flows in a small area (130 km2) of Madison County, Virginia. Field studies showed that the majority (70%) of these debris flows initiated with a thickness of 0.5 to 3.0 m in colluvium on slopes from 17 o to 41 o (Wieczorek et al., 2000). This paper evaluated and compared the approaches of SINMAP, LISA, and Iverson's (2000) transient response model for slope stability analysis by applying each model to the landslide data from Madison County. Of these three stability models, only Iverson's transient response model evaluated stability conditions as a function of time and depth. Iverson?s model would be the preferred method of the three models to evaluate landslide hazards on a regional scale in areas prone to rain-induced landslides as it considers both the transient and spatial response of pore pressure in its calculation of slope stability. The stability calculation used in SINMAP and LISA is similar and utilizes probability distribution functions for certain parameters. Unlike SINMAP that only considers soil cohesion, internal friction angle and rainfall-rate distributions, LISA allows the use of distributed data for all parameters, so it is the preferred model to evaluate slope stability over SINMAP. Results from all three models suggested similar soil and hydrologic properties for triggering the landslides that occurred during the 1995 storm in Madison County, Virginia. The colluvium probably had cohesion of less than 2KPa. The root-soil system is above the failure plane and consequently root strength and tree surcharge had negligible effect on slope stability. The result that the final location of the water table was near the ground surface is supported by the water budget analysis of the rainstorm conducted by Smith et al. (1996).

  9. Comparative Analysis of Modeling Studies on China's Future Energy and Emissions Outlook

    SciTech Connect

    Zheng, Nina; Zhou, Nan; Fridley, David

    2010-09-01

    The past decade has seen the development of various scenarios describing long-term patterns of future Greenhouse Gas (GHG) emissions, with each new approach adding insights to our understanding of the changing dynamics of energy consumption and aggregate future energy trends. With the recent growing focus on China's energy use and emission mitigation potential, a range of Chinese outlook models have been developed across different institutions including in China's Energy Research Institute's 2050 China Energy and CO2 Emissions Report, McKinsey & Co's China's Green Revolution report, the UK Sussex Energy Group and Tyndall Centre's China's Energy Transition report, and the China-specific section of the IEA World Energy Outlook 2009. At the same time, the China Energy Group at Lawrence Berkeley National Laboratory (LBNL) has developed a bottom-up, end-use energy model for China with scenario analysis of energy and emission pathways out to 2050. A robust and credible energy and emission model will play a key role in informing policymakers by assessing efficiency policy impacts and understanding the dynamics of future energy consumption and energy saving and emission reduction potential. This is especially true for developing countries such as China, where uncertainties are greater while the economy continues to undergo rapid growth and industrialization. A slightly different assumption or storyline could result in significant discrepancies among different model results. Therefore, it is necessary to understand the key models in terms of their scope, methodologies, key driver assumptions and the associated findings. A comparative analysis of LBNL's energy end-use model scenarios with the five above studies was thus conducted to examine similarities and divergences in methodologies, scenario storylines, macroeconomic drivers and assumptions as well as aggregate energy and emission scenario results. Besides directly tracing different energy and CO{sub 2} savings potential

  10. Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements.

    PubMed

    Müller, Ferenc; Blader, Patrick; Strähle, Uwe

    2002-06-01

    Homology searches between DNA sequences of evolutionary distant species (phylogenetic footprinting) offer a fast detection method for regulatory sequences. Because of the small size of their genomes, tetraodontid species such as the Japanese pufferfish and green spotted pufferfish have become attractive models for comparative genomics. A disadvantage of the tetraodontid species is, however, that they cannot be bred and manipulated routinely under laboratory conditions, so these species are less attractive for developmental and genetic analysis. In contrast, an increasing arsenal of transgene techniques with the developmental model species zebrafish and medaka are being used for functional analysis of cis regulatory sequences. The main disadvantage is the much larger genome. While comparison between many loci proved the suitability of phylogenetic footprinting using fish and mammalian sequences, fast rate of change in enhancer structure and gene duplication within teleosts may obscure detection of homologies. Here we discuss the contribution and potentials provided by different teleost models for the detection and functional analysis of conserved cis-regulatory elements. PMID:12111739

  11. Modelling submerged coastal environments: Remote sensing technologies, techniques, and comparative analysis

    NASA Astrophysics Data System (ADS)

    Dillon, Chris

    Built upon remote sensing and GIS littoral zone characterization methodologies of the past decade, a series of loosely coupled models aimed to test, compare and synthesize multi-beam SONAR (MBES), Airborne LiDAR Bathymetry (ALB), and satellite based optical data sets in the Gulf of St. Lawrence, Canada, eco-region. Bathymetry and relative intensity metrics for the MBES and ALB data sets were run through a quantitative and qualitative comparison, which included outputs from the Benthic Terrain Modeller (BTM) tool. Substrate classification based on relative intensities of respective data sets and textural indices generated using grey level co-occurrence matrices (GLCM) were investigated. A spatial modelling framework built in ArcGIS(TM) for the derivation of bathymetric data sets from optical satellite imagery was also tested for proof of concept and validation. Where possible, efficiencies and semi-automation for repeatable testing was achieved using ArcGIS(TM) ModelBuilder. The findings from this study could assist future decision makers in the field of coastal management and hydrographic studies. Keywords: Seafloor terrain characterization, Benthic Terrain Modeller (BTM), Multi-beam SONAR, Airborne LiDAR Bathymetry, Satellite Derived Bathymetry, ArcGISTM ModelBuilder, Textural analysis, Substrate classification.

  12. Badminton instructional in Malaysian schools: a comparative analysis of TGfU and SDT pedagogical models.

    PubMed

    Nathan, Sanmuga

    2016-01-01

    Model based physical education curriculum of Teaching Games for Understanding (TGfU) is still at early stage of implementation in Malaysian schools whereby the technical or skill-led model continues to dominate the physical education curriculum. Implementing TGfU seems to be problematic and untested in this environment. Therefore, this study examined, the effects that a revised model of TGfU compared to Skill Drill Technical (SDT) a technical model had on learning movement skills in Badminton, including returning to base, decision making and skill execution whilst performing in a doubles game play and also explored teachers' perceptions of navigating between the two models. Participants aged 15.5 ± 1.0 years, N = 32, school Badminton players were randomly selected and assigned equally into groups of TGfU and SDT. Reflective data was gathered from two experienced physical education teachers who were involved in this study. Findings indicated for movement to the base in doubles game play indicated significant improvement, after intervention via TGfU. As for decision-making and skill execution in doubles game play, analysis revealed no significant difference after intervention. Findings from teachers reflection, indicated the importance of mini game play in both TGfU and SDT models, as the students enjoyed, and built up positive attitudes for both winning or losing in game situations. However, when negotiating the TGfU model, the teacher found it difficult at times to execute the pedagogical model, as students needed guidance to discuss aspects related to tactics. However, to keep this pedagogical model viable further research findings ought to be circulated among teachers in Malaysia and similar Southeast Asian counties. PMID:27516953

  13. Comparing the Fit of Item Response Theory and Factor Analysis Models

    ERIC Educational Resources Information Center

    Maydeu-Olivares, Alberto; Cai, Li; Hernandez, Adolfo

    2011-01-01

    Linear factor analysis (FA) models can be reliably tested using test statistics based on residual covariances. We show that the same statistics can be used to reliably test the fit of item response theory (IRT) models for ordinal data (under some conditions). Hence, the fit of an FA model and of an IRT model to the same data set can now be…

  14. Computer-Aided Modelling and Analysis of PV Systems: A Comparative Study

    PubMed Central

    Koukouvaos, Charalambos

    2014-01-01

    Modern scientific advances have enabled remarkable efficacy for photovoltaic systems with regard to the exploitation of solar energy, boosting them into having a rapidly growing position among the systems developed for the production of renewable energy. However, in many cases the design, analysis, and control of photovoltaic systems are tasks which are quite complex and thus difficult to be carried out. In order to cope with this kind of problems, appropriate software tools have been developed either as standalone products or parts of general purpose software platforms used to model and simulate the generation, transmission, and distribution of solar energy. The utilization of this kind of software tools may be extremely helpful to the successful performance evaluation of energy systems with maximum accuracy and minimum cost in time and effort. The work presented in this paper aims on a first level at the performance analysis of various configurations of photovoltaic systems through computer-aided modelling. On a second level, it provides a comparative evaluation of the credibility of two of the most advanced graphical programming environments, namely, Simulink and LabVIEW, with regard to their application in photovoltaic systems. PMID:24772007

  15. Computer-aided modelling and analysis of PV systems: a comparative study.

    PubMed

    Koukouvaos, Charalambos; Kandris, Dionisis; Samarakou, Maria

    2014-01-01

    Modern scientific advances have enabled remarkable efficacy for photovoltaic systems with regard to the exploitation of solar energy, boosting them into having a rapidly growing position among the systems developed for the production of renewable energy. However, in many cases the design, analysis, and control of photovoltaic systems are tasks which are quite complex and thus difficult to be carried out. In order to cope with this kind of problems, appropriate software tools have been developed either as standalone products or parts of general purpose software platforms used to model and simulate the generation, transmission, and distribution of solar energy. The utilization of this kind of software tools may be extremely helpful to the successful performance evaluation of energy systems with maximum accuracy and minimum cost in time and effort. The work presented in this paper aims on a first level at the performance analysis of various configurations of photovoltaic systems through computer-aided modelling. On a second level, it provides a comparative evaluation of the credibility of two of the most advanced graphical programming environments, namely, Simulink and LabVIEW, with regard to their application in photovoltaic systems.

  16. Comparative Analysis of Global Digital Elevation Models and Ultra-Prominent Mountain Peaks

    NASA Astrophysics Data System (ADS)

    Grohmann, Carlos H.

    2016-06-01

    Global Digital Elevation Models (GDEMs) are datasets of vital importance for regional-scale analysis in areas such as geomorphology, [paleo]climatology, oceanography and biodiversity. In this work I present a comparative assessment of the datasets ETOPO1 (1' resolution), GTOPO30, GLOBE, SRTM30 PLUS, GMTED2010 and ACE2 (30") against the altitude of the world's ultra prominent peaks. GDEMs' elevations show an expected tendency of underestimating the peak's altitude, but differences reach 3,500 m. None of the GDEMs captures the full range of elevation on Earth and they do not represent well the altitude of the most prominent peaks. Some of these problems could be addressed with the release of NASADEM, but the smoothing effect caused by moving-window resampling can only be tackled by using new techniques, such as scale-adaptative kernels and curvature-based terrain generalisation.

  17. Comparative analysis of economic models in selected solar energy computer programs

    NASA Astrophysics Data System (ADS)

    Powell, J. W.; Barnes, K. A.

    1982-01-01

    The economic evaluation models in five computer programs widely used for analyzing solar energy systems (F-CHART 3.0, F-CHART 4.0, SOLCOST, BLAST, and DOE-2) are compared. Differences in analysis techniques and assumptions among the programs are assessed from the point of view of consistency with the Federal requirements for life cycle costing (10 CFR Part 436), effect on predicted economic performance, and optimal system size, case of use, and general applicability to diverse systems types and building types. The FEDSOL program developed by the National Bureau of Standards specifically to meet the Federal life cycle cost requirements serves as a basis for the comparison. Results of the study are illustrated in test cases of two different types of Federally owned buildings: a single family residence and a low rise office building.

  18. Comparative Analysis of Smart Meters Deployment Business Models on the Example of the Russian Federation Markets

    NASA Astrophysics Data System (ADS)

    Daminov, Ildar; Tarasova, Ekaterina; Andreeva, Tatyana; Avazov, Artur

    2016-02-01

    This paper presents the comparison of smart meter deployment business models to determine the most suitable option providing smart meters deployment. Authors consider 3 main business model of companies: distribution grid company, energy supplier (energosbyt) and metering company. The goal of the article is to compare the business models of power companies from massive smart metering roll out in power system of Russian Federation.

  19. Comparative analysis of autophagy and tauopathy related markers in cerebral ischemia and Alzheimer's disease animal models.

    PubMed

    Villamil-Ortiz, Javier G; Cardona-Gomez, Gloria P

    2015-01-01

    Alzheimer's disease (AD) and cerebral ischemia (CI) are neuropathologies that are characterized by aggregates of tau protein, a hallmark of cognitive disorder and dementia. Protein accumulation can be induced by autophagic failure. Autophagy is a metabolic pathway involved in the homeostatic recycling of cellular components. However, the role of autophagy in those tauopathies remains unclear. In this study, we performed a comparative analysis to identify autophagy related markers in tauopathy generated by AD and CI during short-term, intermediate, and long-term progression using the 3xTg-AD mouse model (aged 6,12, and 18 months) and the global CI 2-VO (2-Vessel Occlusion) rat model (1,15, and 30 days post-ischemia). Our findings confirmed neuronal loss and hyperphosphorylated tau aggregation in the somatosensory cortex (SS-Cx) of the 3xTg-AD mice in the late stage (aged 18 months), which was supported by a failure in autophagy. These results were in contrast to those obtained in the SS-Cx of the CI rats, in which we detected neuronal loss and tauopathy at 1 and 15 days post-ischemia, and this phenomenon was reversed at 30 days. We proposed that this phenomenon was associated with autophagy induction in the late stage, since the data showed a decrease in p-mTOR activity, an association of Beclin-1 and Vps34, a progressive reduction in PHF-1, an increase in LC3B puncta and autophago-lysosomes formation were observed. Furthermore, the survival pathways remained unaffected. Together, our comparative study suggest that autophagy could ameliorates tauopathy in CI but not in AD, suggesting a differential temporal approach to the induction of neuroprotection and the prevention of neurodegeneration.

  20. COMPARING THE UTILITY OF MULTIMEDIA MODELS FOR HUMAN AND ECOLOGICAL EXPOSURE ANALYSIS: TWO CASES

    EPA Science Inventory

    A number of models are available for exposure assessment; however, few are used as tools for both human and ecosystem risks. This discussion will consider two modeling frameworks that have recently been used to support human and ecological decision making. The study will compare ...

  1. Regional disaster impact analysis: comparing input-output and computable general equilibrium models

    NASA Astrophysics Data System (ADS)

    Koks, Elco E.; Carrera, Lorenzo; Jonkeren, Olaf; Aerts, Jeroen C. J. H.; Husby, Trond G.; Thissen, Mark; Standardi, Gabriele; Mysiak, Jaroslav

    2016-08-01

    A variety of models have been applied to assess the economic losses of disasters, of which the most common ones are input-output (IO) and computable general equilibrium (CGE) models. In addition, an increasing number of scholars have developed hybrid approaches: one that combines both or either of them in combination with noneconomic methods. While both IO and CGE models are widely used, they are mainly compared on theoretical grounds. Few studies have compared disaster impacts of different model types in a systematic way and for the same geographical area, using similar input data. Such a comparison is valuable from both a scientific and policy perspective as the magnitude and the spatial distribution of the estimated losses are born likely to vary with the chosen modelling approach (IO, CGE, or hybrid). Hence, regional disaster impact loss estimates resulting from a range of models facilitate better decisions and policy making. Therefore, this study analyses the economic consequences for a specific case study, using three regional disaster impact models: two hybrid IO models and a CGE model. The case study concerns two flood scenarios in the Po River basin in Italy. Modelling results indicate that the difference in estimated total (national) economic losses and the regional distribution of those losses may vary by up to a factor of 7 between the three models, depending on the type of recovery path. Total economic impact, comprising all Italian regions, is negative in all models though.

  2. Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus*

    PubMed Central

    Morais-Silva, Fabio O; Rezende, Antonio Mauro; Pimentel, Catarina; Santos, Catia I; Clemente, Carla; Varela–Raposo, Ana; Resende, Daniela M; da Silva, Sofia M; de Oliveira, Luciana Márcia; Matos, Marcia; Costa, Daniela A; Flores, Orfeu; Ruiz, Jerónimo C; Rodrigues-Pousada, Claudina

    2014-01-01

    Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh. PMID:25055974

  3. [Comparative analysis of soil organic matter content based on different hyperspectral inversion models].

    PubMed

    Luan, Fu-Ming; Zhang, Xiao-Lei; Xiong, Hei-Gang; Zhang, Fang; Wang, Fang

    2013-01-01

    The present paper, based on the Qitai county of Xinjiang, selected 40 soil samples, and used two methods respectively, i.e. multiple linear stepwise regression (MLSR) and artificial neural network (ANNs), to establish the inversion and predieting model of soil organic matter (SOM) content and the model test from measured reflectance spectra and relative test were carried through to the models. Through quantitative analysis, the conclusions can be drawn as follows that the precision values of the different models vary from one to another, the model fitting effects order from high to low is that the integrated model for artificial neural networks (ANNs) is best, single artificial neural networks (ANNs) model is better, while stepwise multiple regression (MLSR) models are worse. Artificial neural networks (ANNs) has the strong abilities of linear and nonlinear approximation, while its integrated model for artificial neural networks (ANNs) is an important way to improve the inversion accuracy of soil organic matter (SOM) content, with the correlation coefficient up to 0.938, root mean square error and total root mean square error are minimum, being 2.13 and 1.404 respectively, and the predictive ability of the soil organic matter (SOM) content are very close to the measured spectrum, so the analysis results can achieve a more practical prediction accuracy for the best fitting model.

  4. Recent results on the spatiotemporal modelling and comparative analysis of Black Death and bubonic plague epidemics

    USGS Publications Warehouse

    Christakos, G.; Olea, R.A.; Yu, H.-L.

    2007-01-01

    Background: This work demonstrates the importance of spatiotemporal stochastic modelling in constructing maps of major epidemics from fragmentary information, assessing population impacts, searching for possible etiologies, and performing comparative analysis of epidemics. Methods: Based on the theory previously published by the authors and incorporating new knowledge bases, informative maps of the composite space-time distributions were generated for important characteristics of two major epidemics: Black Death (14th century Western Europe) and bubonic plague (19th-20th century Indian subcontinent). Results: The comparative spatiotemporal analysis of the epidemics led to a number of interesting findings: (1) the two epidemics exhibited certain differences in their spatiotemporal characteristics (correlation structures, trends, occurrence patterns and propagation speeds) that need to be explained by means of an interdisciplinary effort; (2) geographical epidemic indicators confirmed in a rigorous quantitative manner the partial findings of isolated reports and time series that Black Death mortality was two orders of magnitude higher than that of bubonic plague; (3) modern bubonic plague is a rural disease hitting harder the small villages in the countryside whereas Black Death was a devastating epidemic that indiscriminately attacked large urban centres and the countryside, and while the epidemic in India lasted uninterruptedly for five decades, in Western Europe it lasted three and a half years; (4) the epidemics had reverse areal extension features in response to annual seasonal variations. Temperature increase at the end of winter led to an expansion of infected geographical area for Black Death and a reduction for bubonic plague, reaching a climax at the end of spring when the infected area in Western Europe was always larger than in India. Conversely, without exception, the infected area during winter was larger for the Indian bubonic plague; (5) during the

  5. Comparative analysis of dayside magnetic reconnection models in global magnetosphere simulations

    NASA Astrophysics Data System (ADS)

    Komar, C. M.; Fermo, R. L.; Cassak, P. A.

    2015-01-01

    We test and compare a number of existing models predicting the location of magnetic reconnection at Earth's dayside magnetopause for various solar wind conditions. We employ robust image processing techniques to determine the locations where each model predicts reconnection to occur. The predictions are then compared to the magnetic separators, the magnetic field lines separating different magnetic topologies. The predictions are tested in distinct high-resolution simulations with interplanetary magnetic field (IMF) clock angles ranging from 30 to 165° in global magnetohydrodynamic simulations using the three-dimensional Block Adaptive Tree Solarwind Roe-type Upwind Scheme code with a uniform resistivity, although the described techniques can be generally applied to any self-consistent magnetosphere code. Additional simulations are carried out to test location model dependence on IMF strength and dipole tilt. We find that most of the models match large portions of the magnetic separators when the IMF has a southward component, with the models saying reconnection occurs where the local reconnection rate and reconnection outflow speed are maximized performing best. When the IMF has a northward component, none of the models tested faithfully map the entire magnetic separator, but the maximum magnetic shear model is the best at mapping the separator in the cusp region where reconnection has been observed. Predictions for some models with northward IMF orientations improve after accounting for plasma flow shear parallel to the reconnecting components of the magnetic fields. Implications for observations are discussed.

  6. A Comparative Analysis of Spatial Visualization Ability and Drafting Models for Industrial and Technology Education Students

    ERIC Educational Resources Information Center

    Katsioloudis, Petros; Jovanovic, Vukica; Jones, Mildred

    2014-01-01

    The main purpose of this study was to determine significant positive effects among the use of three different types of drafting models, and to identify whether any differences exist towards promotion of spatial visualization ability for students in Industrial Technology and Technology Education courses. In particular, the study compared the use of…

  7. Comparative analysis of some models of gene regulation in mixed-substrate microbial growth.

    PubMed

    Narang, Atul

    2006-09-21

    Mixed-substrate microbial growth is of fundamental interest in microbiology and bioengineering. Several mathematical models have been developed to account for the genetic regulation of such systems, especially those resulting in diauxic growth. In this work, we compare the dynamics of three such models (Narang, 1998a. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species. Biotechnol. Bioeng. 59, 116-121; Thattai and Shraiman, 2003. Metabolic switching in the sugar phosphotransferase system of Escherichia coli. Biophys. J. 85(2), 744-754; Brandt et al., 2004. Modelling microbial adaptation to changing availability of substrates. Water Res. 38, 1004-1013). We show that these models are dynamically similar--the initial motion of the inducible enzymes in all the models is described by the Lotka-Volterra equations for competing species. In particular, the prediction of diauxic growth corresponds to "extinction" of one of the enzymes during the first few hours of growth. The dynamic similarity occurs because in all the models, the inducible enzymes possess properties characteristic of competing species: they are required for their own synthesis, and they inhibit each other. Despite this dynamic similarity, the models vary with respect to the range of dynamics captured. The Brandt et al. model always predicts the diauxic growth pattern, whereas the remaining two models exhibit both diauxic and non-diauxic growth patterns. The models also differ with respect to the mechanisms that generate the mutual inhibition between the enzymes. In the Narang model, mutual inhibition occurs because the enzymes for each substrate enhance the dilution of the enzymes for the other substrate. The Brandt et al. model superimposes upon this dilution effect an additional mechanism of mutual inhibition. In the Thattai and Shraiman model, the mutual inhibition is entirely due to competition for the phosphoryl groups. For quantitative

  8. Modelling formulations using gene expression programming--a comparative analysis with artificial neural networks.

    PubMed

    Colbourn, E A; Roskilly, S J; Rowe, R C; York, P

    2011-10-01

    This study has investigated the utility and potential advantages of gene expression programming (GEP)--a new development in evolutionary computing for modelling data and automatically generating equations that describe the cause-and-effect relationships in a system--to four types of pharmaceutical formulation and compared the models with those generated by neural networks, a technique now widely used in the formulation development. Both methods were capable of discovering subtle and non-linear relationships within the data, with no requirement from the user to specify the functional forms that should be used. Although the neural networks rapidly developed models with higher values for the ANOVA R(2) these were black box and provided little insight into the key relationships. However, GEP, although significantly slower at developing models, generated relatively simple equations describing the relationships that could be interpreted directly. The results indicate that GEP can be considered an effective and efficient modelling technique for formulation data.

  9. The Effectiveness of Physical Models in Teaching Anatomy: A Meta-Analysis of Comparative Studies

    ERIC Educational Resources Information Center

    Yammine, Kaissar; Violato, Claudio

    2016-01-01

    There are various educational methods used in anatomy teaching. While three dimensional (3D) visualization technologies are gaining ground due to their ever-increasing realism, reports investigating physical models as a low-cost 3D traditional method are still the subject of considerable interest. The aim of this meta-analysis is to quantitatively…

  10. A comparative analysis of radiobiological models for cell surviving fractions at high doses.

    PubMed

    Andisheh, B; Edgren, M; Belkić, Dž; Mavroidis, P; Brahme, A; Lind, B K

    2013-04-01

    For many years the linear-quadratic (LQ) model has been widely used to describe the effects of total dose and dose per fraction at low-to-intermediate doses in conventional fractionated radiotherapy. Recent advances in stereotactic radiosurgery (SRS) and stereotactic radiotherapy (SRT) have increased the interest in finding a reliable cell survival model, which will be accurate at high doses, as well. Different models have been proposed for improving descriptions of high dose survival responses, such as the Universal Survival Curve (USC), the Kavanagh-Newman (KN) and several generalizations of the LQ model, e.g. the Linear-Quadratic-Linear (LQL) model and the Pade Linear Quadratic (PLQ) model. The purpose of the present study is to compare a number of models in order to find the best option(s) which could successfully be used as a fractionation correction method in SRT. In this work, six independent experimental data sets were used: CHOAA8 (Chinese hamster fibroblast), H460 (non-small cell lung cancer, NSLC), NCI-H841 (small cell lung cancer, SCLC), CP3 and DU145 (human prostate carcinoma cell lines) and U1690 (SCLC). By detailed comparisons with these measurements, the performance of nine different radiobiological models was examined for the entire dose range, including high doses beyond the shoulder of the survival curves. Using the computed and measured cell surviving fractions, comparison of the goodness-of-fit for all the models was performed by means of the reduced χ (2)-test with a 95% confidence interval. The obtained results indicate that models with dose-independent final slopes and extrapolation numbers generally represent better choices for SRT. This is especially important at high doses where the final slope and extrapolation numbers are presently found to play a major role. The PLQ, USC and LQL models have the least number of shortcomings at all doses. The extrapolation numbers and final slopes of these models do not depend on dose. Their asymptotes

  11. A comparative analysis of 9 multi-model averaging approaches in hydrological continuous streamflow simulation

    NASA Astrophysics Data System (ADS)

    Arsenault, Richard; Gatien, Philippe; Renaud, Benoit; Brissette, François; Martel, Jean-Luc

    2015-10-01

    This study aims to test whether a weighted combination of several hydrological models can simulate flows more accurately than the models taken individually. In addition, the project attempts to identify the most efficient model averaging method and the optimal number of models to include in the weighting scheme. In order to address the first objective, streamflow was simulated using four lumped hydrological models (HSAMI, HMETS, MOHYSE and GR4J-6), each of which were calibrated with three different objective functions on 429 watersheds. The resulting 12 hydrographs (4 models × 3 metrics) were weighted and combined with the help of 9 averaging methods which are the simple arithmetic mean (SAM), Akaike information criterion (AICA), Bates-Granger (BGA), Bayes information criterion (BICA), Bayesian model averaging (BMA), Granger-Ramanathan average variant A, B and C (GRA, GRB and GRC) and the average by SCE-UA optimization (SCA). The same weights were then applied to the hydrographs in validation mode, and the Nash-Sutcliffe Efficiency metric was measured between the averaged and observed hydrographs. Statistical analyses were performed to compare the accuracy of weighted methods to that of individual models. A Kruskal-Wallis test and a multi-objective optimization algorithm were then used to identify the most efficient weighted method and the optimal number of models to integrate. Results suggest that the GRA, GRB, GRC and SCA weighted methods perform better than the individual members. Model averaging from these four methods were superior to the best of the individual members in 76% of the cases. Optimal combinations on all watersheds included at least one of each of the four hydrological models. None of the optimal combinations included all members of the ensemble of 12 hydrographs. The Granger-Ramanathan average variant C (GRC) is recommended as the best compromise between accuracy, speed of execution, and simplicity.

  12. Comparing proportional hazards and accelerated failure time models for survival analysis.

    PubMed

    Orbe, Jesus; Ferreira, Eva; Núñez-Antón, Vicente

    2002-11-30

    This paper describes a method proposed for a censored linear regression model that can be used in the context of survival analysis. The method has the important characteristic of allowing estimation and inference without knowing the distribution of the duration variable. Moreover, it does not need the assumption of proportional hazards. Therefore, it can be an interesting alternative to the Cox proportional hazards models when this assumption does not hold. In addition, implementation and interpretation of the results is simple. In order to analyse the performance of this methodology, we apply it to two real examples and we carry out a simulation study. We present its results together with those obtained with the traditional Cox model and AFT parametric models. The new proposal seems to lead to more precise results.

  13. Color model comparative analysis for breast cancer diagnosis using H and E stained images

    NASA Astrophysics Data System (ADS)

    Li, Xingyu; Plataniotis, Konstantinos N.

    2015-03-01

    Digital cancer diagnosis is a research realm where signal processing techniques are used to analyze and to classify color histopathology images. Different from grayscale image analysis of magnetic resonance imaging or X-ray, colors in histopathology images convey large amount of histological information and thus play significant role in cancer diagnosis. Though color information is widely used in histopathology works, as today, there is few study on color model selections for feature extraction in cancer diagnosis schemes. This paper addresses the problem of color space selection for digital cancer classification using H and E stained images, and investigates the effectiveness of various color models (RGB, HSV, CIE L*a*b*, and stain-dependent H and E decomposition model) in breast cancer diagnosis. Particularly, we build a diagnosis framework as a comparison benchmark and take specific concerns of medical decision systems into account in evaluation. The evaluation methodologies include feature discriminate power evaluation and final diagnosis performance comparison. Experimentation on a publicly accessible histopathology image set suggests that the H and E decomposition model outperforms other assessed color spaces. For reasons behind various performance of color spaces, our analysis via mutual information estimation demonstrates that color components in the H and E model are less dependent, and thus most feature discriminate power is collected in one channel instead of spreading out among channels in other color spaces.

  14. Comparative analysis of data collection methods for individualized modeling of radiologists' visual similarity judgments

    SciTech Connect

    Tourassi, Georgia; Xu, Songhua; Yoon, Hong-Jun; Morin-Ducote, Garnetta; Hudson, Kathy

    2013-01-01

    Rationale and Objectives: We conducted an observer study to investigate how the data collection method affects the efficacy of modeling individual radiologists judgments regarding the perceptual similarity of breast masses on mammograms. Materials and Methods: Institutional review board approval was obtained prior to the study. Six observers of variable experience levels in breast imaging were recruited to assess the perceptual similarity of mammographic masses. The observers subjective judgments were collected using: (i) a rating method, (ii) a preference method, and (iii) a hybrid method combining rating and ranking. Personalized user models were developed with the collected data to predict observers opinions. The relative efficacy of each data collection method was assessed based on the classification accuracy of the resulting user models. Results: The hybrid data collection method produced significantly more accurate individualized user models of perceptual opinions with comparable and sometimes better time efficiency than the other two data collection methods. The user models derived from hybrid data were clearly superior even when developed with a dramatically smaller number of training cases. Conclusions: A hybrid method combining rating and ranking is an intuitive and efficient way for collecting subjective similarity judgments to model human perceptual opinions with a higher accuracy than other more commonly used data collection methods.

  15. On biodiversity in river networks: A trade-off metapopulation model and comparative analysis

    NASA Astrophysics Data System (ADS)

    Muneepeerakul, R.; Levin, S. A.; Rinaldo, A.; Rodriguez-Iturbe, I.

    2007-07-01

    A discrete, structured metapopulation model is coupled with the strictly hierarchical competition-colonization trade-off model, in which competitively superior species have lower fecundity rates and thus lower colonizing ability, to study the resulting biodiversity patterns in river networks. These patterns are then compared with those resulting from the neutral dynamics, in which every species has the same fecundity rate and is competitively equivalent at a per capita level. Significant differences exist between riparian biodiversity patterns and those predicted by theories developed for two-dimensional landscapes. We find that dispersal directionality and network structure promote species that produce a large number of propagules at a species level; such species are considered competitively superior in the neutral model and inferior in the trade-off model. As a result, the two key characteristics of riparian systems, dispersal directionality and network structure, lead to lower and higher overall γ diversity in the former and the latter models, respectively. The network structure, through the containment effect due to limited cross-basin dispersal, always leads to higher between-community, β diversity. The spatial distribution of local, α diversity becomes heterogeneous and thus important under directional dispersal and network structure. A higher degree of dividedness results in higher γ diversity for communities obeying both neutral and trade-off models, but the increase is more dramatic in the latter.

  16. Eliciting mixed emotions: a meta-analysis comparing models, types, and measures.

    PubMed

    Berrios, Raul; Totterdell, Peter; Kellett, Stephen

    2015-01-01

    The idea that people can experience two oppositely valenced emotions has been controversial ever since early attempts to investigate the construct of mixed emotions. This meta-analysis examined the robustness with which mixed emotions have been elicited experimentally. A systematic literature search identified 63 experimental studies that instigated the experience of mixed emotions. Studies were distinguished according to the structure of the underlying affect model-dimensional or discrete-as well as according to the type of mixed emotions studied (e.g., happy-sad, fearful-happy, positive-negative). The meta-analysis using a random-effects model revealed a moderate to high effect size for the elicitation of mixed emotions (d IG+ = 0.77), which remained consistent regardless of the structure of the affect model, and across different types of mixed emotions. Several methodological and design moderators were tested. Studies using the minimum index (i.e., the minimum value between a pair of opposite valenced affects) resulted in smaller effect sizes, whereas subjective measures of mixed emotions increased the effect sizes. The presence of more women in the samples was also associated with larger effect sizes. The current study indicates that mixed emotions are a robust, measurable and non-artifactual experience. The results are discussed in terms of the implications for an affect system that has greater versatility and flexibility than previously thought. PMID:25926805

  17. Comparative Analysis of Pain Behaviours in Humanized Mouse Models of Sickle Cell Anemia.

    PubMed

    Lei, Jianxun; Benson, Barbara; Tran, Huy; Ofori-Acquah, Solomon F; Gupta, Kalpna

    2016-01-01

    Pain is a hallmark feature of sickle cell anemia (SCA) but management of chronic as well as acute pain remains a major challenge. Mouse models of SCA are essential to examine the mechanisms of pain and develop novel therapeutics. To facilitate this effort, we compared humanized homozygous BERK and Townes sickle mice for the effect of gender and age on pain behaviors. Similar to previously characterized BERK sickle mice, Townes sickle mice show more mechanical, thermal, and deep tissue hyperalgesia with increasing age. Female Townes sickle mice demonstrate more hyperalgesia compared to males similar to that reported for BERK mice and patients with SCA. Mechanical, thermal and deep tissue hyperalgesia increased further after hypoxia/reoxygenation (H/R) treatment in Townes sickle mice. Together, these data show BERK sickle mice exhibit a significantly greater degree of hyperalgesia for all behavioral measures as compared to gender- and age-matched Townes sickle mice. However, the genetically distinct "knock-in" strategy of human α and β transgene insertion in Townes mice as compared to BERK mice, may provide relative advantage for further genetic manipulations to examine specific mechanisms of pain. PMID:27494522

  18. Comparative Analysis of Pain Behaviours in Humanized Mouse Models of Sickle Cell Anemia

    PubMed Central

    Lei, Jianxun; Benson, Barbara; Tran, Huy; Ofori-Acquah, Solomon F.; Gupta, Kalpna

    2016-01-01

    Pain is a hallmark feature of sickle cell anemia (SCA) but management of chronic as well as acute pain remains a major challenge. Mouse models of SCA are essential to examine the mechanisms of pain and develop novel therapeutics. To facilitate this effort, we compared humanized homozygous BERK and Townes sickle mice for the effect of gender and age on pain behaviors. Similar to previously characterized BERK sickle mice, Townes sickle mice show more mechanical, thermal, and deep tissue hyperalgesia with increasing age. Female Townes sickle mice demonstrate more hyperalgesia compared to males similar to that reported for BERK mice and patients with SCA. Mechanical, thermal and deep tissue hyperalgesia increased further after hypoxia/reoxygenation (H/R) treatment in Townes sickle mice. Together, these data show BERK sickle mice exhibit a significantly greater degree of hyperalgesia for all behavioral measures as compared to gender- and age-matched Townes sickle mice. However, the genetically distinct “knock-in” strategy of human α and β transgene insertion in Townes mice as compared to BERK mice, may provide relative advantage for further genetic manipulations to examine specific mechanisms of pain. PMID:27494522

  19. NAS Demand Predictions, Transportation Systems Analysis Model (TSAM) Compared with Other Forecasts

    NASA Technical Reports Server (NTRS)

    Viken, Jeff; Dollyhigh, Samuel; Smith, Jeremy; Trani, Antonio; Baik, Hojong; Hinze, Nicholas; Ashiabor, Senanu

    2006-01-01

    The current work incorporates the Transportation Systems Analysis Model (TSAM) to predict the future demand for airline travel. TSAM is a multi-mode, national model that predicts the demand for all long distance travel at a county level based upon population and demographics. The model conducts a mode choice analysis to compute the demand for commercial airline travel based upon the traveler s purpose of the trip, value of time, cost and time of the trip,. The county demand for airline travel is then aggregated (or distributed) to the airport level, and the enplanement demand at commercial airports is modeled. With the growth in flight demand, and utilizing current airline flight schedules, the Fratar algorithm is used to develop future flight schedules in the NAS. The projected flights can then be flown through air transportation simulators to quantify the ability of the NAS to meet future demand. A major strength of the TSAM analysis is that scenario planning can be conducted to quantify capacity requirements at individual airports, based upon different future scenarios. Different demographic scenarios can be analyzed to model the demand sensitivity to them. Also, it is fairly well know, but not well modeled at the airport level, that the demand for travel is highly dependent on the cost of travel, or the fare yield of the airline industry. The FAA projects the fare yield (in constant year dollars) to keep decreasing into the future. The magnitude and/or direction of these projections can be suspect in light of the general lack of airline profits and the large rises in airline fuel cost. Also, changes in travel time and convenience have an influence on the demand for air travel, especially for business travel. Future planners cannot easily conduct sensitivity studies of future demand with the FAA TAF data, nor with the Boeing or Airbus projections. In TSAM many factors can be parameterized and various demand sensitivities can be predicted for future travel. These

  20. Comparative analysis for various redox flow batteries chemistries using a cost performance model

    SciTech Connect

    Crawford, Aladsair J.; Viswanathan, Vilayanur V.; Stephenson, David E.; Wang, Wei; Thomsen, Edwin C.; Reed, David M.; Li, Bin; Balducci, Patrick J.; Kintner-Meyer, Michael CW; Sprenkle, Vincent L.

    2015-10-20

    A robust performance-based cost model is developed for all-vanadium, iron-vanadium and iron chromium redox flow batteries. Systems aspects such as shunt current losses, pumping losses and thermal management are accounted for. The objective function, set to minimize system cost, allows determination of stack design and operating parameters such as current density, flow rate and depth of discharge (DOD). Component costs obtained from vendors are used to calculate system costs for various time frames. A 2 kW stack data was used to estimate unit energy costs and compared with model estimates for the same size electrodes. The tool has been shared with the redox flow battery community to both validate their stack data and guide future direction.

  1. A novel model-gel-tissue assay analysis for comparing tumor elastic properties to collagen content.

    PubMed

    Barnes, Stephanie L; Young, Pampee P; Miga, Michael I

    2009-08-01

    In previous work, a new assay was realized for determining soft-tissue mechanical properties. The method, named the model-gel-tissue (MGT) assay, couples material testing with a finite element model built from a micro-CT image acquisition of a gel-embedded tissue specimen to determine its mechanical properties. Given recent reports demonstrating that increased stromal collagen promotes mammary tumor initiation and proliferation, in this paper, the MGT assay is used to evaluate the modulus of murine mammary tumors and is subsequently correlated quantitatively to type I collagen content. In addition, preliminary testing of the assay sensitivity with respect to gel-volume to tissue-mass ratio is reported here. The results demonstrate a strong linear correlation between tumor mechanical properties and collagen content (R (2) = 0.9462). This result is important because mechanical stiffness as provided by the MGT assay is very similar to parameters under clinical investigation using elastographic imaging techniques. The sensitivity tests indicated that an approximate gel-volume to tissue-mass ratio threshold of 16.5 ml g(-1) is needed for successful analysis. This is an important result in that it presents guideline constraints for conducting this analysis.

  2. Eliciting mixed emotions: a meta-analysis comparing models, types, and measures

    PubMed Central

    Berrios, Raul; Totterdell, Peter; Kellett, Stephen

    2015-01-01

    The idea that people can experience two oppositely valenced emotions has been controversial ever since early attempts to investigate the construct of mixed emotions. This meta-analysis examined the robustness with which mixed emotions have been elicited experimentally. A systematic literature search identified 63 experimental studies that instigated the experience of mixed emotions. Studies were distinguished according to the structure of the underlying affect model—dimensional or discrete—as well as according to the type of mixed emotions studied (e.g., happy-sad, fearful-happy, positive-negative). The meta-analysis using a random-effects model revealed a moderate to high effect size for the elicitation of mixed emotions (dIG+ = 0.77), which remained consistent regardless of the structure of the affect model, and across different types of mixed emotions. Several methodological and design moderators were tested. Studies using the minimum index (i.e., the minimum value between a pair of opposite valenced affects) resulted in smaller effect sizes, whereas subjective measures of mixed emotions increased the effect sizes. The presence of more women in the samples was also associated with larger effect sizes. The current study indicates that mixed emotions are a robust, measurable and non-artifactual experience. The results are discussed in terms of the implications for an affect system that has greater versatility and flexibility than previously thought. PMID:25926805

  3. The octopus: a model for a comparative analysis of the evolution of learning and memory mechanisms.

    PubMed

    Hochner, Binyamin; Shomrat, Tal; Fiorito, Graziano

    2006-06-01

    Comparative analysis of brain function in invertebrates with sophisticated behaviors, such as the octopus, may advance our understanding of the evolution of the neural processes that mediate complex behaviors. Until the last few years, this approach was infeasible due to the lack of neurophysiological tools for testing the neural circuits mediating learning and memory in the brains of octopus and other cephalopods. Now, for the first time, the adaptation of modern neurophysiological methods to the study of the central nervous system of the octopus allows this avenue of research. The emerging results suggest that a convergent evolutionary process has led to the selection of vertebrate-like neural organization and activity-dependent long-term synaptic plasticity. As octopuses and vertebrates are very remote phylogenetically, this convergence suggests the importance of the shared properties for the mediation of learning and memory.

  4. How are population-based funding formulae for healthcare composed? A comparative analysis of seven models

    PubMed Central

    2013-01-01

    Background Population-based funding formulae act as an important means of promoting equitable health funding structures. To evaluate how policy makers in different jurisdictions construct health funding formulae and build an understanding of contextual influences underpinning formula construction we carried out a comparative analysis of key components of funding formulae across seven high-income and predominantly publically financed health systems: New Zealand, England, Scotland, the Netherlands, the state of New South Wales in Australia, the Canadian province of Ontario, and the city of Stockholm, Sweden. Methods Core components from each formula were summarised and key similarities and differences evaluated from a compositional perspective. We categorised approaches to constructing funding formulae under three main themes: identifying factors which predict differential need amongst populations; adjusting for cost factors outside of needs factors; and engaging in normative correction of allocations for ‘unmet’ need. Results We found significant congruence in the factors used to guide need and cost adjustments. However, there is considerable variation in interpretation and implementation of these factors. Conclusion Despite broadly similar frameworks, there are distinct differences in the composition of the formulae across the seven health systems. Ultimately, the development of funding formulae is a dynamic process, subject to availability of data reflecting health needs, the influence of wider socio-political objectives and health system determinants. PMID:24209410

  5. Local participation in biodiversity conservation initiatives: a comparative analysis of different models in South East Mexico.

    PubMed

    Méndez-López, María Elena; García-Frapolli, Eduardo; Pritchard, Diana J; Sánchez González, María Consuelo; Ruiz-Mallén, Isabel; Porter-Bolland, Luciana; Reyes-Garcia, Victoria

    2014-12-01

    In Mexico, biodiversity conservation is primarily implemented through three schemes: 1) protected areas, 2) payment-based schemes for environmental services, and 3) community-based conservation, officially recognized in some cases as Indigenous and Community Conserved Areas. In this paper we compare levels of local participation across conservation schemes. Through a survey applied to 670 households across six communities in Southeast Mexico, we document local participation during the creation, design, and implementation of the management plan of different conservation schemes. To analyze the data, we first calculated the frequency of participation at the three different stages mentioned, then created a participation index that characterizes the presence and relative intensity of local participation for each conservation scheme. Results showed that there is a low level of local participation across all the conservation schemes explored in this study. Nonetheless, the payment for environmental services had the highest local participation while the protected areas had the least. Our findings suggest that local participation in biodiversity conservation schemes is not a predictable outcome of a specific (community-based) model, thus implying that other factors might be important in determining local participation. This has implications on future strategies that seek to encourage local involvement in conservation.

  6. Bioinformatics investigation of therapeutic mechanisms of Xuesaitong capsule treating ischemic cerebrovascular rat model with comparative transcriptome analysis

    PubMed Central

    Liao, Jiangquan; Wei, Benjun; Chen, Hengwen; Liu, Yongmei; Wang, Jie

    2016-01-01

    Background: Xuesaitong soft capsule (XST) which consists of panax notoginseng saponin (PNS) has been used to treat ischemic cerebrovascular diseases in China. The therapeutic mechanism of XST has not been elucidated yet from prospective of genomics and bioinformatics. Methods: A transcriptome analysis was performed to review series concerning middle cerebral artery occlusion (MCAO) rat model and XST intervention after MCAO from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were compared between blank group and model group, model group and XST group. Functional enrichment and pathway analysis were performed. Protein-Protein interaction network was constructed. The overlapping genes from two DEGs sets were screened out and profound analysis was performed. Results: Two series including 22 samples were obtained. 870 DEGs were identified between blank group and model group, and 1189 DEGs were identified between model group and XST group. GO terms and KEGG pathways of MCAO and XST intervention were significantly enriched. PPI networks were constructed to demonstrate the gene-gene interactions. The overlapping genes from two DEGs sets were highlighted. ANTXR2, FHL3, PRCP, TYROBP, TAF9B, FGFR2, BCL11B, RB1CC1 and MBNL2 were the pivotal genes and possible action sites of XST therapeutic mechanisms. Conclusion: MCAO is a pathological process with multiple. PMID:27347353

  7. A Technique Using Principal Component Analysis to Compare Seasonal Cycles of Earth Radiation from CERES and Model Computations

    NASA Technical Reports Server (NTRS)

    Smith, G. Louis; Mlynczak, Pamela E.; Potter, Gerald L.

    2012-01-01

    A method for quantitatively comparing the seasonal cycles of two global data sets is presented. The seasonal cycles of absorbed solar radiation (ASR) and outgoing longwave radiation (OLR) have been computed from an eight-year data set from the Clouds and Earth's Radiant Energy System (CERES) scanning radiometers and from a model data set produced by the NASA Goddard Space Flight Center Global Modeling and Assimilation Office. To compare the seasonal cycles from these two data sets, principal component (PC) analysis is used, where the PCs express the time variations and the corresponding empirical orthogonal functions (EOFs) describe the geographic variations. Ocean has a long thermal response time compared to land, so land and ocean are separated for the analysis. The root-mean square values for the seasonal cycles of ASR and OLR are extremely close for the two data sets. The first three PCs are quite close, showing that the time responses and magnitudes over the globe are very similar. The agreement between the two sets of PCs is quantified by computing the matrix of inner products of the two sets. For ASR over land, the first PCs of CERES and the model agree to better than 99.9%. The EOF maps are similar for most of the globe, but differ in a few places, and the agreement of the EOF maps is likewise quantified. Maps of differences between the annual cycles show regions of agreement and disagreement.

  8. Comparative Analysis of the ESA and NASA Interplanetary Meteoroid Enviroment Models

    NASA Astrophysics Data System (ADS)

    Grun, Eberhard; Srama, Ralf; Horanyi, Mihaly; Kruger, Harald; Soja, Rachel; Sterken, Veerle; Sternovsky, Zotan; Strub, Peter

    2013-08-01

    Meteoroid environment models are used to assess the hazard arising from meteoroid impacts onto space structures. We have analyzed the current meteoroid models of ESA (IMEM) and of NASA (MEM). These models are based on different sets of measurements. MEM is based on radar meteor observations, lunar impact cratering rate, and on zodiacal light observations while IMEM is based on orbital element distributions of comets and asteroids, the lunar impact cratering rate, thermal radiation observations, and on in situ dust measurements. Both models describe the cratering flux at 1AU quite well; however, the flux of mm-sized meteoroids differs by a factor two due to the different assumed relative speeds. At other heliocentric distances from Mercury to Mars the predicted fluxes differ by up to 2 orders of magnitude between the two models. The current knowledge of the interplanetary meteoroid environment as exemplified by these meteoroid models is insufficient to provide reliable assessment of the risk of meteoroid impacts for human travel in interplanetary space.

  9. Comparing Categorization Models

    ERIC Educational Resources Information Center

    Rouder, Jeffrey N.; Ratcliff, Roger

    2004-01-01

    Four experiments are presented that competitively test rule- and exemplar-based models of human categorization behavior. Participants classified stimuli that varied on a unidimensional axis into 2 categories. The stimuli did not consistently belong to a category; instead, they were probabilistically assigned. By manipulating these assignment…

  10. Literacy Models and the Reconstruction of History Education: A Comparative Discourse Analysis of Two Lesson Plans

    ERIC Educational Resources Information Center

    Collin, Ross; Reich, Gabriel A.

    2015-01-01

    This article presents discourse analyses of two lesson plans designed for secondary school history classes. Although the plans focus on the same topic, they rely on different models of content area literacy: disciplinary literacy, or reading and writing like experts in a given domain, and critical literacy, or reading and writing to address…

  11. A Comparative Analysis of Point-of-View Modeling for Industrial and Technology Education Courses

    ERIC Educational Resources Information Center

    Katsioloudis, Petros J.; Fantz, Todd D.; Jones, Millie

    2013-01-01

    Enrollment in technology education at the college level has been declining, so it is becoming essential for technology teacher educators to investigate ways to increase the enrollment in their programs. Technology teacher educators are exploring the extent to which distance-learning technologies such as video modeling can be used by industrial and…

  12. Comparative Analysis of Methods to Induce Myocardial Infarction in a Closed-Chest Rabbit Model

    PubMed Central

    Isorni, Marc-Antoine; Casanova, Amaury; Piquet, Julie; Bellamy, Valérie; Pignon, Charly; Puymirat, Etienne; Menasche, Philippe

    2015-01-01

    Objective. To develop a rabbit model of closed-chest catheter-induced myocardial infarction. Background. Limitations of rodent and large animal models justify the search for clinically relevant alternatives. Methods. Microcatheterization of the heart was performed in 47 anesthetized 3-4 kg New Zealand rabbits to test five techniques of myocardial ischemia: free coils (n = 4), interlocking coils (n = 4), thrombogenic gelatin sponge (n = 4), balloon occlusion (n = 4), and alcohol injection (n = 8). In order to limit ventricular fibrillation, an antiarrhythmic protocol was implemented, with beta-blockers/amiodarone before and xylocaine infusion during the procedure. Clinical, angiographic, and echographic data were gathered. End points included demonstration of vessel occlusion (TIMI flow grades 0 and 1 on the angiogram), impairment of left ventricular function at 2 weeks after procedure (by echocardiography), and pathologically confirmed myocardial infarction. Results. The best arterial access was determined to be through the right carotid artery. The internal mammary guiding catheter 4-Fr was selected as the optimal device for selective intracoronary injection. Free coils deployed prematurely and tended to prolapse into the aorta. Interlocking coils did not deploy completely and failed to provide reliable results. Gelatin sponge was difficult to handle, adhered to the catheter, and could not be clearly visualized by fluoroscopy. Balloon occlusion yielded inconsistent results. Alcohol injection was the most efficient and reproducible method for inducing myocardial infarction (4 out of 6 animals), the extent of which could be fine-tuned by using a coaxial balloon catheter as a microcatheter (0.52 mm) to achieve a superselective injection of 0.2 mL of alcohol. This approach resulted in a 20% decrease in LVEF and infarcted myocardium was confirmed histologically. Conclusions. By following a stepwise approach, a minimally invasive, effective, and reproducible

  13. [Comparative analysis of the monopodial and sympodial models of bulb branching in Galanthus L].

    PubMed

    Chub, V V; Kozhevnikova, A D

    2000-01-01

    We have examined sympodial and monopodial models of bulb branching in Galanthus. The issue of the position of the reduced prophyll is discussed. We proposed a method of formal interpretation: parts of the plant were positioned on diagrams; several variants of axial schemes were matched to each diagram; the schemes were divided into two classes, monopodial and sympodial ones, and stability of each class was estimated. In order to decide about the model of Galanthus bulb branching, we have examined plants with additional inflorescences and plants with additional leaf series. We have shown that the sympodial model predicts the presence of the reduced prophyll at the base of the innovation bud in all studied cases. Consecutive stages of prophyll reduction (prophyll of the innovation bud) can be followed in Amaryllidaceae in the following sequence: Zephyranthes, a well-developed large prophyll with green lamina; Vallota, a developed prophyll with reduced green lamina; Haemanthus, a thin chaffy short-living prophyll. At the end of this sequence is Galanthus with completely reduced prophyll at the innovation bud.

  14. Comparative analysis of methods for modeling the penetration and plane-parallel motion of conical projectiles in soil

    NASA Astrophysics Data System (ADS)

    Bazhenov, V. G.; Bragov, A. M.; Konstantinov, A. Yu.; Kotov, V. L.

    2015-05-01

    This paper presents an analysis of the accuracy of known and new modeling methods using the hypothesis of local and plane sections for solution of problems of the impact and plane-parallel motion of conical bodies at an angle to the free surface of the half-space occupied by elastoplastic soil. The parameters of the local interaction model that is quadratic in velocity are determined by solving the one-dimensional problem of the expansion of a spherical cavity. Axisymmetric problems for each of the meridional section are solved simultaneously neglecting mass and momentum transfer in the circumferential direction and using an approach based on the hypothesis of plane sections. The dynamic and kinematic parameters of oblique penetration obtained using modified models are compared with the results of computer simulation in a three-dimensional formulation. The results obtained with regard to the contact stress distribution along the generator of the pointed cone are in satisfactory agreement.

  15. A comparative analysis of island floras challenges taxonomy-based biogeographical models of speciation.

    PubMed

    Igea, Javier; Bogarín, Diego; Papadopulos, Alexander S T; Savolainen, Vincent

    2015-02-01

    Speciation on islands, and particularly the divergence of species in situ, has long been debated. Here, we present one of the first, complete assessments of the geographic modes of speciation for the flora of a small oceanic island. Cocos Island (Costa Rica) is pristine; it is located 550 km off the Pacific coast of Central America. It harbors 189 native plant species, 33 of which are endemic. Using phylogenetic data from insular and mainland congeneric species, we show that all of the endemic species are derived from independent colonization events rather than in situ speciation. This is in sharp contrast to the results of a study carried out in a comparable system, Lord Howe Island (Australia), where as much as 8.2% of the plant species were the product of sympatric speciation. Differences in physiography and age between the islands may be responsible for the contrasting patterns of speciation observed. Importantly, comparing phylogenetic assessments of the modes of speciation with taxonomy-based measures shows that widely used island biogeography approaches overestimate rates of in situ speciation. PMID:25522772

  16. Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles.

    PubMed

    Orf, Isabel; Timm, Stefan; Bauwe, Hermann; Fernie, Alisdair R; Hagemann, Martin; Kopka, Joachim; Nikoloski, Zoran

    2016-05-01

    Photorespiration is a process that is crucial for the survival of oxygenic phototrophs in environments that favour the oxygenation reaction of Rubisco. While photorespiration is conserved among cyanobacteria, algae, and embryophytes, it evolved to different levels of complexity in these phyla. The highest complexity is found in embryophytes, where the pathway involves four cellular compartments and respective transport processes. The complexity of photorespiration in embryophytes raises the question whether a simpler system, such as cyanobacteria, may serve as a model to facilitate our understanding of the common key aspects of photorespiration. In this study, we conducted a meta-analysis of publicly available metabolite profiles from the embryophyte Arabidopsis thaliana and the cyanobacterium Synechocystis sp. PCC 6803 grown under conditions that either activate or suppress photorespiration. The comparative meta-analysis evaluated the similarity of metabolite profiles, the variability of metabolite pools, and the patterns of metabolite ratios. Our results show that the metabolic signature of photorespiration is in part conserved between the compared model organisms under conditions that favour the oxygenation reaction. Therefore, our findings support the claim that cyanobacteria can serve as prokaryotic models of photorespiration in embryophytes.

  17. Comparative analysis for various redox flow batteries chemistries using a cost performance model

    NASA Astrophysics Data System (ADS)

    Crawford, Alasdair; Viswanathan, Vilayanur; Stephenson, David; Wang, Wei; Thomsen, Edwin; Reed, David; Li, Bin; Balducci, Patrick; Kintner-Meyer, Michael; Sprenkle, Vincent

    2015-10-01

    The total energy storage system cost is determined by means of a robust performance-based cost model for multiple flow battery chemistries. Systems aspects such as shunt current losses, pumping losses and various flow patterns through electrodes are accounted for. The system cost minimizing objective function determines stack design by optimizing the state of charge operating range, along with current density and current-normalized flow. The model cost estimates are validated using 2-kW stack performance data for the same size electrodes and operating conditions. Using our validated tool, it has been demonstrated that an optimized all-vanadium system has an estimated system cost of < 350 kWh-1 for 4-h application. With an anticipated decrease in component costs facilitated by economies of scale from larger production volumes, coupled with performance improvements enabled by technology development, the system cost is expected to decrease to 160 kWh-1 for a 4-h application, and to 100 kWh-1 for a 10-h application. This tool has been shared with the redox flow battery community to enable cost estimation using their stack data and guide future direction.

  18. Heat flow and gravity responses over salt bodies: A comparative model analysis

    SciTech Connect

    Corrigan, J.; Sweat, M.

    1995-07-01

    Two-dimensional numerical modeling of sea-floor heat flow and water-bottom gravity responses to systematic variations in simple subsurface salt body geometries provides insight on the relative usefulness of these two data types for extracting salt geometry information. For a given salt body geometry, diffusion of heat through overlying sediments results in a dramatic decrease in the amplitude of heat flow anomalies as the depth to the top of the salt body increases. For top-of-salt depths greater than about 1 km, the heat flow response is insensitive to the length of salt feeder stocks and to the thickness of salt tongues/sheets. This shallow depth-to-top-of-salt sensitivity range, in addition to a number of environmental factors that can adversely affect interpretation of heat flow anomalies in terms of heat refraction towards and through salt bodies, severely limits the usefulness of sea-floor heat flow data for constraining aspects of salt body geometry. For gravity data, the critical factor for addressing salt body geometry is the distribution of salt relative to the sediment-salt density crossover depth (above and below which salt is more and less dense, respectively, than the surrounding sediment). Except when ht relevant geometry information being sought (presence and/or length of feeder stock, thickness of salt tongue or sheet) is near the density crossover depth, the geometry-related information content of the gravity field is greater than that of the heat flow field. Based on these model results, measurement uncertainty considerations, and data limitations, the authors conclude that gravity data generally offer an order of magnitude greater resolution capability than sea-floor heat flow data for addressing salt body geometry issues of exploration interest.

  19. A comparative study of an accelerated life-test model and a toxicokinetics-based model for the analysis of Porcellio scaber survival data.

    PubMed

    Ren, Shijin

    2004-01-01

    Statistical models have long been used for reliability analysis and risk assessment. In the present study, an accelerated life-test model was used to analyze a set of dose-time-response data obtained with the terrestrial isopod Porcellio scaber. Survival data were experimentally obtained by exposing P. scaber to diazinon (a nonpersistent insecticide) at six concentrations between 2 and 11.31 microg/g (toxicant/soil). Survival data are presented on a weekly basis. The accelerated life-test model assumed a log-normal distribution and constant variance across all diazinon concentrations. Model parameters were obtained by maximum likelihood estimation. The accelerated life-test model was compared to a toxicokinetics-based model reported in the literature. Survival predictions made by both models were compared with the observed data. Both the accelerated life-test model and the toxicokinetics-based model underestimated toxicity at a diazinon concentration of 8 microg/g. Overall, however, the accelerated life-test model outperformed the toxicokinetics-based model, with survival predictions closer to the observed data in most cases and a stronger correlation between predicted and observed survivals. However, as a statistical model, the accelerated life-test model did not reveal mechanistic information, and only statistical and distributional interpretations of its model parameters could be made.

  20. Comparative QSAR Analysis of 3,5-bis (Arylidene)-4-Piperidone Derivatives: the Development of Predictive Cytotoxicity Models

    PubMed Central

    Edraki, Najmeh; Das, Umashankar; Hemateenejad, Bahram; Dimmock, Jonathan R.; Miri, Ramin

    2016-01-01

    1-[4-(2-Alkylaminoethoxy) phenylcarbonyl]-3,5-bis(arylidene)-4-piperidones are a novel class of potent cytotoxic agents. These compounds demonstrate low micromolar to submicromolar IC50 values against human Molt 4/C8 and CEM T-lymphocytes and murine leukemia L1210 cells. In this study, a comparative QSAR investigation was performed on a series of 3,5-bis (arylidene)-4-piperidones using different chemometric tools to develop the best predictive models for further development of analogs with improved cytotoxicity. All the QSAR models were validated by internal validation tests. The QSAR models obtained by GA-PLS method were considered the best as compared to MLR method. The best QSAR model obtained by GA-PLS analysis on L1210, CEM and Molt4/C8 demonstrated good predictively with R2pred values ranging from 0.94-0.80. Molecular density, topological (X2A) and geometrical indices of the molecules were found to be the most important factors for determining cytotoxic properties. PMID:27642313

  1. Comparative QSAR Analysis of 3,5-bis (Arylidene)-4-Piperidone Derivatives: the Development of Predictive Cytotoxicity Models.

    PubMed

    Edraki, Najmeh; Das, Umashankar; Hemateenejad, Bahram; Dimmock, Jonathan R; Miri, Ramin

    2016-01-01

    1-[4-(2-Alkylaminoethoxy) phenylcarbonyl]-3,5-bis(arylidene)-4-piperidones are a novel class of potent cytotoxic agents. These compounds demonstrate low micromolar to submicromolar IC50 values against human Molt 4/C8 and CEM T-lymphocytes and murine leukemia L1210 cells. In this study, a comparative QSAR investigation was performed on a series of 3,5-bis (arylidene)-4-piperidones using different chemometric tools to develop the best predictive models for further development of analogs with improved cytotoxicity. All the QSAR models were validated by internal validation tests. The QSAR models obtained by GA-PLS method were considered the best as compared to MLR method. The best QSAR model obtained by GA-PLS analysis on L1210, CEM and Molt4/C8 demonstrated good predictively with R(2) pred values ranging from 0.94-0.80. Molecular density, topological (X2A) and geometrical indices of the molecules were found to be the most important factors for determining cytotoxic properties. PMID:27642313

  2. Comparative analysis of the actual evapotranspiration of Flemish forest and cropland, using the soil water balance model WAVE

    NASA Astrophysics Data System (ADS)

    Verstraeten, W. W.; Muys, B.; Feyen, J.; Veroustraete, F.; Minnaert, M.; Meiresonne, L.; de Schrijver, A.

    2005-05-01

    This paper focuses on the quantification of the green - vegetation related - water flux of a forest stand in the temperate lowland of Flanders. The underlying reason of the research was to develop a methodology for assessing the impact of forests on the hydrologic cycle in comparison to agriculture. The approach tested for calculating the water consumption by forests was based on the application of the soil water balance model WAVE. The study involved the collection of data from 14 forest stands, the calibration and validation of the WAVE model, and the comparison of the water use (WU) components - transpiration, soil and interception evaporation - between forest and cropland. For model calibration purposes simulated and measured time series of soil water content at different soil depths, period March 2000-August 2001, were compared. A multiple-site validation was conducted as well. Actual tree transpiration calculated with sap flow measurements in three forest stands gave similar results for two of the three stands of pine (Pinus sylvestris L.), but WAVE overestimated the actual measured transpiration for a stand of poplar (Populus sp.). A useful approach to compare the WU components of forest versus cropland is scenario analysis based on the validated WAVE model. The statistical Profile Analysis method was implemented to explore and analyse the simulated WU time-series. With an average annual rainfall of 819 mm, the results show that forests in Flanders consume more water than agricultural crops. A 30 years average of 491 mm for 10 forests stands versus 398 mm for 10 cropped agricultural fields was derived. The WU components, on yearly basis, also differ between the two land use types (transpiration: 315 mm for forest and 261 mm for agricultural land use; soil evaporation: 47 mm and 131 mm, for forest and cropland, respectively). Forest canopy interception evaporation was estimated at 126 mm, while it was negligible for cropland.

  3. Comparative analysis of the actual evapotranspiration of Flemish forest and cropland, using the soil water balance model WAVE

    NASA Astrophysics Data System (ADS)

    Verstraeten, W. W.; Muys, B.; Feyen, J.; Veroustraete, F.; Minnaert, M.; Meiresonne, L.; de Schrijver, A.

    2005-09-01

    This paper focuses on the quantification of the green - vegetation related - water flux of forest stands in the temperate lowland of Flanders. The underlying reason of the research was to develop a methodology for assessing the impact of forests on the hydrologic cycle in comparison to agriculture. The tested approach for calculating the water use by forests was based on the application of the soil water balance model WAVE. The study involved the collection of data from 14 forest stands, the calibration and validation of the WAVE model, and the comparison of the water use (WU) components - transpiration, soil and interception evaporation - between forest and cropland. For model calibration purposes simulated and measured time series of soil water content at different soil depths, period March 2000-August 2001, were compared. A multiple-site validation was conducted as well. Actual tree transpiration calculated with sap flow measurements in three forest stands gave similar results for two of the three stands of pine (Pinus sylvestris L.), but WAVE overestimated the actual measured transpiration for a stand of poplar (Populus sp.). A useful approach to compare the WU components of forest versus cropland is scenario analysis based on the validated WAVE model. The statistical Profile Analysis method was implemented to explore and analyse the simulated WU time series. With an average annual rainfall of 819 mm, the results reveal that forests in Flanders consume more water than agricultural crops. A 30 years average of 491 mm for 10 forests stands versus 398 mm for 10 cropped agricultural fields was derived. The WU components, on yearly basis, also differ between the two land use types (transpiration: 315 mm for forest and 261 mm for agricultural land use; soil evaporation: 47 mm and 131 mm, for forest and cropland, respectively). Forest canopy interception evaporation was estimated at 126 mm, while it was negligible for cropland.

  4. A comparative sensitivity analysis focused on wet deposition models for the Fukushima and Chernobyl atmospheric dispersion events

    NASA Astrophysics Data System (ADS)

    Quérel, Arnaud; Roustan, Yelva; Quélo, Denis; Bocquet, Marc; Winiarek, Victor

    2014-05-01

    In order to model the transport of radionuclides bound to atmospheric particles and the ground contamination at the synoptic scale, the wet deposition is a crucial point. Usually, the wet deposition is divided in two different mechanisms, the below-cloud scavenging (washout) and the in-cloud scavenging (rainout). Since the micro-physics of both deposition processes is not well known yet, the modeling of the wet deposition of particles at the synoptic scale is uncertain and difficult to validate. This leads to an abundance of wet deposition models, none of them being fully adequate. The existing models of particle scavenging can be distinguished by the nature and the number of physical parameters they rely on. For instance the scavenging coefficient variability can be determined only by the rainfall intensity or take into account the rainfall intensity and the particle size distribution. Beyond their intrinsic formulations, the deposition models are sensitive to the input data necessary to use them, cloud height for instance. Finally, the simulated ground deposition is more or less sensitive to the choices of the overall-models involved in the atmospheric transport of particles and the meteorology in general. For accidental atmospheric releases, the uncertainties linked to the source-term are for instance crucial, what justifies the use of different ones in the study. The Polyphemus air quality system is used to perform the simulations of the radioactive dispersion, considering Caesium-137 as particulate matter for the accidental releases from the Fukushima and Chernobyl nuclear power plants. In this study, two different approaches are used. In the first one, the influence of the different components taking part in the scavenging modeling are confronted separately (whether the scavenging models or the overall models). The second approach is a global sensitivity analysis computed both on the Chernobyl and Fukushima cases. It relies on simulations performed with

  5. A comparative analysis of predictive models of morbidity in intensive care unit after cardiac surgery – Part I: model planning

    PubMed Central

    Barbini, Emanuela; Cevenini, Gabriele; Scolletta, Sabino; Biagioli, Bonizella; Giomarelli, Pierpaolo; Barbini, Paolo

    2007-01-01

    Background Different methods have recently been proposed for predicting morbidity in intensive care units (ICU). The aim of the present study was to critically review a number of approaches for developing models capable of estimating the probability of morbidity in ICU after heart surgery. The study is divided into two parts. In this first part, popular models used to estimate the probability of class membership are grouped into distinct categories according to their underlying mathematical principles. Modelling techniques and intrinsic strengths and weaknesses of each model are analysed and discussed from a theoretical point of view, in consideration of clinical applications. Methods Models based on Bayes rule, k-nearest neighbour algorithm, logistic regression, scoring systems and artificial neural networks are investigated. Key issues for model design are described. The mathematical treatment of some aspects of model structure is also included for readers interested in developing models, though a full understanding of mathematical relationships is not necessary if the reader is only interested in perceiving the practical meaning of model assumptions, weaknesses and strengths from a user point of view. Results Scoring systems are very attractive due to their simplicity of use, although this may undermine their predictive capacity. Logistic regression models are trustworthy tools, although they suffer from the principal limitations of most regression procedures. Bayesian models seem to be a good compromise between complexity and predictive performance, but model recalibration is generally necessary. k-nearest neighbour may be a valid non parametric technique, though computational cost and the need for large data storage are major weaknesses of this approach. Artificial neural networks have intrinsic advantages with respect to common statistical models, though the training process may be problematical. Conclusion Knowledge of model assumptions and the theoretical

  6. A comparative transcriptome analysis identifying FGF23 regulated genes in the kidney of a mouse CKD model.

    PubMed

    Dai, Bing; David, Valentin; Martin, Aline; Huang, Jinsong; Li, Hua; Jiao, Yan; Gu, Weikuan; Quarles, L Darryl

    2012-01-01

    Elevations of circulating Fibroblast growth factor 23 (FGF23) are associated with adverse cardiovascular outcomes and progression of renal failure in chronic kidney disease (CKD). Efforts to identify gene products whose transcription is directly regulated by FGF23 stimulation of fibroblast growth factor receptors (FGFR)/α-Klotho complexes in the kidney is confounded by both systemic alterations in calcium, phosphorus and vitamin D metabolism and intrinsic alterations caused by the underlying renal pathology in CKD. To identify FGF23 responsive genes in the kidney that might explain the association between FGF23 and adverse outcomes in CKD, we performed comparative genome wide analysis of gene expression profiles in the kidney of the Collagen 4 alpha 3 null mice (Col4a3(-/-)) model of progressive kidney disease with kidney expression profiles of Hypophosphatemic (Hyp) and FGF23 transgenic mouse models of elevated FGF23. The different complement of potentially confounding factors in these models allowed us to identify genes that are directly targeted by FGF23. This analysis found that α-Klotho, an anti-aging hormone and FGF23 co-receptor, was decreased by FGF23. We also identified additional FGF23-responsive transcripts and activation of networks associated with renal damage and chronic inflammation, including lipocalin 2 (Lcn2), transforming growth factor beta (TGF-β) and tumor necrosis factor-alpha (TNF-α) signaling pathways. Finally, we found that FGF23 suppresses angiotensin-converting enzyme 2 (ACE2) expression in the kidney, thereby providing a pathway for FGF23 regulation of the renin-angiotensin system. These gene products provide a possible mechanistic links between elevated FGF23 and pathways responsible for renal failure progression and cardiovascular diseases.

  7. Comparative Protein Structure Modeling Using MODELLER.

    PubMed

    Webb, Benjamin; Sali, Andrej

    2014-09-08

    Functional characterization of a protein sequence is one of the most frequent problems in biology. This task is usually facilitated by accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described.

  8. A model potential for the internal rotation of nitrosyl hyperfluorite. A comparative analysis of different theoretical methods

    NASA Astrophysics Data System (ADS)

    Cárdenas-Jirón, Gloria I.; Toro-Labbé, Alejandro

    1994-05-01

    We present a comparative analysis of the internal rotation energy curves of nitrosyl hyperfluorite (FONO). Two model potentials, derived from a Fourier series expansion, have been used to rationalize the trans⇌cis isomerization process for different theoretical methods going from traditional molecular orbital calculations to density functional theory. It is shown that Hartree—Fock (HF) and post Hartree—Fock (pHF) calculations, using a sufficiently large basis set, lead to results that are qualitatively similar. However, local density functional (LDF) calculations produce results that are not compatible. The resulting barrier heights vary from 2.36 (LDF) to 12.76 kcal/mol (MP4SDTQ/6-31G*) passing through a value of 8.33 kcal/mol from a HF/6-31G calculations. It is concluded that the LDF results, within the approximations used in that calculation, appear to be anomalous when compared to the HF and pHF results.

  9. Comparative analysis of autophagy and tauopathy related markers in cerebral ischemia and Alzheimer’s disease animal models

    PubMed Central

    Villamil-Ortiz, Javier G.; Cardona-Gomez, Gloria P.

    2015-01-01

    Alzheimer’s disease (AD) and cerebral ischemia (CI) are neuropathologies that are characterized by aggregates of tau protein, a hallmark of cognitive disorder and dementia. Protein accumulation can be induced by autophagic failure. Autophagy is a metabolic pathway involved in the homeostatic recycling of cellular components. However, the role of autophagy in those tauopathies remains unclear. In this study, we performed a comparative analysis to identify autophagy related markers in tauopathy generated by AD and CI during short-term, intermediate, and long-term progression using the 3xTg-AD mouse model (aged 6,12, and 18 months) and the global CI 2-VO (2-Vessel Occlusion) rat model (1,15, and 30 days post-ischemia). Our findings confirmed neuronal loss and hyperphosphorylated tau aggregation in the somatosensory cortex (SS-Cx) of the 3xTg-AD mice in the late stage (aged 18 months), which was supported by a failure in autophagy. These results were in contrast to those obtained in the SS-Cx of the CI rats, in which we detected neuronal loss and tauopathy at 1 and 15 days post-ischemia, and this phenomenon was reversed at 30 days. We proposed that this phenomenon was associated with autophagy induction in the late stage, since the data showed a decrease in p-mTOR activity, an association of Beclin-1 and Vps34, a progressive reduction in PHF-1, an increase in LC3B puncta and autophago-lysosomes formation were observed. Furthermore, the survival pathways remained unaffected. Together, our comparative study suggest that autophagy could ameliorates tauopathy in CI but not in AD, suggesting a differential temporal approach to the induction of neuroprotection and the prevention of neurodegeneration. PMID:26042033

  10. Comparative Protein Structure Modeling Using MODELLER.

    PubMed

    Webb, Benjamin; Sali, Andrej

    2016-01-01

    Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc. PMID:27322406

  11. Comparative Protein Structure Modeling Using MODELLER.

    PubMed

    Webb, Benjamin; Sali, Andrej

    2016-06-20

    Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.

  12. Comparative Analysis of Four Manpower Nursing Requirements Models. Health Manpower References. [Nurse Planning Information Series, No. 6].

    ERIC Educational Resources Information Center

    Deane, Robert T.; Ro, Kong-Kyun

    The analysis and description of four manpower nursing requirements models-- the Pugh-Roberts, the Vector, the Community Systems Foundation (CSF), and the Western Interstate Commission of Higher Education (WICHE)--are presented in this report. The introduction provides an overview of the project which was designed to analyze these different models.…

  13. A Comparative of business process modelling techniques

    NASA Astrophysics Data System (ADS)

    Tangkawarow, I. R. H. T.; Waworuntu, J.

    2016-04-01

    In this era, there is a lot of business process modeling techniques. This article is the research about differences of business process modeling techniques. For each technique will explain about the definition and the structure. This paper presents a comparative analysis of some popular business process modelling techniques. The comparative framework is based on 2 criteria: notation and how it works when implemented in Somerleyton Animal Park. Each technique will end with the advantages and disadvantages. The final conclusion will give recommend of business process modeling techniques that easy to use and serve the basis for evaluating further modelling techniques.

  14. Comparative metabolomic analysis reveals a reactive oxygen species-dominated dynamic model underlying chilling environment adaptation and tolerance in rice.

    PubMed

    Zhang, Jingyu; Luo, Wei; Zhao, Yuan; Xu, Yunyuan; Song, Shuhui; Chong, Kang

    2016-09-01

    Cold, a major environmental stress for plants, has been studied intensively for decades. Its response system has been revealed, especially at the transcriptional level. The mechanisms underlying recovery growth and environmental adaptation, however, remain unknown. Taking advantage of a naturally existing system, two subspecies of Asian cultivated rice (Oryza sativa) with significant divergence in chilling tolerance, we analyzed representative japonica and indica varieties, Nipponbare and 93-11, using comparative metabolomic analysis at six time points covering chilling treatment and recovery. In total, 223 known metabolites were detected. During chilling treatment, significant biochemical changes were centered on antioxidation. During recovery, a wide-ranging chilling response was observed. Large-scale amino acid accumulation occurred, consistent with the appearance of chilling injury. At the mid-treatment stage, the accumulation of antioxidation-related compounds appeared earlier in Nipponbare than in 93-11, consistent with the higher reactive oxygen species (ROS) levels in japonica vs indica varieties. A significant contribution of ROS-mediated gene regulation, rather than the C-repeat binding factor/dehydration-responsive-element binding factor (CBF/DREB) regulon, to the more vigorous transcriptional stress response in Nipponbare was revealed by RNA-seq. Accordingly, during recovery, the induction of stress-tolerant-related metabolites was more active in the chilling-tolerant variety Nipponbare. Senescence-related compounds accumulated only in the chilling-sensitive variety 93-11. Our study uncovers the dynamic metabolic models underlying chilling response and recovery, and reveals a ROS-dominated rice adaptation mechanism to low-temperature environments. PMID:27198693

  15. A new method for comparing rankings through complex networks: Model and analysis of competitiveness of major European soccer leagues

    NASA Astrophysics Data System (ADS)

    Criado, Regino; García, Esther; Pedroche, Francisco; Romance, Miguel

    2013-12-01

    In this paper, we show a new technique to analyze families of rankings. In particular, we focus on sports rankings and, more precisely, on soccer leagues. We consider that two teams compete when they change their relative positions in consecutive rankings. This allows to define a graph by linking teams that compete. We show how to use some structural properties of this competitivity graph to measure to what extend the teams in a league compete. These structural properties are the mean degree, the mean strength, and the clustering coefficient. We give a generalization of the Kendall's correlation coefficient to more than two rankings. We also show how to make a dynamic analysis of a league and how to compare different leagues. We apply this technique to analyze the four major European soccer leagues: Bundesliga, Italian Lega, Spanish Liga, and Premier League. We compare our results with the classical analysis of sport ranking based on measures of competitive balance.

  16. A new method for comparing rankings through complex networks: model and analysis of competitiveness of major European soccer leagues.

    PubMed

    Criado, Regino; García, Esther; Pedroche, Francisco; Romance, Miguel

    2013-12-01

    In this paper, we show a new technique to analyze families of rankings. In particular, we focus on sports rankings and, more precisely, on soccer leagues. We consider that two teams compete when they change their relative positions in consecutive rankings. This allows to define a graph by linking teams that compete. We show how to use some structural properties of this competitivity graph to measure to what extend the teams in a league compete. These structural properties are the mean degree, the mean strength, and the clustering coefficient. We give a generalization of the Kendall's correlation coefficient to more than two rankings. We also show how to make a dynamic analysis of a league and how to compare different leagues. We apply this technique to analyze the four major European soccer leagues: Bundesliga, Italian Lega, Spanish Liga, and Premier League. We compare our results with the classical analysis of sport ranking based on measures of competitive balance.

  17. A new method for comparing rankings through complex networks: model and analysis of competitiveness of major European soccer leagues.

    PubMed

    Criado, Regino; García, Esther; Pedroche, Francisco; Romance, Miguel

    2013-12-01

    In this paper, we show a new technique to analyze families of rankings. In particular, we focus on sports rankings and, more precisely, on soccer leagues. We consider that two teams compete when they change their relative positions in consecutive rankings. This allows to define a graph by linking teams that compete. We show how to use some structural properties of this competitivity graph to measure to what extend the teams in a league compete. These structural properties are the mean degree, the mean strength, and the clustering coefficient. We give a generalization of the Kendall's correlation coefficient to more than two rankings. We also show how to make a dynamic analysis of a league and how to compare different leagues. We apply this technique to analyze the four major European soccer leagues: Bundesliga, Italian Lega, Spanish Liga, and Premier League. We compare our results with the classical analysis of sport ranking based on measures of competitive balance. PMID:24387553

  18. Capturing tumor complexity in vitro: Comparative analysis of 2D and 3D tumor models for drug discovery

    PubMed Central

    Stock, Kristin; Estrada, Marta F.; Vidic, Suzana; Gjerde, Kjersti; Rudisch, Albin; Santo, Vítor E.; Barbier, Michaël; Blom, Sami; Arundkar, Sharath C.; Selvam, Irwin; Osswald, Annika; Stein, Yan; Gruenewald, Sylvia; Brito, Catarina; van Weerden, Wytske; Rotter, Varda; Boghaert, Erwin; Oren, Moshe; Sommergruber, Wolfgang; Chong, Yolanda; de Hoogt, Ronald; Graeser, Ralph

    2016-01-01

    Two-dimensional (2D) cell cultures growing on plastic do not recapitulate the three dimensional (3D) architecture and complexity of human tumors. More representative models are required for drug discovery and validation. Here, 2D culture and 3D mono- and stromal co-culture models of increasing complexity have been established and cross-comparisons made using three standard cell carcinoma lines: MCF7, LNCaP, NCI-H1437. Fluorescence-based growth curves, 3D image analysis, immunohistochemistry and treatment responses showed that end points differed according to cell type, stromal co-culture and culture format. The adaptable methodologies described here should guide the choice of appropriate simple and complex in vitro models. PMID:27364600

  19. Capturing tumor complexity in vitro: Comparative analysis of 2D and 3D tumor models for drug discovery.

    PubMed

    Stock, Kristin; Estrada, Marta F; Vidic, Suzana; Gjerde, Kjersti; Rudisch, Albin; Santo, Vítor E; Barbier, Michaël; Blom, Sami; Arundkar, Sharath C; Selvam, Irwin; Osswald, Annika; Stein, Yan; Gruenewald, Sylvia; Brito, Catarina; van Weerden, Wytske; Rotter, Varda; Boghaert, Erwin; Oren, Moshe; Sommergruber, Wolfgang; Chong, Yolanda; de Hoogt, Ronald; Graeser, Ralph

    2016-01-01

    Two-dimensional (2D) cell cultures growing on plastic do not recapitulate the three dimensional (3D) architecture and complexity of human tumors. More representative models are required for drug discovery and validation. Here, 2D culture and 3D mono- and stromal co-culture models of increasing complexity have been established and cross-comparisons made using three standard cell carcinoma lines: MCF7, LNCaP, NCI-H1437. Fluorescence-based growth curves, 3D image analysis, immunohistochemistry and treatment responses showed that end points differed according to cell type, stromal co-culture and culture format. The adaptable methodologies described here should guide the choice of appropriate simple and complex in vitro models. PMID:27364600

  20. Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity

    DOE PAGESBeta

    Harper, Bryan; Thomas, Dennis G.; Chikkagoudar, Satish; Baker, Nathan A.; Tang, Kaizhi; Heredia-Langner, Alejandro; Lins, Roberto D.; Harper, Stacey

    2015-06-04

    The integration of rapid assays, large data sets, informatics and modeling can overcome current barriers in understanding nanomaterial structure-toxicity relationships by providing a weight-of-the-evidence mechanism to generate hazard rankings for nanomaterials. Here we present the use of a rapid, low-cost assay to perform screening-level toxicity evaluations of nanomaterials in vivo. Calculated EZ Metric scores, a combined measure of morbidity and mortality, were established at realistic exposure levels and used to develop a predictive model of nanomaterial toxicity. Hazard ranking and clustering analysis of 68 diverse nanomaterials revealed distinct patterns of toxicity related to both core composition and outermost surface chemistrymore » of nanomaterials. The resulting clusters guided the development of a predictive model of gold nanoparticle toxicity to embryonic zebrafish. In addition, our findings suggest that risk assessments based on the size and core composition of nanomaterials alone may be wholly inappropriate, especially when considering complex engineered nanomaterials. These findings reveal the need to expeditiously increase the availability of quantitative measures of nanomaterial hazard and broaden the sharing of that data and knowledge to support predictive modeling. In addition, research should continue to focus on methodologies for developing predictive models of nanomaterial hazard based on sub-lethal responses to low dose exposures.« less

  1. Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity

    SciTech Connect

    Harper, Bryan; Thomas, Dennis G.; Chikkagoudar, Satish; Baker, Nathan A.; Tang, Kaizhi; Heredia-Langner, Alejandro; Lins, Roberto D.; Harper, Stacey

    2015-06-04

    The integration of rapid assays, large data sets, informatics and modeling can overcome current barriers in understanding nanomaterial structure-toxicity relationships by providing a weight-of-the-evidence mechanism to generate hazard rankings for nanomaterials. Here we present the use of a rapid, low-cost assay to perform screening-level toxicity evaluations of nanomaterials in vivo. Calculated EZ Metric scores, a combined measure of morbidity and mortality, were established at realistic exposure levels and used to develop a predictive model of nanomaterial toxicity. Hazard ranking and clustering analysis of 68 diverse nanomaterials revealed distinct patterns of toxicity related to both core composition and outermost surface chemistry of nanomaterials. The resulting clusters guided the development of a predictive model of gold nanoparticle toxicity to embryonic zebrafish. In addition, our findings suggest that risk assessments based on the size and core composition of nanomaterials alone may be wholly inappropriate, especially when considering complex engineered nanomaterials. These findings reveal the need to expeditiously increase the availability of quantitative measures of nanomaterial hazard and broaden the sharing of that data and knowledge to support predictive modeling. In addition, research should continue to focus on methodologies for developing predictive models of nanomaterial hazard based on sub-lethal responses to low dose exposures.

  2. Insights into the evolution of the CSP gene family through the integration of evolutionary analysis and comparative protein modeling.

    PubMed

    Kulmuni, Jonna; Havukainen, Heli

    2013-01-01

    Insect chemical communication and chemosensory systems rely on proteins coded by several gene families. Here, we have combined protein modeling with evolutionary analysis in order to study the evolution and structure of chemosensory proteins (CSPs) within arthropods and, more specifically, in ants by using the data available from sequenced genomes. Ants and other social insects are especially interesting model systems for the study of chemosensation, as they communicate in a highly complex social context and much of their communication relies on chemicals. Our ant protein models show how this complexity has shaped CSP evolution; the proteins are highly modifiable by their size, surface charge and binding pocket. Based on these findings, we divide ant CSPs into three groups: typical insect CSPs, an ancient 5-helical CSP and hymenopteran CSPs with a small binding pocket, and suggest that these groups likely serve different functions. The hymenopteran CSPs have duplicated repeatedly in individual ant lineages. In these CSPs, positive selection has driven surface charge changes, an observation which has possible implications for the interaction between CSPs and ligands or odorant receptors. Our phylogenetic analysis shows that within the Arthropoda the only highly conserved gene is the ancient 5-helical CSP, which is likely involved in an essential ubiquitous function rather than chemosensation. During insect evolution, the 6-helical CSPs have diverged and perform chemosensory functions among others. Our results contribute to the general knowledge of the structural differences between proteins underlying chemosensation and highlight those protein properties which have been affected by adaptive evolution. PMID:23723994

  3. Quantum analytical modeling and simulation of CNT on insulator (COI) and CNT on nothing (CON) FET: a comparative analysis

    NASA Astrophysics Data System (ADS)

    Mukherjee, Sudipta; Bandyopadhyay, Dipan; Dutta, Pranab Kishore; Sarkar, Subir Kumar

    2016-06-01

    A comprehensive performance analysis by quantum analytical modeling of CNT on insulator (COI) and CNT on nothing (CON) FET having channel length 20 nm has been proposed and investigated on the basis of 2D Poisson's Equation and solution of 1-D Schrodinger's Equation and validated using ATLAS 2D simulator. As classical approximations fail to describe carrier quantization, charge inversion and potential profile of a device at sub-100 nm regime, here for the first time an analytical model in quantum mechanical aspect for COI/CON devices has been derived. Effects of high-k dielectrics in place of conventional SiO2 over the device characteristics have been thoroughly discussed. Moreover, all noticeable benefits of our device to the so called SOI/SON architecture have also been vividly justified.

  4. Comparative analysis of various real-time data assimilation approaches for assimilating streamflow into a hydrologic routing model

    NASA Astrophysics Data System (ADS)

    Noh, Seong Jin; Mazzoleni, Maurizio; Lee, Haksu; Liu, Yuqiong; Seo, Dong Jun; Solomatine, Dimitri

    2016-04-01

    Reliable water depth estimation is an extremely important issue in operational early flood warning systems. Different water system models have been implemented in the last decades, and, in parallel, data assimilation approaches have been introduced in order to reduce the uncertainty of such models. The goal of this study is to compare the performances of a distributed hydrologic routing model with streamflow assimilation using six different data assimilation methods, including direct insertion, nudging, Kalman filter, Ensemble Kalman filter, Asynchronous Ensemble Kalman filter and variational method. The model used in this study is a 3-parameter Muskingum (O'Donnell 1985) which was implemented in the Trinity River, within the Dallas-Fort-Worth Metroplex area in Texas, USA. The first methodological step is to discretize the river reach into multiple 1-km sub-reaches in order to estimate water depth in a distributed fashion. Then, different data assimilation approaches were implemented using the state-space approach formulation of the Muskingum model proposed by Georgakakos (1990). Finally, streamflow observations were assimilated at two points where flow sensors are located. The results of this work pointed out that assimilation of streamflow observations can noticeably improve the hydrologic routing model prediction and that ensemble definition is particularly important for both Ensemble Kalman filter and Asynchronous Ensemble Kalman filter. This study is part of the FP7 European Project WeSenseIt Citizen Water Observatory (www.http://wesenseit.eu/) and NSF Project Integrated Sensing and Prediction of urban Water for Sustainable Cities (http://ispuw.uta.edu/nsf)

  5. Implementation and comparative analysis of the optimisations produced by evolutionary algorithms for the parameter extraction of PSP MOSFET model

    NASA Astrophysics Data System (ADS)

    Hadia, Sarman K.; Thakker, R. A.; Bhatt, Kirit R.

    2016-05-01

    The study proposes an application of evolutionary algorithms, specifically an artificial bee colony (ABC), variant ABC and particle swarm optimisation (PSO), to extract the parameters of metal oxide semiconductor field effect transistor (MOSFET) model. These algorithms are applied for the MOSFET parameter extraction problem using a Pennsylvania surface potential model. MOSFET parameter extraction procedures involve reducing the error between measured and modelled data. This study shows that ABC algorithm optimises the parameter values based on intelligent activities of honey bee swarms. Some modifications have also been applied to the basic ABC algorithm. Particle swarm optimisation is a population-based stochastic optimisation method that is based on bird flocking activities. The performances of these algorithms are compared with respect to the quality of the solutions. The simulation results of this study show that the PSO algorithm performs better than the variant ABC and basic ABC algorithm for the parameter extraction of the MOSFET model; also the implementation of the ABC algorithm is shown to be simpler than that of the PSO algorithm.

  6. Observed & Modeled Changes in the Onset of Spring: A Preliminary Comparative Analysis by Geographic Regions of the USA

    NASA Astrophysics Data System (ADS)

    Enquist, C.

    2012-12-01

    Phenology, the study of seasonal life cycle events in plants and animals, is a well-recognized indicator of climate change impacts on people and nature. Models, experiments, and observational studies show changes in plant and animal phenology as a function of environmental change. Current research aims to improve our understanding of changes by enhancing existing models, analyzing observations, synthesizing previous research, and comparing outputs. Local to regional climatology is a critical driver of phenological variation of organisms across scales. Because plants respond to the cumulative effects of daily weather over an extended period, timing of life cycle events are effective integrators of climate data. One specific measure, leaf emergence, is particularly important because it often shows a strong response to temperature change, and is crucial for assessment of processes related to start and duration of the growing season. Schwartz et al. (2006) developed a suite of models (the "Spring Indices") linking plant development from historical data from leafing and flowering of cloned lilac and honeysuckle with basic climatic drivers to monitor changes related to the start of the spring growing season. These models can be generated at any location that has daily max-min temperature time series. The new version of these models is called the "Extended Spring Indices," or SI-x (Schwartz et al. in press). The SI-x model output (first leaf date and first bloom date) are produced similarly to the original models (SI-o), but do not incorporate accumulated chilling hours; rather energy accumulation starts for all stations on January 1. This change extends the locations SI model output can be generated into the sub-tropics, allowing full coverage of the conterminous USA. Both SI model versions are highly correlated, with mean bias and mean absolute differences around two days or less, and a similar bias and absolute errors when compared to cloned lilac data. To

  7. Two-Year versus One-Year Head Start Program Impact: Addressing Selection Bias by Comparing Regression Modeling with Propensity Score Analysis

    ERIC Educational Resources Information Center

    Leow, Christine; Wen, Xiaoli; Korfmacher, Jon

    2015-01-01

    This article compares regression modeling and propensity score analysis as different types of statistical techniques used in addressing selection bias when estimating the impact of two-year versus one-year Head Start on children's school readiness. The analyses were based on the national Head Start secondary dataset. After controlling for…

  8. Comparative analysis of H&E and Prussian blue staining in a mouse model of cerebral microbleeds.

    PubMed

    Liu, Shuo; Grigoryan, Mher Mahoney; Vasilevko, Vitaly; Sumbria, Rachita K; Paganini-Hill, Annlia; Cribbs, David H; Fisher, Mark J

    2014-11-01

    Cerebral microbleeds are microscopic hemorrhages with deposits of blood products in the brain, which can be visualized with MRI and are implicated in cerebrovascular diseases. Hematoxylin and eosin (H&E) and Perl's Prussian blue are popular staining methods used to localize cerebral microbleeds in pathology. This paper compared these two staining techniques in a mouse model of cerebral microbleeds. We used lipopolysaccharide (LPS) to induce cerebral microhemorrhages. C57B6 mice were treated with LPS (5 mg/kg, i.p.) or vehicle at baseline and at 24 hr. The brains were extracted 48 hr after the first injection and adjacent coronal sections were stained with H&E and Prussian blue to compare the effectiveness of the two staining techniques. H&E-positive stains were increased with LPS treatment and were correlated with grossly visible microhemorrhages on the brain surface; Prussian blue-positive stains, by comparison, showed no significant increase with LPS treatment and did not correlate with either H&E-positive stains or surface microhemorrhages. H&E staining is thus a more reliable indicator of acute bleeding events induced by LPS in this model within a short time span.

  9. Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2 (-/-) Hippocampus.

    PubMed

    Provenzano, Giovanni; Corradi, Zelia; Monsorno, Katia; Fedrizzi, Tarcisio; Ricceri, Laura; Scattoni, Maria L; Bozzi, Yuri

    2016-01-01

    (-/-) DEGs. Weighted correlation network analysis (WGCNA) performed on BTBR and En2 (-/-) hippocampal transcriptomes together identified six modules significantly enriched in ASD-related genes. Each of these modules showed a specific enrichment profile in neuronal and glial genes, as well as in genes associated to ASD comorbidities such as epilepsy and SCZ. Our data reveal significant transcriptional similarities and differences between the BTBR and En2 (-/-) hippocampus, indicating that transcriptome analysis of ASD mouse models may contribute to identify novel molecular targets for pharmacological studies. PMID:27610074

  10. Comparative analysis of collaboration networks

    SciTech Connect

    Progulova, Tatiana; Gadjiev, Bahruz

    2011-03-14

    In this paper we carry out a comparative analysis of the word network as the collaboration network based on the novel by M. Bulgakov 'Master and Margarita', the synonym network of the Russian language as well as the Russian movie actor network. We have constructed one-mode projections of these networks, defined degree distributions for them and have calculated main characteristics. In the paper a generation algorithm of collaboration networks has been offered which allows one to generate networks statistically equivalent to the studied ones. It lets us reveal a structural correlation between word network, synonym network and movie actor network. We show that the degree distributions of all analyzable networks are described by the distribution of q-type.

  11. Convergence analysis of a finite element skull model of Herpestes javanicus (Carnivora, Mammalia): implications for robust comparative inferences of biomechanical function.

    PubMed

    Tseng, Zhijie Jack; Flynn, John J

    2015-01-21

    Predictions of skull biomechanical capability based on virtual models constitute a valuable data source for testing hypotheses about craniodental form and feeding behavior. Such comparative analyses also inform dietary reconstruction in extinct species. 3D modeling using Finite Element (FE) methods is a common technique applied to the comparative analysis of craniodental function in extinct and extant vertebrates. However, taxonomically diverse skull models in the literature often are not directly comparable to each other, in part because of distinctions in how boundary conditions are defined, but also because of substantial differences in the number of FEs composing the models. In this study, we test whether a conventional convergence test is adequate in identifying the minimum number of FEs needed to achieve internally stable results for a single species. We constructed a series of skull models of Herpestes javanicus, and simulated unilateral biting across the dentition; the models differed in the number of FEs, degrees of freedom at the joint and bite point constraints, and type of tetrahedral FEs used. We found that convergence patterns differed across constraint types, FE quantities, and bite position simulated. Four-noded tetrahedral (tet-4) FE models with relaxed constraints produced the most stable measurements compared to over-constrained tet-4 models and to relaxed tet-10 models. In absence of an optimal FE quantity from convergence testing, we propose a broadly applicable sub-sampling protocol, whereby average measurement values across multiple models per specimen are used for among-species comparisons. A regime of sampling three low FE quantity models produced the closest estimates of mean measurement values relative to larger model sets, being within the 95% bootstrap estimated confidence intervals. Future studies should focus on identifying sources of variation associated with other FE modeling protocols, so that they can be accounted for before

  12. Comparative artificial neural network and partial least squares models for analysis of Metronidazole, Diloxanide, Spiramycin and Cliquinol in pharmaceutical preparations

    NASA Astrophysics Data System (ADS)

    Elkhoudary, Mahmoud M.; Abdel Salam, Randa A.; Hadad, Ghada M.

    2014-09-01

    Metronidazole (MNZ) is a widely used antibacterial and amoebicide drug. Therefore, it is important to develop a rapid and specific analytical method for the determination of MNZ in mixture with Spiramycin (SPY), Diloxanide (DIX) and Cliquinol (CLQ) in pharmaceutical preparations. This work describes simple, sensitive and reliable six multivariate calibration methods, namely linear and nonlinear artificial neural networks preceded by genetic algorithm (GA-ANN) and principle component analysis (PCA-ANN) as well as partial least squares (PLS) either alone or preceded by genetic algorithm (GA-PLS) for UV spectrophotometric determination of MNZ, SPY, DIX and CLQ in pharmaceutical preparations with no interference of pharmaceutical additives. The results manifest the problem of nonlinearity and how models like ANN can handle it. Analytical performance of these methods was statistically validated with respect to linearity, accuracy, precision and specificity. The developed methods indicate the ability of the previously mentioned multivariate calibration models to handle and solve UV spectra of the four components’ mixtures using easy and widely used UV spectrophotometer.

  13. Comparative artificial neural network and partial least squares models for analysis of Metronidazole, Diloxanide, Spiramycin and Cliquinol in pharmaceutical preparations.

    PubMed

    Elkhoudary, Mahmoud M; Abdel Salam, Randa A; Hadad, Ghada M

    2014-09-15

    Metronidazole (MNZ) is a widely used antibacterial and amoebicide drug. Therefore, it is important to develop a rapid and specific analytical method for the determination of MNZ in mixture with Spiramycin (SPY), Diloxanide (DIX) and Cliquinol (CLQ) in pharmaceutical preparations. This work describes simple, sensitive and reliable six multivariate calibration methods, namely linear and nonlinear artificial neural networks preceded by genetic algorithm (GA-ANN) and principle component analysis (PCA-ANN) as well as partial least squares (PLS) either alone or preceded by genetic algorithm (GA-PLS) for UV spectrophotometric determination of MNZ, SPY, DIX and CLQ in pharmaceutical preparations with no interference of pharmaceutical additives. The results manifest the problem of nonlinearity and how models like ANN can handle it. Analytical performance of these methods was statistically validated with respect to linearity, accuracy, precision and specificity. The developed methods indicate the ability of the previously mentioned multivariate calibration models to handle and solve UV spectra of the four components' mixtures using easy and widely used UV spectrophotometer.

  14. Comparative Sensitivity Analysis of Muscle Activation Dynamics.

    PubMed

    Rockenfeller, Robert; Günther, Michael; Schmitt, Syn; Götz, Thomas

    2015-01-01

    We mathematically compared two models of mammalian striated muscle activation dynamics proposed by Hatze and Zajac. Both models are representative for a broad variety of biomechanical models formulated as ordinary differential equations (ODEs). These models incorporate parameters that directly represent known physiological properties. Other parameters have been introduced to reproduce empirical observations. We used sensitivity analysis to investigate the influence of model parameters on the ODE solutions. In addition, we expanded an existing approach to treating initial conditions as parameters and to calculating second-order sensitivities. Furthermore, we used a global sensitivity analysis approach to include finite ranges of parameter values. Hence, a theoretician striving for model reduction could use the method for identifying particularly low sensitivities to detect superfluous parameters. An experimenter could use it for identifying particularly high sensitivities to improve parameter estimation. Hatze's nonlinear model incorporates some parameters to which activation dynamics is clearly more sensitive than to any parameter in Zajac's linear model. Other than Zajac's model, Hatze's model can, however, reproduce measured shifts in optimal muscle length with varied muscle activity. Accordingly we extracted a specific parameter set for Hatze's model that combines best with a particular muscle force-length relation. PMID:26417379

  15. A comparative analysis of the Libyan national essential medicines list and the WHO model list of essential medicines

    PubMed Central

    Mustafa, Asma Abubakr; Kowalski, Stefan Robert

    2010-01-01

    Aim and Objectives To examine the concordance of the Libyan Pharmaceutical List of Essential Medicines (LPLEM) with the World Health Organization Model List of Essential Medicines 2009 (WMLEM 2009). Methods The concordance between generic medicines listed in the WMLEM 2009 (standard reference list) and the LPLEM 2006 (comparator list) was evaluated. Results The total number of Basic Essential Medicines (BEMs) listed on the WMLEM 2009 was 347. The total number of generic medicines listed on the LPLEM was 584. Although the LPLEM has more listed medicines, only 270 (77.6%) of BEMs from the WMLEM were listed as available. However, 25 of the 77 missing medicines were deemed to have appropriate alternatives. A total of 52 medicines from the WMLEM 2009 were therefore missing from the LPLEM. Discrepancies compared to the WMLEM 2009 were identified in 15 out of 29 therapeutic sections. The highest discrepancy rate from the WMLEM 2009 was in the anti-infective section (35 missing medicines). Missing BEMs were noted in many subclassifications of the anti-infective medicines section, but omissions were particularly prevalent in the antibacterial medicines subsection (11 missing medicines). Antituberculosis medications had the highest discrepancy rate for antibacterial BEMs with one-third of the single medicines recommended by the WHO in the WMLEM 2009 not listed on the LPLEM. Of the 314 additional medicines on the LPLEM, 18 were deemed to be irrational non-essential medicines. Conclusion The LPLEM does not include several essential medicines recommended by the WHO in the WMLEM 2009. These discrepancies may have serious public health implications for management of some infectious diseases, particularly, tuberculosis and HIV. PMID:21483564

  16. Gradient Matching Methods for Computational Inference in Mechanistic Models for Systems Biology: A Review and Comparative Analysis.

    PubMed

    Macdonald, Benn; Husmeier, Dirk

    2015-01-01

    Parameter inference in mathematical models of biological pathways, expressed as coupled ordinary differential equations (ODEs), is a challenging problem in contemporary systems biology. Conventional methods involve repeatedly solving the ODEs by numerical integration, which is computationally onerous and does not scale up to complex systems. Aimed at reducing the computational costs, new concepts based on gradient matching have recently been proposed in the computational statistics and machine learning literature. In a preliminary smoothing step, the time series data are interpolated; then, in a second step, the parameters of the ODEs are optimized, so as to minimize some metric measuring the difference between the slopes of the tangents to the interpolants, and the time derivatives from the ODEs. In this way, the ODEs never have to be solved explicitly. This review provides a concise methodological overview of the current state-of-the-art methods for gradient matching in ODEs, followed by an empirical comparative evaluation based on a set of widely used and representative benchmark data.

  17. Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2

    PubMed Central

    2014-01-01

    Background Diabetes mellitus of type 2 (T2D), also known as noninsulin-dependent diabetes mellitus (NIDDM) or adult-onset diabetes, is a common disease. It is estimated that more than 300 million people worldwide suffer from T2D. In this study, we investigated the T2D, pre-diabetic and healthy human (no diabetes) bloodstream samples using genomic, genealogical, and phonemic information. We identified differentially expressed genes and pathways. The study has provided deeper insights into the development of T2D, and provided useful information for further effective prevention and treatment of the disease. Results A total of 142 bloodstream samples were collected, including 47 healthy humans, 22 pre-diabetic and 73 T2D patients. Whole genome scale gene expression profiles were obtained using the Agilent Oligo chips that contain over 20,000 human genes. We identified 79 significantly differentially expressed genes that have fold change ≥ 2. We mapped those genes and pinpointed locations of those genes on human chromosomes. Amongst them, 3 genes were not mapped well on the human genome, but the rest of 76 differentially expressed genes were well mapped on the human genome. We found that most abundant differentially expressed genes are on chromosome one, which contains 9 of those genes, followed by chromosome two that contains 7 of the 76 differentially expressed genes. We performed gene ontology (GO) functional analysis of those 79 differentially expressed genes and found that genes involve in the regulation of cell proliferation were among most common pathways related to T2D. The expression of the 79 genes was combined with clinical information that includes age, sex, and race to construct an optimal discriminant model. The overall performance of the model reached 95.1% accuracy, with 91.5% accuracy on identifying healthy humans, 100% accuracy on pre-diabetic patients and 95.9% accuract on T2D patients. The higher performance on identifying pre-diabetic patients was

  18. Least-Squares Regression and Spectral Residual Augmented Classical Least-Squares Chemometric Models for Stability-Indicating Analysis of Agomelatine and Its Degradation Products: A Comparative Study.

    PubMed

    Naguib, Ibrahim A; Abdelrahman, Maha M; El Ghobashy, Mohamed R; Ali, Nesma A

    2016-01-01

    Two accurate, sensitive, and selective stability-indicating methods are developed and validated for simultaneous quantitative determination of agomelatine (AGM) and its forced degradation products (Deg I and Deg II), whether in pure forms or in pharmaceutical formulations. Partial least-squares regression (PLSR) and spectral residual augmented classical least-squares (SRACLS) are two chemometric models that are being subjected to a comparative study through handling UV spectral data in range (215-350 nm). For proper analysis, a three-factor, four-level experimental design was established, resulting in a training set consisting of 16 mixtures containing different ratios of interfering species. An independent test set consisting of eight mixtures was used to validate the prediction ability of the suggested models. The results presented indicate the ability of mentioned multivariate calibration models to analyze AGM, Deg I, and Deg II with high selectivity and accuracy. The analysis results of the pharmaceutical formulations were statistically compared to the reference HPLC method, with no significant differences observed regarding accuracy and precision. The SRACLS model gives comparable results to the PLSR model; however, it keeps the qualitative spectral information of the classical least-squares algorithm for analyzed components. PMID:26987554

  19. Comparative Genomic and Transcriptomic Analysis of Wangiella dermatitidis, A Major Cause of Phaeohyphomycosis and a Model Black Yeast Human Pathogen

    PubMed Central

    Chen, Zehua; Martinez, Diego A.; Gujja, Sharvari; Sykes, Sean M.; Zeng, Qiandong; Szaniszlo, Paul J.; Wang, Zheng; Cuomo, Christina A.

    2014-01-01

    Black or dark brown (phaeoid) fungi cause cutaneous, subcutaneous, and systemic infections in humans. Black fungi thrive in stressful conditions such as intense light, high radiation, and very low pH. Wangiella (Exophiala) dermatitidis is arguably the most studied phaeoid fungal pathogen of humans. Here, we report our comparative analysis of the genome of W. dermatitidis and the transcriptional response to low pH stress. This revealed that W. dermatitidis has lost the ability to synthesize alpha-glucan, a cell wall compound many pathogenic fungi use to evade the host immune system. In contrast, W. dermatitidis contains a similar profile of chitin synthase genes as related fungi and strongly induces genes involved in cell wall synthesis in response to pH stress. The large portfolio of transporters may provide W. dermatitidis with an enhanced ability to remove harmful products as well as to survive on diverse nutrient sources. The genome encodes three independent pathways for producing melanin, an ability linked to pathogenesis; these are active during pH stress, potentially to produce a barrier to accumulated oxidative damage that might occur under stress conditions. In addition, a full set of fungal light-sensing genes is present, including as part of a carotenoid biosynthesis gene cluster. Finally, we identify a two-gene cluster involved in nucleotide sugar metabolism conserved with a subset of fungi and characterize a horizontal transfer event of this cluster between fungi and algal viruses. This work reveals how W. dermatitidis has adapted to stress and survives in diverse environments, including during human infections. PMID:24496724

  20. Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen.

    PubMed

    Chen, Zehua; Martinez, Diego A; Gujja, Sharvari; Sykes, Sean M; Zeng, Qiandong; Szaniszlo, Paul J; Wang, Zheng; Cuomo, Christina A

    2014-04-01

    Black or dark brown (phaeoid) fungi cause cutaneous, subcutaneous, and systemic infections in humans. Black fungi thrive in stressful conditions such as intense light, high radiation, and very low pH. Wangiella (Exophiala) dermatitidis is arguably the most studied phaeoid fungal pathogen of humans. Here, we report our comparative analysis of the genome of W. dermatitidis and the transcriptional response to low pH stress. This revealed that W. dermatitidis has lost the ability to synthesize alpha-glucan, a cell wall compound many pathogenic fungi use to evade the host immune system. In contrast, W. dermatitidis contains a similar profile of chitin synthase genes as related fungi and strongly induces genes involved in cell wall synthesis in response to pH stress. The large portfolio of transporters may provide W. dermatitidis with an enhanced ability to remove harmful products as well as to survive on diverse nutrient sources. The genome encodes three independent pathways for producing melanin, an ability linked to pathogenesis; these are active during pH stress, potentially to produce a barrier to accumulated oxidative damage that might occur under stress conditions. In addition, a full set of fungal light-sensing genes is present, including as part of a carotenoid biosynthesis gene cluster. Finally, we identify a two-gene cluster involved in nucleotide sugar metabolism conserved with a subset of fungi and characterize a horizontal transfer event of this cluster between fungi and algal viruses. This work reveals how W. dermatitidis has adapted to stress and survives in diverse environments, including during human infections. PMID:24496724

  1. Validity of Intraoral Scans Compared with Plaster Models: An In-Vivo Comparison of Dental Measurements and 3D Surface Analysis

    PubMed Central

    2016-01-01

    Purpose Dental measurements have been commonly taken from plaster dental models obtained from alginate impressions can. Through the use of an intraoral scanner, digital impressions now acquire the information directly from the mouth. The purpose of this study was to determine the validity of the intraoral scans compared to plaster models. Materials and Methods Two types of dental models (intraoral scan and plaster model) of 20 subjects were included in this study. The subjects had impressions taken of their teeth and made as plaster model. In addition, their mouths were scanned with the intraoral scanner and the scans were converted into digital models. Eight transverse and 16 anteroposterior measurements, 24 tooth heights and widths were recorded on the plaster models with a digital caliper and on the intraoral scan with 3D reverse engineering software. For 3D surface analysis, the two models were superimposed by using best-fit algorithm. The average differences between the two models at all points on the surfaces were computed. Paired t-test and Bland-Altman plot were used to determine the validity of measurements from the intraoral scan compared to those from the plaster model. Results There were no significant differences between the plaster models and intraoral scans, except for one measurement of lower intermolar width. The Bland-Altman plots of all measurements showed that differences between the two models were within the limits of agreement. The average surface difference between the two models was within 0.10 mm. Conclusions The results of the present study indicate that the intraoral scans are clinically acceptable for diagnosis and treatment planning in dentistry and can be used in place of plaster models. PMID:27304976

  2. Comparative analysis of meteorological performance of coupled chemistry-meteorology models in the context of AQMEII phase 2

    EPA Science Inventory

    Air pollution simulations critically depend on the quality of the underlying meteorology. In phase 2 of the Air Quality Model Evaluation International Initiative (AQMEII-2), thirteen modeling groups from Europe and four groups from North America operating eight different regional...

  3. Transitions in State Public Health Law: Comparative Analysis of State Public Health Law Reform Following the Turning Point Model State Public Health Act

    PubMed Central

    Meier, Benjamin Mason; Gebbie, Kristine M.

    2009-01-01

    Given the public health importance of law modernization, we undertook a comparative analysis of policy efforts in 4 states (Alaska, South Carolina, Wisconsin, and Nebraska) that have considered public health law reform based on the Turning Point Model State Public Health Act. Through national legislative tracking and state case studies, we investigated how the Turning Point Act's model legal language has been considered for incorporation into state law and analyzed key facilitating and inhibiting factors for public health law reform. Our findings provide the practice community with a research base to facilitate further law reform and inform future scholarship on the role of law as a determinant of the public's health. PMID:19150900

  4. Comparative Analysis of the Secretome from a Model Filarial Nematode (Litomosoides sigmodontis) Reveals Maximal Diversity in Gravid Female Parasites*

    PubMed Central

    Armstrong, Stuart D.; Babayan, Simon A.; Lhermitte-Vallarino, Nathaly; Gray, Nick; Xia, Dong; Martin, Coralie; Kumar, Sujai; Taylor, David W.; Blaxter, Mark L.; Wastling, Jonathan M.; Makepeace, Benjamin L.

    2014-01-01

    Filarial nematodes (superfamily Filarioidea) are responsible for an annual global health burden of ∼6.3 million disability-adjusted life-years, which represents the greatest single component of morbidity attributable to helminths affecting humans. No vaccine exists for the major filarial diseases, lymphatic filariasis and onchocerciasis; in part because research on protective immunity against filariae has been constrained by the inability of the human-parasitic species to complete their lifecycles in laboratory mice. However, the rodent filaria Litomosoides sigmodontis has become a popular experimental model, as BALB/c mice are fully permissive for its development and reproduction. Here, we provide a comprehensive analysis of excretory-secretory products from L. sigmodontis across five lifecycle stages and identifications of host proteins associated with first-stage larvae (microfilariae) in the blood. Applying intensity-based quantification, we determined the abundance of 302 unique excretory-secretory proteins, of which 64.6% were present in quantifiable amounts only from gravid adult female nematodes. This lifecycle stage, together with immature microfilariae, released four proteins that have not previously been evaluated as vaccine candidates: a predicted 28.5 kDa filaria-specific protein, a zonadhesin and SCO-spondin-like protein, a vitellogenin, and a protein containing six metridin-like ShK toxin domains. Female nematodes also released two proteins derived from the obligate Wolbachia symbiont. Notably, excretory-secretory products from all parasite stages contained several uncharacterized members of the transthyretin-like protein family. Furthermore, biotin labeling revealed that redox proteins and enzymes involved in purinergic signaling were enriched on the adult nematode cuticle. Comparison of the L. sigmodontis adult secretome with that of the human-infective filarial nematode Brugia malayi (reported previously in three independent published studies

  5. Comparative power spectrum analysis of EEG activity in spontaneously hypertensive and Wistar rats in kainate model of temporal model of epilepsy.

    PubMed

    Tchekalarova, Jana; Kortenska, Lidia; Marinov, Pencho; Boyanov, Kiril

    2016-06-01

    Recently, we have reported that spontaneously hypertensive rats (SHRs) exhibit higher susceptibility than Wistar rats in kainate (KA) model of epilepsy. The aim of the present study is to compare the baseline of EEG signals in SHRs and Wistar rats using Discrete Fourier transform (DFT) during the three phases of KA model (acute, latent and chronic). The SHRs showed higher baseline relative power of delta waves in the left frontal cortex and lower gamma-HF waves in the left frontal and left/right parietal cortex, respectively, compared to Wistar rats. During the acute phase, both absolute and relative power of fast EEG bands (gamma-HF) was lower in the left/right frontal and the left/right parietal cortex in SHRs compared to Wistar rats. During the latent phase, no difference in the power of the investigated bands was detected between the two strains. During the chronic epileptic phase, the SHRs were characterized with higher power of HF oscillations than Wistar rats both in the frontal and parietal cortex without brain lateralization while theta, alpha and beta bands were with diminished power in the left parietal cortex of SHRs compared to normotensive Wistar rats. Taken together, the presented results suggest that the increased delta waves and lower gamma-HF waves in the frontal/parietal cortex are associated with a higher seizure susceptibility of SHRs compared to Wistar rats while fastest oscillations has a critical role in seizure generation and propagation of hypertensive rats.

  6. A Comparative Analysis of the Meaning of Model Minority among Ethnic Koreans in China and the United States

    ERIC Educational Resources Information Center

    Gao, Fang

    2010-01-01

    Koreans have been successful in nesting their educational achievement into places like China and the United States, where they have earned the title of "model minority". This research is a comparison of the manner in which the model minority stereotype is handled by Korean Chinese and Korean Americans. The gathered data leads us to argue that…

  7. Sociological analysis and comparative education

    NASA Astrophysics Data System (ADS)

    Woock, Roger R.

    1981-12-01

    It is argued that comparative education is essentially a derivative field of study, in that it borrows theories and methods from academic disciplines. After a brief humanistic phase, in which history and philosophy were central for comparative education, sociology became an important source. In the mid-50's and 60's, sociology in the United States was characterised by Structural Functionalism as a theory, and Social Survey as a dominant methodology. Both were incorporated into the development of comparative education. Increasingly in the 70's, and certainly today, the new developments in sociology are characterised by an attack on Positivism, which is seen as the philosophical position underlying both functionalism and survey methods. New or re-discovered theories with their attendant methodologies included Marxism, Phenomenological Sociology, Critical Theory, and Historical Social Science. The current relationship between comparative education and social science is one of uncertainty, but since social science is seen to be returning to its European roots, the hope is held out for the development of an integrated social theory and method which will provide a much stronger basis for developments in comparative education.

  8. A Comparative Analysis of a Game-Based Mobile Learning Model in Low-Socioeconomic Communities of India

    ERIC Educational Resources Information Center

    Kim, Paul; Buckner, Elizabeth; Kim, Hyunkyung; Makany, Tamas; Taleja, Neha; Parikh, Vallabhi

    2012-01-01

    This study explores the effectiveness of a game-based mobile learning model for children living in underdeveloped regions with significant contextual variations. Data for this study came from a total of 210 children between the ages of 6-14 years old from six marginalized communities in India. The findings reveal that children with little or no…

  9. Comparative analysis of quantum cascade laser modeling based on density matrices and non-equilibrium Green's functions

    SciTech Connect

    Lindskog, M. Wacker, A.; Wolf, J. M.; Liverini, V.; Faist, J.; Trinite, V.; Maisons, G.; Carras, M.; Aidam, R.; Ostendorf, R.

    2014-09-08

    We study the operation of an 8.5 μm quantum cascade laser based on GaInAs/AlInAs lattice matched to InP using three different simulation models based on density matrix (DM) and non-equilibrium Green's function (NEGF) formulations. The latter advanced scheme serves as a validation for the simpler DM schemes and, at the same time, provides additional insight, such as the temperatures of the sub-band carrier distributions. We find that for the particular quantum cascade laser studied here, the behavior is well described by simple quantum mechanical estimates based on Fermi's golden rule. As a consequence, the DM model, which includes second order currents, agrees well with the NEGF results. Both these simulations are in accordance with previously reported data and a second regrown device.

  10. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.

    PubMed

    Michel, F; Westhof, E

    1990-12-01

    Alignment of the 87 available sequences of group I self-splicing introns reveals numerous instances of covariation between distant sites. Some of these covariations cannot be ascribed to historical coincidences or the known secondary structure of group I introns, and are, therefore, best explained as reflecting tertiary contacts. With the help of stereochemical modelling, we have taken advantage of these novel interactions to derive a three-dimensional model of the conserved core of group I introns. Two noteworthy features of that model are its extreme compactness and the fact that all of the most evolutionarily conserved residues happen to converge around the two helices that constitute the substrate of the core ribozyme and the site that binds the guanosine cofactor necessary for self-splicing. Specific functional implications are discussed, both with regard to the way the substrate helices are recognized by the core and possible rearrangements of the introns during the self-splicing process. Concerning potential long-range interactions, emphasis is put on the possible recognition of two consecutive purines in the minor groove of a helix by a GAAA or related terminal loop.

  11. Comparative statistical analysis of planetary surfaces

    NASA Astrophysics Data System (ADS)

    Schmidt, Frédéric; Landais, Francois; Lovejoy, Shaun

    2016-04-01

    In the present study, we aim to provide a statistical and comparative description of topographic fields by using the huge amount of topographic data available for different bodies in the solar system, including Earth, Mars, the Moon etc.. Our goal is to characterize and quantify the geophysical processes involved by a relevant statistical description. In each case, topographic fields exhibit an extremely high variability with details at each scale, from millimeter to thousands of kilometers. This complexity seems to prohibit global descriptions or global topography models. Nevertheless, this topographic complexity is well-known to exhibit scaling laws that establish a similarity between scales and permit simpler descriptions and models. Indeed, efficient simulations can be made using the statistical properties of scaling fields (fractals). But realistic simulations of global topographic fields must be multi (not mono) scaling behaviour, reflecting the extreme variability and intermittency observed in real fields that can not be generated by simple scaling models. A multiscaling theory has been developed in order to model high variability and intermittency. This theory is a good statistical candidate to model the topography field with a limited number of parameters (called the multifractal parameters). After a global analysis of Mars (Landais et. al, 2015) we have performed similar analysis on different body in the solar system including the Moon, Venus and mercury indicating that the mulifractal parameters might be relevant to explain the competition between several processes operating on multiple scales

  12. Extracellular vesicles derived from mesenchymal stromal cells may possess increased therapeutic potential for acute kidney injury compared with conditioned medium in rodent models: A meta-analysis

    PubMed Central

    ZHANG, GUANGYUAN; WANG, DANDAN; MIAO, SHUAI; ZOU, XIANGYU; LIU, GUOHUA; ZHU, YINGJIAN

    2016-01-01

    The potential involvement of the endocrine/paracrine mechanisms in the mesenchymal stromal cells (MSCs) therapy for acute kidney injury (AKI) has been increasingly studied. The aim of the present meta-analysis was to systematically review the therapeutic role of MSC-conditioned medium (CM) or MSCs released by extracellular vesicles (Evs) for the treatment of AKI in rodent models. Studies were identified using PubMed and Scopus databases using a custom search strategy and eligibility criteria. Data regarding serum creatinine (SCr) concentration, CM or Evs, measurement time point, AKI model (toxic or non-toxic) and other parameters, including delivery route, animal type and animal numbers, were extracted. Pooled analysis and subgroup analysis as well as multivariable meta-regression were performed. Heterogeneity and publication bias were also investigated. A total of 13 studies were included and analyzed. Pooled analysis showed reduced SCr (0.93 [0.67, 1.20], mg/dl) in rodent models of AKI after CM/Evs therapy. The results of the subgroup analysis suggested that Evs induced an increased therapeutic effect, in the form of SCr reduction, as compared with CM (P=0.05). There were also other significant influential factors for SCr reduction including measurement time point (P=0.0004) and therapeutic time point (P<0.0001) after surgery. By contrast, parameters such as delivery route, injury type and cell type were not significant influential factors. Multivariable meta-regression analysis showed that measurement time point (P=0.041), therapeutic time point (P=0.03), Evs or CM (P=0.0003) and cell type (P<0.0001) were influential factors in the reduction of SCr. The present meta-analysis indicates that CM or Evs derived from MSCs are able to improve the impaired renal function in rodents modelling AKI. Compared with CM, Evs may produce a more marked therapeutic effect in recovery from renal failure. In addition, CM or Evs administration in early stages of AKI may result in

  13. Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods

    PubMed Central

    Pometti, Carolina L.; Bessega, Cecilia F.; Saidman, Beatriz O.; Vilardi, Juan C.

    2014-01-01

    Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other. PMID:24688293

  14. A comparative analysis of inhibitors of the glycolysis pathway in breast and ovarian cancer cell line models.

    PubMed

    Xintaropoulou, Chrysi; Ward, Carol; Wise, Alan; Marston, Hugh; Turnbull, Arran; Langdon, Simon P

    2015-09-22

    Many cancer cells rely on aerobic glycolysis for energy production and targeting of this pathway is a potential strategy to inhibit cancer cell growth. In this study, inhibition of five glycolysis pathway molecules (GLUT1, HKII, PFKFB3, PDHK1 and LDH) using 9 inhibitors (Phloretin, Quercetin, STF31, WZB117, 3PO, 3-bromopyruvate, Dichloroacetate, Oxamic acid, NHI-1) was investigated in panels of breast and ovarian cancer cell line models. All compounds tested blocked glycolysis as indicated by increased extracellular glucose and decreased lactate production and also increased apoptosis. Sensitivity to several inhibitors correlated with the proliferation rate of the cell lines. Seven compounds had IC50 values that were associated with each other consistent with a shared mechanism of action. A synergistic interaction was revealed between STF31 and Oxamic acid when combined with the antidiabetic drug metformin. Sensitivity to glycolysis inhibition was also examined under a range of O2 levels (21% O2, 7% O2, 2% O2 and 0.5% O2) and greater resistance to the inhibitors was found at low oxygen conditions (7% O2, 2% O2 and 0.5% O2) relative to 21% O2 conditions. These results indicate growth of breast and ovarian cancer cell lines is dependent on all the targets examined in the glycolytic pathway with increased sensitivity to the inhibitors under normoxic conditions. PMID:26259240

  15. Comparative analysis of the influence of Fructus Ligustri Lucidi on a rat lumbar disc herniation model.

    PubMed

    Han, Ya-Xin; Liang, Dong; Han, Xiao-Rui; Liang, De-Yong

    2015-07-01

    Lumbar disc herniation (LDH) is a term used for a group of conditions, including back pain, femoral nerve pain and sciatica. Currently available treatments and surgical options are insufficient for patients with LDH. Fructus Ligustri Lucidi (FLL) is a herb that is used for treating age-associated diseases. The results of the present study suggested that FLL may be used for treatment of patients with LDH. In the present study, matrix metalloproteinase-1, -3, -8 and -9 (MMP-1, -3, -8 and -9) protein and mRNA expression downregulation was observed in patients with LDH according to western blotting and reverse transcription-quantitative polymerase chain reaction. By contrast, upregulation of interleukin-2 (IL-2), IL-6, IL-8 and tumor necrosis factor-α (TNF-α) expression was observed in patients with LDH, according to an enzyme-linked immunosorbent assay. Mechanical allodynia was observed in rats with LDH not treated with FLL; however, not in FLL‑treated rats. IL-2, IL-6, IL-8 and TNF-α expression levels in the serum from untreated rats were significantly higher than that of the FLL‑treated rat models. Protein expression levels of MMPs in FLL-treated rats were lower than those in untreated rats. However, the mechanisms underlying the association between FLL and protein expression levels require further investigation. PMID:25816023

  16. Comparative Analysis of the Flax Immune Receptors L6 and L7 Suggests an Equilibrium-Based Switch Activation Model.

    PubMed

    Bernoux, Maud; Burdett, Hayden; Williams, Simon J; Zhang, Xiaoxiao; Chen, Chunhong; Newell, Kim; Lawrence, Gregory J; Kobe, Bostjan; Ellis, Jeffrey G; Anderson, Peter A; Dodds, Peter N

    2016-01-01

    NOD-like receptors (NLRs) are central components of the plant immune system. L6 is a Toll/interleukin-1 receptor (TIR) domain-containing NLR from flax (Linum usitatissimum) conferring immunity to the flax rust fungus. Comparison of L6 to the weaker allele L7 identified two polymorphic regions in the TIR and the nucleotide binding (NB) domains that regulate both effector ligand-dependent and -independent cell death signaling as well as nucleotide binding to the receptor. This suggests that a negative functional interaction between the TIR and NB domains holds L7 in an inactive/ADP-bound state more tightly than L6, hence decreasing its capacity to adopt the active/ATP-bound state and explaining its weaker activity in planta. L6 and L7 variants with a more stable ADP-bound state failed to bind to AvrL567 in yeast two-hybrid assays, while binding was detected to the signaling active variants. This contrasts with current models predicting that effectors bind to inactive receptors to trigger activation. Based on the correlation between nucleotide binding, effector interaction, and immune signaling properties of L6/L7 variants, we propose that NLRs exist in an equilibrium between ON and OFF states and that effector binding to the ON state stabilizes this conformation, thereby shifting the equilibrium toward the active form of the receptor to trigger defense signaling. PMID:26744216

  17. A comparative analysis of inhibitors of the glycolysis pathway in breast and ovarian cancer cell line models.

    PubMed

    Xintaropoulou, Chrysi; Ward, Carol; Wise, Alan; Marston, Hugh; Turnbull, Arran; Langdon, Simon P

    2015-09-22

    Many cancer cells rely on aerobic glycolysis for energy production and targeting of this pathway is a potential strategy to inhibit cancer cell growth. In this study, inhibition of five glycolysis pathway molecules (GLUT1, HKII, PFKFB3, PDHK1 and LDH) using 9 inhibitors (Phloretin, Quercetin, STF31, WZB117, 3PO, 3-bromopyruvate, Dichloroacetate, Oxamic acid, NHI-1) was investigated in panels of breast and ovarian cancer cell line models. All compounds tested blocked glycolysis as indicated by increased extracellular glucose and decreased lactate production and also increased apoptosis. Sensitivity to several inhibitors correlated with the proliferation rate of the cell lines. Seven compounds had IC50 values that were associated with each other consistent with a shared mechanism of action. A synergistic interaction was revealed between STF31 and Oxamic acid when combined with the antidiabetic drug metformin. Sensitivity to glycolysis inhibition was also examined under a range of O2 levels (21% O2, 7% O2, 2% O2 and 0.5% O2) and greater resistance to the inhibitors was found at low oxygen conditions (7% O2, 2% O2 and 0.5% O2) relative to 21% O2 conditions. These results indicate growth of breast and ovarian cancer cell lines is dependent on all the targets examined in the glycolytic pathway with increased sensitivity to the inhibitors under normoxic conditions.

  18. Comparative Analysis between [(18)F]Fludarabine-PET and [(18)F]FDG-PET in a Murine Model of Inflammation.

    PubMed

    Hovhannisyan, Narinée; Dhilly, Martine; Guillouet, Stéphane; Leporrier, Michel; Barré, Louisa

    2016-06-01

    Lymphoma research has advanced thanks to introduction of [(18)F]fludarabine, a positron-emitting tool. This novel radiotracer has been shown to display a great specificity for lymphoid tissues. However, in a benign process such as inflammation, the uptake of this tracer has not been questioned. Indeed, in inflammatory zones, elevated glucose metabolism rate may result in false-positives with [(18)F]FDG-PET Imaging. In the present investigation, it has been argued that cells, involved in inflammation, might be less avid of [(18)F]fludarabine. To generate inflammation, Swiss mice were intramuscularly injected with 0.1 mL of turpentine oil into the right front paw. Imaging sessions with (18)F-labeled tracers named above were conducted on days 5 and 25 after inoculation. For each animal, volumes of interest (VOI), delineating the muscle of the inflamed (IP) and normal paws (NP), were determined on PET scans. For characterization of inflammation, muscle samples from IP and NP were stained with hematoxylin and eosin (H&E). In early (day 5) inflammation, [(18)F]FDG accumulation was 4.00 ± 1.65 times greater in the IP than in the contralateral NP; for [(18)F]fludarabine, this IP/NP ratio was 1.31 ± 0.28, resulting in a significant difference between radiotracer groups (p < 0.01). In late (day 25) inflammation, the IP/NP ratios were 2.07 ± 0.49 and 1.03 ± 0.07, for [(18)F]FDG and [(18)F]fludarabine, respectively (p < 0.001). [(18)F]Fludarabine showed significantly weaker uptake in inflammation when compared with [(18)F]FDG. This encouraging finding suggests that [(18)F]fludarabine-PET might well be a robust approach for distinguishing tumor from inflammatory tissue, avoiding false-positive PET results and thus enabling an accurate imaging of lymphoma.

  19. Comparative Analysis Between Thoracic Spinal Cord and Sacral Neuromodulation in a Rat Spinal Cord Injury Model: A Preliminary Report of a Rat Spinal Cord Stimulation Model

    PubMed Central

    Lee, Chang-Hyun; Kwon, Ji Woong; Yoon, Cheol-Yong; Lim, Jae-Young; Kim, Ki-Jeong; Jahng, Tae-Ahn; Kim, Hyun-Jib

    2013-01-01

    Objective The purpose of this study is to compare a neuroprotective effect of thoracic cord neuromodulation to that of sacral nerve neuromodulation in rat thoracic spinal cord injury (SCI) model. Methods Twenty female Sprague Dawley rats were randomly divided into 4 groups: the normal control group (n=5), SCI with sham stimulation group (SCI, n=5), SCI with electrical stimulation at thoracic spinal cord (SCI + TES, n=5), and SCI with electrical stimulation at sacral nerve (SCI + SES, n=5). Spinal cord was injured by an impactor which dropped from 25mm height. Electrical stimulation was performed by the following protocol: pulse duration, 0.1ms; frequency, 20 Hz; stimulation time, 30 minutes; and stimulation duration at thoracic epidural space and S2 or 3 neural foramina for 4 weeks. Locomotor function, urodynamic study, muscle weights, and fiber cross sectional area (CSA) were investigated. Results All rats of the SCI + TES group expired within 3 days after the injury. The locomotor function of all survived rats improved over time but there was no significant difference between the SCI and the SCI + SES group. All rats experienced urinary retention after the injury and recovered self-voiding after 3-9 days. Voiding contraction interval was 25.5±7.5 minutes in the SCI group, 16.5±5.3 minutes in the SCI+SES group, and 12.5±4.2 minutes in the control group. The recovery of voiding contraction interval was significant in the SCI + SES group comparing to the SCI group (p<0.05). Muscle weight and CSA were slightly greater in the SCI + SES than in the SCI group, but the difference was not significant. Conclusion We failed to establish a rat spinal cord stimulation model. However, sacral neuromodulation have a therapeutic potential to improve neurogenic bladder and muscle atrophy. PMID:24757451

  20. [A model-based meta-analysis to compare urate-lowering response rate of febuxostat and allopurinol in gout patient].

    PubMed

    Sun, Yi; Li, Liang; Zhou, Tian-Yan; Lu, Wei

    2014-12-01

    This study aims to compare the urate-lowering response rate of febuxostat and allopurinol in gout patient using a model-based meta-analysis. The literature search identified 22 clinical trials of gout with a total of 43 unique treatment arms that met our inclusion criteria, and a total of 6 365 gout patients were included in the study. The response rates of allopuriol and febuxostat were characterized by Tmax model and Emax model respectively, and the effect of baseline serum uric acid (sUA) and patient type on the drug effect was tested. The results showed that allopurinol can reach an average maximum response rate of 50.8% while febuxostat can reach a 100% response rate within a very short time, and the ED50 was 34.3 mg. Covariate analysis revealed that baseline sUA has a negative effect on response rate of allopurinol, and a positive effect on the predicted ED50 of febuxostat. For patients who had shown inadequate response to prior allopurinol treatment, the average response rate was about half that of the allopurinol responder patients.

  1. Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods.

    PubMed

    Evans, H R; Karmakharm, T; Lawson, M A; Walker, R E; Harris, W; Fellows, C; Huggins, I D; Richmond, P; Chantry, A D

    2016-02-01

    Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (±19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (±0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images), it

  2. Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods.

    PubMed

    Evans, H R; Karmakharm, T; Lawson, M A; Walker, R E; Harris, W; Fellows, C; Huggins, I D; Richmond, P; Chantry, A D

    2016-02-01

    Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (±19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (±0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images), it

  3. Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods☆

    PubMed Central

    Evans, H.R.; Karmakharm, T.; Lawson, M.A.; Walker, R.E.; Harris, W.; Fellows, C.; Huggins, I.D.; Richmond, P.; Chantry, A.D.

    2016-01-01

    Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (± 19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (± 0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images

  4. Comparing the Discrete and Continuous Logistic Models

    ERIC Educational Resources Information Center

    Gordon, Sheldon P.

    2008-01-01

    The solutions of the discrete logistic growth model based on a difference equation and the continuous logistic growth model based on a differential equation are compared and contrasted. The investigation is conducted using a dynamic interactive spreadsheet. (Contains 5 figures.)

  5. Modeling corrosion inhibition efficacy of small organic molecules as non-toxic chromate alternatives using comparative molecular surface analysis (CoMSA).

    PubMed

    Fernandez, Michael; Breedon, Michael; Cole, Ivan S; Barnard, Amanda S

    2016-10-01

    Traditionally many structural alloys are protected by primer coatings loaded with corrosion inhibiting additives. Strontium Chromate (or other chromates) have been shown to be extremely effectively inhibitors, and find extensive use in protective primer formulations. Unfortunately, hexavalent chromium which imbues these coatings with their corrosion inhibiting properties is also highly toxic, and their use is being increasingly restricted by legislation. In this work we explore a novel tridimensional Quantitative-Structure Property Relationship (3D-QSPR) approach, comparative molecular surface analysis (CoMSA), which was developed to recognize "high-performing" corrosion inhibitor candidates from the distributions of electronegativity, polarizability and van der Waals volume on the molecular surfaces of 28 small organic molecules. Multivariate statistical analysis identified five prototypes molecules, which are capable of explaining 71% of the variance within the inhibitor data set; whilst a further five molecules were also identified as archetypes, describing 75% of data variance. All active corrosion inhibitors, at a 80% threshold, were successfully recognized by the CoMSA model with adequate specificity and precision higher than 70% and 60%, respectively. The model was also capable of identifying structural patterns, that revealed reasonable starting points for where structural changes may augment corrosion inhibition efficacy. The presented methodology can be applied to other functional molecules and extended to cover structure-activity studies in a diverse range of areas such as drug design and novel material discovery.

  6. Modeling corrosion inhibition efficacy of small organic molecules as non-toxic chromate alternatives using comparative molecular surface analysis (CoMSA).

    PubMed

    Fernandez, Michael; Breedon, Michael; Cole, Ivan S; Barnard, Amanda S

    2016-10-01

    Traditionally many structural alloys are protected by primer coatings loaded with corrosion inhibiting additives. Strontium Chromate (or other chromates) have been shown to be extremely effectively inhibitors, and find extensive use in protective primer formulations. Unfortunately, hexavalent chromium which imbues these coatings with their corrosion inhibiting properties is also highly toxic, and their use is being increasingly restricted by legislation. In this work we explore a novel tridimensional Quantitative-Structure Property Relationship (3D-QSPR) approach, comparative molecular surface analysis (CoMSA), which was developed to recognize "high-performing" corrosion inhibitor candidates from the distributions of electronegativity, polarizability and van der Waals volume on the molecular surfaces of 28 small organic molecules. Multivariate statistical analysis identified five prototypes molecules, which are capable of explaining 71% of the variance within the inhibitor data set; whilst a further five molecules were also identified as archetypes, describing 75% of data variance. All active corrosion inhibitors, at a 80% threshold, were successfully recognized by the CoMSA model with adequate specificity and precision higher than 70% and 60%, respectively. The model was also capable of identifying structural patterns, that revealed reasonable starting points for where structural changes may augment corrosion inhibition efficacy. The presented methodology can be applied to other functional molecules and extended to cover structure-activity studies in a diverse range of areas such as drug design and novel material discovery. PMID:27362530

  7. Comparative dynamics in a health investment model.

    PubMed

    Eisenring, C

    1999-10-01

    The method of comparative dynamics fully exploits the inter-temporal structure of optimal control models. I derive comparative dynamic results in a simplified demand for health model. The effect of a change in the depreciation rate on the optimal paths for health capital and investment in health is studied by use of a phase diagram.

  8. Comparing Techniques for Certified Static Analysis

    NASA Technical Reports Server (NTRS)

    Cachera, David; Pichardie, David

    2009-01-01

    A certified static analysis is an analysis whose semantic validity has been formally proved correct with a proof assistant. The recent increasing interest in using proof assistants for mechanizing programming language metatheory has given rise to several approaches for certification of static analysis. We propose a panorama of these techniques and compare their respective strengths and weaknesses.

  9. Three-dimensional comparative analysis of bitemarks.

    PubMed

    Lasser, Allan J; Warnick, Allan J; Berman, Gary M

    2009-05-01

    Historically, the inability to accurately represent bitemarks and other wound patterns has limited their evidentiary value. The development of the ABFO #2 scale by Krauss and Hyzer enabled forensic odontologists to correct for most photographic plane distortions. The technique presented here uses the ABFO #2 scale in conjunction with the evolving technologies of laser scanners and comparative software commonly used by the automobile industry for three-dimensional (3D) analysis. The 3D software comparison was performed in which measurements were analyzed of the normal distance for each point on the teeth relative to the bitemarks. It created a color-mapped display of the bitemark model, with the color indicating the deviation at each point. There was a correlation between the bitemark and the original teeth. PMID:19432742

  10. Statistical Downscaling of General Circulation Model Output for the Northern Great Plains: A Comparative Analysis of Downscaling Methods for Temperature and Precipitation

    NASA Astrophysics Data System (ADS)

    Coburn, J.

    2013-12-01

    General Circulation Models have come to be the foremost dynamical tools to understanding and predicting the complex changes associated with climate change, yet the grid spacing of these models are far too course for use in local and regional impact studies. Recent research has highlighted the possibility to downscale these course resolution data through regional climate models (RCMs) or through statistical means. Given the current changes in climate due to natural and human made forcings and the importance of the Northern Great Plains (NGP) to the global agricultural food supply, it is important to gain insight into the small scale effects these changes will have on this important region. Here is presented an analysis of three statistical downscaling methods for translating the course scale information to a more usable scale planners and the public can use for more effective decision making. Regression and weather typing methods are applied to ten GCM outputs and compared for their effectiveness and ability to accurately generate fine scale daily and monthly temperature and precipitation data for the NGP. The implications are explored by utilizing the most robust method to extrapolate the outcomes of the 2.6, 4.5 and 8.5 RCP experiments for future climate.

  11. Comparative analysis of the protective effects of caffeic acid phenethyl ester (CAPE) on pulmonary contusion lung oxidative stress and serum copper and zinc levels in experimental rat model.

    PubMed

    Sırmalı, Mehmet; Solak, Okan; Tezel, Cagatay; Sırmalı, Rana; Ginis, Zeynep; Atik, Dilek; Agackıran, Yetkin; Koylu, Halis; Delibas, Namık

    2013-01-01

    The aim of this study was to investigate the effects of caffeic acid phenethyl ester (CAPE) in the lungs by biochemical and histopathological analyses in an experimental isolated lung contusion model. Eighty-one male Sprague-Dawley rats were used. The animals were divided randomly into four groups: group 1 (n = 9) was defined as without contusion and without CAPE injection. Group 2 (n = 9) was defined as CAPE 10 μmol/kg injection without lung contusion. Group 3 (n = 36) was defined as contusion without CAPE-administrated group which consisted of four subgroups that were created according to analysis between days 0, 1, 2, and 3. Group 4 (n = 27) was defined as CAPE 10 μmol/kg administrated after contusion group divided into three subgroups according to analysis on days 1, 2, and 3. CAPE 10 μmol/kg was injected intraperitoneally 30 min after trauma and on days 1 and 2. Blood samples were obtained to measure catalase (CAT) and superoxide dismutase (SOD) activities and level of malondialdehyde (MDA) and for blood gas analysis. Trace elements such as zinc and copper were measured in serum. The lung tissue was also removed for histopathological examination. Isolated lung contusion increased serum and tissue SOD and CAT activities and MDA levels (p < 0.05). Both serum and tissue SOD, MDA, and CAT levels on day 3 were lower in group 4 compared to group 3 (p < 0.05). Further, the levels of SOD, MDA, and CAT in group 4 were similar compared to group 1 (p > 0.05). CAPE also had a significant beneficial effect on blood gases (p < 0.05). Both serum zinc and copper levels were (p < 0.05) influenced by the administration of CAPE. Histopathological examination revealed lower scores in group 4 compared to group 3 (p < 0.05) and no significant differences compared to group 1 (p > 0.05). CAPE appears to be effective in protecting against severe oxidative stress and tissue damage caused by pulmonary contusion in an

  12. Comparative analysis of the food webs of two intertidal mudflats during two seasons using inverse modelling: Aiguillon Cove and Brouage Mudflat, France

    NASA Astrophysics Data System (ADS)

    Degré, Delphine; Leguerrier, Delphine; Armynot du Chatelet, Eric; Rzeznik, Jadwiga; Auguet, Jean-Christophe; Dupuy, Christine; Marquis, Elise; Fichet, Denis; Struski, Caroline; Joyeux, Emmanuel; Sauriau, Pierre-Guy; Niquil, Nathalie

    2006-08-01

    Inverse analysis was used to model the food webs of two intertidal mudflat ecosystems: Aiguillon Cove (AC) and Brouage Mudflat (BM) (south-western Atlantic coast, France). The aim of the present study is to describe and compare the functioning of these two ecosystems. The method of inverse analysis has been adapted in order to take into account, in a single calculation, two seasons: spring/summer (mid-March to mid-October) and autumn/winter (the rest of the year). Gathering all available data on the two sites, the most important gaps in knowledge were identified with the help of sensitivity analyses: they concerned mainly the exports of material by grazing fish (such as mullet Liza ramada), resuspension of microphytobenthos, and fluxes linked to microfauna which is poorly known for the two systems. The two sites presented the same overall type of functioning (net import of detritus, export of living organic material and higher faunal activity during spring/summer). In both ecosystems, primary production was dominated by the microphytobenthic production, of which a great part was exported via water-column advection and biotic vectors (grazing fish), while many secondary producers also used detritus as a food resource. Each system also had its own characteristics, one BM being much more seasonally driven than the other AC. It appeared essential to take the seasons into account, as variations in microphytobenthos production and in meiofauna, macrofauna and biotic vectors led to great differences in the food-web organisation.

  13. Structural modeling and docking studies of ribose 5-phosphate isomerase from Leishmania major and Homo sapiens: a comparative analysis for Leishmaniasis treatment.

    PubMed

    Capriles, Priscila V S Z; Baptista, Luiz Phillippe R; Guedes, Isabella A; Guimarães, Ana Carolina R; Custódio, Fabio L; Alves-Ferreira, Marcelo; Dardenne, Laurent E

    2015-02-01

    Leishmaniases are caused by protozoa of the genus Leishmania and are considered the second-highest cause of death worldwide by parasitic infection. The drugs available for treatment in humans are becoming ineffective mainly due to parasite resistance; therefore, it is extremely important to develop a new chemotherapy against these parasites. A crucial aspect of drug design development is the identification and characterization of novel molecular targets. In this work, through an in silico comparative analysis between the genomes of Leishmania major and Homo sapiens, the enzyme ribose 5-phosphate isomerase (R5PI) was indicated as a promising molecular target. R5PI is an important enzyme that acts in the pentose phosphate pathway and catalyzes the interconversion of d-ribose-5-phosphate (R5P) and d-ribulose-5-phosphate (5RP). R5PI activity is found in two analogous groups of enzymes called RpiA (found in H. sapiens) and RpiB (found in L. major). Here, we present the first report of the three-dimensional (3D) structures and active sites of RpiB from L. major (LmRpiB) and RpiA from H. sapiens (HsRpiA). Three-dimensional models were constructed by applying a hybrid methodology that combines comparative and ab initio modeling techniques, and the active site was characterized based on docking studies of the substrates R5P (furanose and ring-opened forms) and 5RP. Our comparative analyses show that these proteins are structural analogs and that distinct residues participate in the interconversion of R5P and 5RP. We propose two distinct reaction mechanisms for the reversible isomerization of R5P to 5RP, which is catalyzed by LmRpiB and HsRpiA. We expect that the present results will be important in guiding future molecular modeling studies to develop new drugs that are specially designed to inhibit the parasitic form of the enzyme without significant effects on the human analog.

  14. High Altitude Long Endurance UAV Analysis Model Development and Application Study Comparing Solar Powered Airplane and Airship Station-Keeping Capabilities

    NASA Technical Reports Server (NTRS)

    Ozoroski, Thomas A.; Nickol, Craig L.; Guynn, Mark D.

    2015-01-01

    There have been ongoing efforts in the Aeronautics Systems Analysis Branch at NASA Langley Research Center to develop a suite of integrated physics-based computational utilities suitable for modeling and analyzing extended-duration missions carried out using solar powered aircraft. From these efforts, SolFlyte has emerged as a state-of-the-art vehicle analysis and mission simulation tool capable of modeling both heavier-than-air (HTA) and lighter-than-air (LTA) vehicle concepts. This study compares solar powered airplane and airship station-keeping capability during a variety of high altitude missions, using SolFlyte as the primary analysis component. Three Unmanned Aerial Vehicle (UAV) concepts were designed for this study: an airplane (Operating Empty Weight (OEW) = 3285 kilograms, span = 127 meters, array area = 450 square meters), a small airship (OEW = 3790 kilograms, length = 115 meters, array area = 570 square meters), and a large airship (OEW = 6250 kilograms, length = 135 meters, array area = 1080 square meters). All the vehicles were sized for payload weight and power requirements of 454 kilograms and 5 kilowatts, respectively. Seven mission sites distributed throughout the United States were selected to provide a basis for assessing the vehicle energy budgets and site-persistent operational availability. Seasonal, 30-day duration missions were simulated at each of the sites during March, June, September, and December; one-year duration missions were simulated at three of the sites. Atmospheric conditions during the simulated missions were correlated to National Climatic Data Center (NCDC) historical data measurements at each mission site, at four flight levels. Unique features of the SolFlyte model are described, including methods for calculating recoverable and energy-optimal flight trajectories and the effects of shadows on solar energy collection. Results of this study indicate that: 1) the airplane concept attained longer periods of on

  15. Comparative Environmental Threat Analysis: Three Case Studies.

    ERIC Educational Resources Information Center

    Latour, J. B.; Reiling, R.

    1994-01-01

    Reviews how carrying capacity for different environmental problems is operationalized. Discusses whether it is possible to compare threats, using the exceeding of carrying capacity as a yardstick. Points out problems in comparative threat analysis using three case studies: threats to European groundwater resources, threats to ecosystems in Europe,…

  16. Comparing models of Red Knot population dynamics

    USGS Publications Warehouse

    McGowan, Conor

    2015-01-01

    Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

  17. Fold assessment for comparative protein structure modeling.

    PubMed

    Melo, Francisco; Sali, Andrej

    2007-11-01

    Accurate and automated assessment of both geometrical errors and incompleteness of comparative protein structure models is necessary for an adequate use of the models. Here, we describe a composite score for discriminating between models with the correct and incorrect fold. To find an accurate composite score, we designed and applied a genetic algorithm method that searched for a most informative subset of 21 input model features as well as their optimized nonlinear transformation into the composite score. The 21 input features included various statistical potential scores, stereochemistry quality descriptors, sequence alignment scores, geometrical descriptors, and measures of protein packing. The optimized composite score was found to depend on (1) a statistical potential z-score for residue accessibilities and distances, (2) model compactness, and (3) percentage sequence identity of the alignment used to build the model. The accuracy of the composite score was compared with the accuracy of assessment by single and combined features as well as by other commonly used assessment methods. The testing set was representative of models produced by automated comparative modeling on a genomic scale. The composite score performed better than any other tested score in terms of the maximum correct classification rate (i.e., 3.3% false positives and 2.5% false negatives) as well as the sensitivity and specificity across the whole range of thresholds. The composite score was implemented in our program MODELLER-8 and was used to assess models in the MODBASE database that contains comparative models for domains in approximately 1.3 million protein sequences.

  18. Comparative analysis of planetary laser ranging concepts

    NASA Astrophysics Data System (ADS)

    Dirkx, D.; Bauer, S.; Noomen, R.; Vermeersen, B. L. A.; Visser, P. N.

    2014-12-01

    Laser ranging is an emerging technology for tracking interplanetary missions, offering improved range accuracy and precision (mm-cm), compared to existing DSN tracking. The ground segment uses existing Satellite Laser Ranging (SLR) technology, whereas the space segment is modified with an active system. In a one-way system, such as that currently being used on the LRO spacecraft (Zuber et al., 2010), only an active detector is required on the spacecraft. For a two-way system, such as that tested by using the laser altimeter system on the MESSENGER spacecraft en route to Mercury (Smith et al., 2006), a laser transmitter system is additionally placed on the space segment, which will asynchronously fire laser pulses towards the ground stations. Although the one-way system requires less hardware, clock errors on both the space and ground segments will accumulate over time, polluting the range measurements. For a two-way system, the range measurements are only sensitive to clock errors integrated over the the two-way light time.We investigate the performance of both one- and two-way laser range systems by simulating their operation. We generate realizations of clock error time histories from Allan variance profiles, and use them to create range measurement error profiles. We subsequently perform the orbit determination process from this data to quanitfy the system's performance. For our simulations, we use two test cases: a lunar orbiter similar to LRO and a Phobos lander similar to the Phobos Laser Ranging concept (Turyshev et al., 2010). For the lunar orbiter, we include an empirical model for unmodelled non-gravitational accelerations in our truth model to include errors ihe dynamics. We include the estimation of clock parameters over a number of arc lengths for our simulations of the one-way range system and use a variety of state arc durations for the lunar orbiter simulations.We perform Monte Carlo simulations and generate true error distributions for both

  19. Effect of genetic algorithm as a variable selection method on different chemometric models applied for the analysis of binary mixture of amoxicillin and flucloxacillin: A comparative study

    NASA Astrophysics Data System (ADS)

    Attia, Khalid A. M.; Nassar, Mohammed W. I.; El-Zeiny, Mohamed B.; Serag, Ahmed

    2016-03-01

    Different chemometric models were applied for the quantitative analysis of amoxicillin (AMX), and flucloxacillin (FLX) in their binary mixtures, namely, partial least squares (PLS), spectral residual augmented classical least squares (SRACLS), concentration residual augmented classical least squares (CRACLS) and artificial neural networks (ANNs). All methods were applied with and without variable selection procedure (genetic algorithm GA). The methods were used for the quantitative analysis of the drugs in laboratory prepared mixtures and real market sample via handling the UV spectral data. Robust and simpler models were obtained by applying GA. The proposed methods were found to be rapid, simple and required no preliminary separation steps.

  20. Effect of genetic algorithm as a variable selection method on different chemometric models applied for the analysis of binary mixture of amoxicillin and flucloxacillin: A comparative study.

    PubMed

    Attia, Khalid A M; Nassar, Mohammed W I; El-Zeiny, Mohamed B; Serag, Ahmed

    2016-03-01

    Different chemometric models were applied for the quantitative analysis of amoxicillin (AMX), and flucloxacillin (FLX) in their binary mixtures, namely, partial least squares (PLS), spectral residual augmented classical least squares (SRACLS), concentration residual augmented classical least squares (CRACLS) and artificial neural networks (ANNs). All methods were applied with and without variable selection procedure (genetic algorithm GA). The methods were used for the quantitative analysis of the drugs in laboratory prepared mixtures and real market sample via handling the UV spectral data. Robust and simpler models were obtained by applying GA. The proposed methods were found to be rapid, simple and required no preliminary separation steps.

  1. MycoCAP - Mycobacterium Comparative Analysis Platform

    PubMed Central

    Choo, Siew Woh; Ang, Mia Yang; Dutta, Avirup; Tan, Shi Yang; Siow, Cheuk Chuen; Heydari, Hamed; Mutha, Naresh V. R.; Wee, Wei Yee; Wong, Guat Jah

    2015-01-01

    Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my PMID:26666970

  2. Network Analysis in Comparative Social Sciences

    ERIC Educational Resources Information Center

    Vera, Eugenia Roldan; Schupp, Thomas

    2006-01-01

    This essay describes the pertinence of Social Network Analysis (SNA) for the social sciences in general, and discusses its methodological and conceptual implications for comparative research in particular. The authors first present a basic summary of the theoretical and methodological assumptions of SNA, followed by a succinct overview of its…

  3. Teacher Policy: A Framework for Comparative Analysis

    ERIC Educational Resources Information Center

    Tatto, Maria Teresa

    2008-01-01

    This article outlines a framework for analysis of teacher focused policy studies within an international and comparative perspective. Using the notion of the professional life cycle of teachers, the article examines examples of key empirical studies that illustrate the impact of policy on addressing such issues as teacher recruitment, education,…

  4. MycoCAP - Mycobacterium Comparative Analysis Platform.

    PubMed

    Choo, Siew Woh; Ang, Mia Yang; Dutta, Avirup; Tan, Shi Yang; Siow, Cheuk Chuen; Heydari, Hamed; Mutha, Naresh V R; Wee, Wei Yee; Wong, Guat Jah

    2015-01-01

    Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my.

  5. Applying the Rasch Model to Measure Mobility of Women: A Comparative Analysis of Mobility of Informal Workers in Fisheries in Kerala, India.

    PubMed

    Menon, Nikhila

    2016-01-01

    Mobility or freedom and ability to move is gendered in many cultural contexts. In this paper I analyse mobility associated with work from the capability approach perspective of Sen. This is an empirical paper which uses the Rasch Rating Scale Model (RSM) to construct the measure of mobility of women for the first time in the development studies discourse. I construct a measure of mobility (latent trait) of women workers engaged in two types of informal work, namely, peeling work and fish vending, in fisheries in the cultural context of India. The scale measure enables first, to test the unidimensionality of my construct of mobility of women and second, to analyse the domains of mobility of women workers. The comparative analysis of the scale of permissibility of mobility constructed using the RSM for the informal women workers shows that women face constraints on mobility in social and personal spaces in the socially advanced state of Kerala in India. Work mobility does not expand the real freedoms, hence work mobility can be termed as bounded capability which is a capability limited or bounded by either the social, cultural and gender norms or a combination of all of these. Therefore at the macro level, growth in informal employment in sectors like fisheries which improve mobility of women through work mobility does not necessarily expand the capability sets by contributing to greater freedoms and transformational mobility. This paper has a significant methodological contribution in that it uses an innovative method for the measurement of mobility of women in the development studies discipline.

  6. Applying the Rasch Model to Measure Mobility of Women: A Comparative Analysis of Mobility of Informal Workers in Fisheries in Kerala, India.

    PubMed

    Menon, Nikhila

    2016-01-01

    Mobility or freedom and ability to move is gendered in many cultural contexts. In this paper I analyse mobility associated with work from the capability approach perspective of Sen. This is an empirical paper which uses the Rasch Rating Scale Model (RSM) to construct the measure of mobility of women for the first time in the development studies discourse. I construct a measure of mobility (latent trait) of women workers engaged in two types of informal work, namely, peeling work and fish vending, in fisheries in the cultural context of India. The scale measure enables first, to test the unidimensionality of my construct of mobility of women and second, to analyse the domains of mobility of women workers. The comparative analysis of the scale of permissibility of mobility constructed using the RSM for the informal women workers shows that women face constraints on mobility in social and personal spaces in the socially advanced state of Kerala in India. Work mobility does not expand the real freedoms, hence work mobility can be termed as bounded capability which is a capability limited or bounded by either the social, cultural and gender norms or a combination of all of these. Therefore at the macro level, growth in informal employment in sectors like fisheries which improve mobility of women through work mobility does not necessarily expand the capability sets by contributing to greater freedoms and transformational mobility. This paper has a significant methodological contribution in that it uses an innovative method for the measurement of mobility of women in the development studies discipline. PMID:26784381

  7. Comparative analysis of CMIP3 and CMIP5 global climate models for simulating the daily mean, maximum, and minimum temperatures and daily precipitation over China

    NASA Astrophysics Data System (ADS)

    Sun, Qiaohong; Miao, Chiyuan; Duan, Qingyun

    2015-05-01

    This study assesses the simulations of the daily mean, maximum, and minimum temperatures and daily precipitation over China during the period 1990-1999, based on phase 3 and phase 5 of the Coupled Model Intercomparison Project (CMIP3 and CMIP5). Fourteen CMIP3 models and 14 CMIP5 models were investigated over eight regions across China. Skill scores quantifying the match between the simulated and observed probability density functions (PDFs) were applied to evaluate the performance of the models. For daily mean, maximum, and minimum temperatures, the results revealed that CMIP3 and CMIP5 models captured the basic pattern of the observed PDFs in all regions. However, the probabilities at lower values were overestimated in most models. In all regions except the west of Northwest China (region 7), all CMIP5 models captured more than 80% of the observed PDFs. Compared with performance at the annual time scale, the models tended to perform relatively worse over the period June to August. The performances of the CMIP5 and CMIP3 models were not as good for daily precipitation as for daily temperature, and the skill scores for precipitation were generally lower than 0.7 in all regions. The amount of drizzle (daily precipitation < 5 mm) was overestimated notably in all regions. The amount of very heavy precipitation (daily precipitation ≥ 20 mm) tended to be underestimated in humid regions but overestimated in arid regions. Compared with CMIP3, CMIP5 models showed some improvements in the simulation of daily mean, maximum, and minimum temperatures, but there was a lack of apparent improvement for simulation of daily precipitation.

  8. National Launch System comparative economic analysis

    NASA Technical Reports Server (NTRS)

    Prince, A.

    1992-01-01

    Results are presented from an analysis of economic benefits (or losses), in the form of the life cycle cost savings, resulting from the development of the National Launch System (NLS) family of launch vehicles. The analysis was carried out by comparing various NLS-based architectures with the current Shuttle/Titan IV fleet. The basic methodology behind this NLS analysis was to develop a set of annual payload requirements for the Space Station Freedom and LEO, to design launch vehicle architectures around these requirements, and to perform life-cycle cost analyses on all of the architectures. A SEI requirement was included. Launch failure costs were estimated and combined with the relative reliability assumptions to measure the effects of losses. Based on the analysis, a Shuttle/NLS architecture evolving into a pressurized-logistics-carrier/NLS architecture appears to offer the best long-term cost benefit.

  9. Image analysis in comparative genomic hybridization

    SciTech Connect

    Lundsteen, C.; Maahr, J.; Christensen, B.

    1995-01-01

    Comparative genomic hybridization (CGH) is a new technique by which genomic imbalances can be detected by combining in situ suppression hybridization of whole genomic DNA and image analysis. We have developed software for rapid, quantitative CGH image analysis by a modification and extension of the standard software used for routine karyotyping of G-banded metaphase spreads in the Magiscan chromosome analysis system. The DAPI-counterstained metaphase spread is karyotyped interactively. Corrections for image shifts between the DAPI, FITC, and TRITC images are done manually by moving the three images relative to each other. The fluorescence background is subtracted. A mean filter is applied to smooth the FITC and TRITC images before the fluorescence ratio between the individual FITC and TRITC-stained chromosomes is computed pixel by pixel inside the area of the chromosomes determined by the DAPI boundaries. Fluorescence intensity ratio profiles are generated, and peaks and valleys indicating possible gains and losses of test DNA are marked if they exceed ratios below 0.75 and above 1.25. By combining the analysis of several metaphase spreads, consistent findings of gains and losses in all or almost all spreads indicate chromosomal imbalance. Chromosomal imbalances are detected either by visual inspection of fluorescence ratio (FR) profiles or by a statistical approach that compares FR measurements of the individual case with measurements of normal chromosomes. The complete analysis of one metaphase can be carried out in approximately 10 minutes. 8 refs., 7 figs., 1 tab.

  10. Comparative performance analysis of mobile displays

    NASA Astrophysics Data System (ADS)

    Safaee-Rad, Reza; Aleksic, Milivoje

    2012-01-01

    Cell-phone display performance (in terms of color quality and optical efficiency) has become a critical factor in creating a positive user experience. As a result, there is a significant amount of effort by cell-phone OEMs to provide a more competitive display solution. This effort is focused on using different display technologies (with significantly different color characteristics) and more sophisticated display processors. In this paper, the results of a mobile-display comparative performance analysis are presented. Three cell-phones from major OEMs are selected and their display performances are measured and quantified. Comparative performance analysis is done using display characteristics such as display color gamut size, RGB-channels crosstalk, RGB tone responses, gray tracking performance, color accuracy, and optical efficiency.

  11. Comparative analysis of twelve Dothideomycete plant pathogens

    SciTech Connect

    Ohm, Robin; Aerts, Andrea; Salamov, Asaf; Goodwin, Stephen B.; Grigoriev, Igor

    2011-03-11

    The Dothideomycetes are one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related Dothideomycete species can have very diverse host plants. Twelve Dothideomycete genomes have currently been sequenced by the Joint Genome Institute and other sequencing centers. They can be accessed via Mycocosm which has tools for comparative analysis

  12. Nuclear matrix elements for 0νβ{sup −}β{sup −} decays: Comparative analysis of the QRPA, shell model and IBM predictions

    SciTech Connect

    Civitarese, Osvaldo; Suhonen, Jouni

    2013-12-30

    In this work we report on general properties of the nuclear matrix elements involved in the neutrinoless double β{sup −} decays (0νβ{sup −}β{sup −} decays) of several nuclei. A summary of the values of the NMEs calculated along the years by the Jyväskylä-La Plata collaboration is presented. These NMEs, calculated in the framework of the quasiparticle random phase approximation (QRPA), are compared with those of the other available calculations, like the Shell Model (ISM) and the interacting boson model (IBA-2)

  13. Comparing fluid mechanics models with experimental data.

    PubMed Central

    Spedding, G R

    2003-01-01

    The art of modelling the physical world lies in the appropriate simplification and abstraction of the complete problem. In fluid mechanics, the Navier-Stokes equations provide a model that is valid under most circumstances germane to animal locomotion, but the complexity of solutions provides strong incentive for the development of further, more simplified practical models. When the flow organizes itself so that all shearing motions are collected into localized patches, then various mathematical vortex models have been very successful in predicting and furthering the physical understanding of many flows, particularly in aerodynamics. Experimental models have the significant added convenience that the fluid mechanics can be generated by a real fluid, not a model, provided the appropriate dimensionless groups have similar values. Then, analogous problems can be encountered in making intelligible but independent descriptions of the experimental results. Finally, model predictions and experimental results may be compared if, and only if, numerical estimates of the likely variations in the tested quantities are provided. Examples from recent experimental measurements of wakes behind a fixed wing and behind a bird in free flight are used to illustrate these principles. PMID:14561348

  14. Comparative analysis of two hydrological models with different glacier parameterisations for climate impact assessment and water resources management in the Syrdarya Basin, Central Asia

    NASA Astrophysics Data System (ADS)

    Gafurov, Abror; Duethmann, Doris; Agaltseva, Natalya; Merkushkin, Alexander; Pak, Alexander; Kriegel, David; Huss, Matthias; Güntner, Andreas; Merz, Bruno; Unger-Shayesteh, Katy; Mannig, Birgit; Paeth, Heiko; Vorogushyn, Sergiy

    2014-05-01

    Central Asian river basins in general and zones of run-off formation in particular are currently experiencing the impact of increasing temperatures and changes in precipitation. The headwaters thus exhibit negative glacier mass balances, decreasing glacierisation, changes in snow cover characteristics and changing runoff response. These changes are likely to intensify in future under the changing climate. Both hydropower industry and irrigated agriculture in the downstream areas strongly depend on the water amount, its seasonal and long-term distribution. This fact calls for an effort to reliably assess water availability in the runoff formation zone of Central Asia in order to improve water management policy in the region. One of the approaches to assessment of water resources is the evaluation of climate scenarios with the climate-and-hydrology model chain. Application of several models allows reducing the modeling uncertainty and proceeding with more robust water balance components assessment. We present the comparison of the two hydrological models AISHF (Automated Information System for Hydrological Forecasting) developed at the Centre for Hydrometeorology of Uzbekistan and WASA run at GFZ Potsdam, implemented for the Naryn and Karadarya basins (Syrdarya). These models use different parameterization and calibration schemes. Whereas in the AISHF model glacier dynamics is considered in scenarios of glacier area loss, the WASA model simulates continuous glacier mass balance, glacier area and volume evolution based on meteorological drivers. Consideration of initial glacier volume and its temporal dynamics can be essential for climate impact assessment in transient model simulations. The impact of climate change scenarios, developed with the regional climate model REMO at the University of Würzburg, are compared with respect to total discharge dynamics and runoff contributions from glacier, snowmelt and rainfall. Implications of water availability assessment

  15. Comparative Genome Analysis of Enterobacter cloacae

    PubMed Central

    Liu, Wing-Yee; Wong, Chi-Fat; Chung, Karl Ming-Kar; Jiang, Jing-Wei; Leung, Frederick Chi-Ching

    2013-01-01

    The Enterobacter cloacae species includes an extremely diverse group of bacteria that are associated with plants, soil and humans. Publication of the complete genome sequence of the plant growth-promoting endophytic E. cloacae subsp. cloacae ENHKU01 provided an opportunity to perform the first comparative genome analysis between strains of this dynamic species. Examination of the pan-genome of E. cloacae showed that the conserved core genome retains the general physiological and survival genes of the species, while genomic factors in plasmids and variable regions determine the virulence of the human pathogenic E. cloacae strain; additionally, the diversity of fimbriae contributes to variation in colonization and host determination of different E. cloacae strains. Comparative genome analysis further illustrated that E. cloacae strains possess multiple mechanisms for antagonistic action against other microorganisms, which involve the production of siderophores and various antimicrobial compounds, such as bacteriocins, chitinases and antibiotic resistance proteins. The presence of Type VI secretion systems is expected to provide further fitness advantages for E. cloacae in microbial competition, thus allowing it to survive in different environments. Competition assays were performed to support our observations in genomic analysis, where E. cloacae subsp. cloacae ENHKU01 demonstrated antagonistic activities against a wide range of plant pathogenic fungal and bacterial species. PMID:24069314

  16. Comparative DNA Sequence Analysis of Wheat and Rice Genomes

    PubMed Central

    Sorrells, Mark E.; La Rota, Mauricio; Bermudez-Kandianis, Catherine E.; Greene, Robert A.; Kantety, Ramesh; Munkvold, Jesse D.; Miftahudin; Mahmoud, Ahmed; Ma, Xuefeng; Gustafson, Perry J.; Qi, Lili L.; Echalier, Benjamin; Gill, Bikram S.; Matthews, David E.; Lazo, Gerard R.; Chao, Shiaoman; Anderson, Olin D.; Edwards, Hugh; Linkiewicz, Anna M.; Dubcovsky, Jorge; Akhunov, Eduard D.; Dvorak, Jan; Zhang, Deshui; Nguyen, Henry T.; Peng, Junhua; Lapitan, Nora L.V.; Gonzalez-Hernandez, Jose L.; Anderson, James A.; Hossain, Khwaja; Kalavacharla, Venu; Kianian, Shahryar F.; Choi, Dong-Woog; Close, Timothy J.; Dilbirligi, Muharrem; Gill, Kulvinder S.; Steber, Camille; Walker-Simmons, Mary K.; McGuire, Patrick E.; Qualset, Calvin O.

    2003-01-01

    The use of DNA sequence-based comparative genomics for evolutionary studies and for transferring information from model species to crop species has revolutionized molecular genetics and crop improvement strategies. This study compared 4485 expressed sequence tags (ESTs) that were physically mapped in wheat chromosome bins, to the public rice genome sequence data from 2251 ordered BAC/PAC clones using BLAST. A rice genome view of homologous wheat genome locations based on comparative sequence analysis revealed numerous chromosomal rearrangements that will significantly complicate the use of rice as a model for cross-species transfer of information in nonconserved regions. PMID:12902377

  17. Comparative analysis of Vening-Meinesz Moritz isostatic models using the constant and variable crust-mantle density contrast - a case study of Zealandia

    NASA Astrophysics Data System (ADS)

    Bagherbandi, Mohammad; Tenzer, Robert

    2013-04-01

    We compare three different numerical schemes of treating the Moho density contrast in gravimetric inverse problems for finding the Moho depths. The results are validated using the global crustal model CRUST2.0, which is determined based purely on seismic data. Firstly, the gravimetric recovery of the Moho depths is realized by solving Moritz's generalization of the Vening-Meinesz inverse problem of isostasy while the constant Moho density contrast is adopted. The Pratt-Hayford isostatic model is then facilitated to estimate the variable Moho density contrast. This variable Moho density contrast is subsequently used to determine the Moho depths. Finally, the combined least-squares approach is applied to estimate jointly the Moho depths and density contract based on a priori error model. The EGM2008 global gravity model and the DTM2006.0 global topographic/bathymetric model are used to generate the isostatic gravity anomalies. The comparison of numerical results reveals that the optimal isostatic inverse scheme should take into consideration both the variable depth and density of compensation. This is achieved by applying the combined least-squares approach for a simultaneous estimation of both Moho parameters. We demonstrate that the result obtained using this method has the best agreement with the CRUST2.0 Moho depths. The numerical experiments are conducted at the regional study area of New Zealand's continental shelf.

  18. Value of Organoids from Comparative Epithelia Models.

    PubMed

    Schwarz, Julia S; de Jonge, Hugo R; Forrest, John N

    2015-12-01

    Organoids have tremendous therapeutic potential. They were recently defined as a collection of organ-specific cell types, which self-organize through cell-sorting, develop from stem cells, and perform an organ specific function. The ability to study organoid development and growth in culture and manipulate their genetic makeup makes them particularly suitable for studying development, disease, and drug efficacy. Organoids show great promise in personalized medicine. From a single patient biopsy, investigators can make hundreds of organoids with the genetic landscape of the patient of origin. This genetic similarity makes organoids an ideal system in which to test drug efficacy. While many investigators assume human organoids are the ultimate model system, we believe that the generation of epithelial organoids of comparative model organisms has great potential. Many key transport discoveries were made using marine organisms. In this paper, we describe how deriving organoids from the spiny dogfish shark, zebrafish, and killifish can contribute to the fields of comparative biology and disease modeling with future prospects for personalized medicine. PMID:26604860

  19. Inpatient care in Kazakhstan: A comparative analysis

    PubMed Central

    Kumar, Ainur B.; Izekenova, Aigulsum; Abikulova, Akmaral

    2013-01-01

    Background: Reforms in inpatient care are critical for the enhancement of the efficiency of health systems. It still remains the main costly sector of the health system, accounting for more than 60% of all expenditures. Inappropriate and ineffective use of the hospital infrastructure is also a big issue. We aimed to analyze statistical data on health indices and dynamics of the hospital stock in Kazakhstan in comparison with those of developed countries. Materials and Methods: Study design is comparative quantitative analysis of inpatient care indicators. We used information and analytical methods, content analysis, mathematical treatment, and comparative analysis of statistical data on health system and dynamics of hospital stock in Kazakhstan and some other countries of the world [Organization for Economic Cooperation and Development (OECD), USA, Canada, Russia, China, Japan, and Korea] over the period 2001-2011. Results: Despite substantial and continuous reductions over the past 10 years, hospitalization rates in Kazakhstan still remain high compared to some developed countries, including those of the OECD. In fact, the hospital stay length for all patients in Kazakhstan in 2011 is around 9.9 days, hospitalization ratio per 100 people is 16.3, and hospital beds capacity is 100 per 10,000 inhabitants. Conclusion: The decreased level of beds may adversely affect both medical organization and health system operations. Alternatives to the existing inpatient care are now being explored. The introduction of the unified national healthcare system allows shifting the primary focus on primary care organizations, which can decrease the demand on inpatient care as a result of improving the health status of people at the primary care level. PMID:24516484

  20. Fundus camera systems: a comparative analysis

    PubMed Central

    DeHoog, Edward; Schwiegerling, James

    2010-01-01

    Retinal photography requires the use of a complex optical system, called a fundus camera, capable of illuminating and imaging the retina simultaneously. The patent literature shows two design forms but does not provide the specifics necessary for a thorough analysis of the designs to be performed. We have constructed our own designs based on the patent literature in optical design software and compared them for illumination efficiency, image quality, ability to accommodate for patient refractive error, and manufacturing tolerances, a comparison lacking in the existing literature. PMID:19137032

  1. Comparing Realistic Subthalamic Nucleus Neuron Models

    NASA Astrophysics Data System (ADS)

    Njap, Felix; Claussen, Jens C.; Moser, Andreas; Hofmann, Ulrich G.

    2011-06-01

    The mechanism of action of clinically effective electrical high frequency stimulation is still under debate. However, recent evidence points at the specific activation of GABA-ergic ion channels. Using a computational approach, we analyze temporal properties of the spike trains emitted by biologically realistic neurons of the subthalamic nucleus (STN) as a function of GABA-ergic synaptic input conductances. Our contribution is based on a model proposed by Rubin and Terman and exhibits a wide variety of different firing patterns, silent, low spiking, moderate spiking and intense spiking activity. We observed that most of the cells in our network turn to silent mode when we increase the GABAA input conductance above the threshold of 3.75 mS/cm2. On the other hand, insignificant changes in firing activity are observed when the input conductance is low or close to zero. We thus reproduce Rubin's model with vanishing synaptic conductances. To quantitatively compare spike trains from the original model with the modified model at different conductance levels, we apply four different (dis)similarity measures between them. We observe that Mahalanobis distance, Victor-Purpura metric, and Interspike Interval distribution are sensitive to different firing regimes, whereas Mutual Information seems undiscriminative for these functional changes.

  2. A Framework for the Comparative Analysis of Farm Organizations.

    ERIC Educational Resources Information Center

    Molnar, Joseph J.

    Presenting a model for the comparative analysis of farm organizations, this paper analyzes the farm firm as a complex organization; identifies key structural dimensions of an agricultural production unit; and reviews various organizational perspectives for their utility in understanding and explaining the behavior of farm operations and farm…

  3. Comparative Transcriptome Analysis of Four Prymnesiophyte Algae

    PubMed Central

    Koid, Amy E.; Liu, Zhenfeng; Terrado, Ramon; Jones, Adriane C.; Caron, David A.; Heidelberg, Karla B.

    2014-01-01

    Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists. PMID:24926657

  4. Comparative transcriptome analysis of four prymnesiophyte algae.

    PubMed

    Koid, Amy E; Liu, Zhenfeng; Terrado, Ramon; Jones, Adriane C; Caron, David A; Heidelberg, Karla B

    2014-01-01

    Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists.

  5. Comparative genome analysis of Basidiomycete fungi

    SciTech Connect

    Riley, Robert; Salamov, Asaf; Henrissat, Bernard; Nagy, Laszlo; Brown, Daren; Held, Benjamin; Baker, Scott; Blanchette, Robert; Boussau, Bastien; Doty, Sharon L.; Fagnan, Kirsten; Floudas, Dimitris; Levasseur, Anthony; Manning, Gerard; Martin, Francis; Morin, Emmanuelle; Otillar, Robert; Pisabarro, Antonio; Walton, Jonathan; Wolfe, Ken; Hibbett, David; Grigoriev, Igor

    2013-08-07

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism. Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.

  6. A comparative analysis of the model calculated and GPS-observed TEC variations before the Haiti, 2010 and Japan, 2011 earthquakes

    NASA Astrophysics Data System (ADS)

    Namgaladze, Alexander; Karpov, Mikhail; Zolotov, Oleg

    2013-04-01

    Model simulations of the ionosphere Total Electron Content (TEC) variations have been performed for the Haiti January 12, 2010 and Japan March 11, 2011 earthquakes. Calculations have been carried out using the global numerical Upper Atmosphere Model (UAM). The seismogenic impacts in the model have been set as lower boundary conditions for the electric potential equation. Namely, the vertical electric currents of ~ 20 nA/m2 flowing from the ionosphere to the Earth have been set at the near-epicenter area of ~ 250 by 2000 km. The simulated relative (%) TEC disturbances for both events have been compared to each other and to the corresponding GPS-observed data. The common features persisting at both observed and modeled TEC variations are: (1) the appearance of positive disturbances 20 - 40% by magnitude at night hours for 2 - 4 days before the earthquake, (2) the geomagnetic conjugation of the effects and (3) the lack of migration (movements) of the TEC deviations during their lifetime (of ~ 8 hours). Main differences between the considered events (Haiti and Japan), both modeled and observed, are most evidently pronounced in the TEC disturbances' maximum location relative to the geomagnetic equator. In case of the Haiti earthquake the strongest by magnitude TEC disturbances are located near the magnetically conjugated to the earthquake's epicenter region at the Southern hemisphere, while in case of the Japan earthquake - near the epicenter at the Northern hemisphere. We have attributed this difference to the different seasons the events have taken place in. The asymmetry of the Haiti model TEC disturbances relative to the magnetic meridian of the earthquake's epicenter is in agreement with the GPS-observed one. In case of the Japan earthquake the asymmetry of the TEC deviations relative to the magnetic meridian of the earthquake's epicenter is negligible in the observations, while in the model results it is similar to the Haiti case. In order to remove this asymmetry

  7. Behavioral abnormalities in APPSwe/PS1dE9 mouse model of AD-like pathology: comparative analysis across multiple behavioral domains.

    PubMed

    Janus, Christopher; Flores, Abigail Y; Xu, Guilian; Borchelt, David R

    2015-09-01

    Alzheimer's disease (AD) is characterized by dysfunction in cognitive and noncognitive domains with clinical diagnosis based on multiple neuropsychological tests. Here, we evaluated cognitive and noncognitive behaviors in 2 age cohorts (8 and 14 months at the start of the study) of APPSwe/PS1dE9 transgenic mice that model AD-like amyloidosis. We used a battery of tests that included fear-conditioned context and tone memories, swimming activity, and orientation to a proximal cue in a visible platform water maze test and burrowing and nest building activity. To compare the performance of mice across all tests, we used z-score normalization of data. The analyses revealed that the behavior of the transgenic mice was significantly compromised in cognitive as well as in noncognitive domains. Combining scores across multiple behavioral tests produced an integrated index characterizing the overall phenotypic abnormality in this model of AD-like amyloidosis. Assessing multiple behavioral domains provides a broader view of the breadth of impairments in multiple behavioral systems. Greater implementation of such approaches could enable reliable and clinically predictive evaluation of therapeutics in mouse models of amyloidosis.

  8. Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2−/− Hippocampus

    PubMed Central

    Provenzano, Giovanni; Corradi, Zelia; Monsorno, Katia; Fedrizzi, Tarcisio; Ricceri, Laura; Scattoni, Maria L.; Bozzi, Yuri

    2016-01-01

    /− DEGs. Weighted correlation network analysis (WGCNA) performed on BTBR and En2−/− hippocampal transcriptomes together identified six modules significantly enriched in ASD-related genes. Each of these modules showed a specific enrichment profile in neuronal and glial genes, as well as in genes associated to ASD comorbidities such as epilepsy and SCZ. Our data reveal significant transcriptional similarities and differences between the BTBR and En2−/− hippocampus, indicating that transcriptome analysis of ASD mouse models may contribute to identify novel molecular targets for pharmacological studies. PMID:27610074

  9. Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2−/− Hippocampus

    PubMed Central

    Provenzano, Giovanni; Corradi, Zelia; Monsorno, Katia; Fedrizzi, Tarcisio; Ricceri, Laura; Scattoni, Maria L.; Bozzi, Yuri

    2016-01-01

    /− DEGs. Weighted correlation network analysis (WGCNA) performed on BTBR and En2−/− hippocampal transcriptomes together identified six modules significantly enriched in ASD-related genes. Each of these modules showed a specific enrichment profile in neuronal and glial genes, as well as in genes associated to ASD comorbidities such as epilepsy and SCZ. Our data reveal significant transcriptional similarities and differences between the BTBR and En2−/− hippocampus, indicating that transcriptome analysis of ASD mouse models may contribute to identify novel molecular targets for pharmacological studies.

  10. Comparative Genome Analysis of Basidiomycete Fungi

    SciTech Connect

    Riley, Robert; Salamov, Asaf; Morin, Emmanuelle; Nagy, Laszlo; Manning, Gerard; Baker, Scott; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Hibbett, David; Martin, Francis; Grigoriev, Igor

    2012-03-19

    Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, symbionts, and plant and animal pathogens. To better understand the diversity of phenotypes in basidiomycetes, we performed a comparative analysis of 35 basidiomycete fungi spanning the diversity of the phylum. Phylogenetic patterns of lignocellulose degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay. Patterns of secondary metabolic enzymes give additional insight into the broad array of phenotypes found in the basidiomycetes. We suggest that the profile of an organism in lignocellulose-targeting genes can be used to predict its nutritional mode, and predict Dacryopinax sp. as a brown rot; Botryobasidium botryosum and Jaapia argillacea as white rots.

  11. Comparative factor analysis models for an empirical study of EEG data, II: A data-guided resolution of the rotation indeterminacy.

    PubMed

    Rogers, L J; Douglas, R R

    1984-02-01

    In this paper (the second in a series), we consider a (generic) pair of datasets, which have been analyzed by the techniques of the previous paper. Thus, their "stable subspaces" have been established by comparative factor analysis. The pair of datasets must satisfy two confirmable conditions. The first is the "Inclusion Condition," which requires that the stable subspace of one of the datasets is nearly identical to a subspace of the other dataset's stable subspace. On the basis of that, we have assumed the pair to have similar generating signals, with stochastically independent generators. The second verifiable condition is that the (presumed same) generating signals have distinct ratios of variances for the two datasets. Under these conditions a small elaboration of some elementary linear algebra reduces the rotation problem to several eigenvalue-eigenvector problems. Finally, we emphasize that an analysis of each dataset by the method of Douglas and Rogers (1983) is an essential prerequisite for the useful application of the techniques in this paper. Nonempirical methods of estimating the number of factors simply will not suffice, as confirmed by simulations reported in the previous paper. PMID:6706478

  12. Comparative analysis of driver's brake perception-reaction time at signalized intersections with and without countdown timer using parametric duration models.

    PubMed

    Fu, Chuanyun; Zhang, Yaping; Bie, Yiming; Hu, Liwei

    2016-10-01

    Countdown timers display the time left on the current signal, which makes drivers be more ready to react to the phase change. However, previous related studies have rarely explored the effects of countdown timer on driver's brake perception-reaction time (BPRT) to yellow light. The goal of this study was therefore to characterize and model driver's BPRT to yellow signal at signalized intersections with and without countdown timer. BPRT data for "first-to-stop" vehicles after yellow onset within the transitional zone were collected through on-site observation at six signalized intersections in Harbin, China. Statistical analysis showed that the observed 15th, 50th, and 85th percentile BPRTs without countdown timer were 0.52, 0.84, and 1.26s, respectively. The observed 15th, 50th, and 85th percentile BPRTs with countdown timer were 0.32, 1.20, and 2.52s, respectively. Log-logistic distribution appeared to best fit the BPRT without countdown timer, while Weibull distribution seemed to best fit the BPRT with countdown timer. After that, a Log-logistic accelerated failure time (AFT) duration model was developed to model driver's BPRT without countdown timer, whereas a Weibull AFT duration model was established to model driver's BPRT with countdown timer. Three significant factors affecting the BPRT identified in both AFT models included yellow-onset distance from the stop line, yellow-onset approach speed, and deceleration rate. No matter whether the presence of countdown timer or not, BPRT increased as yellow-onset distance to the stop line or deceleration rate increased, but decreased as yellow-onset speed increased. The impairment of driver's BPRT due to countdown timer appeared to increase with yellow-onset distance to the stop line or deceleration rate, but decrease with yellow-onset speed. An increase in driver's BPRT because of countdown timer may induce risky driving behaviors (i.e., stop abruptly, or even violate traffic signal), revealing a weakness of

  13. Comparative analysis of selected fuel cell vehicles

    SciTech Connect

    1993-05-07

    Vehicles powered by fuel cells operate more efficiently, more quietly, and more cleanly than internal combustion engines (ICEs). Furthermore, methanol-fueled fuel cell vehicles (FCVs) can utilize major elements of the existing fueling infrastructure of present-day liquid-fueled ICE vehicles (ICEVs). DOE has maintained an active program to stimulate the development and demonstration o fuel cell technologies in conjunction with rechargeable batteries in road vehicles. The purpose of this study is to identify and assess the availability of data on FCVs, and to develop a vehicle subsystem structure that can be used to compare both FCVs and ICEV, from a number of perspectives--environmental impacts, energy utilization, materials usage, and life cycle costs. This report focuses on methanol-fueled FCVs fueled by gasoline, methanol, and diesel fuel that are likely to be demonstratable by the year 2000. The comparative analysis presented covers four vehicles--two passenger vehicles and two urban transit buses. The passenger vehicles include an ICEV using either gasoline or methanol and an FCV using methanol. The FCV uses a Proton Exchange Membrane (PEM) fuel cell, an on-board methanol reformer, mid-term batteries, and an AC motor. The transit bus ICEV was evaluated for both diesel and methanol fuels. The transit bus FCV runs on methanol and uses a Phosphoric Acid Fuel Cell (PAFC) fuel cell, near-term batteries, a DC motor, and an on-board methanol reformer. 75 refs.

  14. Comparative metagenome analysis of an Alaskan glacier.

    PubMed

    Choudhari, Sulbha; Lohia, Ruchi; Grigoriev, Andrey

    2014-04-01

    The temperature in the Arctic region has been increasing in the recent past accompanied by melting of its glaciers. We took a snapshot of the current microbial inhabitation of an Alaskan glacier (which can be considered as one of the simplest possible ecosystems) by using metagenomic sequencing of 16S rRNA recovered from ice/snow samples. Somewhat contrary to our expectations and earlier estimates, a rich and diverse microbial population of more than 2,500 species was revealed including several species of Archaea that has been identified for the first time in the glaciers of the Northern hemisphere. The most prominent bacterial groups found were Proteobacteria, Bacteroidetes, and Firmicutes. Firmicutes were not reported in large numbers in a previously studied Alpine glacier but were dominant in an Antarctic subglacial lake. Representatives of Cyanobacteria, Actinobacteria and Planctomycetes were among the most numerous, likely reflecting the dependence of the ecosystem on the energy obtained through photosynthesis and close links with the microbial community of the soil. Principal component analysis (PCA) of nucleotide word frequency revealed distinct sequence clusters for different taxonomic groups in the Alaskan glacier community and separate clusters for the glacial communities from other regions of the world. Comparative analysis of the community composition and bacterial diversity present in the Byron glacier in Alaska with other environments showed larger overlap with an Arctic soil than with a high Arctic lake, indicating patterns of community exchange and suggesting that these bacteria may play an important role in soil development during glacial retreat.

  15. Comparative Analysis of Genome Sequences with VISTA

    DOE Data Explorer

    Dubchak, Inna

    VISTA is a comprehensive suite of programs and databases developed by and hosted at the Genomics Division of Lawrence Berkeley National Laboratory. They provide information and tools designed to facilitate comparative analysis of genomic sequences. Users have two ways to interact with the suite of applications at the VISTA portal. They can submit their own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. A key menu option is the Enhancer Browser and Database at http://enhancer.lbl.gov/. The VISTA Enhancer Browser is a central resource for experimentally validated human noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation with other vertebrates. The results of this enhancer screen are provided through this publicly available website. The browser also features relevant results by external contributors and a large collection of additional genome-wide conserved noncoding elements which are candidate enhancer sequences. The LBL developers invite external groups to submit computational predictions of developmental enhancers. As of 10/19/2009 the database contains information on 1109 in vivo tested elements - 508 elements with enhancer activity.

  16. Comparative analysis of cystatin superfamily in platyhelminths.

    PubMed

    Guo, Aijiang

    2015-01-01

    The cystatin superfamily is comprised of cysteine proteinase inhibitors and encompasses at least 3 subfamilies: stefins, cystatins and kininogens. In this study, the platyhelminth cystatin superfamily was identified and grouped into stefin and cystatin subfamilies. The conserved domain of stefins (G, QxVxG) was observed in all members of platyhelminth stefins. The three characteristics of cystatins, the cystatin-like domain (G, QxVxG, PW), a signal peptide, and one or two conserved disulfide bonds, were observed in platyhelminths, with the exception of cestodes, which lacked the conserved disulfide bond. However, it is noteworthy that cestode cystatins had two tandem repeated domains, although the second tandem repeated domain did not contain a cystatin-like domain, which has not been previously reported. Tertiary structure analysis of Taenia solium cystatin, one of the cestode cystatins, demonstrated that the N-terminus of T. solium cystatin formed a five turn α-helix, a five stranded β-pleated sheet and a hydrophobic edge, similar to the structure of chicken cystatin. Although no conserved disulfide bond was found in T. solium cystatin, the models of T. solium cystatin and chicken cystatin corresponded at the site of the first disulfide bridge of the chicken cystatin. However, the two models were not similar regarding the location of the second disulfide bridge of chicken cystatin. These results showed that T. solium cystatin and chicken cystatin had similarities and differences, suggesting that the biochemistry of T. solium cystatin could be similar to chicken cystatin in its inhibitory function and that it may have further functional roles. The same results were obtained for other cestode cystatins. Phylogenetic analysis showed that cestode cystatins constituted an independent clade and implied that cestode cystatins should be considered to have formed a new clade during evolution.

  17. Comparative Analysis of Cystatin Superfamily in Platyhelminths

    PubMed Central

    Guo, Aijiang

    2015-01-01

    The cystatin superfamily is comprised of cysteine proteinase inhibitors and encompasses at least 3 subfamilies: stefins, cystatins and kininogens. In this study, the platyhelminth cystatin superfamily was identified and grouped into stefin and cystatin subfamilies. The conserved domain of stefins (G, QxVxG) was observed in all members of platyhelminth stefins. The three characteristics of cystatins, the cystatin-like domain (G, QxVxG, PW), a signal peptide, and one or two conserved disulfide bonds, were observed in platyhelminths, with the exception of cestodes, which lacked the conserved disulfide bond. However, it is noteworthy that cestode cystatins had two tandem repeated domains, although the second tandem repeated domain did not contain a cystatin-like domain, which has not been previously reported. Tertiary structure analysis of Taenia solium cystatin, one of the cestode cystatins, demonstrated that the N-terminus of T. solium cystatin formed a five turn α-helix, a five stranded β-pleated sheet and a hydrophobic edge, similar to the structure of chicken cystatin. Although no conserved disulfide bond was found in T. solium cystatin, the models of T. solium cystatin and chicken cystatin corresponded at the site of the first disulfide bridge of the chicken cystatin. However, the two models were not similar regarding the location of the second disulfide bridge of chicken cystatin. These results showed that T. solium cystatin and chicken cystatin had similarities and differences, suggesting that the biochemistry of T. solium cystatin could be similar to chicken cystatin in its inhibitory function and that it may have further functional roles. The same results were obtained for other cestode cystatins. Phylogenetic analysis showed that cestode cystatins constituted an independent clade and implied that cestode cystatins should be considered to have formed a new clade during evolution. PMID:25853513

  18. Comparative analysis of plant lycopene cyclases.

    PubMed

    Koc, Ibrahim; Filiz, Ertugrul; Tombuloglu, Huseyin

    2015-10-01

    Carotenoids are essential isoprenoid pigments produced by plants, algae, fungi and bacteria. Lycopene cyclase (LYC) commonly cyclize carotenoids, which is an important branching step in the carotenogenesis, at one or both end of the backbone. Plants have two types of LYC (β-LCY and ϵ-LCY). In this study, plant LYCs were analyzed. Based on domain analysis, all LYCs accommodate lycopene cyclase domain (Pf05834). Furthermore, motif analysis indicated that motifs were conserved among the plants. On the basis of phylogenetic analysis, β-LCYs and ϵ-LCYs were classified in β and ϵ groups. Monocot and dicot plants separated from each other in the phylogenetic tree. Subsequently, Oryza sativa Japonica Group and Zea mays of LYCs as monocot plants and Vitis vinifera and Solanum lycopersicum of LYCs as dicot plants were analyzed. According to nucleotide diversity analysis of β-LCY and ϵ-LCY genes, nucleotide diversities were found to be π: 0.30 and π: 0.25, respectively. The result highlighted β-LCY genes showed higher nucleotide diversity than ϵ-LCY genes. LYCs interacting genes and their co-expression partners were also predicted using String server. The obtained data suggested the importance of LYCs in carotenoid metabolism. 3D modeling revealed that depicted structures were similar in O. sativa, Z mays, S. lycopersicum, and V. vinifera β-LCYs and ϵ-LCYs. Likewise, the predicted binding sites were highly similar between O. sativa, Z mays, S. lycopersicum, and V. vinifera LCYs. Most importantly, analysis elucidated the V/IXGXGXXGXXXA motif for both type of LYC (β-LCY and ϵ-LCY). This motif related to Rossmann fold domain and probably provides a flat platform for binding of FAD in O. sativa, Z mays, S. lycopersicum, and V. vinifera β-LCYs and ϵ-LCYs with conserved structure. In addition to lycopene cyclase domain, the V/IXGXGXXGXXXA motif can be used for exploring LYCs proteins and to annotate the function of unknown proteins containing lycopene cyclase

  19. Comparative analysis of plant lycopene cyclases.

    PubMed

    Koc, Ibrahim; Filiz, Ertugrul; Tombuloglu, Huseyin

    2015-10-01

    Carotenoids are essential isoprenoid pigments produced by plants, algae, fungi and bacteria. Lycopene cyclase (LYC) commonly cyclize carotenoids, which is an important branching step in the carotenogenesis, at one or both end of the backbone. Plants have two types of LYC (β-LCY and ϵ-LCY). In this study, plant LYCs were analyzed. Based on domain analysis, all LYCs accommodate lycopene cyclase domain (Pf05834). Furthermore, motif analysis indicated that motifs were conserved among the plants. On the basis of phylogenetic analysis, β-LCYs and ϵ-LCYs were classified in β and ϵ groups. Monocot and dicot plants separated from each other in the phylogenetic tree. Subsequently, Oryza sativa Japonica Group and Zea mays of LYCs as monocot plants and Vitis vinifera and Solanum lycopersicum of LYCs as dicot plants were analyzed. According to nucleotide diversity analysis of β-LCY and ϵ-LCY genes, nucleotide diversities were found to be π: 0.30 and π: 0.25, respectively. The result highlighted β-LCY genes showed higher nucleotide diversity than ϵ-LCY genes. LYCs interacting genes and their co-expression partners were also predicted using String server. The obtained data suggested the importance of LYCs in carotenoid metabolism. 3D modeling revealed that depicted structures were similar in O. sativa, Z mays, S. lycopersicum, and V. vinifera β-LCYs and ϵ-LCYs. Likewise, the predicted binding sites were highly similar between O. sativa, Z mays, S. lycopersicum, and V. vinifera LCYs. Most importantly, analysis elucidated the V/IXGXGXXGXXXA motif for both type of LYC (β-LCY and ϵ-LCY). This motif related to Rossmann fold domain and probably provides a flat platform for binding of FAD in O. sativa, Z mays, S. lycopersicum, and V. vinifera β-LCYs and ϵ-LCYs with conserved structure. In addition to lycopene cyclase domain, the V/IXGXGXXGXXXA motif can be used for exploring LYCs proteins and to annotate the function of unknown proteins containing lycopene cyclase

  20. Ring Current Dynamics in Moderate and Strong Storms: Comparative Analysis of TWINS and IMAGE/HENA Data with the Comprehensive Ring Current Model

    NASA Technical Reports Server (NTRS)

    Buzulukova, N.; Fok, M.-C.; Goldstein, J.; Valek, P.; McComas, D. J.; Brandt, P. C.

    2010-01-01

    We present a comparative study of ring current dynamics during strong and moderate storms. The ring current during the strong storm is studied with IMAGE/HENA data near the solar cycle maximum in 2000. The ring current during the moderate storm is studied using energetic neutral atom (ENA) data from the Two Wide-Angle Imaging Neutral- Atom Spectrometers (TWINS) mission during the solar minimum in 2008. For both storms, the local time distributions of ENA emissions show signatures of postmidnight enhancement (PME) during the main phases. To model the ring current and ENA emissions, we use the Comprehensive Ring Current Model (CRCM). CRCM results show that the main-phase ring current pressure peaks in the premidnight-dusk sector, while the most intense CRCM-simulated ENA emissions show PME signatures. We analyze two factors to explain this difference: the dependence of charge-exchange cross section on energy and pitch angle distributions of ring current. We find that the IMF By effect (twisting of the convection pattern due to By) is not needed to form the PME. Additionally, the PME is more pronounced for the strong storm, although relative shielding and hence electric field skewing is well developed for both events.

  1. Process modeling and analysis of pulp mill-based integrated biorefinery with hemicellulose pre-extraction for ethanol production: a comparative study.

    PubMed

    Huang, Hua-Jiang; Ramaswamy, Shri; Al-Dajani, Waleed Wafa; Tschirner, Ulrike

    2010-01-01

    Pulp and paper mills represent a major platform to use more effectively an abundant, renewable bio-resource - wood. Modification of the modern day pulp mills into integrated forest biorefineries (IFBR) presents an excellent opportunity to produce, in addition to valuable cellulose fiber, co-products including fuel grade ethanol and additional energy, thus resulting in increased revenue streams and profitability and potentially lower the greenhouse gas emissions. A process model to simulate the integrate forest biorefinery manufacturing pulp and other co-products has been developed. This model has been used to compare three integrated biorefinery scenarios: the conventional Kraft pulping process, the pulp mill-based IFBR with hemicelluloses extraction prior to pulping for ethanol production, and the pulp mill-based IFBR with both pre-extracted hemicelluloses and the short fiber for ethanol production. Based on a fixed feedstock throughput of 2000 dry Mg wood/day, results show that the pulp mill-based IFBR with both pre-extracted hemicelluloses and the short fiber cellulose converted to ethanol can produce 0.038 MM m(3) (10.04 MM gal) ethanol per year at a minimum ethanol selling price (MESP) of $491/m(3) ($1.86/gal). The economic feasibility of IFBR can be further improved by using further improvements in the pre-extraction process, other biomass such as corn stover for producing ethanol, and taking advantage of the economies of scale.

  2. Comparative Analysis of Effect of Density, Insertion Angle and Reinsertion on Pull-Out Strength of Single and Two Pedicle Screw Constructs Using Synthetic Bone Model

    PubMed Central

    Varghese, Vicky; Kumar, Gurunathan Saravana

    2016-01-01

    Study Design Biomechanical study. Purpose To determine the effect of density, insertion angle and reinsertion on pull-out strength of pedicle screw in single and two screw-rod configurations. Overview of Literature Pedicle screw pull-out studies have involved single screw construct, whereas two screws and rod constructs are always used in spine fusions. Extrapolation of results using the single screw construct may lead to using expensive implants or increasing the fusion levels specifically in osteoporotic bones. Methods Single screw and two screw pull-out strength tests were carried out according to American Society for Testing and Materials F 543-07 on foam models to test the effect of density, insertion angle and reinsertion using poly axial pedicle screws. Results Bone density was the most significant factor deciding the pull-out strength in both single and two screw constructs. The difference in pull-out strength between single screw and two screw configurations in extremely osteoporotic bone model (80 kg/m3) was 78%, whereas in the normal bone model it was 48%. Axial pull-out value was highest for the single screw configuration; in the two screw configuration the highest pull-out strength was at 10°–15°. There was an 18% reduction in pull-out strength due to reinsertion in single screw configuration. The reinsertion effect was insignificant in the two screw configuration. Conclusions A significant difference in response of various factors on holding power of pedicle screw between single and two-screw configurations is evident. The percentage increase in pull-out strength between single and two screw constructs is higher for osteoporotic bone when compared to normal bone. Reinsertion has no significant effect on pull-out strength in the two screw rod configuration. PMID:27340518

  3. Comparative network analysis via differential graphlet communities

    PubMed Central

    Wong, Serene W H; Cercone, Nick; Jurisica, Igor

    2015-01-01

    While current protein interaction data provides a rich resource for molecular biology, it mostly lacks condition-specific details. Abundance of mRNA data for most diseases provides potential to model condition-specific transcriptional changes. Transcriptional data enables modeling disease mechanisms, and in turn provide potential treatments. While approaches to compare networks constructed from healthy and disease samples have been developed, they do not provide the complete comparison, evaluations are performed on very small networks, or no systematic network analyses are performed on differential network structures. We propose a novel method for efficiently exploiting network structure information in the comparison between any graphs, and validate results in non-small cell lung cancer. We introduce the notion of differential graphlet community to detect deregulated subgraphs between any graphs such that the network structure information is exploited. The differential graphlet community approach systematically captures network structure differences between any graphs. Instead of using connectivity of each protein or each edge, we used shortest path distributions on differential graphlet communities in order to exploit network structure information on identified deregulated subgraphs. We validated the method by analyzing three non-small cell lung cancer datasets and validated results on four independent datasets. We observed that the shortest path lengths are significantly longer for normal graphs than for tumor graphs between genes that are in differential graphlet communities, suggesting that tumor cells create "shortcuts" between biological processes that may not be present in normal conditions. PMID:25283527

  4. An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs.

    PubMed

    Cuadrat, Rafael R C; da Serra Cruz, Sérgio Manuel; Tschoeke, Diogo Antônio; Silva, Edno; Tosta, Frederico; Jucá, Henrique; Jardim, Rodrigo; Campos, Maria Luiza M; Mattoso, Marta; Dávila, Alberto M R

    2014-08-01

    A key focus in 21(st) century integrative biology and drug discovery for neglected tropical and other diseases has been the use of BLAST-based computational methods for identification of orthologous groups in pathogenic organisms to discern orthologs, with a view to evaluate similarities and differences among species, and thus allow the transfer of annotation from known/curated proteins to new/non-annotated ones. We used here a profile-based sensitive methodology to identify distant homologs, coupled to the NCBI's COG (Unicellular orthologs) and KOG (Eukaryote orthologs), permitting us to perform comparative genomics analyses on five protozoan genomes. OrthoSearch was used in five protozoan proteomes showing that 3901 and 7473 orthologs can be identified by comparison with COG and KOG proteomes, respectively. The core protozoa proteome inferred was 418 Protozoa-COG orthologous groups and 704 Protozoa-KOG orthologous groups: (i) 31.58% (132/418) belongs to the category J (translation, ribosomal structure, and biogenesis), and 9.81% (41/418) to the category O (post-translational modification, protein turnover, chaperones) using COG; (ii) 21.45% (151/704) belongs to the categories J, and 13.92% (98/704) to the O using KOG. The phylogenomic analysis showed four well-supported clades for Eukarya, discriminating Multicellular [(i) human, fly, plant and worm] and Unicellular [(ii) yeast, (iii) fungi, and (iv) protozoa] species. These encouraging results attest to the usefulness of the profile-based methodology for comparative genomics to accelerate semi-automatic re-annotation, especially of the protozoan proteomes. This approach may also lend itself for applications in global health, for example, in the case of novel drug target discovery against pathogenic organisms previously considered difficult to research with traditional drug discovery tools. PMID:24960463

  5. Development of intelligent systems based on Bayesian regularization network and neuro-fuzzy models for mass detection in mammograms: A comparative analysis.

    PubMed

    Mahersia, Hela; Boulehmi, Hela; Hamrouni, Kamel

    2016-04-01

    Female breast cancer is the second most common cancer in the world. Several efforts in artificial intelligence have been made to help improving the diagnostic accuracy at earlier stages. However, the identification of breast abnormalities, like masses, on mammographic images is not a trivial task, especially for dense breasts. In this paper we describe our novel mass detection process that includes three successive steps of enhancement, characterization and classification. The proposed enhancement system is based mainly on the analysis of the breast texture. First of all, a filtering step with morphological operators and soft thresholding is achieved. Then, we remove from the filtered breast region, all the details that may interfere with the eventual masses, including pectoral muscle and galactophorous tree. The pixels belonging to this tree will be interpolated and replaced by the average of the neighborhood. In the characterization process, measurement of the Gaussian density in the wavelet domain allows the segmentation of the masses. Finally, a comparative classification mechanism based on the Bayesian regularization back-propagation networks and ANFIS techniques is proposed. The tests were conducted on the MIAS database. The results showed the robustness of the proposed enhancement method. PMID:26831269

  6. Comparing modelled fire dynamics with charcoal records for the Holocene

    NASA Astrophysics Data System (ADS)

    Brücher, Tim; Brovkin, Victor; Kloster, Silvia; Marlon, Jennifer; Power, Mitch

    2014-05-01

    An Earth System model of intermediate complexity, CLIMBER-2, and land surface model JSBACH that includes dynamic vegetation, carbon cycle, and fire regime are used for simulation of natural fire dynamics through the last 8,000 years. To compare the fire model results with the charcoal reconstructions, several output variables of the fire model (burned area, carbon emissions) and several approaches of model output processing are tested. The z-scores out of charcoal dataset have been calculated for the period 8,000 to 200 BP to exclude a period of strong anthropogenic forcing during the last two centuries. The model analysis points mainly to an increasing fire activity during the Holocene for most of the investigated areas, which is in good correspondence to reconstructed fire trends out of charcoal data for most of the tested regions, while for few regions such as Europe the simulated trend and the reconstructed trends are different. The difference between the modeled and reconstructed fire activity could be due to absence of the anthropogenic forcing in the model simulations, but also due to limitations of model assumptions for modeling fire dynamics. For the model trends, the usage of averaging or z-score processing of model output resulted in similar directions of trend. Therefore, the approach of fire model output processing does not effect results of the model-data comparison. Global fire modeling is still in its infancy; improving our representations of fire through validation exercises such as what we present here is thus essential before testing hypotheses about the effects of extreme climate changes on fire behavior and potential feedbacks that result from those changes. Brücher, T., Brovkin, V., Kloster, S., Marlon, J. R., and Power, M. J.: Comparing modelled fire dynamics with charcoal records for the Holocene, Clim. Past Discuss., 9, 6429-6458, doi:10.5194/cpd-9-6429-2013, 2013.

  7. Comparative analysis of the Borrelia garinii genome.

    PubMed

    Glöckner, G; Lehmann, R; Romualdi, A; Pradella, S; Schulte-Spechtel, U; Schilhabel, M; Wilske, B; Sühnel, J; Platzer, M

    2004-01-01

    Three members of the genus Borrelia (B.burgdorferi, B.garinii, B.afzelii) cause tick-borne borreliosis. Depending on the Borrelia species involved, the borreliosis differs in its clinical symptoms. Comparative genomics opens up a way to elucidate the underlying differences in Borrelia species. We analysed a low redundancy whole-genome shotgun (WGS) assembly of a B.garinii strain isolated from a patient with neuroborreliosis in comparison to the B.burgdorferi genome. This analysis reveals that most of the chromosome is conserved (92.7% identity on DNA as well as on amino acid level) in the two species, and no chromosomal rearrangement or larger insertions/deletions could be observed. Furthermore, two collinear plasmids (lp54 and cp26) seem to belong to the basic genome inventory of Borrelia species. These three collinear parts of the Borrelia genome encode 861 genes, which are orthologous in the two species examined. The majority of the genetic information of the other plasmids of B.burgdorferii is also present in B.garinii although orthology is not easy to define due to a high redundancy of the plasmid fraction. Yet, we did not find counterparts of the B.burgdorferi plasmids lp36 and lp38 or their respective gene repertoire in the B.garinii genome. Thus, phenotypic differences between the two species could be attributable to the presence or absence of these two plasmids as well as to the potentially positively selected genes. PMID:15547252

  8. Comparative visual analysis of 3D urban wind simulations

    NASA Astrophysics Data System (ADS)

    Röber, Niklas; Salim, Mohamed; Grawe, David; Leitl, Bernd; Böttinger, Michael; Schlünzen, Heinke

    2016-04-01

    Climate simulations are conducted in large quantity for a variety of different applications. Many of these simulations focus on global developments and study the Earth's climate system using a coupled atmosphere ocean model. Other simulations are performed on much smaller regional scales, to study very small fine grained climatic effects. These microscale climate simulations pose similar, yet also different, challenges for the visualization and the analysis of the simulation data. Modern interactive visualization and data analysis techniques are very powerful tools to assist the researcher in answering and communicating complex research questions. This presentation discusses comparative visualization for several different wind simulations, which were created using the microscale climate model MITRAS. The simulations differ in wind direction and speed, but are all centered on the same simulation domain: An area of Hamburg-Wilhelmsburg that hosted the IGA/IBA exhibition in 2013. The experiments contain a scenario case to analyze the effects of single buildings, as well as examine the impact of the Coriolis force within the simulation. The scenario case is additionally compared with real measurements from a wind tunnel experiment to ascertain the accuracy of the simulation and the model itself. We also compare different approaches for tree modeling and evaluate the stability of the model. In this presentation, we describe not only our workflow to efficiently and effectively visualize microscale climate simulation data using common 3D visualization and data analysis techniques, but also discuss how to compare variations of a simulation and how to highlight the subtle differences in between them. For the visualizations we use a range of different 3D tools that feature techniques for statistical data analysis, data selection, as well as linking and brushing.

  9. Dynamic response of the Trinity River Relief Bridge to controlled pile damage: modeling and experimental data analysis comparing Fourier and Hilbert Huang techniques

    NASA Astrophysics Data System (ADS)

    Zhang, Ray Ruichong; King, Robert; Olson, Larry; Xu, You-Lin

    2005-08-01

    This paper presents the implementation of a method for nonlinear, nonstationary data processing, namely the Hilbert-Huang transform (HHT) in traditional vibration-based approaches to characterizing structural damage and shows the frequency signature of local structural damage in nonstationary vibration recordings. In particular, following the review of traditional approaches to characterizing structural damage from nonstationary vibration recordings, this study first offers the justifications of the HHT as an alternative and complementary data process in addressing the nonstationarity of the vibration. With the use of recordings from controlled field vibration tests of substructures in the Trinity River Relief Bridge in Texas in its intact, minor- and severe-damage pile states, this study then shows that the HHT-based approach can single out some natural frequencies of the structure from a mixed frequency content in recordings that also contain the time-dependent excitation and noise frequencies. Subsequently, this study exposes that the frequency downshift for the damaged pile relative to the undamaged one is an indicative index for the damage extent. The above results are also validated by an ANSYS model-based analysis. Finally, a comprehensive HHT-based characterization of structural damage is discussed, and the potential use for cost-effective, efficient structural damage diagnosis procedures and health-monitoring systems is provided.

  10. Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality.

    PubMed

    Kushwaha, Rekha; Downie, A Bruce; Payne, Christina M

    2013-01-01

    A group of intrinsically disordered, hydrophilic proteins-Late Embryogenesis Abundant (LEA) proteins-has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.

  11. Comparative Analysis of the Effects of Neurotrophic Factors CDNF and GDNF in a Nonhuman Primate Model of Parkinson’s Disease

    PubMed Central

    Garea-Rodríguez, Enrique; Eesmaa, Ave; Lindholm, Päivi; Schlumbohm, Christina; König, Jessica; Meller, Birgit; Krieglstein, Kerstin; Helms, Gunther; Saarma, Mart; Fuchs, Eberhard

    2016-01-01

    Cerebral dopamine neurotrophic factor (CDNF) belongs to a newly discovered family of evolutionarily conserved neurotrophic factors. We demonstrate for the first time a therapeutic effect of CDNF in a unilateral 6-hydroxydopamine (6-OHDA) lesion model of Parkinson’s disease in marmoset monkeys. Furthermore, we tested the impact of high chronic doses of human recombinant CDNF on unlesioned monkeys and analyzed the amino acid sequence of marmoset CDNF. The severity of 6-OHDA lesions and treatment effects were monitored in vivo using 123I-FP-CIT (DaTSCAN) SPECT. Quantitative analysis of 123I-FP-CIT SPECT showed a significant increase of dopamine transporter binding activity in lesioned animals treated with CDNF. Glial cell line-derived neurotrophic factor (GDNF), a well-characterized and potent neurotrophic factor for dopamine neurons, served as a control in a parallel comparison with CDNF. By contrast with CDNF, only single animals responded to the treatment with GDNF, but no statistical difference was observed in the GDNF group. However, increased numbers of tyrosine hydroxylase immunoreactive neurons, observed within the lesioned caudate nucleus of GDNF-treated animals, indicate a strong bioactive potential of GDNF. PMID:26901822

  12. Breastfeeding policy: a globally comparative analysis

    PubMed Central

    Raub, Amy; Earle, Alison

    2013-01-01

    Abstract Objective To explore the extent to which national policies guaranteeing breastfeeding breaks to working women may facilitate breastfeeding. Methods An analysis was conducted of the number of countries that guarantee breastfeeding breaks, the daily number of hours guaranteed, and the duration of guarantees. To obtain current, detailed information on national policies, original legislation as well as secondary sources on 182 of the 193 Member States of the United Nations were examined. Regression analyses were conducted to test the association between national policy and rates of exclusive breastfeeding while controlling for national income level, level of urbanization, female percentage of the labour force and female literacy rate. Findings Breastfeeding breaks with pay are guaranteed in 130 countries (71%) and unpaid breaks are guaranteed in seven (4%). No policy on breastfeeding breaks exists in 45 countries (25%). In multivariate models, the guarantee of paid breastfeeding breaks for at least 6 months was associated with an increase of 8.86 percentage points in the rate of exclusive breastfeeding (P < 0.05). Conclusion A greater percentage of women practise exclusive breastfeeding in countries where laws guarantee breastfeeding breaks at work. If these findings are confirmed in longitudinal studies, health outcomes could be improved by passing legislation on breastfeeding breaks in countries that do not yet ensure the right to breastfeed. PMID:24052676

  13. Comparative analysis of the immunologic response induced by the Sterne 34F2 live spore Bacillus anthracis vaccine in a ruminant model.

    PubMed

    Ndumnego, Okechukwu C; Köhler, Susanne M; Crafford, Jannie; van Heerden, Henriette; Beyer, Wolfgang

    2016-10-01

    The Sterne 34F2 live spore vaccine (SLSV) developed in 1937 is the most widely used veterinary vaccine against anthrax. However, literature on the immunogenicity of this vaccine in a target ruminant host is scarce. In this study, we evaluated the humoral response to the Bacillus anthracis protective antigen (rPA), a recombinant bacillus collagen-like protein of anthracis (rBclA), formaldehyde inactivated spores (FIS) prepared from strain 34F2 and a vegetative antigen formulation prepared from a capsule and toxin deficient strain (CDC 1014) in Boer goats. The toxin neutralizing ability of induced antibodies was evaluated using an in vitro toxin neutralization assay. The protection afforded by the vaccine was also assessed in vaccinates. Anti-rPA, anti-FIS and lethal toxin neutralizing titres were superior after booster vaccinations, compared to single vaccinations. Qualitative analysis of humoral responses to rPA, rBclA and FIS antigens revealed a preponderance of anti-FIS IgG titres following either single or double vaccinations with the SLSV. Antibodies against FIS and rPA both increased by 350 and 300-fold following revaccinations respectively. There was no response to rBclA following vaccinations with the SLSV. Toxin neutralizing titres increased by 80-fold after single vaccination and 700-fold following a double vaccination. Lethal challenge studies in naïve goats indicated a minimum infective dose of 36 B. anthracis spores. Single and double vaccination with the SLSV protected 4/5 and 3/3 of goats challenged with>800 spores respectively. An early booster vaccination following the first immunization is suggested in order to achieve a robust immunity. Results from this study indicate that this crucial second vaccination can be administered as early as 3 months after the initial vaccination.

  14. Comparative analysis of the immunologic response induced by the Sterne 34F2 live spore Bacillus anthracis vaccine in a ruminant model.

    PubMed

    Ndumnego, Okechukwu C; Köhler, Susanne M; Crafford, Jannie; van Heerden, Henriette; Beyer, Wolfgang

    2016-10-01

    The Sterne 34F2 live spore vaccine (SLSV) developed in 1937 is the most widely used veterinary vaccine against anthrax. However, literature on the immunogenicity of this vaccine in a target ruminant host is scarce. In this study, we evaluated the humoral response to the Bacillus anthracis protective antigen (rPA), a recombinant bacillus collagen-like protein of anthracis (rBclA), formaldehyde inactivated spores (FIS) prepared from strain 34F2 and a vegetative antigen formulation prepared from a capsule and toxin deficient strain (CDC 1014) in Boer goats. The toxin neutralizing ability of induced antibodies was evaluated using an in vitro toxin neutralization assay. The protection afforded by the vaccine was also assessed in vaccinates. Anti-rPA, anti-FIS and lethal toxin neutralizing titres were superior after booster vaccinations, compared to single vaccinations. Qualitative analysis of humoral responses to rPA, rBclA and FIS antigens revealed a preponderance of anti-FIS IgG titres following either single or double vaccinations with the SLSV. Antibodies against FIS and rPA both increased by 350 and 300-fold following revaccinations respectively. There was no response to rBclA following vaccinations with the SLSV. Toxin neutralizing titres increased by 80-fold after single vaccination and 700-fold following a double vaccination. Lethal challenge studies in naïve goats indicated a minimum infective dose of 36 B. anthracis spores. Single and double vaccination with the SLSV protected 4/5 and 3/3 of goats challenged with>800 spores respectively. An early booster vaccination following the first immunization is suggested in order to achieve a robust immunity. Results from this study indicate that this crucial second vaccination can be administered as early as 3 months after the initial vaccination. PMID:27496738

  15. Comparative analysis of immunization schedules using a novel adenovirus-based immunotherapeutic targeting hepatitis B in naïve and tolerant mouse models.

    PubMed

    Boukhebza, Houda; Dubois, Clarisse; Koerper, Véronique; Evlachev, Alexei; Schlesinger, Yasmine; Menguy, Thierry; Silvestre, Nathalie; Riedl, Petra; Inchauspé, Geneviève; Martin, Perrine

    2014-05-30

    Development of active targeted immunotherapeutics is a rapid developing field in the arena of chronic infectious diseases. The question of repeated, closely spaced administration of immunotherapeutics to achieve a rapid impact on the replicating agent is an important one. We analyzed here, using a prototype adenovirus-based immunotherapeutic encoding Core and Polymerase from the hepatitis B virus (Ad-HBV), the influence of closely spaced repeated immunizations on the level and quality of induced HBV-specific and vector-specific immune responses in various mouse models. Ad-HBV, whether injected once or multiple times, was able to induce HBV- and adeno-specific T cells both in HBV-free mice and in a HBV tolerant mouse model. Adenovirus-specific T cell responses and titers of neutralizing anti-Ad5 antibodies increased from time of the 3rd injection. Interestingly, single or multiple Ad-HBV injections resulted in detection of Polymerase-specific functional T cells in HBV tolerant mice. Overall no modulation of the levels of HBV-specific cytokine-producing (IFNγ/TNFα) and cytolytic T cells was observed following repeated administrations (3 or 6 weekly injections) when compared with levels detected after a single injection with the exception of two markers: 1. the proportion of HBV-specific IFNγ-producing cells bearing the CD27+/CD43+ phenotype appeared to be sustained in C57BL/6J mice following 6 weekly injections; 2. the percentage of IFNγ/TNFα Core-specific producing cells observed in spleens of HLA-A2 mice as well as of that specific of Polymerase observed in livers of HBV tolerant mice was maintained. In addition, percentage of HBV-specific T cells expressing PD-1 was not increased by multiple injections. Overall these data show that, under experimental conditions used, rapid, closely spaced administrations of an adenovirus-based HBV immunotherapeutics does not inhibit induced T-cell responses including in a HBV-tolerant environment. PMID:24726690

  16. Comparative analysis of in situ versus ex situ perfusion on flow and microcirculation in kidney procurement: research on a porcine model

    PubMed Central

    2013-01-01

    Background The first crucial step in transplantation appears to be the effective rinsing of the graft during organ procurement. Even though there is strong suspicion that ex situ perfusion results in better rinsing of the graft, there is no proof for this hypothesis. The aim of this study was to analyse the differences of in situ and ex situ kidney perfusion in a porcine model. Methods Standardised multiorgan procurement was performed in 15 German landrace pigs. Perfusion was carried out using histidine–tryptophan–ketoglutarate solution (HTK) under the application of pressure. In one kidney, in situ perfusion via the aorta was carried out while the second kidney received ex situ perfusion via the renal artery (RA). Perfusate flow inside the aorta and the RA was recorded at different pressure steps. In order to visualise the effect on the microcirculation, different coloured microparticles (MPs; 10 μm) were administered via the aorta or RA. Subsequently, frozen sections of the explanted kidneys were analysed histologically and MPs were evaluated quantitatively. Results Ex situ kidney perfusion resulted in significantly improved flow rates (P<0.0001) compared with in situ perfusion. By applying ex situ perfusion it was even possible to attain physiological flow levels on the RA under the application of external pressure of 150 to 200 mmHg. The amount of MPs was able to highlight the positive impact of ex situ perfusion on microcirculation of the kidney graft (P<0.0001). Conclusions The use of MPs represents a valuable tool for quantitative investigation and illustration of kidney perfusion in experimental setups. Additional ex situ perfusion is able to improve the quality of kidney perfusion. PMID:23837545

  17. Developmental changes in hepatic glucose metabolism in a newborn piglet model: A comparative analysis for suckling period and early weaning period.

    PubMed

    Xie, Chunyan; Wang, Qinhua; Wang, Jing; Tan, Bie; Fan, Zhiyong; Deng, Ze-yuan; Wu, Xin; Yin, Yulong

    2016-02-19

    The liver glucose metabolism, supplying sufficient energy for glucose-dependent tissues, is important in suckling or weaned animals, although there are few studies with piglet model. To better understand the development of glucose metabolism in the piglets during suckling period and early weaning period, we determined the hepatic glycogen content, and investigated the relative protein expression of key enzymes of glucogenesis (GNG) and mRNA levels of some glucose metabolism-related genes. During suckling period, the protein level of G6Pase in the liver of suckling piglets progressively declined with day of age compared with that of newborn piglets (at 1 day of age), whereas the PEPCK level stabilized until day 21 of age, indicating that hepatic GNG capacity gradually weakened in suckling piglets. The synthesis of hepatic glycogen, which was consistent with the fluctuation of glycolytic key genes PFKL and PKLR that gradually decreased after birth and was more or less steady during latter suckling period, although both the mRNA levels of GCK and key glucose transporter GLUT2 presented uptrend in suckling piglets. However, early weaning significantly suppressed the hepatic GNG in the weaned piglets, especially at d 3-5 of weaning period, then gradually recovered at d 7 of weaning period. Meanwhile, PFKL, PKLR and GLUT2 showed the similar trend during weaning period. On the contrast, the hepatic glycogen reached the maximum value when the G6Pase and PEPCK protein expression were at the lowest level, although the GCK level maintained increasing through 7 days of weaning period. Altogether, our study provides evidence that hepatic GNG and glycolysis in newborn piglets were more active than other days during suckling period, and early weaning could significantly suppressed glucose metabolism in liver, but this inhibition would progressively recover at day 7 after weaning.

  18. Comparing Results from Constant Comparative and Computer Software Methods: A Reflection about Qualitative Data Analysis

    ERIC Educational Resources Information Center

    Putten, Jim Vander; Nolen, Amanda L.

    2010-01-01

    This study compared qualitative research results obtained by manual constant comparative analysis with results obtained by computer software analysis of the same data. An investigated about issues of trustworthiness and accuracy ensued. Results indicated that the inductive constant comparative data analysis generated 51 codes and two coding levels…

  19. Comparative Modelling of the Spectra of Cool Giants

    NASA Technical Reports Server (NTRS)

    Lebzelter, T.; Heiter, U.; Abia, C.; Eriksson, K.; Ireland, M.; Neilson, H.; Nowotny, W; Maldonado, J; Merle, T.; Peterson, R.; Plez, B.; Short, C. I.; Wahlgren, G. M.; Worley, C.; Aringer, B.; Bladh, S.; de Laverny, P.; Goswami, A.; Mora, A.; Norris, R. P.; Recio-Blanco, A.; Scholz, M.; Thevenin, F.; Tsuji, T.; Kordopatis, G.

    2012-01-01

    Our ability to extract information from the spectra of stars depends on reliable models of stellar atmospheres and appropriate techniques for spectral synthesis. Various model codes and strategies for the analysis of stellar spectra are available today. Aims. We aim to compare the results of deriving stellar parameters using different atmosphere models and different analysis strategies. The focus is set on high-resolution spectroscopy of cool giant stars. Methods. Spectra representing four cool giant stars were made available to various groups and individuals working in the area of spectral synthesis, asking them to derive stellar parameters from the data provided. The results were discussed at a workshop in Vienna in 2010. Most of the major codes currently used in the astronomical community for analyses of stellar spectra were included in this experiment. Results. We present the results from the different groups, as well as an additional experiment comparing the synthetic spectra produced by various codes for a given set of stellar parameters. Similarities and differences of the results are discussed. Conclusions. Several valid approaches to analyze a given spectrum of a star result in quite a wide range of solutions. The main causes for the differences in parameters derived by different groups seem to lie in the physical input data and in the details of the analysis method. This clearly shows how far from a definitive abundance analysis we still are.

  20. MHD models compared with Artemis observations at -60 Re

    NASA Astrophysics Data System (ADS)

    Gencturk Akay, Iklim; Sibeck, David; Angelopoulos, Vassilis; Kaymaz, Zerefsan; Kuznetsova, Maria

    2016-07-01

    The distant magnetotail has been one of the least studied magnetic regions of the Earth's magnetosphere compared to the other near Earth both dayside and nightside magnetospheric regions owing to the limited number of spacecraft observations. Since 2011, ARTEMIS spacecraft give an excellent opportunity to study the magnetotail at lunar distances in terms of data quality and parameter space. This also gives opportunities to improve the magnetotail models at -60 Re and encourages the modelling studies of the distant magnetotail. Using ARTEMIS data in distant magnetotail, we create magnetic field and plasma flow vector maps in different planes and separated with IMF orientation to understand the magnetotail dynamics at this distance. For this study, we use CCMC's Run-on-Request resources of the MHD models; specifically SWMF-BATS-R-US, OpenGGCM, and LFM and perform the similar analysis with the models. Our main purpose in this study is to measure the performance of the MHD models at -60 Re distant magnetotail by comparing the model results with Artemis observations. In the literature, such a comprehensive comparative study is lacking in the distant tail. Preliminary results show that in general all three models underestimate the magnetic field structure while overestimating the flow speed. In the cross-sectional view, LFM seems to produce the better agreement with the observations. A clear dipolar magnetic field structure is seen with dawn-dusk asymmetry in all models owing to slight positive IMF By but the effect was found to be exaggerated. All models show tailward flows at this distance of the magnetotail, most possibly owing to the magnetic reconnection at the near Earth tail distances. A detailed comparison of several tail characteristics from the models will be presented and discussions will be given with respect to the observations from Artemis at this distance.

  1. Human Capital Development: Comparative Analysis of BRICs

    ERIC Educational Resources Information Center

    Ardichvili, Alexandre; Zavyalova, Elena; Minina, Vera

    2012-01-01

    Purpose: The goal of this article is to conduct macro-level analysis of human capital (HC) development strategies, pursued by four countries commonly referred to as BRICs (Brazil, Russia, India, and China). Design/methodology/approach: This analysis is based on comparisons of macro indices of human capital and innovativeness of the economy and a…

  2. Comparative 3-D Modeling of tmRNA

    PubMed Central

    Burks, Jody; Zwieb, Christian; Müller, Florian; Wower, Iwona; Wower, Jacek

    2005-01-01

    Background Trans-translation releases stalled ribosomes from truncated mRNAs and tags defective proteins for proteolytic degradation using transfer-messenger RNA (tmRNA). This small stable RNA represents a hybrid of tRNA- and mRNA-like domains connected by a variable number of pseudoknots. Comparative sequence analysis of tmRNAs found in bacteria, plastids, and mitochondria provides considerable insights into their secondary structures. Progress toward understanding the molecular mechanism of template switching, which constitutes an essential step in trans-translation, is hampered by our limited knowledge about the three-dimensional folding of tmRNA. Results To facilitate experimental testing of the molecular intricacies of trans-translation, which often require appropriately modified tmRNA derivatives, we developed a procedure for building three-dimensional models of tmRNA. Using comparative sequence analysis, phylogenetically-supported 2-D structures were obtained to serve as input for the program ERNA-3D. Motifs containing loops and turns were extracted from the known structures of other RNAs and used to improve the tmRNA models. Biologically feasible 3-D models for the entire tmRNA molecule could be obtained. The models were characterized by a functionally significant close proximity between the tRNA-like domain and the resume codon. Potential conformational changes which might lead to a more open structure of tmRNA upon binding to the ribosome are discussed. The method, described in detail for the tmRNAs of Escherichia coli, Bacillus anthracis, and Caulobacter crescentus, is applicable to every tmRNA. Conclusion Improved molecular models of biological significance were obtained. These models will guide in the design of experiments and provide a better understanding of trans-translation. The comparative procedure described here for tmRNA is easily adopted for the modeling the members of other RNA families. PMID:15958166

  3. Compare and Contrast Program Planning Models

    ERIC Educational Resources Information Center

    Baskas, Richard S.

    2011-01-01

    This paper will examine the differences and similarities between two program planning models, Tyler and Caffarella, to reveal their strengths and weaknesses. When adults are involved in training sessions, there are various program planning models that can be used, depending on the goal of the training session. Researchers developed these models…

  4. COMPARING AND LINKING PLUMES ACROSS MODELING APPROACHES

    EPA Science Inventory

    River plumes carry many pollutants, including microorganisms, into lakes and the coastal ocean. The physical scales of many stream and river plumes often lie between the scales for mixing zone plume models, such as the EPA Visual Plumes model, and larger-sized grid scales for re...

  5. Comparing modeled fire dynamics with charcoal records for the Holocene

    NASA Astrophysics Data System (ADS)

    Bruecher, T.; Brovkin, V.; Kloster, S.; Marlon, J. R.; Power, M. J.

    2013-12-01

    An Earth System model of intermediate complexity, CLIMBER-2, and land surface model JSBACH that includes dynamic vegetation, carbon cycle, and fire regime are used for simulation of natural fire dynamics through the last 8,000 years. To compare the fire model results with the charcoal reconstructions, several output variables of the fire model (burned area, carbon emissions) and several approaches of model output processing are tested. The z-scores out of charcoal dataset have been calculated for the period 8,000 to 200 BP to exclude a period of strong anthropogenic forcing during the last two centuries. The model analysis points mainly to an increasing fire activity during the Holocene for most of the investigated areas, which is in good correspondence to reconstructed fire trends out of charcoal data for most of the tested regions, while for few regions such as Europe the simulated trend and the reconstructed trends are different. The difference between the modeled and reconstructed fire activity could be due to absence of the anthropogenic forcing in the model simulations, but also due to limitations of model assumptions for modeling fire dynamics. For the model trends, the usage of averaging or z-score processing of model output resulted in similar directions of trend. Therefore, the approach of fire model output processing does not effect results of the model-data comparison. Global fire modeling is still in its infancy; improving our representations of fire through validation exercises such as what we present here is thus essential before testing hypotheses about the effects of extreme climate changes on fire behavior and potential feedbacks that result from those changes.

  6. MANAGEMENT AND COMPARATIVE ANALYSIS OF DATASET ENSEMBLES

    SciTech Connect

    Geveci, Berk

    2010-05-17

    The primary Phase I technical objective was to develop a prototype that demonstrates the functionality of all components required for an end-to-end meta-data management and comparative visualization system.

  7. Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

    PubMed Central

    Irie, Naoki; Kuratani, Shigeru

    2011-01-01

    One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates. PMID:21427719

  8. Atmosphere of Mars: Mariner IV Models Compared.

    PubMed

    Fjeldbo, G; Fjeldbo, W C; Eshleman, V R

    1966-09-23

    Three classes of models for the atmosphere of Mars differ in identifying the main ionospheric layer measured by Mariner IV as being analogous to a terrestrial F(2), F(1), or E layer. At an altitude of several hundred kilometers, the relative atmospheric mass densities for these models (in the order named) are approximately 1, 10(2), and 10(4), and the temperatures are roughly 100 degrees , 200 degrees , and 400 degrees K. Theory and observation are in best agreement for an F, s model, for which photodissociation of CO(2), and diffusive separation result in an atomic-oxygen upper atmosphere, with O(+) being the principal ion in the isothermal topside of the ionosphere. The mesopause temperature minimum would be at or below the freezing point of CO(2), and dry ice particles would be expected to form. However, an F(1) model, with molecular ions in a mixed and warmer upper atmosphere, might result if photodissociation and diffusive separation are markedly less than would be expected from analogy with Earth's upper atmosphere. The E model proposed by Chamberlain and McElroy appears very unlikely; it is not compatible with the measured ionization profile unless rather unlikely assumptions are made about the values, and changes with height, of the effective recombination coefficient and the average ion mass. Moreover our theoretical heat-budget computations for the atmospheric region probed by Mariner IV indicate markedly lower temperatures and temperature gradients than were obtained for the E model. PMID:17749730

  9. Atmosphere of Mars: Mariner IV Models Compared.

    PubMed

    Fjeldbo, G; Fjeldbo, W C; Eshleman, V R

    1966-09-23

    Three classes of models for the atmosphere of Mars differ in identifying the main ionospheric layer measured by Mariner IV as being analogous to a terrestrial F(2), F(1), or E layer. At an altitude of several hundred kilometers, the relative atmospheric mass densities for these models (in the order named) are approximately 1, 10(2), and 10(4), and the temperatures are roughly 100 degrees , 200 degrees , and 400 degrees K. Theory and observation are in best agreement for an F, s model, for which photodissociation of CO(2), and diffusive separation result in an atomic-oxygen upper atmosphere, with O(+) being the principal ion in the isothermal topside of the ionosphere. The mesopause temperature minimum would be at or below the freezing point of CO(2), and dry ice particles would be expected to form. However, an F(1) model, with molecular ions in a mixed and warmer upper atmosphere, might result if photodissociation and diffusive separation are markedly less than would be expected from analogy with Earth's upper atmosphere. The E model proposed by Chamberlain and McElroy appears very unlikely; it is not compatible with the measured ionization profile unless rather unlikely assumptions are made about the values, and changes with height, of the effective recombination coefficient and the average ion mass. Moreover our theoretical heat-budget computations for the atmospheric region probed by Mariner IV indicate markedly lower temperatures and temperature gradients than were obtained for the E model.

  10. An economic analysis of comparable worth.

    PubMed

    Disch, J M; Feldstein, P J

    1986-06-01

    Comparable worth has been called the civil rights issue of the 1980s. Nursing is in the forefront of this movement. Although several governmental agencies are implementing salary programs based on comparable worth, establishing such a program in the hospital setting could yield problems for nurse executives. Implementation could be costly and demand a significant investment of resources. This paper discusses how wages are determined in a competitive market and what happens to that process when restrictions and barriers make the market noncompetitive. Of most importance, alternative strategies for increasing nursing salaries are presented.

  11. Comparative Rural Landscapes: A Conceptual Geographic Model.

    ERIC Educational Resources Information Center

    Steinbrink, John E.

    The geography unit is designed for use in upper elementary grades. The unit objective is to help the student learn facts about the landscapes of the United States, the Netherlands, Australia, Russia, and Central Africa, and acquire generic ideas which he can apply to the analysis and comparison of other landscapes. The unit is an attempt to apply…

  12. Comparative analysis of Orem's and King's theories.

    PubMed

    Hanucharurnkul, S

    1989-05-01

    Dorothea Orem and Imogene King are two nursing theorists who are contributing significantly to the development of nursing knowledge. This paper compares the similarities and differences in their strategies for theory development, their views of nursing metaparadigm concepts, and their theories of nursing system and goal attainment in terms of scope, usefulness, and their unique contribution to nursing science. PMID:2738232

  13. A Comparative Analysis of Speed Profile Models for Ankle Pointing Movements: Evidence that Lower and Upper Extremity Discrete Movements are Controlled by a Single Invariant Strategy

    PubMed Central

    Michmizos, Konstantinos P.; Vaisman, Lev; Krebs, Hermano Igo

    2014-01-01

    Little is known about whether our knowledge of how the central nervous system controls the upper extremities (UE), can generalize, and to what extent to the lower limbs. Our continuous efforts to design the ideal adaptive robotic therapy for the lower limbs of stroke patients and children with cerebral palsy highlighted the importance of analyzing and modeling the kinematics of the lower limbs, in general, and those of the ankle joints, in particular. We recruited 15 young healthy adults that performed in total 1,386 visually evoked, visually guided, and target-directed discrete pointing movements with their ankle in dorsal–plantar and inversion–eversion directions. Using a non-linear, least-squares error-minimization procedure, we estimated the parameters for 19 models, which were initially designed to capture the dynamics of upper limb movements of various complexity. We validated our models based on their ability to reconstruct the experimental data. Our results suggest a remarkable similarity between the top-performing models that described the speed profiles of ankle pointing movements and the ones previously found for the UE both during arm reaching and wrist pointing movements. Among the top performers were the support-bounded lognormal and the beta models that have a neurophysiological basis and have been successfully used in upper extremity studies with normal subjects and patients. Our findings suggest that the same model can be applied to different “human” hardware, perhaps revealing a key invariant in human motor control. These findings have a great potential to enhance our rehabilitation efforts in any population with lower extremity deficits by, for example, assessing the level of motor impairment and improvement as well as informing the design of control algorithms for therapeutic ankle robots. PMID:25505881

  14. A Comparative Analysis of Speed Profile Models for Ankle Pointing Movements: Evidence that Lower and Upper Extremity Discrete Movements are Controlled by a Single Invariant Strategy.

    PubMed

    Michmizos, Konstantinos P; Vaisman, Lev; Krebs, Hermano Igo

    2014-01-01

    Little is known about whether our knowledge of how the central nervous system controls the upper extremities (UE), can generalize, and to what extent to the lower limbs. Our continuous efforts to design the ideal adaptive robotic therapy for the lower limbs of stroke patients and children with cerebral palsy highlighted the importance of analyzing and modeling the kinematics of the lower limbs, in general, and those of the ankle joints, in particular. We recruited 15 young healthy adults that performed in total 1,386 visually evoked, visually guided, and target-directed discrete pointing movements with their ankle in dorsal-plantar and inversion-eversion directions. Using a non-linear, least-squares error-minimization procedure, we estimated the parameters for 19 models, which were initially designed to capture the dynamics of upper limb movements of various complexity. We validated our models based on their ability to reconstruct the experimental data. Our results suggest a remarkable similarity between the top-performing models that described the speed profiles of ankle pointing movements and the ones previously found for the UE both during arm reaching and wrist pointing movements. Among the top performers were the support-bounded lognormal and the beta models that have a neurophysiological basis and have been successfully used in upper extremity studies with normal subjects and patients. Our findings suggest that the same model can be applied to different "human" hardware, perhaps revealing a key invariant in human motor control. These findings have a great potential to enhance our rehabilitation efforts in any population with lower extremity deficits by, for example, assessing the level of motor impairment and improvement as well as informing the design of control algorithms for therapeutic ankle robots.

  15. A Comparative Analysis of Speed Profile Models for Ankle Pointing Movements: Evidence that Lower and Upper Extremity Discrete Movements are Controlled by a Single Invariant Strategy.

    PubMed

    Michmizos, Konstantinos P; Vaisman, Lev; Krebs, Hermano Igo

    2014-01-01

    Little is known about whether our knowledge of how the central nervous system controls the upper extremities (UE), can generalize, and to what extent to the lower limbs. Our continuous efforts to design the ideal adaptive robotic therapy for the lower limbs of stroke patients and children with cerebral palsy highlighted the importance of analyzing and modeling the kinematics of the lower limbs, in general, and those of the ankle joints, in particular. We recruited 15 young healthy adults that performed in total 1,386 visually evoked, visually guided, and target-directed discrete pointing movements with their ankle in dorsal-plantar and inversion-eversion directions. Using a non-linear, least-squares error-minimization procedure, we estimated the parameters for 19 models, which were initially designed to capture the dynamics of upper limb movements of various complexity. We validated our models based on their ability to reconstruct the experimental data. Our results suggest a remarkable similarity between the top-performing models that described the speed profiles of ankle pointing movements and the ones previously found for the UE both during arm reaching and wrist pointing movements. Among the top performers were the support-bounded lognormal and the beta models that have a neurophysiological basis and have been successfully used in upper extremity studies with normal subjects and patients. Our findings suggest that the same model can be applied to different "human" hardware, perhaps revealing a key invariant in human motor control. These findings have a great potential to enhance our rehabilitation efforts in any population with lower extremity deficits by, for example, assessing the level of motor impairment and improvement as well as informing the design of control algorithms for therapeutic ankle robots. PMID:25505881

  16. General Education Requirements: A Comparative Analysis

    ERIC Educational Resources Information Center

    Warner, Darrell B.; Koeppel, Katie

    2009-01-01

    While "general education" is a phrase heavily used in higher education, Leskes and Wright note that it has multiple meanings: it can refer to those courses that a college or university requires all of its students must pass as a condition for graduation, a common curriculum, a distribution requirement, or even core texts. This analysis of general…

  17. Comparative Lifecycle Energy Analysis: Theory and Practice.

    ERIC Educational Resources Information Center

    Morris, Jeffrey; Canzoneri, Diana

    1992-01-01

    Explores the position that more energy is conserved through recycling secondary materials than is generated from municipal solid waste incineration. Discusses one component of a lifecycle analysis--a comparison of energy requirements for manufacturing competing products. Includes methodological issues, energy cost estimates, and difficulties…

  18. Comparing Work Skills Analysis Tools. Project Report.

    ERIC Educational Resources Information Center

    Barker, Kathryn

    This document outlines the processes and outcomes of a research project conducted to review work skills analysis tools (products and/or services) that profile required job skills and/or assess individuals' acquired skills. The document begins with a brief literature review and discussion of pertinent terminology. Presented next is a list of…

  19. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

    Sahl, Jason W; Pace, Norman R; Spear, John R

    2008-10-01

    A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity. PMID:18757573

  20. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

    Sahl, Jason W; Pace, Norman R; Spear, John R

    2008-10-01

    A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity.

  1. A comparative modeling of supernova 1993J

    NASA Technical Reports Server (NTRS)

    Blinnikov, Sergei; Eastman, Ron; Bartunov, Oleg; Popolitov, Vlad; Woosley, Stan

    1997-01-01

    The light curve of Supernova 1993J is calculated using two computational radiation transport approaches. The two approaches are represented by the computer codes STELLA and EDDINGTON. The emphasis is on the shock breakout and the photometry in the U, B and V bands during the first 120 days of the supernova. The STELLA model includes implicit hydrodynamics and is able to model early supernova evolution before the expansion is homologous. The STELLA model employs multi-group photonics and is able to follow the radiation as it decouples from the matter. The EDDINGTON code uses an algorithm for integrating the transport equation which assumes homologous expansion and uses a finer frequency resolution. The agreement between the two codes is considered to be satisfactory only in the case where compatible physical assumptions are made concerning the opacity. The assumptions are justified. The continuum spectrum for SN 1993J is predicted near the shock breakout to be superior to that predicted by standard single energy group hydrocodes. The uncertainties involved in current time dependent models of supernova light curves are discussed.

  2. A Comparative Study of Some Dynamic Stall Models

    NASA Technical Reports Server (NTRS)

    Reddy, T. S. R.; Kaza, K. R. V.

    1987-01-01

    Three semi-empirical aerodynamic stall models are compared with respect to their lift and moment hysteresis loop prediction, limit cycle behavior, easy implementation, and feasibility in developing the parameters required for stall flutter prediction of advanced turbines. For the comparison of aeroelastic response prediction including stall, a typical section model and a plate structural model are considered. The response analysis includes both plunging and pitching motions of the blades. In model A, a correction to the angle of attack is applied when the angle of attack exceeds the static stall angle. In model B, a synthesis procedure is used for angles of attack above static stall angles and the time history effects are accounted through the Wagner function. In both models the life and moment coefficients for angle of attack below stall are obtained from tabular data for a given Mach number and angle of attack. In model C, referred to an the ONERA model, the life and moment coefficients are given in the form of two differential equations, one for angles below stall, and the other for angles above stall. The parameters of those equations are nonlinear functions of the angle of attack.

  3. Comparative analysis of absorbance calculations for integrated optical waveguide configurations by use of the ray optics model and the electromagnetic wave theory.

    PubMed

    Mendes, S B; Saavedra, S S

    2000-02-01

    Focusing on the use of planar waveguides as platforms for highly sensitive attenuated total reflection spectroscopy of organic thin films, we extend the ray optics model to provide absorbance expressions for the case of dichroic layers immobilized on the waveguide surface. Straightforward expressions are derived for the limiting case of weakly absorbing, anisotropically oriented molecules in the waveguide-cladding region. The second major focus is on the accuracy of the ray optics model. This model assumes that the introduction of absorbing species, either in the bulk cladding or as an adlayer on the waveguide surface, only causes a small perturbation to the original waveguide-mode profile. We investigate the accuracy of this assumption and the conditions under which it is valid. A comparison to an exact calculation by use of the electromagnetic wave theory is implemented, and the discrepancy of the ray optics model is determined for various waveguide configurations. We find that in typical situations in which waveguide-absorbance measurements are used to study organic thin films (k(l)/n(l)

  4. A COMPARATIVE RISK REDUCTION ANALYSIS OF THE OFFICE OF SOLID WASTE'S WASTE MINIMIZATION PRIORITY CHEMICALS INITIATIVE USING THE 3MRA MULTIMEDIA MODELING SYSTEM

    EPA Science Inventory

    A study was initiated by the EPA/ORD National Exposure Research Lab (NERL) in FY05 to quantify risk reduction resulting from this national EPA initiative to reduce WMPC disposal. Using the 3MRA modeling system, which was recommended for use by the EPA Science Advisory Board for ...

  5. Comparative analysis of theories of relativistic photoionization

    NASA Astrophysics Data System (ADS)

    Hafizi, Bahman; Gordon, Daniel; Palastro, John

    2015-11-01

    Laser-plasma experiments routinely rely on photoionization for plasma formation. For large laser intensities or for high-Z atoms relativistic effects become important. We investigate a unique regime of relativistic photoionization from high-Z atoms where relativistic effects modify both the bound and continuum electronic states. Theories of photoionization are based on the imaginary time method and the S-matrix method, amongst others. We compare the results of these approaches for both the Dirac and the Klein-Gordon equations. Analytical results for the momentum distribution of ejected electrons and ionization rate are presented and compared with those from numerical solutions. Work supported by the Department of Energy and the NRL Base Program.

  6. Light beam deflector performance: a comparative analysis.

    PubMed

    Zook, J D

    1974-04-01

    The performance of various types of analog light beam deflectors is summarized, and their relative positions in a deflector hierarchy are defined. The three types of deflectors considered are (1) mechanical (galvanometer) mirror deflectors, (2) acoustooptic deflectors, and (3) analog electrooptic deflectors. Material figures of merit are defined and compared, and the theoretical trade-off between speed and resolution is given for each type of deflector. PMID:20126095

  7. Comparative Analysis of Homology Models of the Ah Receptor Ligand Binding Domain: Verification of Structure-Function Predictions by Site-Directed Mutagenesis of a Non-Functional AHR†

    PubMed Central

    Fraccalvieri, Domenico; Soshilov, Anatoly A.; Karchner, Sibel I.; Franks, Diana G.; Pandini, Alessandro; Bonati, Laura; Hahn, Mark E.; Denison, Michael S.

    2013-01-01

    The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates the biological and toxic effects of a wide variety of structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While significant interspecies differences in AHR ligand binding specificity, selectivity and response have been observed, the structural determinants responsible have not been determined and homology models of the AHR ligand-binding domain (LBD) are available for only a few species. Here we describe the development and comparative analysis of homology models of the LBD of sixteen AHRs from twelve mammalian and nonmammalian species and identify the specific residues contained within their ligand binding cavities. The ligand-binding cavity of the fish AHR exhibits differences from mammalian and avian AHRs, suggesting a slightly different TCDD binding mode. Comparison of the internal cavity in the LBD model of zebrafish (zf) AHR2, which binds TCDD with high affinity, to that of zfAHR1a, which does not bind TCDD, revealed that the latter has a dramatically shortened binding cavity due to the side chains of three residues (Tyr296, Thr386, His388) that reduce the internal space available to TCDD. Mutagenesis of two of these residues in zfAhR1a to those present in zfAHR2 (Y296H, T386A) restored the ability of zfAHR1a to bind TCDD and to exhibit TCDD-dependent binding to DNA. These results demonstrate the importance of these two amino acids and highlight the predictive potential of comparative analysis of homology models from diverse species. The availability of these AHR LBD homology models will facilitate in depth comparative studies of AHR ligand binding and ligand-dependent AHR activation and provide a novel avenue to examine species specific differences in AHR responsiveness. PMID:23286227

  8. A comparative analysis of vertebrate sex determination.

    PubMed

    Sinclair, Andrew; Smith, Craig; Western, Patrick; McClive, Peter

    2002-01-01

    Sex determination in vertebrates is controlled by a variety of mechanisms. We compared the expression of SF1, DAX1, DMRT1, SOX9 and AMH during gonadogenesis in the mouse, chicken and alligator embryo. In contrast to the expression profile of Sf1 in mouse embryos, chicken and alligator embryos show higher levels of Sf1 expression in the developing ovaries compared to testes. This may reflect the higher level of sex hormone synthesis in the ovary compared to the testis in chickens and alligators. The DAX1 gene has a similar expression profile in all three vertebrate species but appears to have different gene structure. As in mouse, DMRT1 was expressed at very high levels in the chicken and alligator male gonad. The male-specific up-regulation of SOX9 expression appears to be a common feature in all three vertebrates. In the chicken and alligator AMH is expressed prior to SOX9, suggesting that in these species SOX9 cannot initiate AMH expression as it does in mammals. SOX9 acts at multiple points in the vertebrate testis pathway but it appears that only some of these functions have been conserved through evolution. PMID:11990786

  9. Comparative analysis of plant oil based fuels

    SciTech Connect

    Ziejewski, M.; Goettler, H.J.; Haines, H.; Huong, C.

    1995-12-31

    This paper presents the evaluation results from the analysis of different blends of fuels using the 13-mode standard SAE testing method. Six high oleic safflower oil blends, six ester blends, six high oleic sunflower oil blends, and six sunflower oil blends were used in this portion of the investigation. Additionally, the results from the repeated 13-mode tests for all the 25/75% mixtures with a complete diesel fuel test before and after each alternative fuel are presented.

  10. The Uranium Resource: A Comparative Analysis

    SciTech Connect

    Schneider, Erich A.; Sailor, William C.

    2007-07-01

    An analogy was drawn between uranium and thirty five minerals for which the USGS maintains extensive records. The USGS mineral price data, which extends from 1900 to the present, was used to create a simple model describing long term price evolution. Making the assumption that the price of uranium, a geologically unexceptional mineral, will evolve in a manner similar to that of the USGS minerals, the model was used to project its price trend for this century. Based upon the precedent set by the USGS data, there is an 80% likelihood that the price of uranium will decline. Moreover, the most likely scenario would see the equilibrium price of uranium decline by about 40% by mid-century. (authors)

  11. Enabling comparative modeling of closely related genomes: Example genus Brucella

    DOE PAGESBeta

    Faria, José P.; Edirisinghe, Janaka N.; Davis, James J.; Disz, Terrence; Hausmann, Anna; Henry, Christopher S.; Olson, Robert; Overbeek, Ross A.; Pusch, Gordon D.; Shukla, Maulik; et al

    2014-03-08

    For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this study, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as wellmore » as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.« less

  12. [Amaranth flour: characteristics, comparative analysis, application possibilities].

    PubMed

    Zharkov, I M; Miroshnichenko, L A; Zviagin, A A; Bavykina, I A

    2014-01-01

    Amaranth flour--a product of amaranth seeds processing--is a valuable industrial raw material that has an unique chemical composition and may be used for nutrition of people suffering from intolerance to traditional cereals protein, including celiac disease patients. The research aim was to study the composition of amaranth flour of two types compared with semolina which is traditionally used for nutrition by Russian population, as well as to compare the composition of milk amaranth flour porridge with milk semolina porridge. The composition of amaranth whole-ground flour and amaranth flour of premium grade processed from amaranth seeds grown in Voronezh region has been researched. It is to be noted that protein content in amaranth flour was 10.8-24.3% higher than in semolina, and its biological value and NPU-coefficient were higher by 22.65 and 46.51% respectively; lysine score in amaranth flour protein of premium grade came up to 107.54%, and in semolina protein only 40.95%. The level of digestible carbohydrates, including starch, was lower in amaranth flour than in semolina by 2.79-12.85 and 4.76-15.85% respectively, while fiber content was 15.5-30 fold higher. Fat content in amaranth flour of premium grade was 2,4 fold lower than in whole-ground amaranth flour but it was 45% higher than in semolina. The main advantage of amaranth flour protein compared to wheat protein is the predominance of albumins and globulins and a minimal content of prolamines and alpha-gliadin complete absence. The specifics of chemical composition allow the amaranth flour to be recommended for being included into nutrition of both healthy children and adults and also celiac disease patients.

  13. Comparative analysis of GOCI ocean color products.

    PubMed

    Amin, Ruhul; Lewis, Mark David; Lawson, Adam; Gould, Richard W; Martinolich, Paul; Li, Rong-Rong; Ladner, Sherwin; Gallegos, Sonia

    2015-10-12

    The Geostationary Ocean Color Imager (GOCI) is the first geostationary ocean color sensor in orbit that provides bio-optical properties from coastal and open waters around the Korean Peninsula at unprecedented temporal resolution. In this study, we compare the normalized water-leaving radiance (nLw) products generated by the Naval Research Laboratory Automated Processing System (APS) with those produced by the stand-alone software package, the GOCI Data Processing System (GDPS), developed by the Korean Ocean Research & Development Institute (KORDI). Both results are then compared to the nLw measured by the above water radiometer at the Ieodo site. This above-water radiometer is part of the Aerosol Robotic NETwork (AeroNET). The results indicate that the APS and GDPS processed  correlates well within the same image slot where the coefficient of determination (r²) is higher than 0.84 for all the bands from 412 nm to 745 nm. The agreement between APS and the AeroNET data is higher when compared to the GDPS results. The Root-Mean-Squared-Error (RMSE) between AeroNET and APS data ranges from 0.24 [mW/(cm²srμm)] at 555 nm to 0.52 [mW/(cm²srμm)]  at 412 nm while RMSE between AeroNET and GDPS data ranges from 0.47 [mW/(cm²srμm)] at 443 nm to 0.69 [mW/(cm²srμm)]  at 490 nm.

  14. Comparative analysis of GOCI ocean color products.

    PubMed

    Amin, Ruhul; Lewis, Mark David; Lawson, Adam; Gould, Richard W; Martinolich, Paul; Li, Rong-Rong; Ladner, Sherwin; Gallegos, Sonia

    2015-01-01

    The Geostationary Ocean Color Imager (GOCI) is the first geostationary ocean color sensor in orbit that provides bio-optical properties from coastal and open waters around the Korean Peninsula at unprecedented temporal resolution. In this study, we compare the normalized water-leaving radiance (nLw) products generated by the Naval Research Laboratory Automated Processing System (APS) with those produced by the stand-alone software package, the GOCI Data Processing System (GDPS), developed by the Korean Ocean Research & Development Institute (KORDI). Both results are then compared to the nLw measured by the above water radiometer at the Ieodo site. This above-water radiometer is part of the Aerosol Robotic NETwork (AeroNET). The results indicate that the APS and GDPS processed  correlates well within the same image slot where the coefficient of determination (r²) is higher than 0.84 for all the bands from 412 nm to 745 nm. The agreement between APS and the AeroNET data is higher when compared to the GDPS results. The Root-Mean-Squared-Error (RMSE) between AeroNET and APS data ranges from 0.24 [mW/(cm²srμm)] at 555 nm to 0.52 [mW/(cm²srμm)]  at 412 nm while RMSE between AeroNET and GDPS data ranges from 0.47 [mW/(cm²srμm)] at 443 nm to 0.69 [mW/(cm²srμm)]  at 490 nm. PMID:26473861

  15. Comparative Analysis of GOCI Ocean Color Products

    PubMed Central

    Amin, Ruhul; Lewis, Mark David; Lawson, Adam; Gould, Richard W.; Martinolich, Paul; Li, Rong-Rong; Ladner, Sherwin; Gallegos, Sonia

    2015-01-01

    The Geostationary Ocean Color Imager (GOCI) is the first geostationary ocean color sensor in orbit that provides bio-optical properties from coastal and open waters around the Korean Peninsula at unprecedented temporal resolution. In this study, we compare the normalized water-leaving radiance (nLw) products generated by the Naval Research Laboratory Automated Processing System (APS) with those produced by the stand-alone software package, the GOCI Data Processing System (GDPS), developed by the Korean Ocean Research & Development Institute (KORDI). Both results are then compared to the nLw measured by the above water radiometer at the Ieodo site. This above-water radiometer is part of the Aerosol Robotic NETwork (AeroNET). The results indicate that the APS and GDPS processed nLw correlates well within the same image slot where the coefficient of determination (r2) is higher than 0.84 for all the bands from 412 nm to 745 nm. The agreement between APS and the AeroNET data is higher when compared to the GDPS results. The Root-Mean-Squared-Error (RMSE) between AeroNET and APS data ranges from 0.24 [mW/(cm2srμm)] at 555 nm to 0.52 [mW/(cm2srμm)] at 412 nm while RMSE between AeroNET and GDPS data ranges from 0.47 [mW/(cm2srμm)] at 443 nm to 0.69 [mW/(cm2srμm)] at 490 nm. PMID:26473861

  16. Analysis of comparative data using generalized estimating equations.

    PubMed

    Paradis, Emmanuel; Claude, Julien

    2002-09-21

    It is widely acknowledged that the analysis of comparative data from related species should be performed taking into account their phylogenetic relationships. We introduce a new method, based on the use of generalized estimating equations (GEE), for the analysis of comparative data. The principle is to incorporate, in the modelling process, a correlation matrix that specifies the dependence among observations. This matrix is obtained from the phylogenetic tree of the studied species. Using this approach, a variety of distributions (discrete or continuous) can be analysed using a generalized linear modelling framework, phylogenies with multichotomies can be analysed, and there is no need to estimate ancestral character state. A simulation study showed that the proposed approach has good statistical properties with a type-I error rate close to the nominal 5%, and statistical power to detect correlated evolution between two characters which increases with the strength of the correlation. The proposed approach performs well for the analysis of discrete characters. We illustrate our approach with some data on macro-ecological correlates in birds. Some extensions of the use of GEE are discussed.

  17. Charge characteristics of humic and fulvic acids: comparative analysis by colloid titration and potentiometric titration with continuous pK-distribution function model.

    PubMed

    Bratskaya, S; Golikov, A; Lutsenko, T; Nesterova, O; Dudarchik, V

    2008-09-01

    Charge characteristics of humic and fulvic acids of a different origin (inshore soils, peat, marine sediments, and soil (lysimetric) waters) were evaluated by means of two alternative methods - colloid titration and potentiometric titration. In order to elucidate possible limitations of the colloid titration as an express method of analysis of low content of humic substances we monitored changes in acid-base properties and charge densities of humic substances with soil depth, fractionation, and origin. We have shown that both factors - strength of acidic groups and molecular weight distribution in humic and fulvic acids - can affect the reliability of colloid titration. Due to deviations from 1:1 stoichiometry in interactions of humic substances with polymeric cationic titrant, the colloid titration can underestimate total acidity (charge density) of humic substances with domination of weak acidic functional groups (pK>6) and high content of the fractions with molecular weight below 1kDa.

  18. Comparative LIBS Analysis Of Calcified Tissues

    NASA Astrophysics Data System (ADS)

    Abdel-Salam, Z. A.; Harith, M. A.

    2008-09-01

    Signal enhancement, limits of detection, and relevance to environmental concentration for element in calcified tissues using LIBS with single and double laser pulses will be presented. These measurements were performed on three calcified tissues representing different matrices, namely enamel of human teeth, shells and eggshells. This method depends on the role of the laser induced shock wave on the ionization rate of the ablated target material atoms. The effect of the laser single and double pulse on the ionic to atomic ratio of calcium and magnesium spectral emission lines, CaII/CaI and MgII/MgI, will be presented and compared with the previous results and its relevance to the target material hardness. The results show that in case of single pulse the intensity ratios in calcium are higher than the double pulse while there is no appreciable difference between both in case of magnesium.

  19. Comparative LIBS Analysis Of Calcified Tissues

    SciTech Connect

    Abdel-Salam, Z. A.; Harith, M. A.

    2008-09-23

    Signal enhancement, limits of detection, and relevance to environmental concentration for element in calcified tissues using LIBS with single and double laser pulses will be presented. These measurements were performed on three calcified tissues representing different matrices, namely enamel of human teeth, shells and eggshells. This method depends on the role of the laser induced shock wave on the ionization rate of the ablated target material atoms. The effect of the laser single and double pulse on the ionic to atomic ratio of calcium and magnesium spectral emission lines, CaII/CaI and MgII/MgI, will be presented and compared with the previous results and its relevance to the target material hardness. The results show that in case of single pulse the intensity ratios in calcium are higher than the double pulse while there is no appreciable difference between both in case of magnesium.

  20. The digital storytelling process: A comparative analysis from various experts

    NASA Astrophysics Data System (ADS)

    Hussain, Hashiroh; Shiratuddin, Norshuhada

    2016-08-01

    Digital Storytelling (DST) is a method of delivering information to the audience. It combines narrative and digital media content infused with the multimedia elements. In order for the educators (i.e the designers) to create a compelling digital story, there are sets of processes introduced by experts. Nevertheless, the experts suggest varieties of processes to guide them; of which some are redundant. The main aim of this study is to propose a single guide process for the creation of DST. A comparative analysis is employed where ten DST models from various experts are analysed. The process can also be implemented in other multimedia materials that used the concept of DST.

  1. Comparative promoter analysis in vertebrate genomes with the CORG workbench.

    PubMed

    Dieterich, Christoph; Vingron, Martin

    2006-01-01

    CORG is a versatile web-based workbench for comparative promoter analysis in vertebrate model organisms. Two kinds of information are explicitly considered in the automated annotation process. First, local conservation patterns in upstream regions of homologous genes: These phylogenetic footprints are likely to stem from sequence elements that are under selective pressure. The CORG pipeline detects and exploits patterns of local similarity to annotate promoter regions. Second, experimental data on transcription start sites: exon positions and DNA binding site descriptions complete the promoter annotation. These data are made available via an interactive web portal. Individual promoter studies are supported by a JAVA applet that supplies all data down to the nucleotide level.

  2. Comparative analysis of de novo transcriptome assembly.

    PubMed

    Clarke, Kaitlin; Yang, Yi; Marsh, Ronald; Xie, Linglin; Zhang, Ke K

    2013-02-01

    The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq data, from either artificial RNA templates or human transcripts, to evaluate five de novo assemblers, ABySS, Mira, Trinity, Velvet and Oases. Of these assemblers, ABySS, Trinity, Velvet and Oases are all based on de Bruijn graph, and Mira uses an overlap graph algorithm. Various numbers of RNA short reads were selected from the External RNA Control Consortium (ERCC) data and human chromosome 22. A number of statistics were then calculated for the resulting contigs from each assembler. Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate. Trinity had relative good performance for both ERCC and human data, but it may not consistently generate full length transcripts. ABySS was the fastest method but its assembly quality was low. Mira gave a good rate for mapping its contigs onto human chromosome 22, but its computational speed is not satisfactory. Our results suggest that transcript assembly remains a challenge problem for bioinformatics society. Therefore, a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique.

  3. Comparative analysis of de novo transcriptome assembly.

    PubMed

    Clarke, Kaitlin; Yang, Yi; Marsh, Ronald; Xie, Linglin; Zhang, Ke K

    2013-02-01

    The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq data, from either artificial RNA templates or human transcripts, to evaluate five de novo assemblers, ABySS, Mira, Trinity, Velvet and Oases. Of these assemblers, ABySS, Trinity, Velvet and Oases are all based on de Bruijn graph, and Mira uses an overlap graph algorithm. Various numbers of RNA short reads were selected from the External RNA Control Consortium (ERCC) data and human chromosome 22. A number of statistics were then calculated for the resulting contigs from each assembler. Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate. Trinity had relative good performance for both ERCC and human data, but it may not consistently generate full length transcripts. ABySS was the fastest method but its assembly quality was low. Mira gave a good rate for mapping its contigs onto human chromosome 22, but its computational speed is not satisfactory. Our results suggest that transcript assembly remains a challenge problem for bioinformatics society. Therefore, a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique. PMID:23393031

  4. Gender and work values: a comparative analysis.

    PubMed

    Elizur, D

    1994-04-01

    The results of recent investigations on work values suggest that the contradictory findings in regard to gender differences may be rooted in variations in the underlying structure of the work-values domain. In the present study a definitional framework for work values was proposed and tested. Smallest space analysis (SSA; Guttman, 1968) was performed on the ratings of 24 work-value items by samples of men and women from Hungary, Israel, and the Netherlands. A double-ordered conceptual system, a radex structure, was obtained in each of the samples, reflecting two hypothesized facets: modality of outcome (cognitive, affective, and instrumental) and type of system performance contingency. Essentially the same structure was obtained for women and men. However, women ranked affective outcomes as well as some of the instrumental and cognitive values higher than men did, whereas men ranked some other cognitive (influence, independence, responsibility) and instrumental (pay) items higher than women did. Personal growth and use of abilities were ranked higher by men in some samples and by women in others. PMID:8201817

  5. Impact of a novel, antimicrobial dressing on in vivo, Pseudomonas aeruginosa wound biofilm: quantitative comparative analysis using a rabbit ear model.

    PubMed

    Seth, Akhil K; Zhong, Aimei; Nguyen, Khang T; Hong, Seok J; Leung, Kai P; Galiano, Robert D; Mustoe, Thomas A

    2014-01-01

    The importance of bacterial biofilms to chronic wound pathogenesis is well established. Different treatment modalities, including topical dressings, have yet to show consistent efficacy against wound biofilm. This study evaluates the impact of a novel, antimicrobial Test Dressing on Pseudomonas aeruginosa biofilm-infected wounds. Six-mm dermal punch wounds in rabbit ears were inoculated with 10(6) colony-forming units of P. aeruginosa. Biofilm was established in vivo using our published model. Dressing changes were performed every other day with either Active Control or Test Dressings. Treated and untreated wounds were harvested for several quantitative endpoints. Confirmatory studies were performed to measure treatment impact on in vitro P. aeruginosa and in vivo polybacterial wounds containing P. aeruginosa and Staphylococcus aureus. The Test Dressing consistently decreased P. aeruginosa bacterial counts, and improved wound healing relative to Inactive Vehicle and Active Control wounds (p < 0.05). In vitro bacterial counts were also significantly reduced following Test Dressing therapy (p < 0.05). Similarly, improvements in bacterial burden and wound healing were also achieved in polybacterial wounds (p < 0.05). This study represents the first quantifiable and consistent in vivo evidence of a topical antimicrobial dressing's impact against established wound biofilm. The development of clinically applicable therapies against biofilm such as this is critical to improving chronic wound care.

  6. Modeling Covariates of Self-Perceived and Epidemiologic Notions of Risk for Acquiring STIs/HIV among Military Personnel: A Comparative Analysis

    PubMed Central

    Mgbere, Osaro; Monjok, Emmanuel; Abughosh, Susan; Ekong, Ernest; Holstad, Marcia M.; Essien, E. James

    2012-01-01

    This study examined the socio-demographic and selected behavioral characteristics associated with self-perceived and epidemiologic notions of risk for acquiring STIs/HIV infection using data from a cross-sectional survey involving 346 consenting female military personnel from two cantonments in Southwestern Nigeria. Findings revealed significant discordance in participants’ risk status based on the two assessment methods, with Kappa coefficients ranging from −0.021 to 0.115. Using epidemiologic assessment as the “gold standard”, 45.4% of the study population were able to accurately assessed their risk levels through self-perception with significant (p≤.01) socio-demographic variations. Multivariate logistic regression analyses indicate that STIs/HIV risk models using both self-perceived and epidemiologic notions of risk were significantly determined by different set of covariates. It is recommended that STIs/HIV prevention intervention should integrate the identified covariates and be targeted at changing individual risk behaviors and perceptions, as well as the social contexts in which risky behaviors occur in the military population. PMID:22271332

  7. A comparative analysis of the dissociation kinetics models for silane molecules on the surface at epitaxial growth, of silicon films, in vacuum

    SciTech Connect

    Orlov, L. K. Smyslova, T. N.

    2006-01-15

    On the basis of different physicochemical models, surface concentrations of monosilane dissociation products on the surface of a silicon film are analyzed. The calculations have made it possible to estimate the crystallization factor and its dependence on temperature and gas pressure in the reactor. It is shown that the qualitative character of the temperature variations of the surface concentrations and crystallization factor depends slighty on the specific choice of the radical SiH{sub n} that controls the time of the pyrolysis process. The general form of the investigated dependences is also slightly sensitive to the stage at which hydrogen is removed from the surface. At the same time, the quantitative characteristics of the surface concentrations substantially depend on the choice of the specific features of silane dissociation on the surface. For silicon atoms on the growth surface, the dependences of the crystallization factor on the temperature of the epitaxial process, gas pressure in the reactor, and dissociation rates for silane molecules on the surface are analyzed. It is shown that, at elevated growth temperatures, the rate of film growth is sensitive to molecule pyrolysis rate, whereas, at low growth temperatures, the filling of the surface by hydrogen is a unique factor that controls the rate of the epitaxial process.

  8. Comparative analysis of gingival phenotype in animal and human experimental models using optical coherence tomography in a non-invasive approach

    NASA Astrophysics Data System (ADS)

    Mota, Cláudia C. B. O.; Fernandes, Luana O.; Melo, Luciana S. A.; Feitosa, Daniela S.; Cimões, Renata; Gomes, Anderson S. L.

    2015-06-01

    Imaging methods are widely used in diagnostic and among the diversity of modalities, optical coherence tomography (OCT) is nowadays commercially available and considered the most innovative technique used for imaging applications, in both medical and non-medical applications. In this study, we exploit the OCT technique in the oral cavity for identification and differentiation between free and attached gingiva, as well as determining the gingival phenotype, an important factor to determination of periodontal prognosis in patients. For the animal studies, five porcine jaws were analyzed using a Swept Source SS-OCT system operating at 1325nm and stereomicroscope, as gold pattern. The SSOCT at 1325nm was chosen due to the longer central wavelength, that allows to deeper penetration imaging, and the faster image acquisition, an essential factor for clinical setting. For the patient studies, a total of 30 males and female were examined using the SS-OCT at 1325nm and computer controlled periodontal probing. 2D and 3D images of tooth/gingiva interface were performed, and quantitative measurements of the gingival sulcus could be noninvasively obtained. Through the image analysis of the animals jaws, it was possible to quantify the free gingiva and the attached gingiva, the calculus deposition over teeth surface and also the subgingival calculus. For the patient's studies, we demonstrated that the gingival phenotype could be measured without the periodontal probe introduction at the gingival sulcus, confirming that OCT can be potentially useful in clinic for direct observation and quantification of gingival phenotype in a non-invasive approach.

  9. Comparative analysis of QSAR models for predicting pK(a) of organic oxygen acids and nitrogen bases from molecular structure.

    PubMed

    Yu, Haiying; Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

    2010-11-22

    For 1143 organic compounds comprising 580 oxygen acids and 563 nitrogen bases that cover more than 17 orders of experimental pK(a) (from -5.00 to 12.23), the pK(a) prediction performances of ACD, SPARC, and two calibrations of a semiempirical quantum chemical (QC) AM1 approach have been analyzed. The overall root-mean-square errors (rms) for the acids are 0.41, 0.58 (0.42 without ortho-substituted phenols with intramolecular H-bonding), and 0.55 and for the bases are 0.65, 0.70, 1.17, and 1.27 for ACD, SPARC, and both QC methods, respectively. Method-specific performances are discussed in detail for six acid subsets (phenols and aromatic and aliphatic carboxylic acids with different substitution patterns) and nine base subsets (anilines, primary, secondary and tertiary amines, meta/para-substituted and ortho-substituted pyridines, pyrimidines, imidazoles, and quinolines). The results demonstrate an overall better performance for acids than for bases but also a substantial variation across subsets. For the overall best-performing ACD, rms ranges from 0.12 to 1.11 and 0.40 to 1.21 pK(a) units for the acid and base subsets, respectively. With regard to the squared correlation coefficient r², the results are 0.86 to 0.96 (acids) and 0.79 to 0.95 (bases) for ACD, 0.77 to 0.95 (acids) and 0.85 to 0.97 (bases) for SPARC, and 0.64 to 0.87 (acids) and 0.43 to 0.83 (bases) for the QC methods, respectively. Attention is paid to structural and method-specific causes for observed pitfalls. The significant subset dependence of the prediction performances suggests a consensus modeling approach. PMID:21033677

  10. Comparative Modeling Studies of Boreal Water and Carbon Balance

    NASA Technical Reports Server (NTRS)

    Coughlan, J.; Peterson, David L. (Technical Monitor)

    1997-01-01

    The coordination of the modeling and field efforts for an Intensive Field Campaign (IFC) may resemble the chicken and egg dilemma. This session's theme advocates that early and proactive involvement by modeling teams can produce a scientific and operational benefit for the IFC and Experiment. This talk will provide some examples and suggestions originating from the NASA funded IFC's of the FIFE First ISLSCP (International Satellite Land Surface Climatology Project) Field Experiment, Oregon Transect Ecosystem Research (OTTER) and predominately Boreal Ecosystem-Atmosphere Study (BOREAS) Experiments. In February 1994 and prior to the final selection of the BOREAS study sites, a group of funded BOREAS investigators agreed to run their models with data for five community types representing the proposed tower flux sites. All participating models were given identical initial values and boundary conditions and driven with identical climate data. The objectives of the intercomparison exercise were: 1) compare simulation results of participating terrestrial, hydrological, and atmospheric models over selected time frames; 2) learn about model behavior and sensitivity to estimated boreal site and vegetation definitions; 3) prioritize BOREAS field data collection efforts supporting modeling studies; 4) identify individual model deficiencies as early as possible. Out of these objectives evolved some important coordination and science issues for the BOREAS Experiment that can be generalized to IFCs and long term archiving of the data. Some problems are acceptable because they are endemic to maintaining fair and open competition prior to the peer review process. Others are logistical and addressable through application of planning, management, and information sciences. This investigator has identified one source of measurement and model incompatibility that is manifest in the IFC scaling approach. Although intuitively obvious, scaling problems are already more formally defined in

  11. Comparative analysis of selected radiative transfer approaches for aquatic environments.

    PubMed

    Sokoletsky, Leonid

    2005-01-01

    A comparative analysis is presented of simple approaches to radiative transfer in plane-parallel layers, such as the self-consistent Haltrin approach, the Chandrasekhar-Klier exact solution for isotropic scatters, an extended version of two-flux radiative Kubelka-Munk theory, the neutron-diffuse Gate-Brinkworth theory, and different versions of the delta-Eddington theory. It is shown that the Haltrin approach is preferable to others and can be used for the solution of an inverse optical problem of the estimation of absorption and backscattering coefficients of aquatic environments from measured apparent optical properties. Two different methods of transformation from measured irradiance reflectance at combined illumination to irradiance reflectance induced by diffuse illumination only are developed. An analysis of the use of the different models for estimation of the effect of the bottom albedo is also presented. PMID:15662895

  12. Statistical correlation analysis for comparing vibration data from test and analysis

    NASA Technical Reports Server (NTRS)

    Butler, T. G.; Strang, R. F.; Purves, L. R.; Hershfeld, D. J.

    1986-01-01

    A theory was developed to compare vibration modes obtained by NASTRAN analysis with those obtained experimentally. Because many more analytical modes can be obtained than experimental modes, the analytical set was treated as expansion functions for putting both sources in comparative form. The dimensional symmetry was developed for three general cases: nonsymmetric whole model compared with a nonsymmetric whole structural test, symmetric analytical portion compared with a symmetric experimental portion, and analytical symmetric portion with a whole experimental test. The theory was coded and a statistical correlation program was installed as a utility. The theory is established with small classical structures.

  13. Comparative Gene Expression Analysis of Mouse and Human Cardiac Maturation.

    PubMed

    Uosaki, Hideki; Taguchi, Y-H

    2016-08-01

    Understanding how human cardiomyocytes mature is crucial to realizing stem cell-based heart regeneration, modeling adult heart diseases, and facilitating drug discovery. However, it is not feasible to analyze human samples for maturation due to inaccessibility to samples while cardiomyocytes mature during fetal development and childhood, as well as difficulty in avoiding variations among individuals. Using model animals such as mice can be a useful strategy; nonetheless, it is not well-understood whether and to what degree gene expression profiles during maturation are shared between humans and mice. Therefore, we performed a comparative gene expression analysis of mice and human samples. First, we examined two distinct mice microarray platforms for shared gene expression profiles, aiming to increase reliability of the analysis. We identified a set of genes displaying progressive changes during maturation based on principal component analysis. Second, we demonstrated that the genes identified had a differential expression pattern between adult and earlier stages (e.g., fetus) common in mice and humans. Our findings provide a foundation for further genetic studies of cardiomyocyte maturation. PMID:27431744

  14. Comparative study of turbulence models in predicting hypersonic inlet flows

    NASA Technical Reports Server (NTRS)

    Kapoor, Kamlesh; Anderson, Bernhard H.; Shaw, Robert J.

    1992-01-01

    A numerical study was conducted to analyze the performance of different turbulence models when applied to the hypersonic NASA P8 inlet. Computational results from the PARC2D code, which solves the full two-dimensional Reynolds-averaged Navier-Stokes equation, were compared with experimental data. The zero-equation models considered for the study were the Baldwin-Lomax model, the Thomas model, and a combination of the Baldwin-Lomax and Thomas models; the two-equation models considered were the Chien model, the Speziale model (both low Reynolds number), and the Launder and Spalding model (high Reynolds number). The Thomas model performed best among the zero-equation models, and predicted good pressure distributions. The Chien and Speziale models compared very well with the experimental data, and performed better than the Thomas model near the walls.

  15. Comparative study of turbulence models in predicting hypersonic inlet flows

    NASA Technical Reports Server (NTRS)

    Kapoor, Kamlesh; Anderson, Bernhard H.; Shaw, Robert J.

    1992-01-01

    A numerical study was conducted to analyze the performance of different turbulence models when applied to the hypersonic NASA P8 inlet. Computational results from the PARC2D code, which solves the full two-dimensional Reynolds-averaged Navier-Stokes equation, were compared with experimental data. The zero-equation models considered for the study were the Baldwin-Lomax model, the Thomas model, and a combination of the Baldwin-Lomax and Thomas models; the two-equation models considered were the Chien model, the Speziale model (both low Reynolds number), and the Launder and Spalding model (high Reynolds number). The Thomas model performed best among the zero-equation models, and predicted good pressure distributions. The Chien and Speziale models compared wery well with the experimental data, and performed better than the Thomas model near the walls.

  16. Acoustooptical spectrum analysis modeling

    NASA Astrophysics Data System (ADS)

    Carmody, M. J.

    1981-06-01

    A summary of Bragg deflection theory and various approaches to direct detection acoustooptic spectrum analysis (AOSA) modeling is presented. A suitable model is chosen and extended to include the effects of diffraction efficiency, transducer efficiency, irradiance profiles of incident laser illumination, aperture size of the Bragg cell, and the acoustic attenuation experienced by the acoustic wavetrain generated by the input r-f signal. A FORTRAN program is developed to model the AOSA and predict the output image plane intensity profiles. A second version of the program includes a time variable permitting dynamic simulation of the system response.

  17. Evolution and physics in comparative protein structure modeling.

    PubMed

    Fiser, András; Feig, Michael; Brooks, Charles L; Sali, Andrej

    2002-06-01

    From a physical perspective, the native structure of a protein is a consequence of physical forces acting on the protein and solvent atoms during the folding process. From a biological perspective, the native structure of proteins is a result of evolution over millions of years. Correspondingly, there are two types of protein structure prediction methods, de novo prediction and comparative modeling. We review comparative protein structure modeling and discuss the incorporation of physical considerations into the modeling process. A good starting point for achieving this aim is provided by comparative modeling by satisfaction of spatial restraints. Incorporation of physical considerations is illustrated by an inclusion of solvation effects into the modeling of loops.

  18. A comparative analysis of biclustering algorithms for gene expression data.

    PubMed

    Eren, Kemal; Deveci, Mehmet; Küçüktunç, Onur; Çatalyürek, Ümit V

    2013-05-01

    The need to analyze high-dimension biological data is driving the development of new data mining methods. Biclustering algorithms have been successfully applied to gene expression data to discover local patterns, in which a subset of genes exhibit similar expression levels over a subset of conditions. However, it is not clear which algorithms are best suited for this task. Many algorithms have been published in the past decade, most of which have been compared only to a small number of algorithms. Surveys and comparisons exist in the literature, but because of the large number and variety of biclustering algorithms, they are quickly outdated. In this article we partially address this problem of evaluating the strengths and weaknesses of existing biclustering methods. We used the BiBench package to compare 12 algorithms, many of which were recently published or have not been extensively studied. The algorithms were tested on a suite of synthetic data sets to measure their performance on data with varying conditions, such as different bicluster models, varying noise, varying numbers of biclusters and overlapping biclusters. The algorithms were also tested on eight large gene expression data sets obtained from the Gene Expression Omnibus. Gene Ontology enrichment analysis was performed on the resulting biclusters, and the best enrichment terms are reported. Our analyses show that the biclustering method and its parameters should be selected based on the desired model, whether that model allows overlapping biclusters, and its robustness to noise. In addition, we observe that the biclustering algorithms capable of finding more than one model are more successful at capturing biologically relevant clusters.

  19. Comparing turbulence models for flow through a rigid glottal model.

    PubMed

    Suh, Jungsoo; Frankel, Steven H

    2008-03-01

    Flow through a rigid model of the human vocal tract featuring a divergent glottis was numerically modeled using the Reynolds-averaged Navier-Stokes approach. A number of different turbulence models, available in a widely used commercial computational fluid dynamics code, were tested to determine their ability to capture various flow features recently observed in laboratory experiments and large eddy simulation studies. The study reveals that results from unsteady simulations employing the k-omega shear stress transport model were in much better agreement with previous measurements and predictions with regard to the ability to predict glottal jet skewing due to the Coanda effect and the intraglottal pressure distribution or related skin friction coefficient, than either steady or unsteady simulations using the Spalart-Allmaras model or any other two-equation turbulence model investigated in this study. PMID:18345812

  20. A novel model-based meta-analysis to indirectly estimate the comparative efficacy of two medications: an example using DPP-4 inhibitors, sitagliptin and linagliptin, in treatment of type 2 diabetes mellitus

    PubMed Central

    Gross, Jorge Luiz; Rogers, James; Polhamus, Daniel; Gillespie, William; Friedrich, Christian; Gong, Yan; Monz, Brigitta Ursula; Patel, Sanjay; Staab, Alexander; Retlich, Silke

    2013-01-01

    Objectives To develop a longitudinal statistical model to indirectly estimate the comparative efficacies of two drugs, using model-based meta-analysis (MBMA). Comparison of two oral dipeptidyl peptidase (DPP)-4 inhibitors, sitagliptin and linagliptin, for type 2 diabetes mellitus (T2DM) treatment was used as an example. Design Systematic review with MBMA. Data sources MEDLINE, EMBASE, http://www.ClinicalTrials.gov, Cochrane review of DPP-4 inhibitors for T2DM, sitagliptin trials on Food and Drug Administration website to December 2011 and linagliptin data from the manufacturer. Eligibility criteria for selecting studies Double-blind, randomised controlled clinical trials, ≥12 weeks’ duration, that analysed sitagliptin or linagliptin efficacies as changes in glycated haemoglobin (HbA1c) levels, in adults with T2DM and HbA1c >7%, irrespective of background medication. Model development and application A Bayesian model was fitted (Markov Chain Monte Carlo method). The final model described HbA1c levels as function of time, dose, baseline HbA1c, washout status/duration and ethnicity. Other covariates showed no major impact on model parameters and were not included. For the indirect comparison, a population of 1000 patients was simulated from the model with a racial composition reflecting the average racial distribution of the linagliptin trials, and baseline HbA1c of 8%. Results The model was developed using longitudinal data from 11 234 patients (10 linagliptin, 15 sitagliptin trials), and assessed by internal evaluation techniques, demonstrating that the model adequately described the observations. Simulations showed both linagliptin 5 mg and sitagliptin 100 mg reduced HbA1c by 0.81% (placebo-adjusted) at week 24. Credible intervals for participants without washout were −0.88 to −0.75 (linagliptin) and −0.89 to −0.73 (sitagliptin), and for those with washout, −0.91 to −0.76 (linagliptin) and −0.91 to −0.75 (sitagliptin). Conclusions This

  1. White matter degeneration in schizophrenia: a comparative diffusion tensor analysis

    NASA Astrophysics Data System (ADS)

    Ingalhalikar, Madhura A.; Andreasen, Nancy C.; Kim, Jinsuh; Alexander, Andrew L.; Magnotta, Vincent A.

    2010-03-01

    Schizophrenia is a serious and disabling mental disorder. Diffusion tensor imaging (DTI) studies performed on schizophrenia have demonstrated white matter degeneration either due to loss of myelination or deterioration of fiber tracts although the areas where the changes occur are variable across studies. Most of the population based studies analyze the changes in schizophrenia using scalar indices computed from the diffusion tensor such as fractional anisotropy (FA) and relative anisotropy (RA). The scalar measures may not capture the complete information from the diffusion tensor. In this paper we have applied the RADTI method on a group of 9 controls and 9 patients with schizophrenia. The RADTI method converts the tensors to log-Euclidean space where a linear regression model is applied and hypothesis testing is performed between the control and patient groups. Results show that there is a significant difference in the anisotropy between patients and controls especially in the parts of forceps minor, superior corona radiata, anterior limb of internal capsule and genu of corpus callosum. To check if the tensor analysis gives a better idea of the changes in anisotropy, we compared the results with voxelwise FA analysis as well as voxelwise geodesic anisotropy (GA) analysis.

  2. AIR Model Preflight Analysis

    NASA Technical Reports Server (NTRS)

    Tai, H.; Wilson, J. W.; Maiden, D. L.

    2003-01-01

    The atmospheric ionizing radiation (AIR) ER-2 preflight analysis, one of the first attempts to obtain a relatively complete measurement set of the high-altitude radiation level environment, is described in this paper. The primary thrust is to characterize the atmospheric radiation and to define dose levels at high-altitude flight. A secondary thrust is to develop and validate dosimetric techniques and monitoring devices for protecting aircrews. With a few chosen routes, we can measure the experimental results and validate the AIR model predictions. Eventually, as more measurements are made, we gain more understanding about the hazardous radiation environment and acquire more confidence in the prediction models.

  3. Transcription factor motif quality assessment requires systematic comparative analysis

    PubMed Central

    Kibet, Caleb Kipkurui; Machanick, Philip

    2016-01-01

    Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis. PMID:27092243

  4. Mental health network governance: comparative analysis across Canadian regions

    PubMed Central

    Wiktorowicz, Mary E; Fleury, Marie-Josée; Adair, Carol E; Lesage, Alain; Goldner, Elliot; Peters, Suzanne

    2010-01-01

    Objective Modes of governance were compared in ten local mental health networks in diverse contexts (rural/urban and regionalized/non-regionalized) to clarify the governance processes that foster inter-organizational collaboration and the conditions that support them. Methods Case studies of ten local mental health networks were developed using qualitative methods of document review, semi-structured interviews and focus groups that incorporated provincial policy, network and organizational levels of analysis. Results Mental health networks adopted either a corporate structure, mutual adjustment or an alliance governance model. A corporate structure supported by regionalization offered the most direct means for local governance to attain inter-organizational collaboration. The likelihood that networks with an alliance model developed coordination processes depended on the presence of the following conditions: a moderate number of organizations, goal consensus and trust among the organizations, and network-level competencies. In the small and mid-sized urban networks where these conditions were met their alliance realized the inter-organizational collaboration sought. In the large urban and rural networks where these conditions were not met, externally brokered forms of network governance were required to support alliance based models. Discussion In metropolitan and rural networks with such shared forms of network governance as an alliance or voluntary mutual adjustment, external mediation by a regional or provincial authority was an important lever to foster inter-organizational collaboration. PMID:21289999

  5. Comparing soil moisture memory in satellite observations and models

    NASA Astrophysics Data System (ADS)

    Stacke, Tobias; Hagemann, Stefan; Loew, Alexander

    2013-04-01

    A major obstacle to a correct parametrization of soil processes in large scale global land surface models is the lack of long term soil moisture observations for large parts of the globe. Currently, a compilation of soil moisture data derived from a range of satellites is released by the ESA Climate Change Initiative (ECV_SM). Comprising the period from 1978 until 2010, it provides the opportunity to compute climatological relevant statistics on a quasi-global scale and to compare these to the output of climate models. Our study is focused on the investigation of soil moisture memory in satellite observations and models. As a proxy for memory we compute the autocorrelation length (ACL) of the available satellite data and the uppermost soil layer of the models. Additional to the ECV_SM data, AMSR-E soil moisture is used as observational estimate. Simulated soil moisture fields are taken from ERA-Interim reanalysis and generated with the land surface model JSBACH, which was driven with quasi-observational meteorological forcing data. The satellite data show ACLs between one week and one month for the greater part of the land surface while the models simulate a longer memory of up to two months. Some pattern are similar in models and observations, e.g. a longer memory in the Sahel Zone and the Arabian Peninsula, but the models are not able to reproduce regions with a very short ACL of just a few days. If the long term seasonality is subtracted from the data the memory is strongly shortened, indicating the importance of seasonal variations for the memory in most regions. Furthermore, we analyze the change of soil moisture memory in the different soil layers of the models to investigate to which extent the surface soil moisture includes information about the whole soil column. A first analysis reveals that the ACL is increasing for deeper layers. However, its increase is stronger in the soil moisture anomaly than in its absolute values and the first even exceeds the

  6. Comment on 'Comparative analysis of the isovolume calibration method for non-invasive respiratory monitoring techniques based on area transduction versus circumference transduction using the connected cylinders model' (2011 Physiol. Meas. 32 1265-74).

    PubMed

    Augousti, A T; Radosz, A

    2015-05-01

    An analysis introduced by the authors in 2011 examining the robustness of the isovolume method for the calibration of the respiratory inductive plethysmograph based on the connected cylinders particular model of Konno and Mead's generalized two-compartment model of respiration is extended. It is demonstrated that extending this to a more physically realistic geometrical model, termed the connected prismatic elliptical segments model, does not enhance the earlier analysis, and that the analysis can easily be proven to cover all area-based transduction sensors, irrespective of the actual geometry of the compartments.

  7. Runoff-rainfall (sic!) modelling: Comparing two different approaches

    NASA Astrophysics Data System (ADS)

    Herrnegger, Mathew; Schulz, Karsten

    2015-04-01

    Rainfall is an important input variable for many applications. However, the estimation of areal rainfall is afflicted with significant uncertainties, since it exhibits a large spatio-temporal variability, especially in Alpine areas. Additionally the density of the monitoring network is frequently low and measurements are subject to major errors. The most reliable hydrological information that is available refers to runoff. Kirchner (2009) presented a method to infer catchment rainfall from streamflow fluctuations. The approach is however limited to catchments, where discharge is determined by the volume of water in storage and which can be characterized as simple first-order nonlinear dynamical systems. The model has recently been applied to several catchments in France and Luxembourg (Adamovic et. al., 2014; Krier et al., 2012). In Herrnegger et al. (2014) a different technique to calculate mean areal rainfall on the basis of an inverse conceptual rainfall-runoff model and runoff observations was presented. Thereby a conceptual model is embedded in an iteration algorithm, in which for every time step a rainfall value is determined, which results in a simulated runoff value that corresponds to the observation. The two modelling approaches differ substantially, not only concerning the model concepts, but especially in the number of model parameters. The Kirchner (2009) model (when deriving the storage-discharge relationship directly from runoff data) only has a single parameter. In contrast, the Herrnegger et al. (2014) model uses 10 parameters that have to be calibrated initially, but will offer more degrees of freedom and flexibility in describing more complex catchment responses. In this contribution, we present the application and comparison of both models in the Krems catchment (38.4 km²) located at the foothills of the Northern Austrian Alps. Apart from comparing the performance of the runoff simulations, the focus of this paper lies in evaluating the inverse

  8. Parmodel: a web server for automated comparative modeling of proteins.

    PubMed

    Uchôa, Hugo Brandão; Jorge, Guilherme Eberhart; Freitas Da Silveira, Nelson José; Camera, João Carlos; Canduri, Fernanda; De Azevedo, Walter Filgueira

    2004-12-24

    Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models for a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at .

  9. EMERGY ANALYSIS AND ECONOMIC ANALYSIS A COMPARATIVE STUDY

    EPA Science Inventory

    Our mission at USEPA is to protect human health and safeguard the natural environment. We aim to base our environmental regulations and policies on sound scientific and, where appropriate, economic analyses. Although EPA has conducted analysis of the impact of regulations on ...

  10. The use of antioptimization to compare alternative structural models

    NASA Technical Reports Server (NTRS)

    Gangadharan, S. N.; Nikolaidis, E.; Lee, K.; Haftka, R. T.

    1993-01-01

    Structural models are usually tested by comparing their response with that of a reference structure (an actual structure or a more refined model) to a limited number of arbitrary loads. This test is not always reliable because the loads are arbitrary. An antioptimization-based method is proposed to test structural models. This method compares a structural model with a reference model or an actual structure under the worst loading case that maximizes the error in the model. Specifically, the method identifies the loading case that maximizes the difference between the responses of two models of the same structure using optimization. This method can be used to design experiments in order to validate a structural model. It can also be applied to identify damage in a structure by determining the load that maximizes the difference in the behavior of the damaged and the intact structure. The proposed method is illustrated by applying it to a plate and an automotive structure.

  11. Comparative Analysis of Different LIDAR System Calibration Techniques

    NASA Astrophysics Data System (ADS)

    Miller, M.; Habib, A.

    2016-06-01

    With light detection and ranging (LiDAR) now being a crucial tool for engineering products and on the fly spatial analysis, it is necessary for the user community to have standardized calibration methods. The three methods in this study were developed and proven by the Digital Photogrammetry Research Group (DPRG) for airborne LiDAR systems and are as follows; Simplified, Quasi-Rigorous, and Rigorous. In lieu of using expensive control surfaces for calibration, these methods compare overlapping LiDAR strips to estimate the systematic errors. These systematic errors are quantified by these methods and include the lever arm biases, boresight biases, range bias and scan angle scale bias. These three methods comprehensively represent all of the possible flight configurations and data availability and this paper will test the limits of the method with the most assumptions, the simplified calibration, by using data that violates the assumptions it's math model is based on and compares the results to the quasi-rigorous and rigorous techniques. The overarching goal is to provide a LiDAR system calibration that does not require raw measurements which can be carried out with minimal control and flight lines to reduce costs. This testing is unique because the terrain used for calibration does not contain gable roofs, all other LiDAR system calibration testing and development has been done with terrain containing features with high geometric integrity such as gable roofs.

  12. Engine System Loads Analysis Compared to Hot-Fire Data

    NASA Technical Reports Server (NTRS)

    Frady, Gregory P.; Jennings, John M.; Mims, Katherine; Brunty, Joseph; Christensen, Eric R.; McConnaughey, Paul R. (Technical Monitor)

    2002-01-01

    Early implementation of structural dynamics finite element analyses for calculation of design loads is considered common design practice for high volume manufacturing industries such as automotive and aeronautical industries. However with the rarity of rocket engine development programs starts, these tools are relatively new to the design of rocket engines. In the NASA MC-1 engine program, the focus was to reduce the cost-to-weight ratio. The techniques for structural dynamics analysis practices, were tailored in this program to meet both production and structural design goals. Perturbation of rocket engine design parameters resulted in a number of MC-1 load cycles necessary to characterize the impact due to mass and stiffness changes. Evolution of loads and load extraction methodologies, parametric considerations and a discussion of load path sensitivities are important during the design and integration of a new engine system. During the final stages of development, it is important to verify the results of an engine system model to determine the validity of the results. During the final stages of the MC-1 program, hot-fire test results were obtained and compared to the structural design loads calculated by the engine system model. These comparisons are presented in this paper.

  13. Comparative analysis of ATRX, a chromatin remodeling protein.

    PubMed

    Park, Daniel J; Pask, Andrew J; Huynh, Kim; Renfree, Marilyn B; Harley, Vincent R; Graves, Jennifer A Marshall

    2004-09-15

    The ATRX protein, associated with X-linked alpha-thalassaemia, mental retardation and developmental abnormalities including genital dysgenesis, has been proposed to function as a global transcriptional regulator within a multi-protein complex. However, an understanding of the composition and mechanics of this machinery has remained elusive. We applied inter-specific comparative analysis to identify conserved elements which may be involved in regulating the conformation of chromatin. As part of this study, we cloned and sequenced the entire translatable coding region (7.4 kb) of the ATRX gene from a model marsupial (tammar wallaby, Macropus eugenii). We identify an ATRX ancestral core, conserved between plants, fish and mammals, comprising the cysteine-rich and SWI2/SNF2 helicase-like regions and protein interaction domains. Our data are consistent with the model of the cysteine-rich region as a DNA-binding zinc finger adjacent to a protein-binding (plant homeodomain-like) domain. Alignment of vertebrate ATRX sequences highlights other conserved elements, including a negatively charged mammalian sequence which we propose to be involved in binding of positively charged histone tails.

  14. SDI CFD MODELING ANALYSIS

    SciTech Connect

    Lee, S.

    2011-05-05

    The Savannah River Remediation (SRR) Organization requested that Savannah River National Laboratory (SRNL) develop a Computational Fluid Dynamics (CFD) method to mix and blend the miscible contents of the blend tanks to ensure the contents are properly blended before they are transferred from the blend tank; such as, Tank 50H, to the Salt Waste Processing Facility (SWPF) feed tank. The work described here consists of two modeling areas. They are the mixing modeling analysis during miscible liquid blending operation, and the flow pattern analysis during transfer operation of the blended liquid. The transient CFD governing equations consisting of three momentum equations, one mass balance, two turbulence transport equations for kinetic energy and dissipation rate, and one species transport were solved by an iterative technique until the species concentrations of tank fluid were in equilibrium. The steady-state flow solutions for the entire tank fluid were used for flow pattern analysis, for velocity scaling analysis, and the initial conditions for transient blending calculations. A series of the modeling calculations were performed to estimate the blending times for various jet flow conditions, and to investigate the impact of the cooling coils on the blending time of the tank contents. The modeling results were benchmarked against the pilot scale test results. All of the flow and mixing models were performed with the nozzles installed at the mid-elevation, and parallel to the tank wall. From the CFD modeling calculations, the main results are summarized as follows: (1) The benchmark analyses for the CFD flow velocity and blending models demonstrate their consistency with Engineering Development Laboratory (EDL) and literature test results in terms of local velocity measurements and experimental observations. Thus, an application of the established criterion to SRS full scale tank will provide a better, physically-based estimate of the required mixing time, and

  15. Comparing pion production models to MiniBooNE data

    SciTech Connect

    Rodrigues, P. A.

    2015-05-15

    Predictions for neutrino-induced charged- and neutral-current single pion production on CH{sub 2} from theoretical models and Monte Carlo event generators are compared with the cross section measurements from the MiniBooNE experiment.

  16. The Constant Comparative Analysis Method Outside of Grounded Theory

    ERIC Educational Resources Information Center

    Fram, Sheila M.

    2013-01-01

    This commentary addresses the gap in the literature regarding discussion of the legitimate use of Constant Comparative Analysis Method (CCA) outside of Grounded Theory. The purpose is to show the strength of using CCA to maintain the emic perspective and how theoretical frameworks can maintain the etic perspective throughout the analysis. My…

  17. Comparing statistical models to predict dengue fever notifications.

    PubMed

    Earnest, Arul; Tan, Say Beng; Wilder-Smith, Annelies; Machin, David

    2012-01-01

    Dengue fever (DF) is a serious public health problem in many parts of the world, and, in the absence of a vaccine, disease surveillance and mosquito vector eradication are important in controlling the spread of the disease. DF is primarily transmitted by the female Aedes aegypti mosquito. We compared two statistical models that can be used in the surveillance and forecast of notifiable infectious diseases, namely, the Autoregressive Integrated Moving Average (ARIMA) model and the Knorr-Held two-component (K-H) model. The Mean Absolute Percentage Error (MAPE) was used to compare models. We developed the models using used data on DF notifications in Singapore from January 2001 till December 2006 and then validated the models with data from January 2007 till June 2008. The K-H model resulted in a slightly lower MAPE value of 17.21 as compared to the ARIMA model. We conclude that the models' performances are similar, but we found that the K-H model was relatively more difficult to fit in terms of the specification of the prior parameters and the relatively longer time taken to run the models.

  18. Comparing statistical models to predict dengue fever notifications.

    PubMed

    Earnest, Arul; Tan, Say Beng; Wilder-Smith, Annelies; Machin, David

    2012-01-01

    Dengue fever (DF) is a serious public health problem in many parts of the world, and, in the absence of a vaccine, disease surveillance and mosquito vector eradication are important in controlling the spread of the disease. DF is primarily transmitted by the female Aedes aegypti mosquito. We compared two statistical models that can be used in the surveillance and forecast of notifiable infectious diseases, namely, the Autoregressive Integrated Moving Average (ARIMA) model and the Knorr-Held two-component (K-H) model. The Mean Absolute Percentage Error (MAPE) was used to compare models. We developed the models using used data on DF notifications in Singapore from January 2001 till December 2006 and then validated the models with data from January 2007 till June 2008. The K-H model resulted in a slightly lower MAPE value of 17.21 as compared to the ARIMA model. We conclude that the models' performances are similar, but we found that the K-H model was relatively more difficult to fit in terms of the specification of the prior parameters and the relatively longer time taken to run the models. PMID:22481978

  19. Comparing Statistical Models to Predict Dengue Fever Notifications

    PubMed Central

    Earnest, Arul; Tan, Say Beng; Wilder-Smith, Annelies; Machin, David

    2012-01-01

    Dengue fever (DF) is a serious public health problem in many parts of the world, and, in the absence of a vaccine, disease surveillance and mosquito vector eradication are important in controlling the spread of the disease. DF is primarily transmitted by the female Aedes aegypti mosquito. We compared two statistical models that can be used in the surveillance and forecast of notifiable infectious diseases, namely, the Autoregressive Integrated Moving Average (ARIMA) model and the Knorr-Held two-component (K-H) model. The Mean Absolute Percentage Error (MAPE) was used to compare models. We developed the models using used data on DF notifications in Singapore from January 2001 till December 2006 and then validated the models with data from January 2007 till June 2008. The K-H model resulted in a slightly lower MAPE value of 17.21 as compared to the ARIMA model. We conclude that the models' performances are similar, but we found that the K-H model was relatively more difficult to fit in terms of the specification of the prior parameters and the relatively longer time taken to run the models. PMID:22481978

  20. Comparing modelled fire dynamics with charcoal records for the Holocene

    NASA Astrophysics Data System (ADS)

    Brücher, T.; Brovkin, V.; Kloster, S.; Marlon, J. R.; Power, M. J.

    2014-04-01

    An earth system model of intermediate complexity (CLIMate and BiosphERe - CLIMBER-2) and a land surface model (JSBACH), which dynamically represent vegetation, are used to simulate natural fire dynamics through the last 8000 yr. Output variables of the fire model (burned area and fire carbon emissions) are used to compare model results with sediment-based charcoal reconstructions. Several approaches for processing model output are also tested. Charcoal data are reported in Z-scores with a base period of 8000-200 BP in order to exclude the strong anthropogenic forcing of fire during the last two centuries. The model-data comparison reveals a robust correspondence in fire activity for most regions considered, while for a few regions, such as Europe, simulated and observed fire histories show different trends. The difference between modelled and observed fire activity may be due to the absence of anthropogenic forcing (e.g. human ignitions and suppression) in the model simulations, and also due to limitations inherent to modelling fire dynamics. The use of spatial averaging (or Z-score processing) of model output did not change the directions of the trends. However, Z-score-transformed model output resulted in higher rank correlations with the charcoal Z-scores in most regions. Therefore, while both metrics are useful, processing model output as Z-scores is preferable to areal averaging when comparing model results to transformed charcoal records.

  1. A Comparative Analysis of Day Care Licensing Standards.

    ERIC Educational Resources Information Center

    Hawaii Univ., Honolulu. Head Start Research and Evaluation Center.

    This report focuses on the major similarities and differences of three sets of day care licensing standards (model, state, and federal) in order to provide an information base for isolating the problems, concerns, and issues involved in day care licensing. Sets of standards compared are: (1) "OCD Guides for Day Care Licensing," 1973 (model); (2)…

  2. Model Analysis ToolKit

    SciTech Connect

    Harp, Dylan R.

    2015-05-15

    MATK provides basic functionality to facilitate model analysis within the Python computational environment. Model analysis setup within MATK includes: - define parameters - define observations - define model (python function) - define samplesets (sets of parameter combinations) Currently supported functionality includes: - forward model runs - Latin-Hypercube sampling of parameters - multi-dimensional parameter studies - parallel execution of parameter samples - model calibration using internal Levenberg-Marquardt algorithm - model calibration using lmfit package - model calibration using levmar package - Markov Chain Monte Carlo using pymc package MATK facilitates model analysis using: - scipy - calibration (scipy.optimize) - rpy2 - Python interface to R

  3. Comparing modelled fire dynamics with charcoal records for the Holocene

    NASA Astrophysics Data System (ADS)

    Brücher, T.; Brovkin, V.; Kloster, S.; Marlon, J. R.; Power, M. J.

    2013-11-01

    An Earth System model of intermediate complexity, CLIMBER-2, and a land surface model JSBACH that represents vegetation dynamically are used to simulate natural fire dynamics through the last 8000 yr. Output variables of the fire model (burned area and fire carbon emissions) are used to compare model results with sediment-based charcoal reconstructions and several approaches of model output processing are tested. Charcoal data are reported in Z-scores and have been used for the period 8000 to 200 BP to exclude the post-Industrial period of strong anthropogenic forcing during the last two centuries. The model-data comparison reveals a robust correspondence in fire trends for most regions considered, while few regions, such as Europe, display different trends between simulated and observed trends. The difference between the modelled and observed fire activity could be linked to an absence of the anthropogenic forcing (e.g., human ignitions and suppression) in the model simulations, but also related to limitations of model assumptions for modelling fire dynamics. For the model trends, the usage of spatial averaging or Z-score processing of model output resulted in similar directions of trend. However, modelled Z-scores resulted in higher rank correlations with the charcoal Z-scores in most of the regions. Therefore, while both metrics are useful, the Z-score processing is more preferable for the modelled fire comparison with the charcoal records than the areal averaging.

  4. Comparative and Evolutionary Analysis of the Bacterial Homologous Recombination Systems

    PubMed Central

    Rocha, Eduardo P. C; Cornet, Emmanuel; Michel, Bénédicte

    2005-01-01

    Homologous recombination is a housekeeping process involved in the maintenance of chromosome integrity and generation of genetic variability. Although detailed biochemical studies have described the mechanism of action of its components in model organisms, there is no recent extensive assessment of this knowledge, using comparative genomics and taking advantage of available experimental data on recombination. Using comparative genomics, we assessed the diversity of recombination processes among bacteria, and simulations suggest that we missed very few homologs. The work included the identification of orthologs and the analysis of their evolutionary history and genomic context. Some genes, for proteins such as RecA, the resolvases, and RecR, were found to be nearly ubiquitous, suggesting that the large majority of bacterial genomes are capable of homologous recombination. Yet many genomes show incomplete sets of presynaptic systems, with RecFOR being more frequent than RecBCD/AddAB. There is a significant pattern of co-occurrence between these systems and antirecombinant proteins such as the ones of mismatch repair and SbcB, but no significant association with nonhomologous end joining, which seems rare in bacteria. Surprisingly, a large number of genomes in which homologous recombination has been reported lack many of the enzymes involved in the presynaptic systems. The lack of obvious correlation between the presence of characterized presynaptic genes and experimental data on the frequency of recombination suggests the existence of still-unknown presynaptic mechanisms in bacteria. It also indicates that, at the moment, the assessment of the intrinsic stability or recombination isolation of bacteria in most cases cannot be inferred from the identification of known recombination proteins in the genomes. PMID:16132081

  5. Comparing interval estimates for small sample ordinal CFA models.

    PubMed

    Natesan, Prathiba

    2015-01-01

    Robust maximum likelihood (RML) and asymptotically generalized least squares (AGLS) methods have been recommended for fitting ordinal structural equation models. Studies show that some of these methods underestimate standard errors. However, these studies have not investigated the coverage and bias of interval estimates. An estimate with a reasonable standard error could still be severely biased. This can only be known by systematically investigating the interval estimates. The present study compares Bayesian, RML, and AGLS interval estimates of factor correlations in ordinal confirmatory factor analysis models (CFA) for small sample data. Six sample sizes, 3 factor correlations, and 2 factor score distributions (multivariate normal and multivariate mildly skewed) were studied. Two Bayesian prior specifications, informative and relatively less informative were studied. Undercoverage of confidence intervals and underestimation of standard errors was common in non-Bayesian methods. Underestimated standard errors may lead to inflated Type-I error rates. Non-Bayesian intervals were more positive biased than negatively biased, that is, most intervals that did not contain the true value were greater than the true value. Some non-Bayesian methods had non-converging and inadmissible solutions for small samples and non-normal data. Bayesian empirical standard error estimates for informative and relatively less informative priors were closer to the average standard errors of the estimates. The coverage of Bayesian credibility intervals was closer to what was expected with overcoverage in a few cases. Although some Bayesian credibility intervals were wider, they reflected the nature of statistical uncertainty that comes with the data (e.g., small sample). Bayesian point estimates were also more accurate than non-Bayesian estimates. The results illustrate the importance of analyzing coverage and bias of interval estimates, and how ignoring interval estimates can be misleading

  6. Comparative analysis of genomic signal processing for microarray data clustering.

    PubMed

    Istepanian, Robert S H; Sungoor, Ala; Nebel, Jean-Christophe

    2011-12-01

    Genomic signal processing is a new area of research that combines advanced digital signal processing methodologies for enhanced genetic data analysis. It has many promising applications in bioinformatics and next generation of healthcare systems, in particular, in the field of microarray data clustering. In this paper we present a comparative performance analysis of enhanced digital spectral analysis methods for robust clustering of gene expression across multiple microarray data samples. Three digital signal processing methods: linear predictive coding, wavelet decomposition, and fractal dimension are studied to provide a comparative evaluation of the clustering performance of these methods on several microarray datasets. The results of this study show that the fractal approach provides the best clustering accuracy compared to other digital signal processing and well known statistical methods.

  7. Operations and Modeling Analysis

    NASA Technical Reports Server (NTRS)

    Ebeling, Charles

    2005-01-01

    The Reliability and Maintainability Analysis Tool (RMAT) provides NASA the capability to estimate reliability and maintainability (R&M) parameters and operational support requirements for proposed space vehicles based upon relationships established from both aircraft and Shuttle R&M data. RMAT has matured both in its underlying database and in its level of sophistication in extrapolating this historical data to satisfy proposed mission requirements, maintenance concepts and policies, and type of vehicle (i.e. ranging from aircraft like to shuttle like). However, a companion analyses tool, the Logistics Cost Model (LCM) has not reached the same level of maturity as RMAT due, in large part, to nonexistent or outdated cost estimating relationships and underlying cost databases, and it's almost exclusive dependence on Shuttle operations and logistics cost input parameters. As a result, the full capability of the RMAT/LCM suite of analysis tools to take a conceptual vehicle and derive its operations and support requirements along with the resulting operating and support costs has not been realized.

  8. Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.

    PubMed

    Boekhorst, Jos; Boersema, Paul J; Tops, Bastiaan B J; van Breukelen, Bas; Heck, Albert J R; Snel, Berend

    2011-01-01

    Unraveling the functional dynamics of phosphorylation networks is a crucial step in understanding the way in which biological networks form a living cell. Recently there has been an enormous increase in the number of measured phosphorylation events. Nevertheless, comparative and integrative analysis of phosphoproteomes is confounded by incomplete coverage and biases introduced by different experimental workflows. As a result, we cannot differentiate whether phosphosites indentified in only one or two samples are the result of condition or species specific phosphorylation, or reflect missing data. Here, we evaluate the impact of incomplete phosphoproteomics datasets on comparative analysis, and we present bioinformatics strategies to quantify the impact of different experimental workflows on measured phosphoproteomes. We show that plotting the saturation in observed phosphosites in replicates provides a reproducible picture of the extent of a particular phosphoproteome. Still, we are still far away from a complete picture of the total human phosphoproteome. The impact of different experimental techniques on the similarity between phosphoproteomes can be estimated by comparing datasets from different experimental pipelines to a common reference. Our results show that comparative analysis is most powerful when datasets have been generated using the same experimental workflow. We show this experimentally by measuring the tyrosine phosphoproteome from Caenorhabditis elegans and comparing it to the tyrosine phosphoproteome of HeLa cells, resulting in an overlap of about 4%. This overlap between very different organisms represents a three-fold increase when compared to dataset of older studies, wherein different workflows were used. The strategies we suggest enable an estimation of the impact of differences in experimental workflows on the overlap between datasets. This will allow us to perform comparative analyses not only on datasets specifically generated for this

  9. CRITICA: coding region identification tool invoking comparative analysis

    NASA Technical Reports Server (NTRS)

    Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1999-01-01

    Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

  10. Computational Methods for the Analysis of Array Comparative Genomic Hybridization

    PubMed Central

    Chari, Raj; Lockwood, William W.; Lam, Wan L.

    2006-01-01

    Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development. PMID:17992253

  11. Model Analysis ToolKit

    2015-05-15

    MATK provides basic functionality to facilitate model analysis within the Python computational environment. Model analysis setup within MATK includes: - define parameters - define observations - define model (python function) - define samplesets (sets of parameter combinations) Currently supported functionality includes: - forward model runs - Latin-Hypercube sampling of parameters - multi-dimensional parameter studies - parallel execution of parameter samples - model calibration using internal Levenberg-Marquardt algorithm - model calibration using lmfit package - modelmore » calibration using levmar package - Markov Chain Monte Carlo using pymc package MATK facilitates model analysis using: - scipy - calibration (scipy.optimize) - rpy2 - Python interface to R« less

  12. Comparative study of two assimilative models of the ionosphere

    NASA Astrophysics Data System (ADS)

    Angling, M. J.; Khattatov, B.

    2006-10-01

    Two assimilative models of the ionosphere are described: the Electron Density Assimilative Model (EDAM), developed by QinetiQ, and the IonoNumerics model developed by Fusion Numerics, Inc. Output from each technique has been compared to independent validation data measured by oblique and vertical ionosondes. Results indicate that when tested against vertical ionosondes, both models can reduce RMS errors compared to a median model. For example, the daytime RMS errors in the F region critical frequency above the Eglin Air Force Base ionosonde are 1.2 MHz for the Parameterised Ionospheric Model, 0.7 MHz for EDAM, and 1.0 MHz for IonoNumerics. Testing conducted against an oblique ionosonde has helped to expose a potential problem with ionospheric hmF2 due to poorly specified empirical driver models within IonoNumerics. The testing shows the usefulness of ray-tracing experiments for improving numerical models and the limitations of only testing models against independent total electron content measurements.

  13. Disaggregation of Rainy Hours: Compared Performance of Various Models.

    NASA Astrophysics Data System (ADS)

    Ben Haha, M.; Hingray, B.; Musy, A.

    In the urban environment, the response times of catchments are usually short. To de- sign or to diagnose waterworks in that context, it is necessary to describe rainfall events with a good time resolution: a 10mn time step is often necessary. Such in- formation is not always available. Rainfall disaggregation models have thus to be applied to produce from rough rainfall data that short time resolution information. The communication will present the performance obtained with several rainfall dis- aggregation models that allow for the disaggregation of rainy hours into six 10mn rainfall amounts. The ability of the models to reproduce some statistical character- istics of rainfall (mean, variance, overall distribution of 10mn-rainfall amounts; ex- treme values of maximal rainfall amounts over different durations) is evaluated thanks to different graphical and numerical criteria. The performance of simple models pre- sented in some scientific papers or developed in the Hydram laboratory as well as the performance of more sophisticated ones is compared with the performance of the basic constant disaggregation model. The compared models are either deterministic or stochastic; for some of them the disaggregation is based on scaling properties of rainfall. The compared models are in increasing complexity order: constant model, linear model (Ben Haha, 2001), Ormsbee Deterministic model (Ormsbee, 1989), Ar- tificial Neuronal Network based model (Burian et al. 2000), Hydram Stochastic 1 and Hydram Stochastic 2 (Ben Haha, 2001), Multiplicative Cascade based model (Olsson and Berndtsson, 1998), Ormsbee Stochastic model (Ormsbee, 1989). The 625 rainy hours used for that evaluation (with a hourly rainfall amount greater than 5mm) were extracted from the 21 years chronological rainfall series (10mn time step) observed at the Pully meteorological station, Switzerland. The models were also evaluated when applied to different rainfall classes depending on the season first and on the

  14. Comparing the line broadened quasilinear model to Vlasov code

    SciTech Connect

    Ghantous, K.; Berk, H. L.; Gorelenkov, N. N.

    2014-03-15

    The Line Broadened Quasilinear (LBQ) model is revisited to study its predicted saturation level as compared with predictions of a Vlasov solver BOT [Lilley et al., Phys. Rev. Lett. 102, 195003 (2009) and M. Lilley, BOT Manual. The parametric dependencies of the model are modified to achieve more accuracy compared to the results of the Vlasov solver both in regards to a mode amplitude's time evolution to a saturated state and its final steady state amplitude in the parameter space of the model's applicability. However, the regions of stability as predicted by LBQ model and BOT are found to significantly differ from each other. The solutions of the BOT simulations are found to have a larger region of instability than the LBQ simulations.

  15. Comparing the line broadened quasilinear model to Vlasov code

    NASA Astrophysics Data System (ADS)

    Ghantous, K.; Berk, H. L.; Gorelenkov, N. N.

    2014-03-01

    The Line Broadened Quasilinear (LBQ) model is revisited to study its predicted saturation level as compared with predictions of a Vlasov solver BOT [Lilley et al., Phys. Rev. Lett. 102, 195003 (2009) and M. Lilley, BOT Manual. The parametric dependencies of the model are modified to achieve more accuracy compared to the results of the Vlasov solver both in regards to a mode amplitude's time evolution to a saturated state and its final steady state amplitude in the parameter space of the model's applicability. However, the regions of stability as predicted by LBQ model and BOT are found to significantly differ from each other. The solutions of the BOT simulations are found to have a larger region of instability than the LBQ simulations.

  16. Comparing Sediment Yield Predictions from Different Hydrologic Modeling Schemes

    NASA Astrophysics Data System (ADS)

    Dahl, T. A.; Kendall, A. D.; Hyndman, D. W.

    2015-12-01

    Sediment yield, or the delivery of sediment from the landscape to a river, is a difficult process to accurately model. It is primarily a function of hydrology and climate, but influenced by landcover and the underlying soils. These additional factors make it much more difficult to accurately model than water flow alone. It is not intuitive what impact different hydrologic modeling schemes may have on the prediction of sediment yield. Here, two implementations of the Modified Universal Soil Loss Equation (MUSLE) are compared to examine the effects of hydrologic model choice. Both the Soil and Water Assessment Tool (SWAT) and the Landscape Hydrology Model (LHM) utilize the MUSLE for calculating sediment yield. SWAT is a lumped parameter hydrologic model developed by the USDA, which is commonly used for predicting sediment yield. LHM is a fully distributed hydrologic model developed primarily for integrated surface and groundwater studies at the watershed to regional scale. SWAT and LHM models were developed and tested for two large, adjacent watersheds in the Great Lakes region; the Maumee River and the St. Joseph River. The models were run using a variety of single model and ensemble downscaled climate change scenarios from the Coupled Model Intercomparison Project 5 (CMIP5). The initial results of this comparison are discussed here.

  17. A comparative analysis of gamma and hadron families at the superhigh energies recorded in experiment Pamir

    NASA Technical Reports Server (NTRS)

    Azimov, S. A.; Mulladjanov, E. J.; Nosov, A. N.; Nuritdinov, H.; Talipov, D. A.; Halilov, D. A.; Yuldashbaev, T. S.

    1985-01-01

    A comparative analysis of hadron and gamma families which have undergone the decascading procedure is made. Results are compared with different models of interactions. In hadron families with energies Summary E sub H sup gamma 20 TeV as well as in gamma families with energies Summary E sub gamma 70 TeV, increasing azimuthal anisotropy is observed.

  18. Accuracy of functional surfaces on comparatively modeled protein structures

    PubMed Central

    Zhao, Jieling; Dundas, Joe; Kachalo, Sema; Ouyang, Zheng; Liang, Jie

    2012-01-01

    Identification and characterization of protein functional surfaces are important for predicting protein function, understanding enzyme mechanism, and docking small compounds to proteins. As the rapid speed of accumulation of protein sequence information far exceeds that of structures, constructing accurate models of protein functional surfaces and identify their key elements become increasingly important. A promising approach is to build comparative models from sequences using known structural templates such as those obtained from structural genome projects. Here we assess how well this approach works in modeling binding surfaces. By systematically building three-dimensional comparative models of proteins using Modeller, we determine how well functional surfaces can be accurately reproduced. We use an alpha shape based pocket algorithm to compute all pockets on the modeled structures, and conduct a large-scale computation of similarity measurements (pocket RMSD and fraction of functional atoms captured) for 26,590 modeled enzyme protein structures. Overall, we find that when the sequence fragment of the binding surfaces has more than 45% identity to that of the tempalte protein, the modeled surfaces have on average an RMSD of 0.5 Å, and contain 48% or more of the binding surface atoms, with nearly all of the important atoms in the signatures of binding pockets captured. PMID:21541664

  19. Comparative and Familial Analysis of Handedness in Great Apes

    ERIC Educational Resources Information Center

    Hopkins, William D.

    2006-01-01

    Historically, population-level handedness has been considered a hallmark of human evolution. Whether nonhuman primates exhibit population-level handedness remains a topic of considerable debate. This paper summarizes published data on handedness in great apes. Comparative analysis indicated that chimpanzees and bonobos show population-level right…

  20. A Comparative Analysis of Three Unique Theories of Organizational Learning

    ERIC Educational Resources Information Center

    Leavitt, Carol C.

    2011-01-01

    The purpose of this paper is to present three classical theories on organizational learning and conduct a comparative analysis that highlights their strengths, similarities, and differences. Two of the theories -- experiential learning theory and adaptive -- generative learning theory -- represent the thinking of the cognitive perspective, while…

  1. The Comparative Analysis of Main Access Control Technologies

    NASA Astrophysics Data System (ADS)

    Zhang, Su; Niu, Li; Chen, Jing

    Effective access control security design is an important precondition for the stable running of an information system. So it's necessary to establish a well-designed security mechanism to ensure the security of the system. This paper analysis and compares the main access control theories.

  2. Initial implementation of a comparative data analysis ontology.

    PubMed

    Prosdocimi, Francisco; Chisham, Brandon; Pontelli, Enrico; Thompson, Julie D; Stoltzfus, Arlin

    2009-01-01

    Comparative analysis is used throughout biology. When entities under comparison (e.g. proteins, genomes, species) are related by descent, evolutionary theory provides a framework that, in principle, allows N-ary comparisons of entities, while controlling for non-independence due to relatedness. Powerful software tools exist for specialized applications of this approach, yet it remains under-utilized in the absence of a unifying informatics infrastructure. A key step in developing such an infrastructure is the definition of a formal ontology. The analysis of use cases and existing formalisms suggests that a significant component of evolutionary analysis involves a core problem of inferring a character history, relying on key concepts: "Operational Taxonomic Units" (OTUs), representing the entities to be compared; "character-state data" representing the observations compared among OTUs; "phylogenetic tree", representing the historical path of evolution among the entities; and "transitions", the inferred evolutionary changes in states of characters that account for observations. Using the Web Ontology Language (OWL), we have defined these and other fundamental concepts in a Comparative Data Analysis Ontology (CDAO). CDAO has been evaluated for its ability to represent token data sets and to support simple forms of reasoning. With further development, CDAO will provide a basis for tools (for semantic transformation, data retrieval, validation, integration, etc.) that make it easier for software developers and biomedical researchers to apply evolutionary methods of inference to diverse types of data, so as to integrate this powerful framework for reasoning into their research.

  3. Comparative Analysis of Cryptography Library in IoT

    NASA Astrophysics Data System (ADS)

    Kumar, Uday; Borgohain, Tuhin; Sanyal, Sugata

    2015-05-01

    The paper aims to do a survey along with a comparative analysis of the various cryptography libraries that are applicable in the field of Internet of Things (IoT). The first half of the paper briefly introduces the various cryptography libraries available in the field of cryptography along with a list of all the algorithms contained within the libraries. The second half of the paper deals with cryptography libraries specifically aimed for application in the field of Internet of Things. The various libraries and their performance analysis listed down in this paper are consolidated from various sources with the aim of providing a single comprehensive repository for reference to the various cryptography libraries and the comparative analysis of their features in IoT.

  4. Image based 3D city modeling : Comparative study

    NASA Astrophysics Data System (ADS)

    Singh, S. P.; Jain, K.; Mandla, V. R.

    2014-06-01

    3D city model is a digital representation of the Earth's surface and it's related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing rapidly for various engineering and non-engineering applications. Generally four main image based approaches were used for virtual 3D city models generation. In first approach, researchers were used Sketch based modeling, second method is Procedural grammar based modeling, third approach is Close range photogrammetry based modeling and fourth approach is mainly based on Computer Vision techniques. SketchUp, CityEngine, Photomodeler and Agisoft Photoscan are the main softwares to represent these approaches respectively. These softwares have different approaches & methods suitable for image based 3D city modeling. Literature study shows that till date, there is no complete such type of comparative study available to create complete 3D city model by using images. This paper gives a comparative assessment of these four image based 3D modeling approaches. This comparative study is mainly based on data acquisition methods, data processing techniques and output 3D model products. For this research work, study area is the campus of civil engineering department, Indian Institute of Technology, Roorkee (India). This 3D campus acts as a prototype for city. This study also explains various governing parameters, factors and work experiences. This research work also gives a brief introduction, strengths and weakness of these four image based techniques. Some personal comment is also given as what can do or what can't do from these softwares. At the last, this study shows; it concluded that, each and every software has some advantages and limitations. Choice of software depends on user requirements of 3D project. For normal visualization project, SketchUp software is a good option. For 3D documentation record, Photomodeler gives good result. For Large city

  5. Case Problems for Problem-Based Pedagogical Approaches: A Comparative Analysis

    ERIC Educational Resources Information Center

    Dabbagh, Nada; Dass, Susan

    2013-01-01

    A comparative analysis of 51 case problems used in five problem-based pedagogical models was conducted to examine whether there are differences in their characteristics and the implications of such differences on the selection and generation of ill-structured case problems. The five pedagogical models were: situated learning, goal-based scenario,…

  6. Comparing Spatial and Multilevel Regression Models for Binary Outcomes in Neighborhood Studies

    PubMed Central

    Xu, Hongwei

    2013-01-01

    The standard multilevel regressions that are widely used in neighborhood research typically ignore potential between-neighborhood correlations due to underlying spatial processes, and hence produce inappropriate inferences about neighborhood effects. In contrast, spatial models make estimations and predictions across areas by explicitly modeling the spatial correlations among observations in different locations. A better understanding of the strengths and limitations of spatial models as compared to the standard multilevel model is needed to improve the research on neighborhood and spatial effects. This research systematically compares model estimations and predictions for binary outcomes between (distance- and lattice-based) spatial and the standard multilevel models in the presence of both within- and between-neighborhood correlations, through simulations. Results from simulation analysis reveal that the standard multilevel and spatial models produce similar estimates of fixed effects, but different estimates of random effects variances. Both the standard multilevel and pure spatial models tend to overestimate the corresponding random effects variances, compared to hybrid models when both non-spatial within neighborhood and spatial between-neighborhood effects exist. Spatial models also outperform the standard multilevel model by a narrow margin in case of fully out-of-sample predictions. Distance-based spatial models provide extra spatial information and have stronger predictive power than lattice-based models under certain circumstances. These merits of spatial modeling are exhibited in an empirical analysis of the child mortality data from 1880 Newark, New Jersey. PMID:25284905

  7. Comparing new models of transverse instability with simulations

    SciTech Connect

    Blaskiewicz M.

    2012-05-20

    Recently, Balbekov and Burov have produced an ordinary integro-differential equation that approximates the Vlasov equation for beams with wakefields and large space charge tune shift. The present work compares this model with simulations. In particular, the claim that certain types of transverse wakes cannot lead to mode coupling instabilities is explored.

  8. Conceptualizations of Creativity: Comparing Theories and Models of Giftedness

    ERIC Educational Resources Information Center

    Miller, Angie L.

    2012-01-01

    This article reviews seven different theories of giftedness that include creativity as a component, comparing and contrasting how each one conceptualizes creativity as a part of giftedness. The functions of creativity vary across the models, suggesting that while the field of gifted education often cites the importance of creativity, the…

  9. BLAT-based comparative analysis for transposable elements: BLATCAT.

    PubMed

    Lee, Sangbum; Oh, Sumin; Kang, Keunsoo; Han, Kyudong

    2014-01-01

    The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs) is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT) based comparative analysis for transposable elements (BLATCAT) program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes.

  10. Dermoscopy analysis of RGB-images based on comparative features

    NASA Astrophysics Data System (ADS)

    Myakinin, Oleg O.; Zakharov, Valery P.; Bratchenko, Ivan A.; Artemyev, Dmitry N.; Neretin, Evgeny Y.; Kozlov, Sergey V.

    2015-09-01

    In this paper, we propose an algorithm for color and texture analysis for dermoscopic images of human skin based on Haar wavelets, Local Binary Patterns (LBP) and Histogram Analysis. This approach is a modification of «7-point checklist» clinical method. Thus, that is an "absolute" diagnostic method because one is using only features extracted from tumor's ROI (Region of Interest), which can be selected manually and/or using a special algorithm. We propose additional features extracted from the same image for comparative analysis of tumor and healthy skin. We used Euclidean distance, Cosine similarity, and Tanimoto coefficient as comparison metrics between color and texture features extracted from tumor's and healthy skin's ROI separately. A classifier for separating melanoma images from other tumors has been built by SVM (Support Vector Machine) algorithm. Classification's errors with and without comparative features between skin and tumor have been analyzed. Significant increase of recognition quality with comparative features has been demonstrated. Moreover, we analyzed two modes (manual and automatic) for ROI selecting on tumor and healthy skin areas. We have reached 91% of sensitivity using comparative features in contrast with 77% of sensitivity using the only "absolute" method. The specificity was the invariable (94%) in both cases.

  11. A Bayesian nonparametric meta-analysis model.

    PubMed

    Karabatsos, George; Talbott, Elizabeth; Walker, Stephen G

    2015-03-01

    In a meta-analysis, it is important to specify a model that adequately describes the effect-size distribution of the underlying population of studies. The conventional normal fixed-effect and normal random-effects models assume a normal effect-size population distribution, conditionally on parameters and covariates. For estimating the mean overall effect size, such models may be adequate, but for prediction, they surely are not if the effect-size distribution exhibits non-normal behavior. To address this issue, we propose a Bayesian nonparametric meta-analysis model, which can describe a wider range of effect-size distributions, including unimodal symmetric distributions, as well as skewed and more multimodal distributions. We demonstrate our model through the analysis of real meta-analytic data arising from behavioral-genetic research. We compare the predictive performance of the Bayesian nonparametric model against various conventional and more modern normal fixed-effects and random-effects models.

  12. A microbial model of economic trading and comparative advantage.

    PubMed

    Enyeart, Peter J; Simpson, Zachary B; Ellington, Andrew D

    2015-01-01

    The economic theory of comparative advantage postulates that beneficial trading relationships can be arrived at by two self-interested entities producing the same goods as long as they have opposing relative efficiencies in producing those goods. The theory predicts that upon entering trade, in order to maximize consumption both entities will specialize in producing the good they can produce at higher efficiency, that the weaker entity will specialize more completely than the stronger entity, and that both will be able to consume more goods as a result of trade than either would be able to alone. We extend this theory to the realm of unicellular organisms by developing mathematical models of genetic circuits that allow trading of a common good (specifically, signaling molecules) required for growth in bacteria in order to demonstrate comparative advantage interactions. In Conception 1, the experimenter controls production rates via exogenous inducers, allowing exploration of the parameter space of specialization. In Conception 2, the circuits self-regulate via feedback mechanisms. Our models indicate that these genetic circuits can demonstrate comparative advantage, and that cooperation in such a manner is particularly favored under stringent external conditions and when the cost of production is not overly high. Further work could involve implementing the models in living bacteria and searching for naturally occurring cooperative relationships between bacteria that conform to the principles of comparative advantage.

  13. Comparative analysis of two DOPA dioxygenases from Phytolacca Americana.

    PubMed

    Takahashi, Kana; Yoshida, Kazuko; Sakuta, Masaaki

    2015-05-01

    The comparative analysis of two Phytolacca americana DOPA dioxygenases (PaDOD1 and PaDOD2) that may be involved in betalain biosynthesis was carried out. The recombinant protein of PaDOD catalyzed the conversion of DOPA to betalamic acid, whereas DOD activity was not detected in PaDOD2 in vitro. The role of DOD genes is discussed in the evolutionary context using phylogenetic analysis, suggesting that DOD might have been duplicated early in evolution and that accumulation of base substitutions could have led to the different characteristics of DODs within the betalain-producing Caryophyllales. PMID:26058141

  14. Comparative analysis of two DOPA dioxygenases from Phytolacca Americana.

    PubMed

    Takahashi, Kana; Yoshida, Kazuko; Sakuta, Masaaki

    2015-05-01

    The comparative analysis of two Phytolacca americana DOPA dioxygenases (PaDOD1 and PaDOD2) that may be involved in betalain biosynthesis was carried out. The recombinant protein of PaDOD catalyzed the conversion of DOPA to betalamic acid, whereas DOD activity was not detected in PaDOD2 in vitro. The role of DOD genes is discussed in the evolutionary context using phylogenetic analysis, suggesting that DOD might have been duplicated early in evolution and that accumulation of base substitutions could have led to the different characteristics of DODs within the betalain-producing Caryophyllales.

  15. Comparative modeling of InP solar cell structures

    NASA Technical Reports Server (NTRS)

    Jain, R. K.; Weinberg, I.; Flood, D. J.

    1991-01-01

    The comparative modeling of p(+)n and n(+)p indium phosphide solar cell structures is studied using a numerical program PC-1D. The optimal design study has predicted that the p(+)n structure offers improved cell efficiencies as compared to n(+)p structure, due to higher open-circuit voltage. The various cell material and process parameters to achieve the maximum cell efficiencies are reported. The effect of some of the cell parameters on InP cell I-V characteristics was studied. The available radiation resistance data on n(+)p and p(+)p InP solar cells are also critically discussed.

  16. Comparative Genomics via Wavelet Analysis for Closely Related Bacteria

    NASA Astrophysics Data System (ADS)

    Song, Jiuzhou; Ware, Tony; Liu, Shu-Lin; Surette, M.

    2004-12-01

    Comparative genomics has been a valuable method for extracting and extrapolating genome information among closely related bacteria. The efficiency of the traditional methods is extremely influenced by the software method used. To overcome the problem here, we propose using wavelet analysis to perform comparative genomics. First, global comparison using wavelet analysis gives the difference at a quantitative level. Then local comparison using keto-excess or purine-excess plots shows precise positions of inversions, translocations, and horizontally transferred DNA fragments. We firstly found that the level of energy spectra difference is related to the similarity of bacteria strains; it could be a quantitative index to describe the similarities of genomes. The strategy is described in detail by comparisons of closely related strains: S.typhi CT18, S.typhi Ty2, S.typhimurium LT2, H.pylori 26695, and H.pylori J99.

  17. Spatial Distribution of Hydrologic Ecosystem Service Estimates: Comparing Two Models

    NASA Astrophysics Data System (ADS)

    Dennedy-Frank, P. J.; Ghile, Y.; Gorelick, S.; Logsdon, R. A.; Chaubey, I.; Ziv, G.

    2014-12-01

    We compare estimates of the spatial distribution of water quantity provided (annual water yield) from two ecohydrologic models: the widely-used Soil and Water Assessment Tool (SWAT) and the much simpler water models from the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) toolbox. These two models differ significantly in terms of complexity, timescale of operation, effort, and data required for calibration, and so are often used in different management contexts. We compare two study sites in the US: the Wildcat Creek Watershed (2083 km2) in Indiana, a largely agricultural watershed in a cold aseasonal climate, and the Upper Upatoi Creek Watershed (876 km2) in Georgia, a mostly forested watershed in a temperate aseasonal climate. We evaluate (1) quantitative estimates of water yield to explore how well each model represents this process, and (2) ranked estimates of water yield to indicate how useful the models are for management purposes where other social and financial factors may play significant roles. The SWAT and InVEST models provide very similar estimates of the water yield of individual subbasins in the Wildcat Creek Watershed (Pearson r = 0.92, slope = 0.89), and a similar ranking of the relative water yield of those subbasins (Spearman r = 0.86). However, the two models provide relatively different estimates of the water yield of individual subbasins in the Upper Upatoi Watershed (Pearson r = 0.25, slope = 0.14), and very different ranking of the relative water yield of those subbasins (Spearman r = -0.10). The Upper Upatoi watershed has a significant baseflow contribution due to its sandy, well-drained soils. InVEST's simple seasonality terms, which assume no change in storage over the time of the model run, may not accurately estimate water yield processes when baseflow provides such a strong contribution. Our results suggest that InVEST users take care in situations where storage changes are significant.

  18. [Comparative analysis of 2 methods of DNA extraction].

    PubMed

    Sánchez García, I; Martín Seisdedos, C; Pérez Grande, R; Corral de la Calle, J; Rodríguez Arias, C; González-Sarmiento, R

    1990-10-01

    The study of the organization of immunoglobulin and T cell receptor genes in leukaemias and lymphomas depends on our ability to obtain high molecular weight DNA. We have compared two different methods of DNA extraction: one being enzymatic, using the enzyme proteinase K, and the other chemical, using urea as a substance purifying DNA. Since the amount and purity of the DNA obtained are similar with each of the two methods of DNA extraction, both are valid to make such a genetic analysis.

  19. Comparative Study of MHD Modeling of the Background Solar Wind

    NASA Astrophysics Data System (ADS)

    Gressl, C.; Veronig, A. M.; Temmer, M.; Odstrčil, D.; Linker, J. A.; Mikić, Z.; Riley, P.

    2014-05-01

    Knowledge about the background solar wind plays a crucial role in the framework of space-weather forecasting. In-situ measurements of the background solar wind are only available for a few points in the heliosphere where spacecraft are located, therefore we have to rely on heliospheric models to derive the distribution of solar-wind parameters in interplanetary space. We test the performance of different solar-wind models, namely Magnetohydrodynamic Algorithm outside a Sphere/ENLIL (MAS/ENLIL), Wang-Sheeley-Arge/ENLIL (WSA/ENLIL), and MAS/MAS, by comparing model results with in-situ measurements from spacecraft located at 1 AU distance to the Sun (ACE, Wind). To exclude the influence of interplanetary coronal mass ejections (ICMEs), we chose the year 2007 as a time period with low solar activity for our comparison. We found that the general structure of the background solar wind is well reproduced by all models. The best model results were obtained for the parameter solar-wind speed. However, the predicted arrival times of high-speed solar-wind streams have typical uncertainties of the order of about one day. Comparison of model runs with synoptic magnetic maps from different observatories revealed that the choice of the synoptic map significantly affects the model performance.

  20. A Comparative Analysis of Three Proposed Federal Renewable Electricity Standards

    SciTech Connect

    Sullivan, Patrick; Logan, Jeffrey; Bird, Lori; Short, Walter

    2009-05-01

    This paper analyzes potential impacts of proposed national renewable electricity standard (RES) legislation. An RES is a mandate requiring certain electricity retailers to provide a minimum share of their electricity sales from qualifying renewable power generation. The analysis focuses on draft bills introduced individually by Senator Jeff Bingaman and Representative Edward Markey, and jointly by Representative Henry Waxman and Markey. The analysis uses NREL's Regional Energy Deployment System (ReEDS) model to evaluate the impacts of the proposed RES requirements on the U.S. energy sector in four scenarios.

  1. Comparative Analysis of Three Proposed Federal Renewable Electricity Standards

    SciTech Connect

    Sullivan, P.; Logan, J.; Bird, L.; Short, W.

    2009-05-01

    This paper analyzes potential impacts of proposed national renewable electricity standard (RES) legislation. An RES is a mandate requiring certain electricity retailers to provide a minimum share of their electricity sales from qualifying renewable power generation. The analysis focuses on draft bills introduced individually by Senator Jeff Bingaman and Representative Edward Markey, and jointly by Representative Henry Waxman and Markey. The analysis uses NREL's Regional Energy Deployment System (ReEDS) model to evaluate the impacts of the proposed RES requirements on the U.S. energy sector in four scenarios.

  2. Material modeling and structural analysis with the microplane constitutive model

    NASA Astrophysics Data System (ADS)

    Brocca, Michele

    The microplane model is a versatile and powerful approach to constitutive modeling in which the stress-strain relations are defined in terms of vectors rather than tensors on planes of all possible orientations. Such planes are called the microplanes and are representative of the microstructure of the material. The microplane model with kinematic constraint has been successfully employed in the past in the modeling of concrete, soils, ice, rocks, fiber composites and other quasibrittle materials. The microplane model provides a powerful and efficient numerical and theoretical framework for the development and implementation of constitutive models for any kind of material. The dissertation presents a review of the background from which the microplane model stems, highlighting differences and similarities with other approaches. The basic structure of the microplane model is then presented, together with its extension to finite strain deformation. To show the effectiveness of the microplane model approach, some examples are given demonstrating applications of microplane models in structural analysis with the finite element method. Some new constitutive models are also introduced for materials characterized by very different properties and microstructures, showing that the approach is indeed very versatile and provides a robust basis for the study of a broad range of problems. New models are introduced for metal plasticity, shape memory alloys and cellular materials. The new models are compared quantitatively with the existing models and experimental data. In particular, the newly introduced microplane models for metal plasticity are compared with the classical J2-flow theory for incremental plasticity. An existing microplane model for concrete is employed in finite element analysis of the 'tube-squash' test, in which concrete undergoes very large deviatoric deformation, and of the size effect in compressive failure of concrete columns. The microplane model for shape

  3. Modelled vs. reconstructed past fire dynamics - how can we compare?

    NASA Astrophysics Data System (ADS)

    Brücher, Tim; Brovkin, Victor; Kloster, Silvia; Marlon, Jennifer R.; Power, Mitch J.

    2015-04-01

    Fire is an important process that affects climate through changes in CO2 emissions, albedo, and aerosols (Ward et al. 2012). Fire-history reconstructions from charcoal accumulations in sediment indicate that biomass burning has increased since the Last Glacial Maximum (Power et al. 2008; Marlon et al. 2013). Recent comparisons with transient climate model output suggest that this increase in global ?re activity is linked primarily to variations in temperature and secondarily to variations in precipitation (Daniau et al. 2012). In this study, we discuss the best way to compare global ?re model output with charcoal records. Fire models generate quantitative output for burned area and fire-related emissions of CO2, whereas charcoal data indicate relative changes in biomass burning for specific regions and time periods only. However, models can be used to relate trends in charcoal data to trends in quantitative changes in burned area or fire carbon emissions. Charcoal records are often reported as Z-scores (Power et al. 2008). Since Z-scores are non-linear power transformations of charcoal influxes, we must evaluate if, for example, a two-fold increase in the standardized charcoal reconstruction corresponds to a 2- or 200-fold increase in the area burned. In our study we apply the Z-score metric to the model output. This allows us to test how well the model can quantitatively reproduce the charcoal-based reconstructions and how Z-score metrics affect the statistics of model output. The Global Charcoal Database (GCD version 2.5; www.gpwg.org/gpwgdb.html) is used to determine regional and global paleofire trends from 218 sedimentary charcoal records covering part or all of the last 8 ka BP. To retrieve regional and global composites of changes in fire activity over the Holocene the time series of Z-scores are linearly averaged to achieve regional composites. A coupled climate-carbon cycle model, CLIMBA (Brücher et al. 2014), is used for this study. It consists of the

  4. Comparative analysis of cryopreservation methods in Chlamydomonas reinhardtii.

    PubMed

    Scarbrough, Chasity; Wirschell, Maureen

    2016-10-01

    Chlamydomonas is a model organism used for studies of many important biological processes. Traditionally, strains have been propagated on solid agar, which requires routine passaging for long-term maintenance. Cryopreservation of Chlamydomonas is possible, yet long-term viability is highly variable. Thus, improved cryopreservation methods for Chlamydomonas are an important requirement for sustained study of genetically defined strains. Here, we tested a commercial cryopreservation kit and directly compared it's effectiveness to a methanol-based method. We also tested thaw-back procedures comparing the growth of cells in liquid culture or on solid agar media. We demonstrated that methanol was the superior cryopreservation method for Chlamydomonas compared to the commercial kit and that post-thaw culture conditions dramatically affect viability. We also demonstrated that cryopreserved cells could be successfully thawed and plated directly onto solid agar plates. Our findings have important implications for the long-term storage of Chlamydomonas that can likely be extended to other algal species.

  5. Canister Model, Systems Analysis

    1993-09-29

    This packges provides a computer simulation of a systems model for packaging nuclear waste and spent nuclear fuel in canisters. The canister model calculates overall programmatic cost, number of canisters, and fuel and waste inventories for the Idaho Chemical Processing Plant (other initial conditions can be entered).

  6. Comparing the ecological relevance of four wave exposure models

    NASA Astrophysics Data System (ADS)

    Sundblad, G.; Bekkby, T.; Isæus, M.; Nikolopoulos, A.; Norderhaug, K. M.; Rinde, E.

    2014-03-01

    Wave exposure is one of the main structuring forces in the marine environment. Methods that enable large scale quantification of environmental variables have become increasingly important for predicting marine communities in the context of spatial planning and coastal zone management. Existing methods range from cartographic solutions to numerical hydrodynamic simulations, and differ in the scale and spatial coverage of their outputs. Using a biological exposure index we compared the performance of four wave exposure models ranging from simple to more advanced techniques. All models were found to be related to the biological exposure index and their performance, measured as bootstrapped R2 distributions, overlapped. Qualitatively, there were differences in the spatial patterns indicating higher complexity with more advanced techniques. In order to create complex spatial patterns wave exposure models should include diffraction, especially in coastal areas rich in islands. The inclusion of wind strength and frequency, in addition to wind direction and bathymetry, further tended to increase the amount of explained variation. The large potential of high-resolution numerical models to explain the observed patterns of species distribution in complex coastal areas provide exciting opportunities for future research. Easy access to relevant wave exposure models will aid large scale habitat classification systems and the continuously growing field of marine species distribution modelling, ultimately serving marine spatial management and planning.

  7. In vitro comparative models for canine and human breast cancers.

    PubMed

    Visan, Simona; Balacescu, Ovidiu; Berindan-Neagoe, Ioana; Catoi, Cornel

    2016-01-01

    During the past four decades, an increased number of similarities between canine mammary tumors and human breast cancer have been reported: molecular, histological, morphological, clinical and epidemiological, which lead to comparative oncological studies. One of the most important goals in human and veterinary oncology is to discover potential molecular biomarkers that could detect breast cancer in an early stage and to develop new effective therapies. Recently, cancer cell lines have successfully been used as an in vitro model to study the biology of cancer, to investigate molecular pathways and to test the efficiency of anticancer drugs. Moreover, establishment of an experimental animal model for the study of human breast cancer will improve testing potential anti-cancer therapies and the discovery of effective therapeutic schemes suitable for human clinical trials. In this review, we collected data from previous studies that strengthen the value of canine mammary cancer cell lines as an in vitro model for the study of human breast cancer. PMID:27004024

  8. Halo Coronal Mass Ejections: Comparing Observations and Models

    NASA Technical Reports Server (NTRS)

    Gilbert, Holly; Orlove, Matthew; SaintCyr, O.; Mays, L.; Gopalswamy, N.

    2011-01-01

    Since 1996, the SOHO LASCO coronagraphs have detected "halo" CMEs that appear to be directed toward Earth, but information about the size and speed of these events seen face-on has been limited. From a single vantage point along the Sun-Earth line, the primary limitation has been ambiguity in fitting the cone model (or other forward-modeling techniques, e.g., Thernisian et al., 2006). But in the past few years, the STEREO mission has provided a view of Earth-directed events from the side. These events offer the opportunity to compare measurements (width and speed) of halo CMEs observed by STEREO with models that derive halo CME properties. We report here results of such a comparison on a large sample of LASCO CMEs in the STEREO era.

  9. Magnetic Field Configuration Models and Reconstruction Methods: a comparative study

    NASA Astrophysics Data System (ADS)

    Al-haddad, Nada; Möstl, Christian; Roussev, Ilia; Nieves-Chinchilla, Teresa; Poedts, Stefaan; Hidalgo, Miguel Angel; Marubashi, Katsuhide; Savani, Neel

    2012-07-01

    This study aims to provide a reference to different magnetic field models and reconstruction methods. In order to understand the dissimilarities of those models and codes, we analyze 59 events from the CDAW list, using four different magnetic field models and reconstruction techniques; force- free reconstruction (Lepping et al.(1990); Lynch et al.(2003)), magnetostatic reconstruction, referred as Grad-Shafranov (Hu & Sonnerup(2001); Mostl et al.(2009)), cylinder reconstruction (Marubashi & Lepping(2007)), elliptical, non-force free (Hidalgo et al.(2002)). The resulted parameters of the reconstructions, for the 59 events are compared, statistically, as well as in more details for some cases. The differences between the reconstruction codes are discussed, and suggestions are provided as how to enhance them. Finally we look at 2 unique cases under the microscope, to provide a comprehensive idea of the different aspects of how the fitting codes work.

  10. In vitro comparative models for canine and human breast cancers

    PubMed Central

    VISAN, SIMONA; BALACESCU, OVIDIU; BERINDAN-NEAGOE, IOANA; CATOI, CORNEL

    2016-01-01

    During the past four decades, an increased number of similarities between canine mammary tumors and human breast cancer have been reported: molecular, histological, morphological, clinical and epidemiological, which lead to comparative oncological studies. One of the most important goals in human and veterinary oncology is to discover potential molecular biomarkers that could detect breast cancer in an early stage and to develop new effective therapies. Recently, cancer cell lines have successfully been used as an in vitro model to study the biology of cancer, to investigate molecular pathways and to test the efficiency of anticancer drugs. Moreover, establishment of an experimental animal model for the study of human breast cancer will improve testing potential anti-cancer therapies and the discovery of effective therapeutic schemes suitable for human clinical trials. In this review, we collected data from previous studies that strengthen the value of canine mammary cancer cell lines as an in vitro model for the study of human breast cancer. PMID:27004024

  11. Comparing Supply-Side Specifications in Models of Global Agriculture and the Food System

    SciTech Connect

    Robinson, Sherman; van Meijl, Hans; Willenbockel, Dirk; Valin, Hugo; Fujimori, Shinichiro; Masui, Toshihiko; Sands, Ronald; Wise, Marshall A.; Calvin, Katherine V.; Havlik, Petr; Mason d'Croz, Daniel; Tabeau, Andrzej; Kavallari, Aikaterini; Schmitz, Christoph; Dietrich, Jan P.; von Lampe, Martin

    2014-01-01

    This paper compares the theoretical specification of production and technical change across the partial equilibrium (PE) and computable general equilibrium (CGE) models of the global agricultural and food system included in the AgMIP model comparison study. The two modeling approaches have different theoretical underpinnings concerning the scope of economic activity they capture and how they represent technology and the behavior of supply and demand in markets. This paper focuses on their different specifications of technology and supply behavior, comparing their theoretical and empirical treatments. While the models differ widely in their specifications of technology, both within and between the PE and CGE classes of models, we find that the theoretical responsiveness of supply to changes in prices can be similar, depending on parameter choices that define the behavior of supply functions over the domain of applicability defined by the common scenarios used in the AgMIP comparisons. In particular, we compare the theoretical specification of supply in CGE models with neoclassical production functions and PE models that focus on land and crop yields in agriculture. In practice, however, comparability of results given parameter choices is an empirical question, and the models differ in their sensitivity to variations in specification. To illustrate the issues, sensitivity analysis is done with one global CGE model, MAGNET, to indicate how the results vary with different specification of technical change, and how they compare with the results from PE models.

  12. Model-Based Safety Analysis

    NASA Technical Reports Server (NTRS)

    Joshi, Anjali; Heimdahl, Mats P. E.; Miller, Steven P.; Whalen, Mike W.

    2006-01-01

    System safety analysis techniques are well established and are used extensively during the design of safety-critical systems. Despite this, most of the techniques are highly subjective and dependent on the skill of the practitioner. Since these analyses are usually based on an informal system model, it is unlikely that they will be complete, consistent, and error free. In fact, the lack of precise models of the system architecture and its failure modes often forces the safety analysts to devote much of their effort to gathering architectural details about the system behavior from several sources and embedding this information in the safety artifacts such as the fault trees. This report describes Model-Based Safety Analysis, an approach in which the system and safety engineers share a common system model created using a model-based development process. By extending the system model with a fault model as well as relevant portions of the physical system to be controlled, automated support can be provided for much of the safety analysis. We believe that by using a common model for both system and safety engineering and automating parts of the safety analysis, we can both reduce the cost and improve the quality of the safety analysis. Here we present our vision of model-based safety analysis and discuss the advantages and challenges in making this approach practical.

  13. Comparing the cognitive differences resulting from modeling instruction: Using computer microworld and physical object instruction to model real world problems

    NASA Astrophysics Data System (ADS)

    Oursland, Mark David

    This study compared the modeling achievement of students receiving mathematical modeling instruction using the computer microworld, Interactive Physics, and students receiving instruction using physical objects. Modeling instruction included activities where students applied the (a) linear model to a variety of situations, (b) linear model to two-rate situations with a constant rate, (c) quadratic model to familiar geometric figures. Both quantitative and qualitative methods were used to analyze achievement differences between students (a) receiving different methods of modeling instruction, (b) with different levels of beginning modeling ability, or (c) with different levels of computer literacy. Student achievement was analyzed quantitatively through a three-factor analysis of variance where modeling instruction, beginning modeling ability, and computer literacy were used as the three independent factors. The SOLO (Structure of the Observed Learning Outcome) assessment framework was used to design written modeling assessment instruments to measure the students' modeling achievement. The same three independent factors were used to collect and analyze the interviews and observations of student behaviors. Both methods of modeling instruction used the data analysis approach to mathematical modeling. The instructional lessons presented problem situations where students were asked to collect data, analyze the data, write a symbolic mathematical equation, and use equation to solve the problem. The researcher recommends the following practice for modeling instruction based on the conclusions of this study. A variety of activities with a common structure are needed to make explicit the modeling process of applying a standard mathematical model. The modeling process is influenced strongly by prior knowledge of the problem context and previous modeling experiences. The conclusions of this study imply that knowledge of the properties about squares improved the students

  14. Modelling effects of internalized antibody: a simple comparative study

    PubMed Central

    2014-01-01

    Background The modelling framework is proposed to study protection properties of antibodies to neutralize the effects of the plant toxin (ricin). The present study extends our previous work by including (i) the model of intracellular transport of toxin to the Endoplasmic Reticulum and (ii) the model of the internalised antibodies (when antibody is delivered directly into the cytosol). Method Simulation of the receptor-toxin-antibody interaction is implemented by solving the systems of PDEs (advection-diffusion models) or ODEs (rate models) for the underlying transport coupled with mass-action kinetics. Results As the main application of the enhanced framework we present a comparative study of two kinds (external and internalised) of antibodies. This comparison is based on calculation of the non-dimensional protection factor using the same set of parameters (geometry, binding constants, initial concentrations of species, and total initial amount of the antibody). Conclusion This research will provide a framework for consistent evaluation and comparison of different types of antibodies for toxicological applications. PMID:24521456

  15. Building v/s Exploring Models: Comparing Learning of Evolutionary Processes through Agent-based Modeling

    NASA Astrophysics Data System (ADS)

    Wagh, Aditi

    Two strands of work motivate the three studies in this dissertation. Evolutionary change can be viewed as a computational complex system in which a small set of rules operating at the individual level result in different population level outcomes under different conditions. Extensive research has documented students' difficulties with learning about evolutionary change (Rosengren et al., 2012), particularly in terms of levels slippage (Wilensky & Resnick, 1999). Second, though building and using computational models is becoming increasingly common in K-12 science education, we know little about how these two modalities compare. This dissertation adopts agent-based modeling as a representational system to compare these modalities in the conceptual context of micro-evolutionary processes. Drawing on interviews, Study 1 examines middle-school students' productive ways of reasoning about micro-evolutionary processes to find that the specific framing of traits plays a key role in whether slippage explanations are cued. Study 2, which was conducted in 2 schools with about 150 students, forms the crux of the dissertation. It compares learning processes and outcomes when students build their own models or explore a pre-built model. Analysis of Camtasia videos of student pairs reveals that builders' and explorers' ways of accessing rules, and sense-making of observed trends are of a different character. Builders notice rules through available blocks-based primitives, often bypassing their enactment while explorers attend to rules primarily through the enactment. Moreover, builders' sense-making of observed trends is more rule-driven while explorers' is more enactment-driven. Pre and posttests reveal that builders manifest a greater facility with accessing rules, providing explanations manifesting targeted assembly. Explorers use rules to construct explanations manifesting non-targeted assembly. Interviews reveal varying degrees of shifts away from slippage in both

  16. A New Method of Comparing Forcing Agents in Climate Models

    SciTech Connect

    Kravitz, Benjamin S.; MacMartin, Douglas; Rasch, Philip J.; Jarvis, Andrew

    2015-10-14

    We describe a new method of comparing different climate forcing agents (e.g., CO2, CH4, and solar irradiance) that avoids many of the ambiguities introduced by temperature-related climate feedbacks. This is achieved by introducing an explicit feedback loop external to the climate model that adjusts one forcing agent to balance another while keeping global mean surface temperature constant. Compared to current approaches, this method has two main advantages: (i) the need to define radiative forcing is bypassed and (ii) by maintaining roughly constant global mean temperature, the effects of state dependence on internal feedback strengths are minimized. We demonstrate this approach for several different forcing agents and derive the relationships between these forcing agents in two climate models; comparisons between forcing agents are highly linear in concordance with predicted functional forms. Transitivity of the relationships between the forcing agents appears to hold within a wide range of forcing. The relationships between the forcing agents obtained from this method are consistent across both models but differ from relationships that would be obtained from calculations of radiative forcing, highlighting the importance of controlling for surface temperature feedback effects when separating radiative forcing and climate response.

  17. Sequence and comparative analysis of Leuconostoc dairy bacteriophages.

    PubMed

    Kot, Witold; Hansen, Lars H; Neve, Horst; Hammer, Karin; Jacobsen, Susanne; Pedersen, Per D; Sørensen, Søren J; Heller, Knut J; Vogensen, Finn K

    2014-04-17

    Bacteriophages attacking Leuconostoc species may significantly influence the quality of the final product. There is however limited knowledge of this group of phages in the literature. We have determined the complete genome sequences of nine Leuconostoc bacteriophages virulent to either Leuconostoc mesenteroides or Leuconostoc pseudomesenteroides strains. The phages have dsDNA genomes with sizes ranging from 25.7 to 28.4 kb. Comparative genomics analysis helped classify the 9 phages into two classes, which correlates with the host species. High percentage of similarity within the classes on both nucleotide and protein levels was observed. Genome comparison also revealed very high conservation of the overall genomic organization between the classes. The genes were organized in functional modules responsible for replication, packaging, head and tail morphogenesis, cell lysis and regulation and modification, respectively. No lysogeny modules were detected. To our knowledge this report provides the first comparative genomic work done on Leuconostoc dairy phages.

  18. Comparative and functional analysis of cardiovascular-related genes

    SciTech Connect

    Cheng, Jan-Fang; Pennacchio, Len A.

    2003-09-01

    The ability to detect putative cis-regulatory elements in cardiovascular-related genes has been accelerated by the availability of genomic sequence data from numerous vertebrate species and the recent development of comparative genomic tools. This improvement is anticipated to lead to a better understanding of the complex regulatory architecture of cardiovascular (CV) genes and how genetic variants in these non-coding regions can potentially play a role in cardiovascular disease. This manuscript reviews a recently established database dedicated to the comparative sequence analysis of 250 human CV genes of known importance, 37 of which currently contain sequence comparison data for organisms beyond those of human, mouse and rat. These data have provided a glimpse into the variety of possible insights from deep vertebrate sequence comparisons and the identification of putative gene regulatory elements.

  19. Stigma, sex work, and substance use: a comparative analysis.

    PubMed

    Benoit, Cecilia; McCarthy, Bill; Jansson, Mikael

    2015-03-01

    Stigma is a widely used concept in social science research and an extensive literature claims that stigmatisation contributes to numerous negative health outcomes. However, few studies compare groups that vary in the extent to which they are stigmatised and even fewer studies examine stigma's independent and mediating effects. This article addresses these gaps in a comparative study of perceived stigma and drug use among three low-income feminised service occupations: sex work, food and alcoholic beverage serving, and barbering and hairstyling. An analysis of longitudinal data shows positive associations between sex work, perceived stigma, and socially less acceptable drug use (for example, heroin and cocaine), and that stigma mediates part of the link between sex work and the use of these drugs. Our overall findings suggest that perceived stigma is pronounced among those who work in the sex industry and negatively affects health independently of sex work involvement.

  20. Estimating, Testing, and Comparing Specific Effects in Structural Equation Models: The Phantom Model Approach

    ERIC Educational Resources Information Center

    Macho, Siegfried; Ledermann, Thomas

    2011-01-01

    The phantom model approach for estimating, testing, and comparing specific effects within structural equation models (SEMs) is presented. The rationale underlying this novel method consists in representing the specific effect to be assessed as a total effect within a separate latent variable model, the phantom model that is added to the main…

  1. Feature-level sentiment analysis by using comparative domain corpora

    NASA Astrophysics Data System (ADS)

    Quan, Changqin; Ren, Fuji

    2016-06-01

    Feature-level sentiment analysis (SA) is able to provide more fine-grained SA on certain opinion targets and has a wider range of applications on E-business. This study proposes an approach based on comparative domain corpora for feature-level SA. The proposed approach makes use of word associations for domain-specific feature extraction. First, we assign a similarity score for each candidate feature to denote its similarity extent to a domain. Then we identify domain features based on their similarity scores on different comparative domain corpora. After that, dependency grammar and a general sentiment lexicon are applied to extract and expand feature-oriented opinion words. Lastly, the semantic orientation of a domain-specific feature is determined based on the feature-oriented opinion lexicons. In evaluation, we compare the proposed method with several state-of-the-art methods (including unsupervised and semi-supervised) using a standard product review test collection. The experimental results demonstrate the effectiveness of using comparative domain corpora.

  2. CMS Analysis School Model

    SciTech Connect

    Malik, S.; Shipsey, I.; Cavanaugh, R.; Bloom, K.; Chan, Kai-Feng; D'Hondt, J.; Klima, B.; Narain, M.; Palla, F.; Rolandi, G.; Schörner-Sadenius, T.

    2014-01-01

    To impart hands-on training in physics analysis, CMS experiment initiated the concept of CMS Data Analysis School (CMSDAS). It was born over three years ago at the LPC (LHC Physics Centre), Fermilab and is based on earlier workshops held at the LPC and CLEO Experiment. As CMS transitioned from construction to the data taking mode, the nature of earlier training also evolved to include more of analysis tools, software tutorials and physics analysis. This effort epitomized as CMSDAS has proven to be a key for the new and young physicists to jump start and contribute to the physics goals of CMS by looking for new physics with the collision data. With over 400 physicists trained in six CMSDAS around the globe, CMS is trying to engage the collaboration in its discovery potential and maximize physics output. As a bigger goal, CMS is striving to nurture and increase engagement of the myriad talents, in the development of physics, service, upgrade, education of those new to CMS and the career development of younger members. An extension of the concept to the dedicated software and hardware schools is also planned, keeping in mind the ensuing upgrade phase.

  3. CMS Analysis School Model

    NASA Astrophysics Data System (ADS)

    Malik, S.; Shipsey, I.; Cavanaugh, R.; Bloom, K.; Chan, Kai-Feng; D'Hondt, J.; Klima, B.; Narain, M.; Palla, F.; Rolandi, G.; Schörner-Sadenius, T.

    2014-06-01

    To impart hands-on training in physics analysis, CMS experiment initiated the concept of CMS Data Analysis School (CMSDAS). It was born over three years ago at the LPC (LHC Physics Centre), Fermilab and is based on earlier workshops held at the LPC and CLEO Experiment. As CMS transitioned from construction to the data taking mode, the nature of earlier training also evolved to include more of analysis tools, software tutorials and physics analysis. This effort epitomized as CMSDAS has proven to be a key for the new and young physicists to jump start and contribute to the physics goals of CMS by looking for new physics with the collision data. With over 400 physicists trained in six CMSDAS around the globe, CMS is trying to engage the collaboration in its discovery potential and maximize physics output. As a bigger goal, CMS is striving to nurture and increase engagement of the myriad talents, in the development of physics, service, upgrade, education of those new to CMS and the career development of younger members. An extension of the concept to the dedicated software and hardware schools is also planned, keeping in mind the ensuing upgrade phase.

  4. Initial sequencing and comparative analysis of the mouse genome

    SciTech Connect

    Waterston, Robert H.; Lindblad-Toh, Kerstin; Birney, Ewan; Rogers, Jane; Abril, Josep F.; Agarwal, Pankaj; Agarwala, Richa; Ainscough, Rachel; Alexandersson, Marina; An, Peter; Antonarakis, Stylianos E.; Attwood, John; Baertsch, Robert; Bailey, Jonathon; Barlow, Karen; Beck, Stephan; Berry, Eric; Birren, Bruce; Bloom, Toby; Bork, Peer; Botcherby, Marc; Bray, Nicolas; Brent, Michael R.; Brown, Daniel G.; Brown, Stephen D.; Bult, Carol; Burton, John; Butler, Jonathan; Campbell, Robert D.; Carninci, Piero; Cawley, Simon; Chiaromonte, Francesca; Chinwalla, Asif T.; Church, Deanna M.; Clamp, Michele; Clee, Christopher; Collins, Francis S.; Cook, Lisa L.; Copley, Richard R.; Coulson, Alan; Couronne, Olivier; Cuff, James; Curwen, Val; Cutts, Tim; Daly, Mark; David, Robert; Davies, Joy; Delehaunty, Kimberly D.; Deri, Justin; Dermitzakis, Emmanouil T.; Dewey, Colin; Dickens, Nicholas J.; Diekhans, Mark; Dodge, Sheila; Dubchak, Inna; Dunn, Diane M.; Eddy, Sean R.; Elnitski, Laura; Emes, Richard D.; Eswara, Pallavi; Eyras, Eduardo; Felsenfeld, Adam; Fewell, Ginger A.; Flicek, Paul; Foley, Karen; Frankel, Wayne N.; Fulton, Lucinda A.; Fulton, Robert S.; Furey, Terrence S.; Gage, Diane; Gibbs, Richard A.; Glusman, Gustavo; Gnerre, Sante; Goldman, Nick; Goodstadt, Leo; Grafham, Darren; Graves, Tina A.; Green, Eric D.; Gregory, Simon; Guigo, Roderic; Guyer, Mark; Hardison, Ross C.; Haussler, David; Hayashizaki, Yoshihide; Hillier, LaDeana W.; Hinrichs, Angela; Hlavina, Wratko; Holzer, Timothy; Hsu, Fan; Hua, Axin; Hubbard, Tim; Hunt, Adrienne; Jackson, Ian; Jaffe, David B.; Johnson, L. Steven; Jones, Matthew; Jones, Thomas A.; Joy, Ann; Kamal, Michael; Karlsson, Elinor K.; Karolchik, Donna; Kasprzyk, Arkadiusz; Kawai, Jun; Keibler, Evan; Kells, Cristyn; Kent, W. James; Kirby, Andrew; Kolbe, Diana L.; Korf, Ian; Kucherlapati, Raju S.; Kulbokas III, Edward J.; Kulp, David; Landers, Tom; Leger, J.P.; Leonard, Steven; Letunic, Ivica; Levine, Rosie; et al.

    2002-12-15

    The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

  5. Establishing a framework for comparative analysis of genome sequences

    SciTech Connect

    Bansal, A.K.

    1995-06-01

    This paper describes a framework and a high-level language toolkit for comparative analysis of genome sequence alignment The framework integrates the information derived from multiple sequence alignment and phylogenetic tree (hypothetical tree of evolution) to derive new properties about sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment and to derive mutation related information from a phylogenetic tree by superimposing parsimonious analysis. The framework has been applied on protein alignments to derive constrained columns (in a multiple sequence alignment) that exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog toolkit based on the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns.

  6. Systems design and comparative analysis of large antenna concepts

    NASA Technical Reports Server (NTRS)

    Garrett, L. B.; Ferebee, M. J., Jr.

    1983-01-01

    Conceptual designs are evaluated and comparative analyses conducted for several large antenna spacecraft for Land Mobile Satellite System (LMSS) communications missions. Structural configurations include trusses, hoop and column and radial rib. The study was conducted using the Interactive Design and Evaluation of Advanced Spacecraft (IDEAS) system. The current capabilities, development status, and near-term plans for the IDEAS system are reviewed. Overall capabilities are highlighted. IDEAS is an integrated system of computer-aided design and analysis software used to rapidly evaluate system concepts and technology needs for future advanced spacecraft such as large antennas, platforms, and space stations. The system was developed at Langley to meet a need for rapid, cost-effective, labor-saving approaches to the design and analysis of numerous missions and total spacecraft system options under consideration. IDEAS consists of about 40 technical modules efficient executive, data-base and file management software, and interactive graphics display capabilities.

  7. Comparative biomorphologic analysis about three dentinal adhesives of last generations.

    PubMed

    Carini, F; Varia, P; Valenza, V

    2001-01-01

    The aim of this work consists in a comparative biomorphological analysis of the properties of infiltration and of adhesion to dental tissues of three among the more used enamel dentinal adhesives of the last generation known with the commercial name of Syntac, Excite and Prompt. The results have given evidence that Syntac has got short adhesion, Excite has got good capacity of infiltration and moderate adhesion, Prompt seems to possess a capacity of infiltration equal to Excite's one, but a better adhesion besides an easier modality of use.

  8. Comparative study of analysis methods in biospeckle phenomenon

    NASA Astrophysics Data System (ADS)

    da Silva, Emerson Rodrigo; Muramatsu, Mikiya

    2008-04-01

    In this work we present a review of main statistical properties of speckle patterns and accomplish a comparative study of the more used methods for analysis and extraction of information from optical grainy. The first and second order space-time statistics are dicussed in an overview perspective. The biospeckle phenomenon has detailed attention, specially in its application on monitoring of activity in tissues. The main techniques used to obtain information from speckle patterns are presented, with special prominence to autocorrelation function, co-occurrence matrices, Fujii's method, Briers' contrast and spatial and temporal contrast analisys (LASCA and LASTCA). An incipient method for analysis, based on the study of sucessive correlations contrast, is introduced. Numerical simulations, using diferent probability density functions for velocities of scatterers, were made with two objectives: to test the analysis methods and to give subsidies for interpretation of in vivo results. Vegetable and animal tissues are investigated, achieving the monitoring of senescence process and vascularization maps on leaves, the accompaniment of fungi contamined fruits, the mapping of activity in flowers and the analisys of healing in rats subjected to abdominal surgery. Experiments using the biospeckle phenomenon in microscopy are carried out. At last, it is evaluated the potentiality of biospeckle as diagnosis tool in chronic vein ulcer cared with low intensity laser therapy and the better analysis methods for each kind of tissue are pointed.

  9. Comparative analysis of evaluation techniques for transport policies

    SciTech Connect

    Browne, David; Ryan, Lisa

    2011-04-15

    The objective of this paper is to examine and compare the use of a number of policy evaluation tools, which can be used to measure the impact of transport policies and programmes as part of a strategic environmental assessment (SEA) or sustainability appraisal. The evaluation tools that were examined include cost-benefit analysis (CBA), cost-effectiveness analysis (CEA) and multi-criteria decision analysis (MCDA). It was concluded that both CEA and CBA are useful for estimating the costs and/or benefits associated with transport policies but are constrained by the difficulty in quantifying non-market impacts and monetising total costs and benefits. Furthermore, CEA is limited to identifying the most 'cost-effective policy' for achieving a single, narrowly defined objective, usually greenhouse gas (GHG) reduction and is, therefore, not suitable for evaluating policy options with ancillary costs or a variety of potential benefits. Thus, CBA or CEA evaluation should be complemented by a complete environmental and socio-economic impact assessment approach such as MCDA. This method allows for participatory analysis and qualitative assessment but is subject to caveats such as subjectivity and value-laden judgments.

  10. Genome-wide Comparative Analysis of Annexin Superfamily in Plants

    PubMed Central

    Jami, Sravan Kumar; Clark, Greg B.; Ayele, Belay T.; Ashe, Paula; Kirti, Pulugurtha Bharadwaja

    2012-01-01

    Most annexins are calcium-dependent, phospholipid-binding proteins with suggested functions in response to environmental stresses and signaling during plant growth and development. They have previously been identified and characterized in Arabidopsis and rice, and constitute a multigene family in plants. In this study, we performed a comparative analysis of annexin gene families in the sequenced genomes of Viridiplantae ranging from unicellular green algae to multicellular plants, and identified 149 genes. Phylogenetic studies of these deduced annexins classified them into nine different arbitrary groups. The occurrence and distribution of bona fide type II calcium binding sites within the four annexin domains were found to be different in each of these groups. Analysis of chromosomal distribution of annexin genes in rice, Arabidopsis and poplar revealed their localization on various chromosomes with some members also found on duplicated chromosomal segments leading to gene family expansion. Analysis of gene structure suggests sequential or differential loss of introns during the evolution of land plant annexin genes. Intron positions and phases are well conserved in annexin genes from representative genomes ranging from Physcomitrella to higher plants. The occurrence of alternative motifs such as K/R/HGD was found to be overlapping or at the mutated regions of the type II calcium binding sites indicating potential functional divergence in certain plant annexins. This study provides a basis for further functional analysis and characterization of annexin multigene families in the plant lineage. PMID:23133603

  11. Comparative study of two approaches to model the offshore fish cages

    NASA Astrophysics Data System (ADS)

    Zhao, Yun-peng; Wang, Xin-xin; Decew, Jud; Tsukrov, Igor; Bai, Xiao-dong; Bi, Chun-wei

    2015-06-01

    The goal of this paper is to provide a comparative analysis of two commonly used approaches to discretize offshore fish cages: the lumped-mass approach and the finite element technique. Two case studies are chosen to compare predictions of the LMA (lumped-mass approach) and FEA (finite element analysis) based numerical modeling techniques. In both case studies, we consider several loading conditions consisting of different uniform currents and monochromatic waves. We investigate motion of the cage, its deformation, and the resultant tension in the mooring lines. Both model predictions are sufficient close to the experimental data, but for the first experiment, the DUT-FlexSim predictions are slightly more accurate than the ones provided by Aqua-FE™. According to the comparisons, both models can be successfully utilized to the design and analysis of the offshore fish cages provided that an appropriate safety factor is chosen.

  12. Burnout syndrome in psychotherapists: a comparative analysis of five nations.

    PubMed

    Puig, Ana; Yoon, Eunhui; Callueng, Carmelo; An, Sunghee; Lee, Sang Min

    2014-02-01

    Burnout is a common phenomenon among psychotherapists. The purpose of this study was to test the Counselor Burnout Inventory (CBI; Lee et al., 2007) measurement invariance, as well as compare means of five latent variables (i.e., CBI subscales of Exhaustion, Incompetence, Negative Work Environment, Devaluing Client, and Deterioration in Personal Life) across five nations (United States, Korea, Japan, Philippines, and Hong Kong) using structural equation modeling. The results indicated that the assumptions of configural, factor loading, and intercept invariance were satisfied across the five nations. When comparing means of five latent variables, the results indicated differential burnout tendencies across the five nations. Implications for psychotherapists' burnout prevention and future research are discussed.

  13. Analysis of T-RFLP data using analysis of variance and ordination methods: a comparative study.

    PubMed

    Culman, S W; Gauch, H G; Blackwood, C B; Thies, J E

    2008-09-01

    The analysis of T-RFLP data has developed considerably over the last decade, but there remains a lack of consensus about which statistical analyses offer the best means for finding trends in these data. In this study, we empirically tested and theoretically compared ten diverse T-RFLP datasets derived from soil microbial communities using the more common ordination methods in the literature: principal component analysis (PCA), nonmetric multidimensional scaling (NMS) with Sørensen, Jaccard and Euclidean distance measures, correspondence analysis (CA), detrended correspondence analysis (DCA) and a technique new to T-RFLP data analysis, the Additive Main Effects and Multiplicative Interaction (AMMI) model. Our objectives were i) to determine the distribution of variation in T-RFLP datasets using analysis of variance (ANOVA), ii) to determine the more robust and informative multivariate ordination methods for analyzing T-RFLP data, and iii) to compare the methods based on theoretical considerations. For the 10 datasets examined in this study, ANOVA revealed that the variation from Environment main effects was always small, variation from T-RFs main effects was large, and variation from T-RFxEnvironment (TxE) interactions was intermediate. Larger variation due to TxE indicated larger differences in microbial communities between environments/treatments and thus demonstrated the utility of ANOVA to provide an objective assessment of community dissimilarity. The comparison of statistical methods typically yielded similar empirical results. AMMI, T-RF-centered PCA, and DCA were the most robust methods in terms of producing ordinations that consistently reached a consensus with other methods. In datasets with high sample heterogeneity, NMS analyses with Sørensen and Jaccard distance were the most sensitive for recovery of complex gradients. The theoretical comparison showed that some methods hold distinct advantages for T-RFLP analysis, such as estimations of variation

  14. Investigation of pulmonary acoustic simulation: comparing airway model generation techniques

    NASA Astrophysics Data System (ADS)

    Henry, Brian; Dai, Zoujun; Peng, Ying; Mansy, Hansen A.; Sandler, Richard H.; Royston, Thomas

    2014-03-01

    Alterations in the structure and function of the pulmonary system that occur in disease or injury often give rise to measurable spectral, spatial and/or temporal changes in lung sound production and transmission. These changes, if properly quantified, might provide additional information about the etiology, severity and location of trauma, injury, or pathology. With this in mind, the authors are developing a comprehensive computer simulation model of pulmonary acoustics, known as The Audible Human Project™. Its purpose is to improve our understanding of pulmonary acoustics and to aid in interpreting measurements of sound and vibration in the lungs generated by airway insonification, natural breath sounds, and external stimuli on the chest surface, such as that used in elastography. As a part of this development process, finite element (FE) models were constructed of an excised pig lung that also underwent experimental studies. Within these models, the complex airway structure was created via two methods: x-ray CT image segmentation and through an algorithmic means called Constrained Constructive Optimization (CCO). CCO was implemented to expedite the segmentation process, as airway segments can be grown digitally. These two approaches were used in FE simulations of the surface motion on the lung as a result of sound input into the trachea. Simulation results were compared to experimental measurements. By testing how close these models are to experimental measurements, we are evaluating whether CCO can be used as a means to efficiently construct physiologically relevant airway trees.

  15. Comparative proteomic analysis of ductal and lobular invasive breast carcinoma.

    PubMed

    Oliveira, N C S; Gomig, T H B; Milioli, H H; Cordeiro, F; Costa, G G; Urban, C A; Lima, R S; Cavalli, I J; Ribeiro, E M S F

    2016-04-04

    Breast cancer is the second most common cancer worldwide and the first among women. Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) are the two major histological subtypes, and the clinical and molecular differences between them justify the search for new markers to distinguish them. As proteomic analysis allows for a powerful and analytical approach to identify potential biomarkers, we performed a comparative analysis of IDC and ILC samples by using two-dimensional electrophoresis and mass spectrometry. Twenty-three spots were identified corresponding to 10 proteins differentially expressed between the two subtypes. ACTB, ACTG, TPM3, TBA1A, TBA1B, VIME, TPIS, PDIA3, PDIA6, and VTDB were upregulated in ductal carcinoma compared to in lobular carcinoma samples. Overall, these 10 proteins have a key role in oncogenesis. Their specific functions and relevance in cancer initiation and progression are further discussed in this study. The identified peptides represent promising biomarkers for the differentiation of ductal and lobular breast cancer subtypes, and for future interventions based on tailored therapy.

  16. Comparative proteomic analysis of ductal and lobular invasive breast carcinoma.

    PubMed

    Oliveira, N C S; Gomig, T H B; Milioli, H H; Cordeiro, F; Costa, G G; Urban, C A; Lima, R S; Cavalli, I J; Ribeiro, E M S F

    2016-01-01

    Breast cancer is the second most common cancer worldwide and the first among women. Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) are the two major histological subtypes, and the clinical and molecular differences between them justify the search for new markers to distinguish them. As proteomic analysis allows for a powerful and analytical approach to identify potential biomarkers, we performed a comparative analysis of IDC and ILC samples by using two-dimensional electrophoresis and mass spectrometry. Twenty-three spots were identified corresponding to 10 proteins differentially expressed between the two subtypes. ACTB, ACTG, TPM3, TBA1A, TBA1B, VIME, TPIS, PDIA3, PDIA6, and VTDB were upregulated in ductal carcinoma compared to in lobular carcinoma samples. Overall, these 10 proteins have a key role in oncogenesis. Their specific functions and relevance in cancer initiation and progression are further discussed in this study. The identified peptides represent promising biomarkers for the differentiation of ductal and lobular breast cancer subtypes, and for future interventions based on tailored therapy. PMID:27173185

  17. Comparative analysis of health risk assessments for municipal waste combustors

    SciTech Connect

    Levin, A.; Fratt, D.B.; Leonard, A.; Bruins, R.J.F.; Fradkin, L.

    1991-01-01

    Quantitative health risk assessments have been performed for a number of proposed municipal waste combustor (MWC) facilities over the past several years. The article presents the results of a comparative analysis of a total of 21 risk assessments, focusing on seven of the most comprehensive methodologies. The analysis concentrates on stack emissions of noncriteria pollutants and is comparative rather than critical in nature. Overall, the risk assessment methodologies used were similar whereas the assumptions and input values used varied from study to study. Some of the variability results directly from differences in site-specific characteristics, but much of it is due to absence of data, lack of field validation, lack of specific guidelines from regulatory agencies, and reliance on professional judgment. The results indicate that carcinogenic risks are more significant than chronic non-carcinogenic risks. In most instances polychlorodibenzodioxins, polychlorodibenzofurans, and cadmium contribute more significantly to the total carcinogenic risk from MWC stack emissions than other contaminants. In addition, the contribution to total risk of all indirect routes of exposure (ingestion and dermal contact) exceeds that of the direct inhalation route for most studies reviewed.

  18. Comparative analysis of health risk assessments for municipal waste combustors.

    PubMed

    Levin, A; Fratt, D B; Leonard, A; Bruins, R J; Fradkin, L

    1991-01-01

    Quantitative health risk assessments have been performed for a number of proposed municipal waste combustor (MWC) facilities over the past several years. This article presents the results of a comparative analysis of a total of 21 risk assessments, focusing on seven of the most comprehensive methodologies. The analysis concentrates on stack emissions of noncriteria pollutants and is comparative rather than critical in nature. Overall, the risk assessment methodologies used were similar whereas the assumptions and input values used varied from study to study. Some of this variability results directly from differences in site-specific characteristics, but much of it is due to absence of data, lack of field validation, lack of specific guidelines from regulatory agencies, and reliance on professional judgment. The results indicate that carcinogenic risks are more significant than chronic non-carcinogenic risks. In most instances polychlorodibenzodioxins, polychlorodibenzofurans, and cadmium contribute more significantly to the total carcinogenic risk from MWC stack emissions than other contaminants. In addition, the contribution to total risk of all indirect routes of exposure (ingestion and dermal contact) exceeds that of the direct inhalation route for most studies reviewed.

  19. Comparative analysis of health risk assessments for municipal waste combustors

    SciTech Connect

    Levin, A.; Fratt, D.B.; Leonard, A.; Bruins, R.J.; Fradkin, L. )

    1991-01-01

    Quantitative health risk assessments have been performed for a number of proposed municipal waste combustor (MWC) facilities over the past several years. This article presents the results of a comparative analysis of a total of 21 risk assessments, focusing on seven of the most comprehensive methodologies. The analysis concentrates on stack emissions of noncriteria pollutants and is comparative rather than critical in nature. Overall, the risk assessment methodologies used were similar whereas the assumptions and input values used varied from study to study. Some of this variability results directly from differences in site-specific characteristics, but much of it is due to absence of data, lack of field validation, lack of specific guidelines from regulatory agencies, and reliance on professional judgment. The results indicate that carcinogenic risks are more significant than chronic non-carcinogenic risks. In most instances polychlorodibenzodioxins, polychlorodibenzofurans, and cadmium contribute more significantly to the total carcinogenic risk from MWC stack emissions than other contaminants. In addition, the contribution to total risk of all indirect routes of exposure (ingestion and dermal contact) exceeds that of the direct inhalation route for most studies reviewed. 42 refs.

  20. Developing the Curriculum for Pupils Experiencing Difficulties in Learning in Ordinary Schools: A Systematic, Comparative Analysis.

    ERIC Educational Resources Information Center

    Ireson, Judith; And Others

    1992-01-01

    Presents a comparative analysis of curriculum development methods in 10 elementary and 10 secondary schools in Great Britain. Reports that interviews and documentation were analyzed using grounded data categories and grouped into a model. Identifies differences in the manner of schools' provision for children with learning disabilities. Discusses…

  1. Factor Analysis with Ordinal Indicators: A Monte Carlo Study Comparing DWLS and ULS Estimation

    ERIC Educational Resources Information Center

    Forero, Carlos G.; Maydeu-Olivares, Alberto; Gallardo-Pujol, David

    2009-01-01

    Factor analysis models with ordinal indicators are often estimated using a 3-stage procedure where the last stage involves obtaining parameter estimates by least squares from the sample polychoric correlations. A simulation study involving 324 conditions (1,000 replications per condition) was performed to compare the performance of diagonally…

  2. A Comparative Meta-Analysis of 5E and Traditional Approaches in Turkey

    ERIC Educational Resources Information Center

    Anil, Özgür; Batdi, Veli

    2015-01-01

    The aim of this study is to compare the 5E learning model with traditional learning methods in terms of their effect on students' academic achievement, retention and attitude scores. In this context, the meta-analytic method known as the "analysis of analyses" was used and a review undertaken of the studies and theses (N = 14) executed…

  3. Suitability of molecular descriptors for database mining. A comparative analysis.

    PubMed

    Cruciani, Gabriele; Pastor, Manuel; Mannhold, Raimund

    2002-06-20

    Database mining methods rely on the molecular descriptors used to characterize a structural database. In the present investigation, five different types of descriptors (log P, UNITY fingerprints, ISIS keys, VolSurf, and GRIND) are applied to characterize various databases (n = 1007, 100, and 229) comprising drugs almost exclusively. The validity of the descriptors is comparatively analyzed via principal component analysis and its hierarchical variant, consensus principal component analysis. Both pharmacodynamic and pharmacokinetic aspects of database mining are treated. For pharmacodynamic aspects, clustering behavior achieved with the different descriptors is tested on the chemically homogeneous beta-blockers, benzodiazepines, and penicillins and on the chemically more diverse class I antiarrhythmics. The following ranking is observed: UNITY fingerprints > ISIS keys and GRIND > VolSurf > log P. Regarding information content, the CPCA superweight plot indicates similarity between fingerprints and ISIS keys as well as between VolSurf and log P, while GRIND differs from all the remaining descriptors. Solubility data and blood/brain barrier penetrating behavior serve as test cases for pharmacokinetic aspects. Comparison of the descriptors applied to these data reveals that VolSurf has the most realistic and consistent behavior, GRIND shows intermediate behavior, while UNITY fingerprints and ISIS keys are not well suited for pharmacokinetic profiling. From this comparative analysis, we conclude that VolSurf descriptors exhibit particular advantages in treating pharmacokinetic aspects; UNITY fingerprints, ISIS keys, and GRIND descriptors are of special value for tackling pharmacodynamic aspects of database mining. The parameter log P is of limited applicability in database mining because of rather poor reliability and lack of completeness of data.

  4. Comparative analysis of EPA cost-benefit methodologies

    SciTech Connect

    Poch, L.; Gillette, J.; Veil, J.

    1998-05-01

    In recent years, reforming the regulatory process has received much attention from diverse groups such as environmentalists, the government, and industry. A cost-benefit analysis can be a useful way to organize and compare the favorable and unfavorable impacts a proposed action night have on society. Since 1981, two Executive Orders have required the U.S. Environmental Protection Agency (EPA) and other regulatory agencies to perform cost-benefit analyses in support of regulatory decision making. At the EPA, a cost-benefit analysis is published as a document called a regulatory impact analysis (RIA). This report reviews cost-benefit methodologies used by three EPA program offices: Office of Air and Radiation, Office of Solid Waste, and Office of Water. These offices were chosen because they promulgate regulations that affect the policies of this study`s sponsor (U.S. Department of Energy, Office of Fossil Energy) and the technologies it uses. The study was conducted by reviewing 11 RIAs recently published by the three offices and by interviewing staff members in the offices. To draw conclusions about the EPA cost-benefit methodologies, their components were compared with those of a standard methodology (i.e., those that should be included in a comprehensive cost-benefit methodology). This study focused on the consistency of the approaches as well as their strengths and weaknesses, since differences in the cost-benefit methodologies themselves or in their application can cause confusion and preclude consistent comparison of regulations both within and among program offices.

  5. Mycobacterial species as case-study of comparative genome analysis.

    PubMed

    Zakham, F; Belayachi, L; Ussery, D; Akrim, M; Benjouad, A; El Aouad, R; Ennaji, M M

    2011-02-08

    The genus Mycobacterium represents more than 120 species including important pathogens of human and cause major public health problems and illnesses. Further, with more than 100 genome sequences from this genus, comparative genome analysis can provide new insights for better understanding the evolutionary events of these species and improving drugs, vaccines, and diagnostics tools for controlling Mycobacterial diseases. In this present study we aim to outline a comparative genome analysis of fourteen Mycobacterial genomes: M. avium subsp. paratuberculosis K—10, M. bovis AF2122/97, M. bovis BCG str. Pasteur 1173P2, M. leprae Br4923, M. marinum M, M. sp. KMS, M. sp. MCS, M. tuberculosis CDC1551, M. tuberculosis F11, M. tuberculosis H37Ra, M. tuberculosis H37Rv, M. tuberculosis KZN 1435 , M. ulcerans Agy99,and M. vanbaalenii PYR—1, For this purpose a comparison has been done based on their length of genomes, GC content, number of genes in different data bases (Genbank, Refseq, and Prodigal). The BLAST matrix of these genomes has been figured to give a lot of information about the similarity between species in a simple scheme. As a result of multiple genome analysis, the pan and core genome have been defined for twelve Mycobacterial species. We have also introduced the genome atlas of the reference strain M. tuberculosis H37Rv which can give a good overview of this genome. And for examining the phylogenetic relationships among these bacteria, a phylogenic tree has been constructed from 16S rRNA gene for tuberculosis and non tuberculosis Mycobacteria to understand the evolutionary events of these species.

  6. Rice fortification: a comparative analysis in mandated settings.

    PubMed

    Forsman, Carmen; Milani, Peiman; Schondebare, Jill A; Matthias, Dipika; Guyondet, Christophe

    2014-09-01

    Legal mandates can play an important role in the success of rice fortification programs that involve the private sector. However, merely enacting mandatory legislation does not guarantee success; it requires a coordinated, multidimensional cross-sector effort that addresses stewardship, develops an appropriate rice fortification technology, enables sustainable production and distribution channels through a range of private-sector players, ensures quality, generates consumer demand, and monitors progress. Furthermore, economic sustainability must be built into the supply chain and distribution network to enable the program to outlast government administrations and/or time-limited funding. Hence, mandates can serve as valuable long-term enablers of cross-sector mobilization and collaboration and as catalysts of civil society engagement in and ownership of fortification programs. This paper compares the rice fortification experiences of Costa Rica and the Philippines--two countries with mandates, yet distinctly different industry landscapes. Costa Rica has achieved national success through strong government stewardship and active market development--key elements of success regardless of industry structure. With a comparatively more diffuse rice industry structure, the Philippines has also had success in limited geographies where key stakeholders have played an active role in market development. A comparative analysis provides lessons that may be relevant to other rice fortification programs. PMID:24913356

  7. Rice fortification: a comparative analysis in mandated settings.

    PubMed

    Forsman, Carmen; Milani, Peiman; Schondebare, Jill A; Matthias, Dipika; Guyondet, Christophe

    2014-09-01

    Legal mandates can play an important role in the success of rice fortification programs that involve the private sector. However, merely enacting mandatory legislation does not guarantee success; it requires a coordinated, multidimensional cross-sector effort that addresses stewardship, develops an appropriate rice fortification technology, enables sustainable production and distribution channels through a range of private-sector players, ensures quality, generates consumer demand, and monitors progress. Furthermore, economic sustainability must be built into the supply chain and distribution network to enable the program to outlast government administrations and/or time-limited funding. Hence, mandates can serve as valuable long-term enablers of cross-sector mobilization and collaboration and as catalysts of civil society engagement in and ownership of fortification programs. This paper compares the rice fortification experiences of Costa Rica and the Philippines--two countries with mandates, yet distinctly different industry landscapes. Costa Rica has achieved national success through strong government stewardship and active market development--key elements of success regardless of industry structure. With a comparatively more diffuse rice industry structure, the Philippines has also had success in limited geographies where key stakeholders have played an active role in market development. A comparative analysis provides lessons that may be relevant to other rice fortification programs.

  8. A comparative study of Gaussian geostatistical models and Gaussian Markov random field models1

    PubMed Central

    Song, Hae-Ryoung; Fuentes, Montserrat; Ghosh, Sujit

    2008-01-01

    Gaussian geostatistical models (GGMs) and Gaussian Markov random fields (GM-RFs) are two distinct approaches commonly used in spatial models for modeling point referenced and areal data, respectively. In this paper, the relations between GGMs and GMRFs are explored based on approximations of GMRFs by GGMs, and approximations of GGMs by GMRFs. Two new metrics of approximation are proposed: (i) the Kullback-Leibler discrepancy of spectral densities and (ii) the chi-squared distance between spectral densities. The distances between the spectral density functions of GGMs and GMRFs measured by these metrics are minimized to obtain the approximations of GGMs and GMRFs. The proposed methodologies are validated through several empirical studies. We compare the performance of our approach to other methods based on covariance functions, in terms of the average mean squared prediction error and also the computational time. A spatial analysis of a dataset on PM2.5 collected in California is presented to illustrate the proposed method. PMID:19337581

  9. Multivariate Comparative Analysis of Stock Exchanges: The European Perspective

    NASA Astrophysics Data System (ADS)

    Koralun-Bereźnicka, Julia

    The aim of the research is to perform a multivariate comparative analysis of 20 European stock exchanges in order to identify the main similarities between the objects. Due to the convergence process of capital markets in Europe the similarities between stock exchanges could be expected to increase over time. The research is meant to show whether and how these similarities change. Consequently, the distances between clusters of similar stock exchanges should become less significant, which the analysis also aims at verifying. The basis of comparison is a set of 48 monthly variables from the period January, 2003 to December, 2006. The variables are classified into three categories: size of the market, equity trading and bonds. The paper aims at identifying the clusters of alike stock exchanges and at finding the characteristic features of each of the distinguished groups. The obtained categorization to some extent corresponds with the division of the European Union into “new” and “old” member countries. Clustering method, performed for each quarter separately, also reveals that the classification is fairly stable in time. The factor analysis, which was carried out to reduce the number of variables, reveals three major factors behind the data, which are related with the earlier mentioned categories of variables.

  10. Comparative genomic analysis reveals bilateral breast cancers are genetically independent.

    PubMed

    Song, Fangfang; Li, Xiangchun; Song, Fengju; Zhao, Yanrui; Li, Haixin; Zheng, Hong; Gao, Zhibo; Wang, Jun; Zhang, Wei; Chen, Kexin

    2015-10-13

    Bilateral breast cancer (BBC) poses a major challenge for oncologists because of the cryptic relationship between the two lesions. The purpose of this study was to determine the origin of the contralateral breast cancer (either dependent or independent of the index tumor). Here, we used ultra-deep whole-exome sequencing and array comparative genomic hybridization (aCGH) to study four paired samples of BBCs with different tumor subtypes and time intervals between the developments of each tumor. We used two paired primary breast tumors and corresponding metastatic liver lesions as the control. We tested the origin independent nature of BBC in three ways: mutational concordance, mutational signature clustering, and clonality analysis using copy number profiles. We found that the paired BBC samples had near-zero concordant mutation rates, which were much lower than those of the paired primary/metastasis samples. The results of a mutational signature analysis also suggested that BBCs are independent of one another. A clonality analysis using aCGH data further revealed that paired BBC samples was clonally independent, in contrast to clonal related origin found for paired primary/metastasis samples. Our preliminary findings show that BBCs in Han Chinese women are origin independent and thus should be treated separately. PMID:26378809

  11. Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study

    PubMed Central

    Jhwueng, Dwueng-Chwuan

    2013-01-01

    Background Phylogenetic comparative methods (PCMs) have been applied widely in analyzing data from related species but their fit to data is rarely assessed. Question Can one determine whether any particular comparative method is typically more appropriate than others by examining comparative data sets? Data I conducted a meta-analysis of 122 phylogenetic data sets found by searching all papers in JEB, Blackwell Synergy and JSTOR published in 2002–2005 for the purpose of assessing the fit of PCMs. The number of species in these data sets ranged from 9 to 117. Analysis Method I used the Akaike information criterion to compare PCMs, and then fit PCMs to bivariate data sets through REML analysis. Correlation estimates between two traits and bootstrapped confidence intervals of correlations from each model were also compared. Conclusions For phylogenies of less than one hundred taxa, the Independent Contrast method and the independent, non-phylogenetic models provide the best fit.For bivariate analysis, correlations from different PCMs are qualitatively similar so that actual correlations from real data seem to be robust to the PCM chosen for the analysis. Therefore, researchers might apply the PCM they believe best describes the evolutionary mechanisms underlying their data. PMID:23826183

  12. ROCK PROPERTIES MODEL ANALYSIS MODEL REPORT

    SciTech Connect

    Clinton Lum

    2002-02-04

    The purpose of this Analysis and Model Report (AMR) is to document Rock Properties Model (RPM) 3.1 with regard to input data, model methods, assumptions, uncertainties and limitations of model results, and qualification status of the model. The report also documents the differences between the current and previous versions and validation of the model. The rock properties models are intended principally for use as input to numerical physical-process modeling, such as of ground-water flow and/or radionuclide transport. The constraints, caveats, and limitations associated with this model are discussed in the appropriate text sections that follow. This work was conducted in accordance with the following planning documents: WA-0344, ''3-D Rock Properties Modeling for FY 1998'' (SNL 1997, WA-0358), ''3-D Rock Properties Modeling for FY 1999'' (SNL 1999), and the technical development plan, Rock Properties Model Version 3.1, (CRWMS M&O 1999c). The Interim Change Notice (ICNs), ICN 02 and ICN 03, of this AMR were prepared as part of activities being conducted under the Technical Work Plan, TWP-NBS-GS-000003, ''Technical Work Plan for the Integrated Site Model, Process Model Report, Revision 01'' (CRWMS M&O 2000b). The purpose of ICN 03 is to record changes in data input status due to data qualification and verification activities. These work plans describe the scope, objectives, tasks, methodology, and implementing procedures for model construction. The constraints, caveats, and limitations associated with this model are discussed in the appropriate text sections that follow. The work scope for this activity consists of the following: (1) Conversion of the input data (laboratory measured porosity data, x-ray diffraction mineralogy, petrophysical calculations of bound water, and petrophysical calculations of porosity) for each borehole into stratigraphic coordinates; (2) Re-sampling and merging of data sets; (3) Development of geostatistical simulations of porosity; (4

  13. Pharmacodynamic population analysis in chronic renal failure using artificial neural networks--a comparative study.

    PubMed

    Gaweda, Adam E; Jacobs, Alfred A; Brier, Michael E; Zurada, Jacek M

    2003-01-01

    This work presents a pharmacodynamic population analysis in chronic renal failure patients using Artificial Neural Networks (ANNs). In pursuit of an effective and cost-efficient strategy for drug delivery in patients with renal failure, two different types of ANN are applied to perform drug dose-effect modeling and their performance compared. Applied in a clinical environment, such models will allow for prediction of patient response to the drug at the effect site and, subsequently, for adjusting the dosing regimen.

  14. Comparative analysis of cryopreservation methods in Chlamydomonas reinhardtii.

    PubMed

    Scarbrough, Chasity; Wirschell, Maureen

    2016-10-01

    Chlamydomonas is a model organism used for studies of many important biological processes. Traditionally, strains have been propagated on solid agar, which requires routine passaging for long-term maintenance. Cryopreservation of Chlamydomonas is possible, yet long-term viability is highly variable. Thus, improved cryopreservation methods for Chlamydomonas are an important requirement for sustained study of genetically defined strains. Here, we tested a commercial cryopreservation kit and directly compared it's effectiveness to a methanol-based method. We also tested thaw-back procedures comparing the growth of cells in liquid culture or on solid agar media. We demonstrated that methanol was the superior cryopreservation method for Chlamydomonas compared to the commercial kit and that post-thaw culture conditions dramatically affect viability. We also demonstrated that cryopreserved cells could be successfully thawed and plated directly onto solid agar plates. Our findings have important implications for the long-term storage of Chlamydomonas that can likely be extended to other algal species. PMID:27452475

  15. Modeling and Analysis of Space Based Transceivers

    NASA Technical Reports Server (NTRS)

    Moore, Michael S.; Price, Jeremy C.; Abbott, Ben; Liebetreu, John; Reinhart, Richard C.; Kacpura, Thomas J.

    2007-01-01

    This paper presents the tool chain, methodology, and initial results of a study to provide a thorough, objective, and quantitative analysis of the design alternatives for space Software Defined Radio (SDR) transceivers. The approach taken was to develop a set of models and tools for describing communications requirements, the algorithm resource requirements, the available hardware, and the alternative software architectures, and generate analysis data necessary to compare alternative designs. The Space Transceiver Analysis Tool (STAT) was developed to help users identify and select representative designs, calculate the analysis data, and perform a comparative analysis of the representative designs. The tool allows the design space to be searched quickly while permitting incremental refinement in regions of higher payoff.

  16. Modeling and Analysis of Space Based Transceivers

    NASA Technical Reports Server (NTRS)

    Reinhart, Richard C.; Liebetreu, John; Moore, Michael S.; Price, Jeremy C.; Abbott, Ben

    2005-01-01

    This paper presents the tool chain, methodology, and initial results of a study to provide a thorough, objective, and quantitative analysis of the design alternatives for space Software Defined Radio (SDR) transceivers. The approach taken was to develop a set of models and tools for describing communications requirements, the algorithm resource requirements, the available hardware, and the alternative software architectures, and generate analysis data necessary to compare alternative designs. The Space Transceiver Analysis Tool (STAT) was developed to help users identify and select representative designs, calculate the analysis data, and perform a comparative analysis of the representative designs. The tool allows the design space to be searched quickly while permitting incremental refinement in regions of higher payoff.

  17. Industrial Acetogenic Biocatalysts: A Comparative Metabolic and Genomic Analysis.

    PubMed

    Bengelsdorf, Frank R; Poehlein, Anja; Linder, Sonja; Erz, Catarina; Hummel, Tim; Hoffmeister, Sabrina; Daniel, Rolf; Dürre, Peter

    2016-01-01

    Synthesis gas (syngas) fermentation by anaerobic acetogenic bacteria employing the Wood-Ljungdahl pathway is a bioprocess for production of biofuels and biocommodities. The major fermentation products of the most relevant biocatalytic strains (Clostridium ljungdahlii, C. autoethanogenum, C. ragsdalei, and C. coskatii) are acetic acid and ethanol. A comparative metabolic and genomic analysis using the mentioned biocatalysts might offer targets for metabolic engineering and thus improve the production of compounds apart from ethanol. Autotrophic growth and product formation of the four wild type (WT) strains were compared in uncontrolled batch experiments. The genomes of C. ragsdalei and C. coskatii were sequenced and the genome sequences of all four biocatalytic strains analyzed in comparative manner. Growth and product spectra (acetate, ethanol, 2,3-butanediol) of C. autoethanogenum, C. ljungdahlii, and C. ragsdalei were rather similar. In contrast, C. coskatii produced significantly less ethanol and its genome sequence lacks two genes encoding aldehyde:ferredoxin oxidoreductases (AOR). Comparative genome sequence analysis of the four WT strains revealed high average nucleotide identity (ANI) of C. ljungdahlii and C. autoethanogenum (99.3%) and C. coskatii (98.3%). In contrast, C. ljungdahlii WT and C. ragsdalei WT showed an ANI-based similarity of only 95.8%. Additionally, recombinant C. ljungdahlii strains were constructed that harbor an artificial acetone synthesis operon (ASO) consisting of the following genes: adc, ctfA, ctfB, and thlA (encoding acetoacetate decarboxylase, acetoacetyl-CoA:acetate/butyrate:CoA-transferase subunits A and B, and thiolase) under the control of thlA promoter (P thlA ) from C. acetobutylicum or native pta-ack promoter (P pta-ack ) from C. ljungdahlii. Respective recombinant strains produced 2-propanol rather than acetone, due to the presence of a NADPH-dependent primary-secondary alcohol dehydrogenase that converts acetone to 2

  18. Industrial Acetogenic Biocatalysts: A Comparative Metabolic and Genomic Analysis

    PubMed Central

    Bengelsdorf, Frank R.; Poehlein, Anja; Linder, Sonja; Erz, Catarina; Hummel, Tim; Hoffmeister, Sabrina; Daniel, Rolf; Dürre, Peter

    2016-01-01

    Synthesis gas (syngas) fermentation by anaerobic acetogenic bacteria employing the Wood–Ljungdahl pathway is a bioprocess for production of biofuels and biocommodities. The major fermentation products of the most relevant biocatalytic strains (Clostridium ljungdahlii, C. autoethanogenum, C. ragsdalei, and C. coskatii) are acetic acid and ethanol. A comparative metabolic and genomic analysis using the mentioned biocatalysts might offer targets for metabolic engineering and thus improve the production of compounds apart from ethanol. Autotrophic growth and product formation of the four wild type (WT) strains were compared in uncontrolled batch experiments. The genomes of C. ragsdalei and C. coskatii were sequenced and the genome sequences of all four biocatalytic strains analyzed in comparative manner. Growth and product spectra (acetate, ethanol, 2,3-butanediol) of C. autoethanogenum, C. ljungdahlii, and C. ragsdalei were rather similar. In contrast, C. coskatii produced significantly less ethanol and its genome sequence lacks two genes encoding aldehyde:ferredoxin oxidoreductases (AOR). Comparative genome sequence analysis of the four WT strains revealed high average nucleotide identity (ANI) of C. ljungdahlii and C. autoethanogenum (99.3%) and C. coskatii (98.3%). In contrast, C. ljungdahlii WT and C. ragsdalei WT showed an ANI-based similarity of only 95.8%. Additionally, recombinant C. ljungdahlii strains were constructed that harbor an artificial acetone synthesis operon (ASO) consisting of the following genes: adc, ctfA, ctfB, and thlA (encoding acetoacetate decarboxylase, acetoacetyl-CoA:acetate/butyrate:CoA-transferase subunits A and B, and thiolase) under the control of thlA promoter (PthlA) from C. acetobutylicum or native pta-ack promoter (Ppta-ack) from C. ljungdahlii. Respective recombinant strains produced 2-propanol rather than acetone, due to the presence of a NADPH-dependent primary-secondary alcohol dehydrogenase that converts acetone to 2

  19. Industrial Acetogenic Biocatalysts: A Comparative Metabolic and Genomic Analysis.

    PubMed

    Bengelsdorf, Frank R; Poehlein, Anja; Linder, Sonja; Erz, Catarina; Hummel, Tim; Hoffmeister, Sabrina; Daniel, Rolf; Dürre, Peter

    2016-01-01

    Synthesis gas (syngas) fermentation by anaerobic acetogenic bacteria employing the Wood-Ljungdahl pathway is a bioprocess for production of biofuels and biocommodities. The major fermentation products of the most relevant biocatalytic strains (Clostridium ljungdahlii, C. autoethanogenum, C. ragsdalei, and C. coskatii) are acetic acid and ethanol. A comparative metabolic and genomic analysis using the mentioned biocatalysts might offer targets for metabolic engineering and thus improve the production of compounds apart from ethanol. Autotrophic growth and product formation of the four wild type (WT) strains were compared in uncontrolled batch experiments. The genomes of C. ragsdalei and C. coskatii were sequenced and the genome sequences of all four biocatalytic strains analyzed in comparative manner. Growth and product spectra (acetate, ethanol, 2,3-butanediol) of C. autoethanogenum, C. ljungdahlii, and C. ragsdalei were rather similar. In contrast, C. coskatii produced significantly less ethanol and its genome sequence lacks two genes encoding aldehyde:ferredoxin oxidoreductases (AOR). Comparative genome sequence analysis of the four WT strains revealed high average nucleotide identity (ANI) of C. ljungdahlii and C. autoethanogenum (99.3%) and C. coskatii (98.3%). In contrast, C. ljungdahlii WT and C. ragsdalei WT showed an ANI-based similarity of only 95.8%. Additionally, recombinant C. ljungdahlii strains were constructed that harbor an artificial acetone synthesis operon (ASO) consisting of the following genes: adc, ctfA, ctfB, and thlA (encoding acetoacetate decarboxylase, acetoacetyl-CoA:acetate/butyrate:CoA-transferase subunits A and B, and thiolase) under the control of thlA promoter (P thlA ) from C. acetobutylicum or native pta-ack promoter (P pta-ack ) from C. ljungdahlii. Respective recombinant strains produced 2-propanol rather than acetone, due to the presence of a NADPH-dependent primary-secondary alcohol dehydrogenase that converts acetone to 2

  20. Comparing methods for metabolic network analysis and an application to metabolic engineering.

    PubMed

    Tomar, Namrata; De, Rajat K

    2013-05-25

    Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of various organisms based on information encoded in their genomes. Characterization of cellular metabolism is useful to understand the phenotypic capabilities of these organisms. It has been done quantitatively through the analysis of pathway operations. There are several in silico approaches for analyzing metabolic networks, including structural and stoichiometric analysis, metabolic flux analysis, metabolic control analysis, and several kinetic modeling based analyses. They can serve as a virtual laboratory to give insights into basic principles of cellular functions. This article summarizes the progress and advances in software and algorithm development for metabolic network analysis, along with their applications relevant to cellular physiology, and metabolic engineering with an emphasis on microbial strain optimization. Moreover, it provides a detailed comparative analysis of existing approaches under different categories.

  1. Command Process Modeling & Risk Analysis

    NASA Technical Reports Server (NTRS)

    Meshkat, Leila

    2011-01-01

    Commanding Errors may be caused by a variety of root causes. It's important to understand the relative significance of each of these causes for making institutional investment decisions. One of these causes is the lack of standardized processes and procedures for command and control. We mitigate this problem by building periodic tables and models corresponding to key functions within it. These models include simulation analysis and probabilistic risk assessment models.

  2. Cytogenetic analysis from DNA by comparative genomic hybridization.

    PubMed

    Tachdjian, G; Aboura, A; Lapierre, J M; Viguié, F

    2000-01-01

    Comparative genomic hybridization (CGH) is a modified in situ hybridization technique which allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment. In CGH analysis, two differentially labelled genomic DNA (study and reference) are co-hybridized to normal metaphase spreads. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome. Since its development, CGH has been applied mostly as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. CGH may also have a role in clinical cytogenetics for detection and identification of unbalanced chromosomal abnormalities.

  3. Phylogeny and comparative genome analysis of a Basidiomycete fungi

    SciTech Connect

    Riley, Robert W.; Salamov, Asaf; Grigoriev, Igor; Hibbett, David

    2011-03-14

    Fungi of the phylum Basidiomycota, make up some 37percent of the described fungi, and are important from the perspectives of forestry, agriculture, medicine, and bioenergy. This diverse phylum includes the mushrooms, wood rots, plant pathogenic rusts and smuts, and some human pathogens. To better understand these important fungi, we have undertaken a comparative genomic analysis of the Basidiomycetes with available sequenced genomes. We report a phylogeny that sheds light on previously unclear evolutionary relationships among the Basidiomycetes. We also define a `core proteome? based on protein families conserved in all Basidiomycetes. We identify key expansions and contractions in protein families that may be responsible for the degradation of plant biomass such as cellulose, hemicellulose, and lignin. Finally, we speculate as to the genomic changes that drove such expansions and contractions.

  4. A comparative and comprehensive analysis of nonsexual assaults.

    PubMed

    Asirdizer, Mahmut; Yavuz, M Sunay

    2011-07-01

    The aim of this study was to make a comparative and comprehensive analysis of nonsexual assaults in 488 medico-legal cases presented to Forensic Medicine Outpatient Clinic of Celal Bayar University Hospital (Manisa, Turkey), between 2005 and 2009. There were blunt force injuries (BFI) in 262 cases (53.7%), sharp force injuries (SFI) in 163 cases (33.4%), and firearm-related wounds (FRW) in 63 cases (12.9%). The results showed significant differences in the monthly distribution of assaults, localization of injuries, and severity of injuries depending on the types of assaults. Most of the injuries were localized to the face, head, and neck in BFI and SFI and to the lower limbs in FRW. The results of this study will help researchers to investigate characteristics of victims, offenders, and injuries and types of assaults because of nonsexual violence.

  5. Imaging hydrated microbial extracellular polymers: Comparative analysis by electron microscopy

    SciTech Connect

    Dohnalkova, A.C.; Marshall, M. J.; Arey, B. W.; Williams, K. H.; Buck, E. C.; Fredrickson, J. K.

    2011-01-01

    Microbe-mineral and -metal interactions represent a major intersection between the biosphere and geosphere but require high-resolution imaging and analytical tools for investigating microscale associations. Electron microscopy has been used extensively for geomicrobial investigations and although used bona fide, the traditional methods of sample preparation do not preserve the native morphology of microbiological components, especially extracellular polymers. Herein, we present a direct comparative analysis of microbial interactions using conventional electron microscopy approaches of imaging at room temperature and a suite of cryogenic electron microscopy methods providing imaging in the close-to-natural hydrated state. In situ, we observed an irreversible transformation of the hydrated bacterial extracellular polymers during the traditional dehydration-based sample preparation that resulted in their collapse into filamentous structures. Dehydration-induced polymer collapse can lead to inaccurate spatial relationships and hence could subsequently affect conclusions regarding nature of interactions between microbial extracellular polymers and their environment.

  6. Imaging Hydrated Microbial Extracellular Polymers: Comparative Analysis by Electron Microscopy

    SciTech Connect

    Dohnalkova, Alice; Marshall, Matthew J.; Arey, Bruce W.; Williams, Kenneth H.; Buck, Edgar C.; Fredrickson, Jim K.

    2011-02-01

    Microbe-mineral and -metal interactions represent a major intersection between the biosphere and geosphere but require high-resolution imaging and analytical tools for investigating microscale associations. Electron microscopy has been used extensively for geomicrobial investigations and although used bona fide, the traditional methods of sample preparation do not preserve the native morphology of microbiological components, especially extracellular polymers. Herein, we present a direct comparative analysis of microbial interactions using conventional electron microscopy approaches of imaging at room temperature and a suite of cryo-electron microscopy methods providing imaging in the close-to-natural hydrated state. In situ, we observed an irreversible transformation of bacterial extracellular polymers during the traditional dehydration-based sample preparation that resulted in the collapse of hydrated gel-like EPS into filamentous structures. Dehydration-induced polymer collapse can lead to inaccurate spatial relationships and hence could subsequently affect conclusions regarding nature of interactions between microbial extracellular polymers and their environment.

  7. Comparative analysis of DG and solar PV water pumping system

    NASA Astrophysics Data System (ADS)

    Tharani, Kusum; Dahiya, Ratna

    2016-03-01

    Looking at present day electricity scenario, there is a major electricity crisis in rural areas. The farmers are still dependant on the monsoon rains for their irrigation needs and livestock maintenance. Some of the agrarian population has opted to use Diesel Generators for pumping water in their fields. But taking into consideration the economics and environmental conditions, the above choice is not suitable for longer run. An effort to shift from non-renewable sources such as diesel to renewable energy source such as solar has been highlighted. An approximate comparative analysis showing the life cycle costs of a PV pumping system with Diesel Generator powered water pumping is done using MATLAB/STMULTNK.

  8. Cardiovascular disease research in Latin America: A comparative bibliometric analysis

    PubMed Central

    Jahangir, Eiman; Comandé, Daniel; Rubinstein, Adolfo

    2011-01-01

    AIM: To investigate the number of publications in cardiovascular disease (CVD) in Latin America and the Caribbean over the last decade. METHODS: We performed a bibliometric analysis in PubMed from 2001 to 2010 for Latin America and the Caribbean, the United States, Canada, Europe, China, and India. RESULTS: Latin America published 4% of articles compared with 26% from the United States/Canada and 42% from Europe. In CVD, Latin America published 4% of articles vs 23% from the United States/Canada and 40% from Europe. The number of publications in CVD in Latin America increased from 41 in 2001 to 726 in 2010. CONCLUSION: Latin America, while publishing more articles than previously, lags behind developed countries. Further advances in research infrastructure are necessary to develop prevention strategies for this region. PMID:22216374

  9. A comparative analysis of metal transportomes from metabolically versatile Pseudomonas

    PubMed Central

    Haritha, Adhikarla; Rodrigue, Agnes; Mohan, Pamarthi Maruthi

    2008-01-01

    Background The availability of complete genome sequences of versatile Pseudomonas occupying remarkably diverse ecological niches enabled to gain insights into their adaptative assets. The objective of this study was to analyze the complete genetic repertoires of metal transporters (metal transportomes) from four representative Pseudomonas species and to identify metal transporters with "Genomic Island" associated features. Methods A comparative metal transporter inventory was built for the following four Pseudomonas species: P.putida (Ppu) KT2440, P.aeruginosa (Pae) PA01, P.fluorescens (Pfl) Pf-5 and P.syringae (Psy)pv.tomato DC3000 using TIGR-CMR and Transport DB. Genomic analysis of essential and toxic metal ion transporters was accomplished from the above inventory. Metal transporters with "Genomic Island" associated features were identified using Islandpath analysis. Results Dataset cataloguing has been executed for 262 metal transporters from the four spp. Additional metal ion transporters belonging to NiCoT, Ca P-type ATPase, Cu P-type ATPases, ZIP and MgtC families were identified. In Psy DC3000, 48% of metal transporters showed strong GI features while it was 45% in Ppu KT2440. In Pfl Pf-5 and Pae PA01 only 26% of their metal transporters exhibited GI features. Conclusion Our comparative inventory of 262 metal transporters from four versatile Pseudomonas spp is the complete suite of metal transportomes analysed till date in a prokaryotic genus. This study identified differences in the basic composition of metal transportomes from Pseudomonas occupying diverse ecological niches and also elucidated their novel features. Based on this inventory we analysed the role of horizontal gene transfer in expansion and variability of metal transporter families. PMID:18816395

  10. Comparative and Evolutionary Analysis of Major Peanut Allergen Gene Families

    PubMed Central

    Ratnaparkhe, Milind B.; Lee, Tae-Ho; Tan, Xu; Wang, Xiyin; Li, Jingping; Kim, Changsoo; Rainville, Lisa K.; Lemke, Cornelia; Compton, Rosana O.; Robertson, Jon; Gallo, Maria; Bertioli, David J.; Paterson, Andrew H.

    2014-01-01

    Peanut (Arachis hypogaea L.) causes one of the most serious food allergies. Peanut seed proteins, Arah1, Arah2, and Arah3, are considered to be among the most important peanut allergens. To gain insights into genome organization and evolution of allergen-encoding genes, approximately 617 kb from the genome of cultivated peanut and 215 kb from a wild relative were sequenced including three Arah1, one Arah2, eight Arah3, and two Arah6 gene family members. To assign polarity to differences between homoeologous regions in peanut, we used as outgroups the single orthologous regions in Medicago, Lotus, common bean, chickpea, and pigeonpea, which diverged from peanut about 50 Ma and have not undergone subsequent polyploidy. These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events. The lack of conservation of allergenic epitopes between species, and the fact that many different proteins can be allergenic, makes the identification of allergens across species by comparative studies difficult. The peanut allergen genes are interspersed with low-copy genes and transposable elements. Phylogenetic analyses revealed lineage-specific expansion and loss of low-copy genes between species and homoeologs. Arah1 syntenic regions are conserved in soybean, pigeonpea, tomato, grape, Lotus, and Arabidopsis, whereas Arah3 syntenic regions show genome rearrangements. We infer that tandem and segmental duplications led to the establishment of the Arah3 gene family. Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes. Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes. PMID:25193311

  11. Comparative and evolutionary analysis of major peanut allergen gene families.

    PubMed

    Ratnaparkhe, Milind B; Lee, Tae-Ho; Tan, Xu; Wang, Xiyin; Li, Jingping; Kim, Changsoo; Rainville, Lisa K; Lemke, Cornelia; Compton, Rosana O; Robertson, Jon; Gallo, Maria; Bertioli, David J; Paterson, Andrew H

    2014-09-01

    Peanut (Arachis hypogaea L.) causes one of the most serious food allergies. Peanut seed proteins, Arah1, Arah2, and Arah3, are considered to be among the most important peanut allergens. To gain insights into genome organization and evolution of allergen-encoding genes, approximately 617 kb from the genome of cultivated peanut and 215 kb from a wild relative were sequenced including three Arah1, one Arah2, eight Arah3, and two Arah6 gene family members. To assign polarity to differences between homoeologous regions in peanut, we used as outgroups the single orthologous regions in Medicago, Lotus, common bean, chickpea, and pigeonpea, which diverged from peanut about 50 Ma and have not undergone subsequent polyploidy. These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events. The lack of conservation of allergenic epitopes between species, and the fact that many different proteins can be allergenic, makes the identification of allergens across species by comparative studies difficult. The peanut allergen genes are interspersed with low-copy genes and transposable elements. Phylogenetic analyses revealed lineage-specific expansion and loss of low-copy genes between species and homoeologs. Arah1 syntenic regions are conserved in soybean, pigeonpea, tomato, grape, Lotus, and Arabidopsis, whereas Arah3 syntenic regions show genome rearrangements. We infer that tandem and segmental duplications led to the establishment of the Arah3 gene family. Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes. Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes. PMID:25193311

  12. Comparative and evolutionary analysis of major peanut allergen gene families.

    PubMed

    Ratnaparkhe, Milind B; Lee, Tae-Ho; Tan, Xu; Wang, Xiyin; Li, Jingping; Kim, Changsoo; Rainville, Lisa K; Lemke, Cornelia; Compton, Rosana O; Robertson, Jon; Gallo, Maria; Bertioli, David J; Paterson, Andrew H

    2014-09-04

    Peanut (Arachis hypogaea L.) causes one of the most serious food allergies. Peanut seed proteins, Arah1, Arah2, and Arah3, are considered to be among the most important peanut allergens. To gain insights into genome organization and evolution of allergen-encoding genes, approximately 617 kb from the genome of cultivated peanut and 215 kb from a wild relative were sequenced including three Arah1, one Arah2, eight Arah3, and two Arah6 gene family members. To assign polarity to differences between homoeologous regions in peanut, we used as outgroups the single orthologous regions in Medicago, Lotus, common bean, chickpea, and pigeonpea, which diverged from peanut about 50 Ma and have not undergone subsequent polyploidy. These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events. The lack of conservation of allergenic epitopes between species, and the fact that many different proteins can be allergenic, makes the identification of allergens across species by comparative studies difficult. The peanut allergen genes are interspersed with low-copy genes and transposable elements. Phylogenetic analyses revealed lineage-specific expansion and loss of low-copy genes between species and homoeologs. Arah1 syntenic regions are conserved in soybean, pigeonpea, tomato, grape, Lotus, and Arabidopsis, whereas Arah3 syntenic regions show genome rearrangements. We infer that tandem and segmental duplications led to the establishment of the Arah3 gene family. Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes. Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes.

  13. Model building techniques for analysis.

    SciTech Connect

    Walther, Howard P.; McDaniel, Karen Lynn; Keener, Donald; Cordova, Theresa Elena; Henry, Ronald C.; Brooks, Sean; Martin, Wilbur D.

    2009-09-01

    The practice of mechanical engineering for product development has evolved into a complex activity that requires a team of specialists for success. Sandia National Laboratories (SNL) has product engineers, mechanical designers, design engineers, manufacturing engineers, mechanical analysts and experimentalists, qualification engineers, and others that contribute through product realization teams to develop new mechanical hardware. The goal of SNL's Design Group is to change product development by enabling design teams to collaborate within a virtual model-based environment whereby analysis is used to guide design decisions. Computer-aided design (CAD) models using PTC's Pro/ENGINEER software tools are heavily relied upon in the product definition stage of parts and assemblies at SNL. The three-dimensional CAD solid model acts as the design solid model that is filled with all of the detailed design definition needed to manufacture the parts. Analysis is an important part of the product development process. The CAD design solid model (DSM) is the foundation for the creation of the analysis solid model (ASM). Creating an ASM from the DSM currently is a time-consuming effort; the turnaround time for results of a design needs to be decreased to have an impact on the overall product development. This effort can be decreased immensely through simple Pro/ENGINEER modeling techniques that summarize to the method features are created in a part model. This document contains recommended modeling techniques that increase the efficiency of the creation of the ASM from the DSM.

  14. A statistical model to compare road mortality in OECD countries.

    PubMed

    Page, Y

    2001-05-01

    The objective of this paper is to compare safety levels and trends in OECD countries from 1980 to 1994 with the help of a statistical model and to launch international discussion and further research about international comparisons. Between 1980 and 1994, the annual number of fatalities decreased drastically in all the selected countries except Japan (+ 12%), Greece (+ 56%) and ex-East Germany (+ 50%). The highest decreases were observed in ex-West Germany (- 48%), Switzerland (- 44%), Australia (- 40%), and UK (- 39%). In France, the decrease in fatalities over the same period reached 34%. The fatality rate, an indicator of risk, decreased in the selected countries from 1980 to 1994 except in the east-European countries during the motorization boom in the late 1980s. As fatality rates are not sufficient for international comparisons, a statistical multiple regression model is set up to compare road safety levels in 21 OECD countries over 15 years. Data were collected from IRTAD (International Road Traffic and Accident Database) and other OECD statistical sources. The number of fatalities is explained by seven exogenous (to road safety) variables. The model, pooling cross-sectional and time series data, supplies estimates of elasticity to the fatalities for each variable: 0.96 for the population; 0.28 for the vehicle fleet per capita; -0.16 for the percentage of buses and coaches in the motorised vehicle fleet; 0.83 for the percentage of youngsters in the population; - 0.41 for the percentage of urban population; 0.39 for alcohol consumption per capita; and 0.39 for the percentage of employed people. The model also supplies a rough estimate of the safety performance of a country: the regression residuals are supposed to contain the effects of essentially endogenous and unobserved variables, independent to the exogenous variables. These endogenous variables are safety performance variables (safety actions, traffic safety policy, network improvements and social

  15. AeroCom INSITU Project: Comparing modeled and measured aerosol optical properties

    NASA Astrophysics Data System (ADS)

    Andrews, Elisabeth; Schmeisser, Lauren; Schulz, Michael; Fiebig, Markus; Ogren, John; Bian, Huisheng; Chin, Mian; Easter, Richard; Ghan, Steve; Kokkola, Harri; Laakso, Anton; Myhre, Gunnar; Randles, Cynthia; da Silva, Arlindo; Stier, Phillip; Skeie, Ragnehild; Takemura, Toshihiko; van Noije, Twan; Zhang, Kai

    2016-04-01

    AeroCom, an open international collaboration of scientists seeking to improve global aerosol models, recently initiated a project comparing model output to in-situ, surface-based measurements of aerosol optical properties. The model/measurement comparison project, called INSITU, aims to evaluate the performance of a suite of AeroCom aerosol models with site-specific observational data in order to inform iterative improvements to model aerosol modules. Surface in-situ data has the unique property of being traceable to physical standards, which is an asset in accomplishing the overall goal of bettering the accuracy of aerosols processes and the predicative capability of global climate models. Here we compare dry, in-situ aerosol scattering and absorption data from ~75 surface, in-situ sites from various global aerosol networks (including NOAA, EUSAAR/ACTRIS and GAW) with a simulated optical properties from a suite of models participating in the AeroCom project. We report how well models reproduce aerosol climatologies for a variety of time scales, aerosol characteristics and behaviors (e.g., aerosol persistence and the systematic relationships between aerosol optical properties), and aerosol trends. Though INSITU is a multi-year endeavor, preliminary phases of the analysis suggest substantial model biases in absorption and scattering coefficients compared to surface measurements, though the sign and magnitude of the bias varies with location. Spatial patterns in the biases highlight model weaknesses, e.g., the inability of models to properly simulate aerosol characteristics at sites with complex topography. Additionally, differences in modeled and measured systematic variability of aerosol optical properties suggest that some models are not accurately capturing specific aerosol behaviors, for example, the tendency of in-situ single scattering albedo to decrease with decreasing aerosol extinction coefficient. The endgoal of the INSITU project is to identify specific

  16. N-terminal protein processing: A comparative proteogenomic analysis

    SciTech Connect

    Bonissone, Stefano; Gupta, Nitin; Romine, Margaret F.; Bradshaw, Ralph A.; Pevzner, Pavel A.

    2013-01-01

    N-Terminal Methionine Excision (NME) is a universally conserved mechanism with the same specificity across all life forms that removes the first Methionine in proteins when the second residue is Gly, Ala, Ser, Cys, Thr, Pro, or Val. In spite of its necessity for proper cell functioning, the functional role of NME remains unclear. In 1988, Arfin and Bradshaw connected NME with the N-end protein degradation rule and postulated that the role of NME is to expose the stabilizing residues with the goal to resist protein degradation. While this explanation (that treats 7 stabilizing residues in the same manner) has become the de facto dogma of NME, comparative proteogenomics analysis of NME tells a different story. We suggest that the primary role of NME is to expose only two (rather than seven) amino acids Ala and Ser for post-translational modifications (e.g., acetylation) rather than to regulate protein degradation. We argue that, contrary to the existing view, NME is not crucially important for proteins with 5 other stabilizing residue at the 2nd positions that are merely bystanders (their function is not affected by NME) that become exposed to NME because their sizes are comparable or smaller than the size of Ala and Ser.

  17. Comparative proteomic analysis of floral color variegation in peach.

    PubMed

    Zhou, Yong; Wu, Xinxin; Zhang, Zhen; Gao, Zhihong

    2015-09-01

    Variegation in flower is a special trait in ornamental peach (Prunus persica L.). To investigate the mechanism of color variegation, we used a combination of two dimensional gel electrophoresis and mass spectrometry to explore the proteomic profiles between variegated flower (VF) and red flower (RF) buds of the peach cultivar 'Sahong Tao'. More than 500 highly reproducible protein spots (P < 0.05) were detected and 72 protein spots showed a greater than two-fold difference in their values. We identified 70 proteins that may play roles in petal coloration. The mRNA levels of the corresponding genes were detected using quantitative RT-PCR. The results show that most of the proteins are involved in energy and metabolism, which provide energy and substrates. We found that LDOX, WD40, ACC, and PPO II are related to the pigment biosynthetic pathway. The activity of PPO enzyme was further validated and showed the higher with significant differences in RF compared with the VF ones. Moreover, the four UCH proteins are involved in protein fate and may be important in post-translational modifications in peach flowers. Our study is the first comparative proteomic analysis of floral variegation and will contribute to further investigations into the molecular mechanism of flower petal coloration in ornamental peach.

  18. Comparative analysis of methods for genome-wide nucleosome cartography.

    PubMed

    Quintales, Luis; Vázquez, Enrique; Antequera, Francisco

    2015-07-01

    Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation. In recent years, several experimental protocols have been developed for this purpose that include the enzymatic digestion, chemical cleavage or immunoprecipitation of chromatin followed by next-generation sequencing of the resulting DNA fragments. Here, we compare the performance and resolution of these methods from the initial biochemical steps through the alignment of the millions of short-sequence reads to a reference genome to the final computational analysis to generate genome-wide maps of nucleosome occupancy. Because of the lack of a unified protocol to process data sets obtained through the different approaches, we have developed a new computational tool (NUCwave), which facilitates their analysis, comparison and assessment and will enable researchers to choose the most suitable method for any particular purpose. NUCwave is freely available at http://nucleosome.usal.es/nucwave along with a step-by-step protocol for its use. PMID:25296770

  19. Comparative analysis of essential genes in prokaryotic genomic islands.

    PubMed

    Zhang, Xi; Peng, Chong; Zhang, Ge; Gao, Feng

    2015-07-30

    Essential genes are thought to encode proteins that carry out the basic functions to sustain a cellular life, and genomic islands (GIs) usually contain clusters of horizontally transferred genes. It has been assumed that essential genes are not likely to be located in GIs, but systematical analysis of essential genes in GIs has not been explored before. Here, we have analyzed the essential genes in 28 prokaryotes by statistical method and reached a conclusion that essential genes in GIs are significantly fewer than those outside GIs. The function of 362 essential genes found in GIs has been explored further by BLAST against the Virulence Factor Database (VFDB) and the phage/prophage sequence database of PHAge Search Tool (PHAST). Consequently, 64 and 60 eligible essential genes are found to share the sequence similarity with the virulence factors and phage/prophages-related genes, respectively. Meanwhile, we find several toxin-related proteins and repressors encoded by these essential genes in GIs. The comparative analysis of essential genes in genomic islands will not only shed new light on the development of the prediction algorithm of essential genes, but also give a clue to detect the functionality of essential genes in genomic islands.

  20. Comparative analysis of methods for genome-wide nucleosome cartography.

    PubMed

    Quintales, Luis; Vázquez, Enrique; Antequera, Francisco

    2015-07-01

    Nucleosomes contribute to compacting the genome into the nucleus and regulate the physical access of regulatory proteins to DNA either directly or through the epigenetic modifications of the histone tails. Precise mapping of nucleosome positioning across the genome is, therefore, essential to understanding the genome regulation. In recent years, several experimental protocols have been developed for this purpose that include the enzymatic digestion, chemical cleavage or immunoprecipitation of chromatin followed by next-generation sequencing of the resulting DNA fragments. Here, we compare the performance and resolution of these methods from the initial biochemical steps through the alignment of the millions of short-sequence reads to a reference genome to the final computational analysis to generate genome-wide maps of nucleosome occupancy. Because of the lack of a unified protocol to process data sets obtained through the different approaches, we have developed a new computational tool (NUCwave), which facilitates their analysis, comparison and assessment and will enable researchers to choose the most suitable method for any particular purpose. NUCwave is freely available at http://nucleosome.usal.es/nucwave along with a step-by-step protocol for its use.

  1. [Comparative analysis of arterial bioprostheses with various antithrombotic modification].

    PubMed

    Barbarash, L S; Burkov, N N; Kudriavtseva, Iu A; Anufriev, A I; Zhuravleva, I Iu

    2012-01-01

    The present study was aimed at comparing the results of remote patency ol arterial bioprosthcses «KemAngioprosthesis» in infrainguinal position with various antithromhotic modifi cation. We analyzed the outcomes in a total of 133 patients who were subdivided into two groups: Group I (n=91) underwent implantation of hioprostheses with antithrombotic modifi calion by non-fractionated heparin. and Group II (n=42) received prostheses treated with low-molecular-weight heparin «Clexane». Patients of the both groups underwent comprehensive analysis of the haemostatic system, blood plasma lipid spectrum, as well as duplex scanning of the prosthesis. 39 (42.9%) Group I patients and 6 (13.6%) Group II patients were found to have developed thromboses. Besides, 14 (I5.4%) Group I patients were diagnosed as hawing restenosis of the anastomosis site, with this complication observed in 3 (7.3%) Group II patients. The results of the analysis demonstrated better remote patency of bioprostheses with antithromhotic modifi cation by low-molecular-weight heparin «Clexane». Dynamic follow up of the patients made it possible to carry out timely correction of medicamentous therapy, as well as at early stages to reveal restenosis of anastomoses followed by endovascular correction. PMID:22929666

  2. Comparative proteomic analysis of Saccharomyces cerevisiae under different nitrogen sources.

    PubMed

    Zhao, Shaohui; Zhao, Xinrui; Zou, Huijun; Fu, Jianwei; Du, Guocheng; Zhou, Jingwen; Chen, Jian

    2014-04-14

    In cultures containing multiple sources of nitrogen, Saccharomyces cerevisiae exhibits a sequential use of nitrogen sources through a mechanism known as nitrogen catabolite repression (NCR). To identify proteins differentially expressed due to NCR, proteomic analysis of S. cerevisiae S288C under different nitrogen source conditions was performed using two-dimensional gel electrophoresis (2-DE), revealing 169 candidate protein spots. Among these 169 protein spots, 121 were identified by matrix assisted laser desorption ionization-time of flight/time of flight mass spectrometry (MALDI-TOF/TOF). The identified proteins were closely associated with four main biological processes through Gene Ontology (GO) categorical analysis. The identification of the potential proteins and cellular processes related to NCR offer a global overview of changes elicited by different nitrogen sources, providing clues into how yeast adapt to different nutritional conditions. Moreover, by comparing our proteomic data with corresponding mRNA data, proteins regulated at the transcriptional and post-transcriptional level could be distinguished. Biological significance In S. cerevisiae, different nitrogen sources provide different growth characteristics and generate different metabolites. The nitrogen catabolite repression (NCR) process plays an important role for S. cerevisiae in the ordinal utilization of different nitrogen sources. NCR process can result in significant shift of global metabolic networks. Previous works on NCR primarily focused on transcriptomic level. The results obtained in this study provided a global atlas of the proteome changes triggered by different nitrogen sources and would facilitate the understanding of mechanisms for how yeast could adapt to different nutritional conditions.

  3. Comparative analysis reveals the underlying mechanism of vertebrate seasonal reproduction.

    PubMed

    Ikegami, Keisuke; Yoshimura, Takashi

    2016-02-01

    Animals utilize photoperiodic changes as a calendar to regulate seasonal reproduction. Birds have highly sophisticated photoperiodic mechanisms and functional genomics analysis in quail uncovered the signal transduction pathway regulating avian seasonal reproduction. Birds detect light with deep brain photoreceptors. Long day (LD) stimulus induces secretion of thyroid-stimulating hormone (TSH) from the pars tuberalis (PT) of the pituitary gland. PT-derived TSH locally activates thyroid hormone (TH) in the hypothalamus, which induces gonadotropin-releasing hormone (GnRH) and hence gonadotropin secretion. However, during winter, low temperatures increase serum TH for adaptive thermogenesis, which accelerates germ cell apoptosis by activating the genes involved in metamorphosis. Therefore, TH has a dual role in the regulation of seasonal reproduction. Studies using TSH receptor knockout mice confirmed the involvement of PT-derived TSH in mammalian seasonal reproduction. In addition, studies in mice revealed that the tissue-specific glycosylation of TSH diversifies its function in the circulation to avoid crosstalk. In contrast to birds and mammals, one of the molecular machineries necessary for the seasonal reproduction of fish are localized in the saccus vasculosus from the photoreceptor to the neuroendocrine output. Thus, comparative analysis is a powerful tool to uncover the universality and diversity of fundamental properties in various organisms.

  4. Sequence and comparative genomic analysis of actin-related proteins.

    PubMed

    Muller, Jean; Oma, Yukako; Vallar, Laurent; Friederich, Evelyne; Poch, Olivier; Winsor, Barbara

    2005-12-01

    Actin-related proteins (ARPs) are key players in cytoskeleton activities and nuclear functions. Two complexes, ARP2/3 and ARP1/11, also known as dynactin, are implicated in actin dynamics and in microtubule-based trafficking, respectively. ARP4 to ARP9 are components of many chromatin-modulating complexes. Conventional actins and ARPs codefine a large family of homologous proteins, the actin superfamily, with a tertiary structure known as the actin fold. Because ARPs and actin share high sequence conservation, clear family definition requires distinct features to easily and systematically identify each subfamily. In this study we performed an in depth sequence and comparative genomic analysis of ARP subfamilies. A high-quality multiple alignment of approximately 700 complete protein sequences homologous to actin, including 148 ARP sequences, allowed us to extend the ARP classification to new organisms. Sequence alignments revealed conserved residues, motifs, and inserted sequence signatures to define each ARP subfamily. These discriminative characteristics allowed us to develop ARPAnno (http://bips.u-strasbg.fr/ARPAnno), a new web server dedicated to the annotation of ARP sequences. Analyses of sequence conservation among actins and ARPs highlight part of the actin fold and suggest interactions between ARPs and actin-binding proteins. Finally, analysis of ARP distribution across eukaryotic phyla emphasizes the central importance of nuclear ARPs, particularly the multifunctional ARP4.

  5. Comparative performance analysis: Commercial cut-flower rose production

    SciTech Connect

    Whittier, J.; Fischer, C.L.

    1990-04-01

    A comparative performance analysis has been conducted to examine the various factors associated with establishing and operating a commercial rose cut-flower greenhouse in ten different locations across the United States. Plant productivity, defined as net blooms produced per plant per year, is largely dependent upon local climatic conditions and technological improvements. Regional variations in productivity have been explicitly analyzed. The greenhouse operation is assumed to be four acres in size and the facilities utilize current technologies. The operation is designed as a professionally-organized company with an owner/manager, grower, and salesperson. The primary product is a red hybrid tea rose for sales. Selling markets vary by location, but in general they are large metropolitan areas. The analysis strongly indicates that new installations for cut-flower rose production are profitable in several areas in the U.S. Southwest, particularly in New Mexico, Arizona, and Texas. No ones stands out as a favored location. Las Cruces, New Mexico, has the highest net present volume and return on investment results. 68 refs., 1 fig., 8 tabs.

  6. Quantifying Drosophila food intake: comparative analysis of current methodology

    PubMed Central

    Deshpande, Sonali A.; Carvalho, Gil B.; Amador, Ariadna; Phillips, Angela M.; Hoxha, Sany; Lizotte, Keith J.; Ja, William W.

    2014-01-01

    Food intake is a fundamental parameter in animal studies. Despite the prevalent use of Drosophila in laboratory research, precise measurements of food intake remain challenging in this model organism. Here, we compare several common Drosophila feeding assays: the Capillary Feeder (CAFE), food-labeling with a radioactive tracer or a colorimetric dye, and observations of proboscis extension (PE). We show that the CAFE and radioisotope-labeling provide the most consistent results, have the highest sensitivity, and can resolve differences in feeding that dye-labeling and PE fail to distinguish. We conclude that performing the radiolabeling and CAFE assays in parallel is currently the best approach for quantifying Drosophila food intake. Understanding the strengths and limitations of food intake methodology will greatly advance Drosophila studies of nutrition, behavior, and disease. PMID:24681694

  7. Apples, oranges, and angles: Comparative kinematic analysis of disparate limbs.

    PubMed

    Gatesy, Stephen M; Pollard, Nancy S

    2011-08-01

    Tetrapod limbs exhibit diverse postures and movements during terrestrial locomotion. As with morphological traits, the history of kinematic evolution should be accessible to reconstruction through analysis of limb motion patterns in a phylogenetic framework. However, the angular data comprising most kinematic descriptions appear to suffer from limitations that preclude meaningful comparison among disparate species. Using simple planar models, we discuss how geometric constraints render joint and elevation angles independent of neither morphology, degree of crouch, nor one another during the stance phase of locomotion. The implicit null hypothesis of potential similarity is invalidated because angular data are not viably transferable among limbs of dissimilar proportion and/or degree of crouch. Overlooking or dismissing the effect of constraints on angular parameterization hampers efforts to quantitatively elucidate the evolution of locomotion. We advocate a search for alternative methods of measuring limb movement that can decouple intersegmental coordination from morphology and posture.

  8. Apples, oranges, and angles: Comparative kinematic analysis of disparate limbs.

    PubMed

    Gatesy, Stephen M; Pollard, Nancy S

    2011-08-01

    Tetrapod limbs exhibit diverse postures and movements during terrestrial locomotion. As with morphological traits, the history of kinematic evolution should be accessible to reconstruction through analysis of limb motion patterns in a phylogenetic framework. However, the angular data comprising most kinematic descriptions appear to suffer from limitations that preclude meaningful comparison among disparate species. Using simple planar models, we discuss how geometric constraints render joint and elevation angles independent of neither morphology, degree of crouch, nor one another during the stance phase of locomotion. The implicit null hypothesis of potential similarity is invalidated because angular data are not viably transferable among limbs of dissimilar proportion and/or degree of crouch. Overlooking or dismissing the effect of constraints on angular parameterization hampers efforts to quantitatively elucidate the evolution of locomotion. We advocate a search for alternative methods of measuring limb movement that can decouple intersegmental coordination from morphology and posture. PMID:21600220

  9. Comparative implant research in dogs: a prosthodontic model.

    PubMed

    Parr, G R; Gardner, L K; Steflik, D E; Sisk, A L

    1992-09-01

    One-hundred twenty endosteal dental implants were inserted bilaterally in the mandibles of 30 adult mongrel dogs after bilateral extraction of all premolars. The 120 implants were evenly divided into one- and two-stage systems and included ceramic and titanium cylindrical root-form implants and titanium blade implants. The research design of this investigation divided the 30 animals into 10 groups of three dogs. This article describes an animal model that is useful in evaluating dental implant designs and compares the results with those from humans. In particular, this article delineates the prosthodontic approach appropriate for this model using one- and two-stage titanium implants. Rexillium alloy fixed prostheses were placed on 32 endosteal implants and 16 natural mandibular molar teeth. The implants and prosthetic components of the Sterio-Oss implant system were used. All prostheses are functional with minimal maintenance. To date, after 1-year of follow-up, none of the implants have been lost and none of the fixed prostheses have required recementation or maintenance other than normal hygiene. Histologic and survival data as well as results with other implant systems will be presented in other reports.

  10. A comparative study of prebiotic and present day translational models

    NASA Technical Reports Server (NTRS)

    Rein, R.; Raghunathan, G.; Mcdonald, J.; Shibata, M.; Srinivasan, S.

    1986-01-01

    It is generally recognized that the understanding of the molecular basis of primitive translation is a fundamental step in developing a theory of the origin of life. However, even in modern molecular biology, the mechanism for the decoding of messenger RNA triplet codons into an amino acid sequence of a protein on the ribosome is understood incompletely. Most of the proposed models for prebiotic translation lack, not only experimental support, but also a careful theoretical scrutiny of their compatibility with well understood stereochemical and energetic principles of nucleic acid structure, molecular recognition principles, and the chemistry of peptide bond formation. Present studies are concerned with comparative structural modelling and mechanistic simulation of the decoding apparatus ranging from those proposed for prebiotic conditions to the ones involved in modern biology. Any primitive decoding machinery based on nucleic acids and proteins, and most likely the modern day system, has to satisfy certain geometrical constraints. The charged amino acyl and the peptidyl termini of successive adaptors have to be adjacent in space in order to satisfy the stereochemical requirements for amide bond formation. Simultaneously, the same adaptors have to recognize successive codons on the messenger. This translational complex has to be realized by components that obey nucleic acid conformational principles, stabilities, and specificities. This generalized condition greatly restricts the number of acceptable adaptor structures.

  11. A comparative analysis of the evolution of imperfect mimicry.

    PubMed

    Penney, Heather D; Hassall, Christopher; Skevington, Jeffrey H; Abbott, Kevin R; Sherratt, Thomas N

    2012-03-21

    Although exceptional examples of adaptation are frequently celebrated, some outcomes of natural selection seem far from perfect. For example, many hoverflies (Diptera: Syrphidae) are harmless (Batesian) mimics of stinging Hymenoptera. However, although some hoverfly species are considered excellent mimics, other species bear only a superficial resemblance to their models and it is unclear why this is so. To evaluate hypotheses that have been put forward to explain interspecific variation in the mimetic fidelity of Palearctic Syrphidae we use a comparative approach. We show that the most plausible explanation is that predators impose less selection for mimetic fidelity on smaller hoverfly species because they are less profitable prey items. In particular, our findings, in combination with previous results, allow us to reject several key hypotheses for imperfect mimicry: first, human ratings of mimetic fidelity are positively correlated with both morphometric measures and avian rankings, indicating that variation in mimetic fidelity is not simply an illusion based on human perception; second, no species of syrphid maps out in multidimensional space as being intermediate in appearance between several different hymenopteran model species, as the multimodel hypothesis requires; and third, we find no evidence for a negative relationship between mimetic fidelity and abundance, which calls into question the kin-selection hypothesis. By contrast, a strong positive relationship between mimetic fidelity and body size supports the relaxed-selection hypothesis, suggesting that reduced predation pressure on less profitable prey species limits the selection for mimetic perfection.

  12. Hierarchical Bayesian model averaging for hydrostratigraphic modeling: Uncertainty segregation and comparative evaluation

    NASA Astrophysics Data System (ADS)

    Tsai, Frank T.-C.; Elshall, Ahmed S.

    2013-09-01

    Analysts are often faced with competing propositions for each uncertain model component. How can we judge that we select a correct proposition(s) for an uncertain model component out of numerous possible propositions? We introduce the hierarchical Bayesian model averaging (HBMA) method as a multimodel framework for uncertainty analysis. The HBMA allows for segregating, prioritizing, and evaluating different sources of uncertainty and their corresponding competing propositions through a hierarchy of BMA models that forms a BMA tree. We apply the HBMA to conduct uncertainty analysis on the reconstructed hydrostratigraphic architectures of the Baton Rouge aquifer-fault system, Louisiana. Due to uncertainty in model data, structure, and parameters, multiple possible hydrostratigraphic models are produced and calibrated as base models. The study considers four sources of uncertainty. With respect to data uncertainty, the study considers two calibration data sets. With respect to model structure, the study considers three different variogram models, two geological stationarity assumptions and two fault conceptualizations. The base models are produced following a combinatorial design to allow for uncertainty segregation. Thus, these four uncertain model components with their corresponding competing model propositions result in 24 base models. The results show that the systematic dissection of the uncertain model components along with their corresponding competing propositions allows for detecting the robust model propositions and the major sources of uncertainty.

  13. SILAC-based comparative analysis of pathogenic Escherichia coli secretomes.

    PubMed

    Boysen, Anders; Borch, Jonas; Krogh, Thøger Jensen; Hjernø, Karin; Møller-Jensen, Jakob

    2015-09-01

    Comparative studies of pathogenic bacteria and their non-pathogenic counterparts has led to the discovery of important virulence factors thereby generating insight into mechanisms of pathogenesis. Protein-based antigens for vaccine development are primarily selected among unique virulence-related factors produced by the pathogen of interest. However, recent work indicates that proteins that are not unique to the pathogen but instead selectively expressed compared to its non-pathogenic counterpart could also be vaccine candidates or targets for drug development. Modern methods in quantitative proteome analysis have the potential to discover both classes of proteins and hence form an important tool for discovering therapeutic targets. Adherent-invasive Escherichia coli (AIEC) and Enterotoxigenic E. coli (ETEC) are pathogenic variants of E. coli which cause intestinal disease in humans. AIEC is associated with Crohn's disease (CD), a chronic inflammatory condition of the gastrointestinal tract whereas ETEC is the major cause of human diarrhea which affects hundreds of millions annually. In spite of the disease burden associated with these pathogens, effective vaccines conferring long-term protection are still needed. In order to identify proteins with therapeutic potential, we have used mass spectrometry-based Stable Isotope Labeling with Amino acids in Cell culture (SILAC) quantitative proteomics method which allows us to compare the proteomes of pathogenic strains to commensal E. coli. In this study, we grew the pathogenic strains ETEC H10407, AIEC LF82 and the non-pathogenic reference strain E. coli K-12 MG1655 in parallel and used SILAC to compare protein levels in OMVs and culture supernatant. We have identified well-known virulence factors from both AIEC and ETEC, thus validating our experimental approach. In addition we find proteins that are not unique to the pathogenic strains but expressed at levels different from the commensal strain, including the

  14. SILAC-based comparative analysis of pathogenic Escherichia coli secretomes.

    PubMed

    Boysen, Anders; Borch, Jonas; Krogh, Thøger Jensen; Hjernø, Karin; Møller-Jensen, Jakob

    2015-09-01

    Comparative studies of pathogenic bacteria and their non-pathogenic counterparts has led to the discovery of important virulence factors thereby generating insight into mechanisms of pathogenesis. Protein-based antigens for vaccine development are primarily selected among unique virulence-related factors produced by the pathogen of interest. However, recent work indicates that proteins that are not unique to the pathogen but instead selectively expressed compared to its non-pathogenic counterpart could also be vaccine candidates or targets for drug development. Modern methods in quantitative proteome analysis have the potential to discover both classes of proteins and hence form an important tool for discovering therapeutic targets. Adherent-invasive Escherichia coli (AIEC) and Enterotoxigenic E. coli (ETEC) are pathogenic variants of E. coli which cause intestinal disease in humans. AIEC is associated with Crohn's disease (CD), a chronic inflammatory condition of the gastrointestinal tract whereas ETEC is the major cause of human diarrhea which affects hundreds of millions annually. In spite of the disease burden associated with these pathogens, effective vaccines conferring long-term protection are still needed. In order to identify proteins with therapeutic potential, we have used mass spectrometry-based Stable Isotope Labeling with Amino acids in Cell culture (SILAC) quantitative proteomics method which allows us to compare the proteomes of pathogenic strains to commensal E. coli. In this study, we grew the pathogenic strains ETEC H10407, AIEC LF82 and the non-pathogenic reference strain E. coli K-12 MG1655 in parallel and used SILAC to compare protein levels in OMVs and culture supernatant. We have identified well-known virulence factors from both AIEC and ETEC, thus validating our experimental approach. In addition we find proteins that are not unique to the pathogenic strains but expressed at levels different from the commensal strain, including the

  15. Comparative analysis of slot dimension in lingual bracket systems

    PubMed Central

    2009-01-01

    Background Orthodontic treatment with fixed appliances requires - among others - the correct clinical expression of torque, which depends on the precise fitting of archwire and slot. Especially in the lingual technique torque problems become clinically more evident than in labial appliances also with respect to the vertical alignment of teeth due to different distances from the center of resistance. The purpose of the present study was to compare the preciseness of slot dimensions of different lingual bracket systems. Methods Three lingual bracket systems were included in the study (7th Generation and STb, Ormco, Glendora, CA, USA; Incognito, TOP-Service/3 M Unitek, Monrovia, CA, USA). Non destructive analysis of vertical slot dimensions was performed using precision pin gauges (Azurea, Belprahon, Switzerland) that were tapered in increments of 0.002 mm (0.00008 inch). The sizes of 240 incisor and canine brackets were measured per system (total: 720). Data were compared using one-way ANOVA. A p-value < 0.05 was considered statistically significant. Results Average slot dimensions were 0.467 mm ± 0.007 mm (0.0184 inch ± 0.0003 inch) for the 7th Generation bracket system, 0.466 mm ± 0.004 mm (0.0183 inch ± 0.0001) inch for the STb bracket system and 0.459 mm ± 0.004 mm (0.0181 inch ± 0.0001) inch for the Incognito bracket system. Differences between systems were statistically significant (p < 0.05). Conclusions The analyzed bracket systems for lingual treatment exhibited significant differences in slot dimension that will clinically result in torque play. These aspects must be considered in lingual orthodontic treatment. PMID:20003510

  16. Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species

    PubMed Central

    Cummings, Craig A.; Shih, Rita; Degoricija, Lovorka; Rico, Alain; Brzoska, Pius; Hamby, Stephen E.; Masood, Naqash; Hariri, Sumyya; Sonbol, Hana; Chuzhanova, Nadia; McClelland, Michael; Furtado, Manohar R.; Forsythe, Stephen J.

    2012-01-01

    Background Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages. Methodology/Principal Findings We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes. Conclusions/Significance Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of

  17. Comparative analysis of Acinetobacters: three genomes for three lifestyles.

    PubMed

    Vallenet, David; Nordmann, Patrice; Barbe, Valérie; Poirel, Laurent; Mangenot, Sophie; Bataille, Elodie; Dossat, Carole; Gas, Shahinaz; Kreimeyer, Annett; Lenoble, Patricia; Oztas, Sophie; Poulain, Julie; Segurens, Béatrice; Robert, Catherine; Abergel, Chantal; Claverie, Jean-Michel; Raoult, Didier; Médigue, Claudine; Weissenbach, Jean; Cruveiller, Stéphane

    2008-03-19

    Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.

  18. Feedback interventions and driving speed: A parametric and comparative analysis

    PubMed Central

    Houten, Ron Van; Nau, Paul A.

    1983-01-01

    Five experiments were conducted to assess the effects of several variables on the efficacy of feedback in reducing driving speed. Experiment 1 systematically varied the criterion used to define speeding, and results showed that the use of a lenient criterion (20 km/hr over the speed limit), which allowed for the posting of high percentages of drivers not speeding, was more effective in reducing speeding than the use of a stringent criterion (10 km/hr over the speed limit). In Experiment 2 an analysis revealed that posting feedback reduced speeding on a limited access highway and the effects persisted to some degree up to 6 km. Experiments 3 and 4 compared the effectiveness of an unmanned parked police vehicle (Experiment 3) and a police air patrol speeding program (Experiment 4) with the feedback sign and determined whether the presence of either of these enforcement variables could potentiate the efficacy of the sign. The results of both experiments demonstrated that although the two enforcement programs initially produced larger effects than the feedback sign, the magnitude of their effect attenuated over time. Experiment 5 compared the effectiveness of a traditional enforcement program with a warning program which included handing out a flier providing feedback on the number and types of accidents occuring on the road during the past year. This experiment demonstrated that the warning program produced a marked reduction in speeding and the traditional enforcement program did not. Furthermore, the warning program and a feedback sign together produced an even greater reduction in speeding than either alone. PMID:16795666

  19. Comparative and retrospective molecular analysis of Parapoxvirus (PPV) isolates.

    PubMed

    Friederichs, Schirin; Krebs, Stefan; Blum, Helmut; Wolf, Eckhard; Lang, Heike; von Buttlar, Heiner; Büttner, Mathias

    2014-03-01

    Species members of the genus Parapoxvirus (PPV) within the family Poxviridae cause contagious pustular dermatitis in small ruminants (Orf virus, ORFV) and mostly mild localized inflammation in cattle (bovine papular stomatitis virus, BPSV and pseudocowpox virus, PCPV). All PPVs are known to be zoonotic, leading to circumscribed skin lesions in humans, historically known as milker's nodules. Human PPV isolates are often ill defined concerning their allocation to an animal origin. Here we present a comparative molecular analysis of a unique collection of 21 historic and recent human and animal PPV cell culture isolates (and two PPV DNA samples). Cell culture PPV propagation was restricted to primary ruminant fibroblasts and was strictly kept at low passages to avoid genomic changes by in vitro influences. For molecular arrangement of the isolate DNAs and their attribution to established PPV species DNA fragments of the PPVs were generated by two different discriminating PCR protocols, targeting the major part of the open reading frame (ORF) 011 (B2L gene) and the complete ORF 032. Multiple sequence alignments and phylogenetic analysis of both genes resulted in affiliation to the known PPV species. The sequences from the ORF 032 allowed discrimination of the isolate DNAs at a higher resolution. Human PPV isolates could be clearly assigned to the PPV species belonging to the reported or assumed animal host of transmission. For the first time, a whole PPV genome sequence comparison of a human biopsy derived virus (B029) and its ovine counterpart (B015) originating from a defined Orf outbreak in Germany is provided, revealing their well conserved relationship. Thus human PPVs can be molecularly retraced to the PPV species indicating the animal of transmission. After transmission to the human host, molecular conservation of the animal's virus peculiarities indicative for a PPV species became evident. PMID:24373950

  20. Comparative Analysis of State Fish Consumption Advisories Targeting Sensitive Populations

    PubMed Central

    Scherer, Alison C.; Tsuchiya, Ami; Younglove, Lisa R.; Burbacher, Thomas M.; Faustman, Elaine M.

    2008-01-01

    Objective Fish consumption advisories are issued to warn the public of possible toxicological threats from consuming certain fish species. Although developing fetuses and children are particularly susceptible to toxicants in fish, fish also contain valuable nutrients. Hence, formulating advice for sensitive populations poses challenges. We conducted a comparative analysis of advisory Web sites issued by states to assess health messages that sensitive populations might access. Data sources We evaluated state advisories accessed via the National Listing of Fish Advisories issued by the U.S. Environmental Protection Agency. Data extraction We created criteria to evaluate advisory attributes such as risk and benefit message clarity. Data synthesis All 48 state advisories issued at the time of this analysis targeted children, 90% (43) targeted pregnant women, and 58% (28) targeted women of childbearing age. Only six advisories addressed single contaminants, while the remainder based advice on 2–12 contaminants. Results revealed that advisories associated a dozen contaminants with specific adverse health effects. Beneficial health effects of any kind were specifically associated only with omega-3 fatty acids found in fish. Conclusions These findings highlight the complexity of assessing and communicating information about multiple contaminant exposure from fish consumption. Communication regarding potential health benefits conferred by specific fish nutrients was minimal and focused primarily on omega-3 fatty acids. This overview suggests some lessons learned and highlights a lack of both clarity and consistency in providing the breadth of information that sensitive populations such as pregnant women need to make public health decisions about fish consumption during pregnancy. PMID:19079708

  1. Comparative analysis of polygalacturonase in the fruit of strawberry cultivars.

    PubMed

    Zhou, H C; Li, G; Zhao, X; Li, L J

    2015-10-19

    The role of polygalacturonase (PG) in the development, ripening, and softening of fruit from two strawberry cultivars with different flesh firmness and softening characteristics was compared. Changes in PG activity and gene expression during development, ripening and softening were measured. The PG genes from each cultivar were cloned and analyzed, and were classified with other PG genes using phylogenetic analysis. In Toyonoka fruit, PG activity increased gradually, reaching a peak during the pink stage, and remained at this level during post-harvest softening. Changes in PG gene expression were consistent with PG activity in these softer fruits. In the firmer Sweet Charlie fruits, PG activity was detected during the initial development stage, reaching a peak at the white stage, thereafter decreasing gradually with ripening and remaining at this lower level throughout softening. Changes in PG gene expression and PG activity were not consistent in these fruit. For both Toyonoka and Sweet Charlie PG genes (FaTPG and FaSCPG, respectively), the open reading frame was 1218 bp, encoding 405 amino acids. Five different nucleotide sites were observed between the two sequences, leading to two amino acid sequence mutations. FaTPG, FaSCPG, and PG genes from the Fragaria vesca genome were classified into three clades using phylogenetic analysis. The clade containing PG genes involved in fruit softening had functional similarity but there were no functional differences between FaTPG and FaSCPG. Differences in PG activity, gene sequence, and gene expression may have led to different roles of PG during ripening and softening in strawberries with different textures.

  2. Comparative Analysis of Uninhibited and Constrained Avian Wing Aerodynamics

    NASA Astrophysics Data System (ADS)

    Cox, Jordan A.

    The flight of birds has intrigued and motivated man for many years. Bird flight served as the primary inspiration of flying machines developed by Leonardo Da Vinci, Otto Lilienthal, and even the Wright brothers. Avian flight has once again drawn the attention of the scientific community as unmanned aerial vehicles (UAV) are not only becoming more popular, but smaller. Birds are once again influencing the designs of aircraft. Small UAVs operating within flight conditions and low Reynolds numbers common to birds are not yet capable of the high levels of control and agility that birds display with ease. Many researchers believe the potential to improve small UAV performance can be obtained by applying features common to birds such as feathers and flapping flight to small UAVs. Although the effects of feathers on a wing have received some attention, the effects of localized transient feather motion and surface geometry on the flight performance of a wing have been largely overlooked. In this research, the effects of freely moving feathers on a preserved red tailed hawk wing were studied. A series of experiments were conducted to measure the aerodynamic forces on a hawk wing with varying levels of feather movement permitted. Angle of attack and air speed were varied within the natural flight envelope of the hawk. Subsequent identical tests were performed with the feather motion constrained through the use of externally-applied surface treatments. Additional tests involved the study of an absolutely fixed geometry mold-and-cast wing model of the original bird wing. Final tests were also performed after applying surface coatings to the cast wing. High speed videos taken during tests revealed the extent of the feather movement between wing models. Images of the microscopic surface structure of each wing model were analyzed to establish variations in surface geometry between models. Recorded aerodynamic forces were then compared to the known feather motion and surface

  3. Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue†

    PubMed Central

    Muratore, Kathryn E.; Seeliger, Markus A.; Wang, Zhihong; Fomina, Dina; Neiswinger, Johnathan; Havranek, James J.; Baker, David; Kuriyan, John; Cole, Philip A.

    2009-01-01

    Protein tyrosine kinases are critical cell signaling enzymes. These enzymes have a highly conserved Arg residue in their catalytic loop which is present two residues or four residues downstream from an absolutely conserved Asp catalytic base. Prior studies on protein tyrosine kinases Csk and Src revealed the potential for chemical rescue of catalytically-deficient mutant kinases (Arg to Ala mutations) by small diamino compounds, particularly imidazole, however the potency and efficiency of rescue was greater for Src. This current study further examines the structural and kinetic basis of rescue for mutant Src as compared to mutant Abl tyrosine kinase. An X-ray crystal structure of R388A Src revealed the surprising finding that a histidine residue of the N-terminus of a symmetry-related kinase inserts into the active site of the adjacent Src and mimics the hydrogen bonding pattern seen in wild-type protein tyrosine kinases. Abl R367A shows potent and efficient rescue more comparable to Src, even though its catalytic loop is more like that of Csk. Various enzyme redesigns of the active sites indicate that the degree and specificity of rescue is somewhat flexible, but the overall properties of the enzymes and rescue agents play an overarching role. The newly discovered rescue agent 2-aminoimidazole is about as efficient as imidazole in rescuing R/A Src and Abl. Rate vs. pH studies with these imidazole analogs suggest that the protonated imidazolium is the preferred form for chemical rescue, consistent with structural models. The efficient rescue seen with mutant Abl points to the potential of this approach to be used effectively to analyze Abl phosphorylation pathways in cells. PMID:19260709

  4. Comparative Analysis of Old-Age Mortality Estimations in Africa

    PubMed Central

    Bendavid, Eran; Seligman, Benjamin; Kubo, Jessica

    2011-01-01

    Background Survival to old ages is increasing in many African countries. While demographic tools for estimating mortality up to age 60 have improved greatly, mortality patterns above age 60 rely on models based on little or no demographic data. These estimates are important for social planning and demographic projections. We provide direct estimations of older-age mortality using survey data. Methods Since 2005, nationally representative household surveys in ten sub-Saharan countries record counts of living and recently deceased household members: Burkina Faso, Côte d'Ivoire, Ethiopia, Namibia, Nigeria, Swaziland, Tanzania, Uganda, Zambia, and Zimbabwe. After accounting for age heaping using multiple imputation, we use this information to estimate probability of death in 5-year intervals (5qx). We then compare our 5qx estimates to those provided by the World Health Organization (WHO) and the United Nations Population Division (UNPD) to estimate the differences in mortality estimates, especially among individuals older than 60 years old. Findings We obtained information on 505,827 individuals (18.4% over age 60, 1.64% deceased). WHO and UNPD mortality models match our estimates closely up to age 60 (mean difference in probability of death -1.1%). However, mortality probabilities above age 60 are lower using our estimations than either WHO or UNPD. The mean difference between our sample and the WHO is 5.9% (95% CI 3.8–7.9%) and between our sample is UNPD is 13.5% (95% CI 11.6–15.5%). Regardless of the comparator, the difference in mortality estimations rises monotonically above age 60. Interpretation Mortality estimations above age 60 in ten African countries exhibit large variations depending on the method of estimation. The observed patterns suggest the possibility that survival in some African countries among adults older than age 60 is better than previously thought. Improving the quality and coverage of vital information in developing countries will become

  5. SRMAFTE facility checkout model flow field analysis

    NASA Technical Reports Server (NTRS)

    Dill, Richard A.; Whitesides, Harold R.

    1992-01-01

    The Solid Rocket Motor Air Flow Equipment (SRMAFTE) facility was constructed for the purpose of evaluating the internal propellant, insulation, and nozzle configurations of solid propellant rocket motor designs. This makes the characterization of the facility internal flow field very important in assuring that no facility induced flow field features exist which would corrupt the model related measurements. In order to verify the design and operation of the facility, a three-dimensional computational flow field analysis was performed on the facility checkout model setup. The checkout model measurement data, one-dimensional and three-dimensional estimates were compared, and the design and proper operation of the facility was verified. The proper operation of the metering nozzles, adapter chamber transition, model nozzle, and diffuser were verified. The one-dimensional and three-dimensional flow field estimates along with the available measurement data are compared.

  6. Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species.

    PubMed

    Alves, Joana I; Alves, M Madalena; Plugge, Caroline M; Stams, Alfons J M; Sousa, Diana Z

    2016-01-01

    An anaerobic thermophilic strain (strain PCO) was isolated from a syngas-converting enrichment culture. Syngas components cannot be used by strain PCO, but the new strain is very tolerant to carbon monoxide (pCO = 1.7 × 10(5) Pa, 100% CO). 16S rRNA gene analysis and DNA-DNA hybridization revealed that strain PCO is a strain of Thermoanaerobacter thermohydrosulfuricus. The physiology of strain PCO and other Thermoanaerobacter species was compared, focusing on their tolerance to carbon monoxide. T. thermohydrosulfuricus, T. brockii subsp. finnii, T. pseudethanolicus, and T. wiegelii were exposed to increased CO concentrations in the headspace, while growth, glucose consumption and product formation were monitored. Remarkably, glucose conversion rates by Thermoanaerobacter species were not affected by CO. All the tested strains fermented glucose to mainly lactate, ethanol, acetate, and hydrogen, but final product concentrations differed. In the presence of CO, ethanol production was generally less affected, but H2 production decreased with increasing CO partial pressure. This study highlights the CO resistance of Thermoanaerobacter species. PMID:27621723

  7. Comparative proteomic analysis of rice shoots exposed to high arsenate.

    PubMed

    Liu, Yanli; Li, Ming; Han, Chao; Wu, Fengxia; Tu, Bingkun; Yang, Pingfang

    2013-10-01

    Consumption of arsenic contaminated water and cereals is a serious threat to humans all over the world. Rice (Oryza sativa "Nipponbare"), as a main cereal crop, can accumulate arsenic more than 10-fold that of in other cereals. To gain a comprehensive understanding of the response of rice subjected to 100 µM arsenate stress, a comparative proteomic analysis of rice shoots in combination with morphological and biochemical investigations have been performed in this study. The results demonstrated that arsenate suppressed the growth of rice seedlings, destroyed the cellular ultra-structure and changed the homeostasis of reactive oxygen species. Moreover, a total of 38 differentially displayed proteins, which were mainly involved in metabolism, redox and protein-metabolism, were identified. The data suggest the arsenic can inhibit rice growth through negatively affecting chloroplast structure and photosynthesis. In addition, upregulation of the proteins involved in redox and protein metabolism might help the rice to be resistant or tolerant to arsenic toxicity. In general, this study improves our understanding about the rice arsenic responsive mechanism.

  8. [Comparative analysis of seven marine biological source of mineral drugs].

    PubMed

    Si, Wei; A, Ru-na; Li, Shang-rong; Zhang, Jing-Xian; Wu, Wan-ying; Cui, Ya-jun

    2014-09-01

    The marine biological source of mineral drugs recorded in Chinese Pharmacopoeia (2010 version) mainly including pearl, nacre, clam shell, common oyster shell, ark shell, cuttle bone, and sea-ear shell are widely used in clinical. Calcium carbonate and a small amount of protein are the main components in this type of drugs. In this paper, a systematical and comparable study were carried out by determination of calcium carbonate by EDTA titration method, the crystal of calcium carbonate by X-Ray powder diffraction and the total amino acids (TAAs) of the hydrolyzed samples by ultraviolet spectrophotometry method. As a result, the crystal structure is calcite for common oyster shell, mixture of calcite and aragonite for nacre and sea-ear shell, aragonite for the other drugs. The content of calcium carbonate ranged from 86% to 96%. Cuttle bone has the highest amount of TAAs among the seven drugs which reached 1.7% while clam shell has the lowest content of 0.16% on average. In conclusion, an effective method was developed for the quality control of marine mineral drugs by comprehensive analysis of calcium carbonate and TAAs in the seven marine mineral drugs.

  9. A comparative analysis of network robustness against different link attacks

    NASA Astrophysics Data System (ADS)

    Duan, Boping; Liu, Jing; Zhou, Mingxing; Ma, Liangliang

    2016-04-01

    Recently, the study of optimizing network robustness has attracted increasing attentions, and the constraint that every node's degree cannot be changed is considered. Although this constraint maintains the node degree distribution consistently in order to reserve the structure of networks, it makes the network structure be lack of flexibility since many network structure always transform in the modern society. Given this consideration, in this paper, we analyze the robustness of networks through setting a new constraint; that is, only the number of edges should be unchanged. Then, we use the link-robustness index (Rl) as the measure of the network robustness against either random failures or intentional attacks, and make a comparative analysis of network robustness against different types of link attacks. Moreover, we use four types of networks as initial networks, namely scale-free networks, random networks, regular networks, and small-world networks. The experimental results show that the values of robustness measures for the optimized networks starting from different initial networks are similar under different link attacks, but the network topologies may be different. That is to say, networks with different topologies may have similar robustness in terms of the robustness measures. We also find that the optimized networks obtained by one link attack may not robust against other link attacks, sometimes, even weaker than the original networks. Therefore, before building networks, it is better to study which type of link attacks may happen.

  10. Comparative genomic analysis of seven Mycoplasma hyosynoviae strains

    PubMed Central

    Bumgardner, Eric A; Kittichotirat, Weerayuth; Bumgarner, Roger E; Lawrence, Paulraj K

    2015-01-01

    Infection with Mycoplasma hyosynoviae can result in debilitating arthritis in pigs, particularly those aged 10 weeks or older. Strategies for controlling this pathogen are becoming increasingly important due to the rise in the number of cases of arthritis that have been attributed to infection in recent years. In order to begin to develop interventions to prevent arthritis caused by M. hyosynoviae, more information regarding the specific proteins and potential virulence factors that its genome encodes was needed. However, the genome of this emerging swine pathogen had not been sequenced previously. In this report, we present a comparative analysis of the genomes of seven strains of M. hyosynoviae isolated from different locations in North America during the years 2010 to 2013. We identified several putative virulence factors that may contribute to the ability of this pathogen to adhere to host cells. Additionally, we discovered several prophage genes present within the genomes of three strains that show significant similarity to MAV1, a phage isolated from the related species, M. arthritidis. We also identified CRISPR-Cas and type III restriction and modification systems present in two strains that may contribute to their ability to defend against phage infection. PMID:25693846

  11. Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species

    PubMed Central

    Alves, Joana I.; Alves, M. Madalena; Plugge, Caroline M.; Stams, Alfons J. M.; Sousa, Diana Z.

    2016-01-01

    An anaerobic thermophilic strain (strain PCO) was isolated from a syngas-converting enrichment culture. Syngas components cannot be used by strain PCO, but the new strain is very tolerant to carbon monoxide (pCO = 1.7 × 105 Pa, 100% CO). 16S rRNA gene analysis and DNA-DNA hybridization revealed that strain PCO is a strain of Thermoanaerobacter thermohydrosulfuricus. The physiology of strain PCO and other Thermoanaerobacter species was compared, focusing on their tolerance to carbon monoxide. T. thermohydrosulfuricus, T. brockii subsp. finnii, T. pseudethanolicus, and T. wiegelii were exposed to increased CO concentrations in the headspace, while growth, glucose consumption and product formation were monitored. Remarkably, glucose conversion rates by Thermoanaerobacter species were not affected by CO. All the tested strains fermented glucose to mainly lactate, ethanol, acetate, and hydrogen, but final product concentrations differed. In the presence of CO, ethanol production was generally less affected, but H2 production decreased with increasing CO partial pressure. This study highlights the CO resistance of Thermoanaerobacter species. PMID:27621723

  12. Comparative Analysis of Carbon Monoxide Tolerance among Thermoanaerobacter Species

    PubMed Central

    Alves, Joana I.; Alves, M. Madalena; Plugge, Caroline M.; Stams, Alfons J. M.; Sousa, Diana Z.

    2016-01-01

    An anaerobic thermophilic strain (strain PCO) was isolated from a syngas-converting enrichment culture. Syngas components cannot be used by strain PCO, but the new strain is very tolerant to carbon monoxide (pCO = 1.7 × 105 Pa, 100% CO). 16S rRNA gene analysis and DNA-DNA hybridization revealed that strain PCO is a strain of Thermoanaerobacter thermohydrosulfuricus. The physiology of strain PCO and other Thermoanaerobacter species was compared, focusing on their tolerance to carbon monoxide. T. thermohydrosulfuricus, T. brockii subsp. finnii, T. pseudethanolicus, and T. wiegelii were exposed to increased CO concentrations in the headspace, while growth, glucose consumption and product formation were monitored. Remarkably, glucose conversion rates by Thermoanaerobacter species were not affected by CO. All the tested strains fermented glucose to mainly lactate, ethanol, acetate, and hydrogen, but final product concentrations differed. In the presence of CO, ethanol production was generally less affected, but H2 production decreased with increasing CO partial pressure. This study highlights the CO resistance of Thermoanaerobacter species.

  13. Comparative proteomic analysis in Miscanthus sinensis exposed to antimony stress.

    PubMed

    Xue, Liang; Ren, Huadong; Li, Sheng; Gao, Ming; Shi, Shengqing; Chang, Ermei; Wei, Yuan; Yao, Xiaohua; Jiang, Zeping; Liu, Jianfeng

    2015-06-01

    To explore the molecular basis of Sb tolerance mechanism in plant, a comparative proteomic analysis of both roots and leaves in Miscanthus sinensis has been conducted in combination with physiological and biochemical analyses. M. sinensis seedlings were exposed to different doses of Sb, and both roots and leaves were collected after 3 days of treatment. Two-dimensional gel electrophoresis (2-DE) and image analyses found that 29 protein spots showed 1.5-fold change in abundance in leaves and 19 spots in roots, of which 31 were identified by MALDI-TOF-MS and MALDI-TOF-TOF-MS. Proteins involved in antioxidant defense and stress response generally increased their expression all over the Sb treatments. In addition, proteins relative to transcription, signal transduction, energy metabolism and cell division and cell structure showed a variable expression pattern over Sb concentrations. Overall these findings provide new insights into the probable survival mechanisms by which M. sinensis could be adapting to Sb phytotoxicity.

  14. The Chlamydia psittaci Genome: A Comparative Analysis of Intracellular Pathogens

    PubMed Central

    Saluz, Hans Peter

    2012-01-01

    Background Chlamydiaceae are a family of obligate intracellular pathogens causing a wide range of diseases in animals and humans, and facing unique evolutionary constraints not encountered by free-living prokaryotes. To investigate genomic aspects of infection, virulence and host preference we have sequenced Chlamydia psittaci, the pathogenic agent of ornithosis. Results A comparison of the genome of the avian Chlamydia psittaci isolate 6BC with the genomes of other chlamydial species, C. trachomatis, C. muridarum, C. pneumoniae, C. abortus, C. felis and C. caviae, revealed a high level of sequence conservation and synteny across taxa, with the major exception of the human pathogen C. trachomatis. Important differences manifest in the polymorphic membrane protein family specific for the Chlamydiae and in the highly variable chlamydial plasticity zone. We identified a number of psittaci-specific polymorphic membrane proteins of the G family that may be related to differences in host-range and/or virulence as compared to closely related Chlamydiaceae. We calculated non-synonymous to synonymous substitution rate ratios for pairs of orthologous genes to identify putative targets of adaptive evolution and predicted type III secreted effector proteins. Conclusions This study is the first detailed analysis of the Chlamydia psittaci genome sequence. It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions. PMID:22506068

  15. A comparative reliability analysis of computer-generated bitemark overlays.

    PubMed

    McNamee, Anne H; Sweet, David; Pretty, Iain

    2005-03-01

    This study compared the reliability of two methods used to produce computer-generated bitemark overlays with Adobe Photoshop (Adobe Systems Inc., San Jose, CA). Scanned images of twelve dental casts were sent to 30 examiners with different experience levels. Examiners were instructed to produce an overlay for each cast image based on the instructions provided for the two techniques. Measurements of the area and the x-y coordinate position of the biting edges of the anterior teeth were obtained using Scion Image software program (Scion Corporation, Frederick, MD) for each overlay. The inter- and intra-reliability assessment of the measurements was performed using an analysis of variance and calculation of reliability coefficients. The assessment of the area measurements showed significant variances seen in the examiner variable for both techniques resulting in low reliability coefficients. Conversely, the results for the positional measurements showed no significant differences in the variances between examiners with exceptionally high reliability coefficients. It was concluded that both techniques were reliable methods to produce bitemark overlays in assessing tooth position. PMID:15818864

  16. Comparative analysis of shell rendering and shear-warp rendering

    NASA Astrophysics Data System (ADS)

    Falcao, Alexandre X.; Rocha, Leonardo M.; Udupa, Jayaram K.

    2002-05-01

    In Medical Imaging, shell rendering and shear-warp rendering are two of the most efficient and effective voxel-based techniques for volume visualization. This work presents a comparative analysis of shell rendering and shear-warp rendering in terms of storage, speed, and image quality. We have chosen 10 different objects of various sizes, shapes and topologies and one 1-GHz Pentium-III PC with 512 MB RAM for our experiments. Hard and fuzzy boundaries of up to 2,833 K voxels in size have been created to test both methods in surface and volume rendering, respectively. Hard surface shell rendering and surface shear-warp rendering required less than 0.5 second. In the worst case, volume shell rendering required 1.45 second, while volume shear-warp rendering spent 0.65 second for the same task. Shear-warp rendering uses on average from 3 to 6 times more memory space than shell rendering, but it can be up to 2.79 times faster than shell rendering. On average, shear-warp rendering is as fast as shell rendering for hard boundaries and 1.7 times faster than shell rendering for fuzzy boundaries. We have also observed that both can produce similar high-quality images.

  17. Comparative analysis of known miRNAs across platyhelminths.

    PubMed

    Jin, Xiaoliang; Lu, Lixia; Su, Hailong; Lou, Zhongzi; Wang, Fang; Zheng, Yadong; Xu, Guo-Tong

    2013-08-01

    MicroRNAs (miRNAs) are a subtype of small regulatory RNAs that are involved in numerous biological processes through small RNA-induced silencing networks. In an attempt to explore the phylogeny of miRNAs across five platyhelminths, we integrated annotated miRNAs and their full genomes. We identified conserved miRNA clusters and, in particular, miR-71/2 was conserved from planarian to parasitic flatworms and was expanded in free-living Schmidtea mediterranea. Analysis of 22 miRNA loci provided compelling evidence that most known miRNAs are conserved across platyhelminths. Meanwhile, we also observed alterations of known protein-coding genes flanking miRNA(s), such as transcriptional direction conversion and locus relocation, in around ~ 41% of 22 known miRNA loci. Compared with Echinococcus multilocularis, the majority of these events occurred in evolution-distant Hymenolepis microstoma, Schistosoma japonicum or/and S. mediterranea. These results imply rearrangement events occurred near the known miRNA loci.

  18. Surgical approaches for nasopharyngeal angiofibroma: comparative analysis and current trends.

    PubMed

    Tosun, Fuat; Ozer, Cem; Gerek, Mustafa; Yetiser, Sertac

    2006-01-01

    This study presents a comparative analysis of current surgical approaches for the treatment of nasopharyngeal angiofibroma, including extension of tumors, postoperative morbidity, complications, and recurrence rate. Twenty-four patients who underwent surgery with the diagnosis of juvenile nasopharyngeal angiofibroma at our department between 1993 and 2003 were retrospectively reviewed according to their clinical presentation, surgical approaches, and prognosis. Radkowski staging scale was used for staging tumors. The transpalatal approach was used in 10 patients before 1999 with tumor stages between Ia and IIa. Transpalatal fistula was encountered in one. Nine patients underwent transnasal endoscopic surgery after 1999 with tumor stages between Ia and IIIa. Lateral rhinotomy in four patients and a degloving approach in one patient were used with tumor stages between IIa and IIIa; postoperative nasal crusting was the most annoying problem in these groups. Recurrent tumor was seen in only one patient who had undergone the transpalatal approach in the 12- to 56-month follow-up period. In this regard, the transnasal endoscopic approach can be used successfully in place of the transpalatal approach due to the former's lesser surgical morbidity and wide lateral exposure of the field in patients with nasopharyngeal angiofibroma. Also, many patients who underwent lateral rhinotomy for the removal of stage IIa, IIb, and IIIa tumors can successfully be treated using the transnasal endoscopic approach. In tumors that extend, infratemporal fossa lateral rhinotomy and degloving approaches provide the optimal exposure but have higher potential for morbidity than does transnasal endoscopic surgery.

  19. Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages.

    PubMed

    Romero, Patricia; Croucher, Nicholas J; Hiller, N Luisa; Hu, Fen Z; Ehrlich, Garth D; Bentley, Stephen D; García, Ernesto; Mitchell, Tim J

    2009-08-01

    Streptococcus pneumoniae is an important human pathogen that often carries temperate bacteriophages. As part of a program to characterize the genetic makeup of prophages associated with clinical strains and to assess the potential roles that they play in the biology and pathogenesis in their host, we performed comparative genomic analysis of 10 temperate pneumococcal phages. All of the genomes are organized into five major gene clusters: lysogeny, replication, packaging, morphogenesis, and lysis clusters. All of the phage particles observed showed a Siphoviridae morphology. The only genes that are well conserved in all the genomes studied are those involved in the integration and the lysis of the host in addition to two genes, of unknown function, within the replication module. We observed that a high percentage of the open reading frames contained no similarities to any sequences catalogued in public databases; however, genes that were homologous to known phage virulence genes, including the pblB gene of Streptococcus mitis and the vapE gene of Dichelobacter nodosus, were also identified. Interestingly, bioinformatic tools showed the presence of a toxin-antitoxin system in the phage phiSpn_6, and this represents the first time that an addition system in a pneumophage has been identified. Collectively, the temperate pneumophages contain a diverse set of genes with various levels of similarity among them. PMID:19502408

  20. Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching.

    PubMed

    Page, R D

    2000-10-15

    Comparative analysis is the preferred method of inferring RNA secondary structure, but its use requires considerable expertise and manual effort. As the importance of secondary structure for accurate sequence alignment and phylogenetic analysis becomes increasingly realised, the need for secondary structure models for diverse taxonomic groups becomes more pressing. The number of available structures bears little relation to the relative diversity or importance of the different taxonomic groups. Insects, for example, comprise the largest group of animals and yet are very poorly represented in secondary structure databases. This paper explores the utility of maximum weighted matching (MWM) to help automate the process of comparative analysis by inferring secondary structure for insect mitochondrial small subunit (12S) rRNA sequences. By combining information on correlated changes in substitutions and helix dot plots, MWM can rapidly generate plausible models of secondary structure. These models can be further refined using standard comparative techniques. This paper presents a secondary structure model for insect 12S rRNA based on an alignment of 225 insect sequences and an alignment for 16 exemplar insect sequences. This alignment is used as a template for a web server that automatically generates secondary structures for insect sequences.

  1. Locating Pleistocene Refugia: Comparing Phylogeographic and Ecological Niche Model Predictions

    PubMed Central

    Waltari, Eric; Hijmans, Robert J.; Peterson, A. Townsend; Nyári, Árpád S.; Perkins, Susan L.; Guralnick, Robert P.

    2007-01-01

    Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution. PMID:17622339

  2. Is racism dead? Comparing (expressive) means and (structural equation) models.

    PubMed

    Leach, C W; Peng, T R; Volckens, J

    2000-09-01

    Much scholarship suggests that racism--belief in out-group inferiority--is unrelated to contemporary attitudes. Purportedly, a new form of racism, one which relies upon a belief in cultural difference, has become a more acceptable basis for such attitudes. The authors argue that an appropriate empirical assessment of racism (both 'old' and 'new') depends upon (1) clear conceptualization and operationalization, and (2) attention to both mean-level expression and explanatory value in structural equation models. This study assessed the endorsement of racism and belief in cultural difference as well as their association with a measure of general attitude in a secondary analysis of parallel representative surveys of attitudes toward different ethnic out-groups in France, The Netherlands, Western Germany and Britain (N = 3242; see Reif & Melich, 1991). For six of the seven out-group targets, racism was strongly related to ethnic majority attitudes, despite low mean-level endorsement. In a pattern consistent with a 'new', indirect racism, the relationship between British racism and attitudes toward Afro-Caribbeans was mediated by belief in cultural difference.

  3. Comparative transcriptomic analysis of human and Drosophila extracellular vesicles

    PubMed Central

    Lefebvre, Fabio Alexis; Benoit Bouvrette, Louis Philip; Perras, Lilyanne; Blanchet-Cohen, Alexis; Garnier, Delphine; Rak, Janusz; Lécuyer, Éric

    2016-01-01

    Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that human and Drosophila cells release similar EVs with diameters ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNAs, related pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these sizeable similarities suggest that EVs could potentially enable RNA-mediated intercellular communication in Drosophila. PMID:27282340

  4. Comparative Analysis of Transposable Element Vector Systems in Human Cells

    PubMed Central

    Grabundzija, Ivana; Irgang, Markus; Mátés, Lajos; Belay, Eyayu; Matrai, Janka; Gogol-Döring, Andreas; Kawakami, Koichi; Chen, Wei; Ruiz, Patricia; Chuah, Marinee K. L.; VandenDriessche, Thierry; Izsvák, Zsuzsanna; Ivics, Zoltán

    2010-01-01

    Transposon-based gene vectors have become indispensable tools in vertebrate genetics for applications ranging from insertional mutagenesis and transgenesis in model species to gene therapy in humans. The transposon toolkit is expanding, but a careful, side-by-side characterization of the diverse transposon systems has been lacking. Here we compared the Sleeping Beauty (SB), piggyBac (PB), and Tol2 transposons with respect to overall activity, overproduction inhibition (OPI), target site selection, transgene copy number as well as long-term expression in human cells. SB was the most efficient system under conditions where the availability of the transposon DNA is limiting the transposition reaction including hard-to-transfect hematopoietic stem/progenitor cells (HSCs), and the most sensitive to OPI, underpinning the need for careful optimization of the transposon components. SB and PB were about equally active, and both more efficient than Tol2, under nonrestrictive conditions. All three systems provided long-term transgene expression in human cells with minimal signs of silencing. Indeed, mapping of Tol2 insertion sites revealed significant underrepresentation within chromosomal regions with H3K27me3 histone marks typically associated with transcriptionally repressed heterochromatin. SB, Tol2, and PB constitute complementary research tools for gene transfer in mammalian cells with important implications for fundamental and translational research. PMID:20372108

  5. Regulating transgenic crops: a comparative analysis of different regulatory processes.

    PubMed

    Jaffe, Gregory

    2004-02-01

    Transgenic crops have the potential to benefit both developed and developing countries. To ensure safe crops to humans and the environment, a strong, but not stifling, regulatory system needs to be established and properly implemented. This paper explores some essential components of a strong regulatory structure for transgenic crops. First, five different regulatory systems for transgenic crops--the United States, the European Union, South Africa, Taiwan, and Argentina--are described and explained. The major components of those systems are then compared to components necessary to a regulatory system that ensures safe products and engenders public trust. The key components discussed include: (1) mandatory pre-market approval; (2) established safety standards; (3) transparency; (4) public participation; (5) use of outside scientists for expert scientific advice; (6) independent agency decisions; (7) post-approval activities; and (8) enforcement authority and resources. Although no one of the existing systems analyzed adequately achieves all the necessary components of a strong regulatory system, those systems serve as models for deciding which regulatory procedures should be emulated and which should be avoided. A mandatory pre-market approval system that applies established safety standards in procedures that are transparent and allows for public participation with no pre-conceived notions or biases will best achieve both safe products and consumer trust.

  6. Comparing vector–host and SIR models for dengue transmission.

    PubMed

    Pandey, Abhishek; Mubayi, Anuj; Medlock, Jan

    2013-12-01

    Various simple mathematical models have been used to investigate dengue transmission. Some of these models explicitly model the mosquito population, while others model the mosquitoes implicitly in the transmission term. We study the impact of modeling assumptions on the dynamics of dengue in Thailand by fitting dengue hemorrhagic fever (DHF) data to simple vector–host and SIR models using Bayesian Markov chain Monte Carlo estimation. The parameter estimates obtained for both models were consistent with previous studies. Most importantly, model selection found that the SIR model was substantially better than the vector–host model for the DHF data from Thailand. Therefore, explicitly incorporating the mosquito population may not be necessary in modeling dengue transmission for some populations.

  7. Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

    PubMed Central

    Bergstrand, Lee H.; Cardenas, Erick; Holert, Johannes; Van Hamme, Jonathan D.

    2016-01-01

    ABSTRACT Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A pathway for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degradation genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid metabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacteria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria. PMID:26956583

  8. Comparing standardized coefficients in structural equation modeling: a model reparameterization approach.

    PubMed

    Kwan, Joyce L Y; Chan, Wai

    2011-09-01

    We propose a two-stage method for comparing standardized coefficients in structural equation modeling (SEM). At stage 1, we transform the original model of interest into the standardized model by model reparameterization, so that the model parameters appearing in the standardized model are equivalent to the standardized parameters of the original model. At stage 2, we impose appropriate linear equality constraints on the standardized model and use a likelihood ratio test to make statistical inferences about the equality of standardized coefficients. Unlike other existing methods for comparing standardized coefficients, the proposed method does not require specific modeling features (e.g., specification of nonlinear constraints), which are available only in certain SEM software programs. Moreover, this method allows researchers to compare two or more standardized coefficients simultaneously in a standard and convenient way. Three real examples are given to illustrate the proposed method, using EQS, a popular SEM software program. Results show that the proposed method performs satisfactorily for testing the equality of standardized coefficients.

  9. Economic Analysis. Computer Simulation Models.

    ERIC Educational Resources Information Center

    Sterling Inst., Washington, DC. Educational Technology Center.

    A multimedia course in economic analysis was developed and used in conjunction with the United States Naval Academy. (See ED 043 790 and ED 043 791 for final reports of the project evaluation and development model.) This volume of the text discusses the simulation of behavioral relationships among variable elements in an economy and presents…

  10. Comparing Longitudinal Coupling and Temporal Delay in a Transmission-Line Model of the Cochlea

    NASA Astrophysics Data System (ADS)

    Homer, Martin; Szalai, Robert; Champneys, Alan; Epp, Bastian

    2011-11-01

    In this paper we compare and contrast the effects of longitudinal coupling and temporal delay on a fluid-structure transmission-line model of the mammalian cochlea. This work is based on recent reports that, in order to qualitatively explain experimental data, models of the basilar membrane impedance must include an exponential term that represents a time-delayed feedback. There are also models that include, e.g., a spatial feed-forward mechanism, whose solution is often approximated by replacing the feed-forward coupling by an exponential term. We show that there is no direct equivalence between the time-delay and the longitudinal coupling mechanisms, although qualitatively similar results can be achieved, albeit in very different regions of parameter space. An investigation of the steady-state outputs shows that both models can display sharp tuning, but that the time-delay model requires negative damping for such an effect to occur. Conversely, the longitudinal coupling model provides the most promising results with small positive damping. These results are extended by a careful stability analysis. We find that, whereas a small time delay can stabilize an unstable transmission-line model (with negative damping), that the longitudinal coupling model is stable when the damping is positive. The techniques developed in the paper are directed towards a more comprehensive analysis of nonlinear models.

  11. Comparing factor analytic models of the DSM-IV personality disorders.

    PubMed

    Huprich, Steven K; Schmitt, Thomas A; Richard, David C S; Chelminski, Iwona; Zimmerman, Mark A

    2010-01-01

    There is little agreement about the latent factor structure of the Diagnostic and Statistical Manual of Mental Disorders (DSM) personality disorders (PDs). Factor analytic studies over the past 2 decades have yielded different results, in part reflecting differences in factor analytic technique, the measure used to assess the PDs, and the changing DSM criteria. In this study, we explore the latent factor structure of the DSM (4th ed.; IV) PDs in a sample of 1200 psychiatric outpatients evaluated with the Structured Interview for DSM-IV PDs (B. Pfohl, N. Blum, & M. Zimmerman, 1997). We first evaluated 2 a priori models of the PDs with confirmatory factor analysis (CFA), reflecting their inherent organization in the DSM-IV: a 3-factor model and a 10-factor model. Fit statistics did not suggest that these models yielded an adequate fit. We then evaluated the latent structure with exploratory factor analysis (EFA). Multiple solutions produced more statistically and theoretically reasonable results, as well as providing clinically useful findings. On the basis of fit statistics and theory, 3 models were evaluated further--the 4-, 5-, and 10-factor models. The 10-factor model, which did not resemble the 10-factor model of the CFA, was determined to be the strongest of all 3 models. Future research should use contemporary methods of evaluating factor analytic results in order to more thoroughly compare various factor solutions.

  12. Model selection for amplitude analysis

    NASA Astrophysics Data System (ADS)

    Guegan, B.; Hardin, J.; Stevens, J.; Williams, M.

    2015-09-01

    Model complexity in amplitude analyses is often a priori under-constrained since the underlying theory permits a large number of possible amplitudes to contribute to most physical processes. The use of an overly complex model results in reduced predictive power and worse resolution on unknown parameters of interest. Therefore, it is common to reduce the complexity by removing from consideration some subset of the allowed amplitudes. This paper studies a method for limiting model complexity from the data sample itself through regularization during regression in the context of a multivariate (Dalitz-plot) analysis. The regularization technique applied greatly improves the performance. An outline of how to obtain the significance of a resonance in a multivariate amplitude analysis is also provided.

  13. Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources.

    PubMed

    Klima, Cassidy L; Cook, Shaun R; Zaheer, Rahat; Laing, Chad; Gannon, Vick P; Xu, Yong; Rasmussen, Jay; Potter, Andrew; Hendrick, Steve; Alexander, Trevor W; McAllister, Tim A

    2016-01-01

    Bovine respiratory disease is a common health problem in beef production. The primary bacterial agent involved, Mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. The role of M. haemolytica in pathogenesis is linked to serotype with serotypes 1 (S1) and 6 (S6) isolated from pneumonic lesions and serotype 2 (S2) found in the upper respiratory tract of healthy animals. Here, we sequenced the genomes of 11 strains of M. haemolytica, representing all three serotypes and performed comparative genomics analysis to identify genetic features that may contribute to pathogenesis. Possible virulence associated genes were identified within 14 distinct prophage, including a periplasmic chaperone, a lipoprotein, peptidoglycan glycosyltransferase and a stress response protein. Prophage content ranged from 2-8 per genome, but was higher in S1 and S6 strains. A type I-C CRISPR-Cas system was identified in each strain with spacer diversity and organization conserved among serotypes. The majority of spacers occur in S1 and S6 strains and originate from phage suggesting that serotypes 1 and 6 may be more resistant to phage predation. However, two spacers complementary to the host chromosome targeting a UDP-N-acetylglucosamine 2-epimerase and a glycosyl transferases group 1 gene are present in S1 and S6 strains only indicating these serotypes may employ CRISPR-Cas to regulate gene expression to avoid host immune responses or enhance adhesion during infection. Integrative conjugative elements are present in nine of the eleven genomes. Three of these harbor extensive multi-drug resistance cassettes encoding resistance against the majority of drugs used to combat infection in beef cattle, including macrolides and tetracyclines used in human medicine. The findings here identify key features that are likely contributing to serotype related pathogenesis and specific targets for vaccine design intended to reduce the

  14. A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae

    PubMed Central

    Ševčíková, Tereza; Klimeš, Vladimír; Zbránková, Veronika; Strnad, Hynek; Hroudová, Miluše; Vlček, Čestmír; Eliáš, Marek

    2016-01-01

    Eustigmatophyceae (Ochrophyta, Stramenopiles) is a small algal group with species of the genus Nannochloropsis being its best studied representatives. Nuclear and organellar genomes have been recently sequenced for several Nannochloropsis spp., but phylogenetically wider genomic studies are missing for eustigmatophytes. We sequenced mitochondrial genomes (mitogenomes) of three species representing most major eustigmatophyte lineages, Monodopsis sp. MarTras21, Vischeria sp. CAUP Q 202 and Trachydiscus minutus, and carried out their comparative analysis in the context of available data from Nannochloropsis and other stramenopiles, revealing a number of noticeable findings. First, mitogenomes of most eustigmatophytes are highly collinear and similar in the gene content, but extensive rearrangements and loss of three otherwise ubiquitous genes happened in the Vischeria lineage; this correlates with an accelerated evolution of mitochondrial gene sequences in this lineage. Second, eustigmatophytes appear to be the only ochrophyte group with the Atp1 protein encoded by the mitogenome. Third, eustigmatophyte mitogenomes uniquely share a truncated nad11 gene encoding only the C-terminal part of the Nad11 protein, while the N-terminal part is encoded by a separate gene in the nuclear genome. Fourth, UGA as a termination codon and the cognate release factor mRF2 were lost from mitochondria independently by the Nannochloropsis and T. minutus lineages. Finally, the rps3 gene in the mitogenome of Vischeria sp. is interrupted by the UAG codon, but the genome includes a gene for an unusual tRNA with an extended anticodon loop that we speculate may serve as a suppressor tRNA to properly decode the rps3 gene. PMID:26872774

  15. A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae.

    PubMed

    Ševčíková, Tereza; Klimeš, Vladimír; Zbránková, Veronika; Strnad, Hynek; Hroudová, Miluše; Vlček, Čestmír; Eliáš, Marek

    2016-03-01

    Eustigmatophyceae (Ochrophyta, Stramenopiles) is a small algal group with species of the genus Nannochloropsis being its best studied representatives. Nuclear and organellar genomes have been recently sequenced for several Nannochloropsis spp., but phylogenetically wider genomic studies are missing for eustigmatophytes. We sequenced mitochondrial genomes (mitogenomes) of three species representing most major eustigmatophyte lineages, Monodopsis sp. MarTras21, Vischeria sp. CAUP Q 202 and Trachydiscus minutus, and carried out their comparative analysis in the context of available data from Nannochloropsis and other stramenopiles, revealing a number of noticeable findings. First, mitogenomes of most eustigmatophytes are highly collinear and similar in the gene content, but extensive rearrangements and loss of three otherwise ubiquitous genes happened in the Vischeria lineage; this correlates with an accelerated evolution of mitochondrial gene sequences in this lineage. Second, eustigmatophytes appear to be the only ochrophyte group with the Atp1 protein encoded by the mitogenome. Third, eustigmatophyte mitogenomes uniquely share a truncated nad11 gene encoding only the C-terminal part of the Nad11 protein, while the N-terminal part is encoded by a separate gene in the nuclear genome. Fourth, UGA as a termination codon and the cognate release factor mRF2 were lost from mitochondria independently by the Nannochloropsis and T. minutus lineages. Finally, the rps3 gene in the mitogenome of Vischeria sp. is interrupted by the UAG codon, but the genome includes a gene for an unusual tRNA with an extended anticodon loop that we speculate may serve as a suppressor tRNA to properly decode the rps3 gene. PMID:26872774

  16. Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources

    PubMed Central

    Klima, Cassidy L.; Cook, Shaun R.; Zaheer, Rahat; Laing, Chad; Gannon, Vick P.; Xu, Yong; Rasmussen, Jay; Potter, Andrew; Hendrick, Steve; Alexander, Trevor W.; McAllister, Tim A.

    2016-01-01

    Bovine respiratory disease is a common health problem in beef production. The primary bacterial agent involved, Mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. The role of M. haemolytica in pathogenesis is linked to serotype with serotypes 1 (S1) and 6 (S6) isolated from pneumonic lesions and serotype 2 (S2) found in the upper respiratory tract of healthy animals. Here, we sequenced the genomes of 11 strains of M. haemolytica, representing all three serotypes and performed comparative genomics analysis to identify genetic features that may contribute to pathogenesis. Possible virulence associated genes were identified within 14 distinct prophage, including a periplasmic chaperone, a lipoprotein, peptidoglycan glycosyltransferase and a stress response protein. Prophage content ranged from 2–8 per genome, but was higher in S1 and S6 strains. A type I-C CRISPR-Cas system was identified in each strain with spacer diversity and organization conserved among serotypes. The majority of spacers occur in S1 and S6 strains and originate from phage suggesting that serotypes 1 and 6 may be more resistant to phage predation. However, two spacers complementary to the host chromosome targeting a UDP-N-acetylglucosamine 2-epimerase and a glycosyl transferases group 1 gene are present in S1 and S6 strains only indicating these serotypes may employ CRISPR-Cas to regulate gene expression to avoid host immune responses or enhance adhesion during infection. Integrative conjugative elements are present in nine of the eleven genomes. Three of these harbor extensive multi-drug resistance cassettes encoding resistance against the majority of drugs used to combat infection in beef cattle, including macrolides and tetracyclines used in human medicine. The findings here identify key features that are likely contributing to serotype related pathogenesis and specific targets for vaccine design intended to reduce the

  17. A comparative study of RNA-seq analysis strategies

    PubMed Central

    Jänes, Jürgen; Hu, Fengyuan; Lewin, Alexandra

    2015-01-01

    Three principal approaches have been proposed for inferring the set of transcripts expressed in RNA samples using RNA-seq. The simplest approach uses curated annotations, which assumes the transcripts in a sample are a subset of the transcripts listed in a curated database. A more ambitious method involves aligning reads to a reference genome and using the alignments to infer the transcript structures, possibly with the aid of a curated transcript database. The most challenging approach is to assemble reads into putative transcripts de novo without the aid of reference data. We have systematically assessed the properties of these three approaches through a simulation study. We have found that the sensitivity of computational transcript set estimation is severely limited. Computational approaches (both genome-guided and de novo assembly) produce a large number of artefacts, which are assigned large expression estimates and absorb a substantial proportion of the signal when performing expression analysis. The approach using curated annotations shows good expression correlation even when the annotations are incomplete. Furthermore, any incorrect transcripts present in a curated set do not absorb much signal, so it is preferable to have a curation set with high sensitivity than high precision. Software to simulate transcript sets, expression values and sequence reads under a wider range of parameter values and to compare sensitivity, precision and signal-to-noise ratios of different methods is freely available online (https://github.com/boboppie/RSSS) and can be expanded by interested parties to include methods other than the exemplars presented in this article. PMID:25788326

  18. A Comparative Metroscope Model for Urban Information Flows

    NASA Astrophysics Data System (ADS)

    Fink, J. H.; Shandas, V.; Beaudoin, F.

    2011-12-01

    One of the most promising ways to achieve global sustainability goals of climate stabilization, poverty reduction, and biodiversity preservation is to make the world's cities more efficient, equitable, and healthful. While each city must follow a unique and somewhat idiosyncratic path toward these linked goals based on its history, geography, demography, and politics, movement in this direction can accelerate if cities can learn from each other more effectively. Such learning requires the identification of common characteristics and methodologies. We have created a framework for organizing and applying urban information flows, which we refer to as "Metroscopes." Metroscopes, which are analogous to the large instruments that have advanced the physical and life sciences, integrate six elements: data collection and input; classification through the use of metrics; data storage and retrieval; analytics and modeling; decision support including visualization and scenario generation; and assessment of the effectiveness of policy choices. Standards for each of these elements can be agreed upon by relevant urban science and policy sub-communities, and then can evolve as technologies and practices advance. We are implementing and calibrating this approach using data and relationships from Portland (OR), Phoenix (AZ) and London (UK). Elements that are being integrated include the Global City Indicators Facility at University of Toronto, the J-Earth database system and Decision Theater from Arizona State University, urban mobility analyses performed by the SENSEable City Lab at MIT, and Portland's Ecodistrict approach for urban management. Individual Metroscopes can be compared directly from one city to another, or with larger assemblages of cities like those being classified by ICLEI's STAR program, the Clinton Climate Initiative's C40, and Siemens Green Cities Index. This large-scale integration of urban data sets and approaches and its systematic comparison are key steps

  19. Comparative assessment of three-phase oil relative permeability models

    NASA Astrophysics Data System (ADS)

    Ranaee, Ehsan; Riva, Monica; Porta, Giovanni M.; Guadagnini, Alberto

    2016-07-01

    We assess the ability of 11 models to reproduce three-phase oil relative permeability (kro) laboratory data obtained in a water-wet sandstone sample. We do so by considering model performance when (i) solely two-phase data are employed to render predictions of kro and (ii) two and three-phase data are jointly used for model calibration. In the latter case, a Maximum Likelihood (ML) approach is used to estimate model parameters. The tested models are selected among (i) classical models routinely employed in practical applications and implemented in commercial reservoir software and (ii) relatively recent models which are considered to allow overcoming some drawbacks of the classical formulations. Among others, the latter set of models includes the formulation recently proposed by Ranaee et al., which has been shown to embed the critical effects of hysteresis, including the reproduction of oil remobilization induced by gas injection in water-wet media. We employ formal model discrimination criteria to rank models according to their skill to reproduce the observed data and use ML Bayesian model averaging to provide model-averaged estimates (and associated uncertainty bounds) of kro by taking advantage of the diverse interpretive abilities of all models analyzed. The occurrence of elliptic regions is also analyzed for selected models in the framework of the classical fractional flow theory of displacement. Our study confirms that model outcomes based on channel flow theory and classical saturation-weighted interpolation models do not generally yield accurate reproduction of kro data, especially in the regime associated with low oil saturations, where water alternating gas injection (WAG) techniques are usually employed for enhanced oil recovery. This negative feature is not observed in the model of Ranaee et al. (2015) due to its ability to embed key effects of pore-scale phase distributions, such as hysteresis effects and cycle dependency, for modeling kro observed

  20. Comparative analysis of multisensor satellite monitoring of Arctic sea-ice

    USGS Publications Warehouse

    Belchansky, G.I.; Mordvintsev, I.N.; Douglas, D.C.

    1999-01-01

    This report represents comparative analysis of nearly coincident Russian OKEAN-01 polar orbiting satellite data, Special Sensor Microwave Imager (SSM/I) and Advanced Very High Resolution Radiometer (AVHRR) imagery. OKEAN-01 ice concentration algorithms utilize active and passive microwave measurements and a linear mixture model for measured values of the brightness temperature and the radar backscatter. SSM/I and AVHRR ice concentrations were computed with NASA Team algorithm and visible and thermal-infrared wavelength AVHRR data, accordingly

  1. Highly comparative time-series analysis: the empirical structure of time series and their methods.

    PubMed

    Fulcher, Ben D; Little, Max A; Jones, Nick S

    2013-06-01

    The process of collecting and organizing sets of observations represents a common theme throughout the history of science. However, despite the ubiquity of scientists measuring, recording and analysing the dynamics of different processes, an extensive organization of scientific time-series data and analysis methods has never been performed. Addressing this, annotated collections of over 35 000 real-world and model-generated time series, and over 9000 time-series analysis algorithms are analysed in this work. We introduce reduced representations of both time series, in terms of their properties measured by diverse scientific methods, and of time-series analysis methods, in terms of their behaviour on empirical time series, and use them to organize these interdisciplinary resources. This new approach to comparing across diverse scientific data and methods allows us to organize time-series datasets automatically according to their properties, retrieve alternatives to particular analysis methods developed in other scientific disciplines and automate the selection of useful methods for time-series classification and regression tasks. The broad scientific utility of these tools is demonstrated on datasets of electroencephalograms, self-affine time series, heartbeat intervals, speech signals and others, in each case contributing novel analysis techniques to the existing literature. Highly comparative techniques that compare across an interdisciplinary literature can thus be used to guide more focused research in time-series analysis for applications across the scientific disciplines.

  2. Comparative study of nitrate leaching models on a regional scale.

    PubMed

    Roelsma, J; Hendriks, R F A

    2014-11-15

    In Europe and North America the application of high levels of manure and fertilisers on agricultural land has led to high levels of nitrate concentrations in groundwater, in particular on sandy soils. For the evaluation of the development of the quality of groundwater a sound quantitative basis is needed. In this paper a comparison has been made between observations of nitrate concentrations in the upper groundwater and predictions of nitrate leaching models. Observations of nitrate concentrations in the upper groundwater at three different locations in regions with mainly sandy soils in the eastern and northern part of the Netherlands were used to test the performance of the simulation models to predict nitrate leaching to the upper groundwater. Four different types of simulation models of different levels of complexity and input data requirement were tested. These models are ANIMO (dynamic complex process oriented model), MM-WSV (meta-model), WOG (simple process oriented model) and NURP (semi-empiric model). The performance of the different simulation models was evaluated using statistical criteria. The dynamic complex process oriented ANIMO model showed the best model performance. The MM-WSV meta-model was the second best model, whilst the simple process oriented WOG model produced the worst model performance. The best model performance showed the dynamic complex process oriented ANIMO model in predicting the nitrate concentrations in the upper groundwater of the Klooster catchment. The good performance of the ANIMO model for this catchment can be explained by the additional information about the use of manure and fertilisers at farm level in this study area. The ANIMO model may be a good tool to predict nitrate concentrations in the upper groundwater on a regional scale. However, the use of a detailed process oriented simulation model requires a comprehensive set of input data. If such a comprehensive data-set is not available the MM-WSV model (meta-model

  3. Comparative analysis of seismic response characteristics of pile-soil-structure interaction system

    NASA Astrophysics Data System (ADS)

    Kong, Desen; Luan, Maotian; Wang, Weiming

    2006-01-01

    The study on the earthquake-resistant performance of a pile-soil-structure interaction system is a relatively complicated and primarily important issue in civil engineering practice. In this paper, a computational model and computation procedures for pile-supported structures, which can duly consider the pile-soil interaction effect, are established by the finite element method. Numerical implementation is made in the time domain. A simplified approximation for the seismic response analysis of pile-soil-structure systems is briefly presented. Then a comparative study is performed for an engineering example with numerical results computed respectively by the finite element method and the simplified method. Through comparative analysis, it is shown that the results obtained by the simplified method well agree with those achieved by the finite element method. The numerical results and findings will offer instructive guidelines for earthquake-resistant analysis and design of pile-supported structures.

  4. Comparative analysis of programmed cell death pathways in filamentous fungi

    PubMed Central

    Fedorova, Natalie D; Badger, Jonathan H; Robson, Geoff D; Wortman, Jennifer R; Nierman, William C

    2005-01-01

    Background Fungi can undergo autophagic- or apoptotic-type programmed cell death (PCD) on exposure to antifungal agents, developmental signals, and stress factors. Filamentous fungi can also exhibit a form of cell death called heterokaryon incompatibility (HI) triggered by fusion between two genetically incompatible individuals. With the availability of recently sequenced genomes of Aspergillus fumigatus and several related species, we were able to define putative components of fungi-specific death pathways and the ancestral core apoptotic machinery shared by all fungi and metazoa. Results Phylogenetic profiling of HI-associated proteins from four Aspergilli and seven other fungal species revealed lineage-specific protein families, orphan genes, and core genes conserved across all fungi and metazoa. The Aspergilli-specific domain architectures include NACHT family NTPases, which may function as key integrators of stress and nutrient availability signals. They are often found fused to putative effector domains such as Pfs, SesB/LipA, and a newly identified domain, HET-s/LopB. Many putative HI inducers and mediators are specific to filamentous fungi and not found in unicellular yeasts. In addition to their role in HI, several of them appear to be involved in regulation of cell cycle, development and sexual differentiation. Finally, the Aspergilli possess many putative downstream components of the mammalian apoptotic machinery including several proteins not found in the model yeast, Saccharomyces cerevisiae. Conclusion Our analysis identified more than 100 putative PCD associated genes in the Aspergilli, which may help expand the range of currently available treatments for aspergillosis and other invasive fungal diseases. The list includes species-specific protein families as well as conserved core components of the ancestral PCD machinery shared by fungi and metazoa. PMID:16336669

  5. A comparative analysis of spindle morphometrics across metazoans

    PubMed Central

    Crowder, Marina E.; Strzelecka, Magdalena; Wilbur, Jeremy D.; Good, Matthew C.; von Dassow, George; Heald, Rebecca

    2015-01-01

    Summary Cell division in all eukaryotes depends on function of the spindle, a microtubule-based structure that segregates chromosomes to generate daughter cells in mitosis or haploid gametes in meiosis. Spindle size adapts to changes in cell size and shape, which vary dramatically across species and within a multicellular organism, but the nature of scaling events and their underlying mechanisms are poorly understood. Cell size variations are most pronounced in early animal development, as egg diameters range from tens of microns up to millimeters across animal phyla, and decrease several orders of magnitude during rapid reductive divisions. During early embryogenesis in the model organisms X. laevis and C. elegans, the spindle scales with cell size [1,2], a phenomenon regulated by molecules that modulate microtubule dynamics [3–6], as well as by limiting cytoplasmic volume [7,8]. However, it is not known to what extent spindle scaling is conserved across organisms and among different cell types. Here we show that in a range of metazoan phyla, mitotic spindle length decreased with cell size across a ~30 fold difference in zygote size. Maximum spindle length varied, but linear spindle scaling occurred similarly in all species once embryonic cell diameter reduced to 140 μm. In contrast, we find that the female meiotic spindle does not scale as closely to egg size, adopting a more uniform size across species that likely reflects its specialized function. Our analysis reveals that spindle morphometrics change abruptly, within one cell cycle, at the transition from meiosis to mitosis in most animals. PMID:26004761

  6. Urban Detection, Delimitation and Morphology: Comparative Analysis of Selective "MEGACITIES"

    NASA Astrophysics Data System (ADS)

    Alhaddad, B.; Arellano, B. E.; Roca, J.

    2012-08-01

    Over the last 50 years, the world has faced an impressive growth of urban population. The walled city, close to the outside, an "island"for economic activities and population density within the rural land, has led to the spread of urban life and urban networks in almost all the territory. There was, as said Margalef (1999), "a topological inversion of the landscape". The "urban" has gone from being an island in the ocean of rural land vastness, to represent the totally of the space in which are inserted natural and rural "systems". New phenomena such as the fall of the fordist model of production, the spread of urbanization known as urban sprawl, and the change of scale of the metropolis, covering increasingly large regions, called "megalopolis" (Gottmann, 1961), have characterized the century. However there are no rigorous databases capable of measuring and evaluating the phenomenon of megacities and in general the process of urbanization in the contemporary world. The aim of this paper is to detect, identify and analyze the morphology of the megacities through remote sensing instruments as well as various indicators of landscape. To understand the structure of these heterogeneous landscapes called megacities, land consumption and spatial complexity needs to be quantified accurately. Remote sensing might be helpful in evaluating how the different land covers shape urban megaregions. The morphological landscape analysis allows establishing the analogies and the differences between patterns of cities and studying the symmetry, growth direction, linearity, complexity and compactness of the urban form. The main objective of this paper is to develop a new methodology to detect urbanized land of some megacities around the world (Tokyo, Mexico, Chicago, New York, London, Moscow, Sao Paulo and Shanghai) using Landsat 7 images.

  7. Addressing Informatics Barriers to Conducting Observational Comparative Effectiveness Research: A Comparative Case Analysis

    ERIC Educational Resources Information Center

    Boone, Christopher P. D.

    2013-01-01

    Background: The U.S. health care system has been under immense scrutiny for ever-increasing costs and poor health outcomes for its patients. Comparative Effectiveness Research (CER) has emerged as a generally accepted practice by providers, policy makers, and scientists as an approach to identify the most clinical- and cost-effective interventions…

  8. Comparative Spectroscopic Analysis of B[e] Supergiants and LBV

    NASA Astrophysics Data System (ADS)

    Borges Fernandes, M.

    2000-02-01

    The upper HRD is populated by massive stars. These objects have, as a characteristic, a substantial mass loss, due mostly to radiation pressure, throughout their whole lives. However about the evolution of these stars, the only secure informations are that they are B or O type stars in the zero age main sequence and they finish their lifes in a supernova explosion. The difficulties, to ascertain the others evolutive stages of these objects, are that they do not exhibit (in most cases) photosferic absorption lines, du