Science.gov

Sample records for comparative model analysis

  1. Minimalist models for proteins: a comparative analysis.

    PubMed

    Tozzini, Valentina

    2010-08-01

    The last decade has witnessed a renewed interest in the coarse-grained (CG) models for biopolymers, also stimulated by the needs of modern molecular biology, dealing with nano- to micro-sized bio-molecular systems and larger than microsecond timescale. This combination of size and timescale is, in fact, hard to access by atomic-based simulations. Coarse graining the system is a route to be followed to overcome these limits, but the ways of practically implementing it are many and different, making the landscape of CG models very vast and complex. In this paper, the CG models are reviewed and their features, applications and performances compared. This analysis, restricted to proteins, focuses on the minimalist models, namely those reducing at minimum the number of degrees of freedom without losing the possibility of explicitly describing the secondary structures. This class includes models using a single or a few interacting centers (beads) for each amino acid. From this analysis several issues emerge. The difficulty in building these models resides in the need for combining transferability/predictive power with the capability of accurately reproducing the structures. It is shown that these aspects could be optimized by accurately choosing the force field (FF) terms and functional forms, and combining different parameterization procedures. In addition, in spite of the variety of the minimalist models, regularities can be found in the parameters values and in FF terms. These are outlined and schematically presented with the aid of a generic phase diagram of the polypeptide in the parameter space and, hopefully, could serve as guidelines for the development of minimalist models incorporating the maximum possible level of predictive power and structural accuracy.

  2. 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…

  3. 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.

  4. 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.

  5. Multiattribute Decision Modeling Techniques: A Comparative Analysis

    DTIC Science & Technology

    1988-08-01

    Rating Technique (SMART) as a direct response to Raiffa’s (1969) article on multiattribute utility theory , which Edwards found extremcy stimulating but...approaches such as multiattribute utility /value assessment and hierarchical analysis and have applied these techniques to a number of non-military... multiattributed ) outcomes O(l)...O(k), and if the utility function is denoted by u and the probabilities of the k events are p(l)...p(k), then the

  6. A Comparative Analysis of Toxicity Models

    DTIC Science & Technology

    2008-04-01

    A-1 B. Selected Gridgen Parameter Values...ranged between 3 and 80 minutes. Agent dispersion was modeled using IDA’s GRIDGEN program, which is a modification of VLSTRACK v. 1.6.3 to give...BioStrike 2 compatible output. The values of some of the parameters used in GRIDGEN are given in Appendix B. GRIDGEN output is in the form of the

  7. Tools for comparative protein structure modeling and analysis.

    PubMed

    Eswar, Narayanan; John, Bino; Mirkovic, Nebojsa; Fiser, Andras; Ilyin, Valentin A; Pieper, Ursula; Stuart, Ashley C; Marti-Renom, Marc A; Madhusudhan, M S; Yerkovich, Bozidar; Sali, Andrej

    2003-07-01

    The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB, a web server for automated comparative modeling that relies on PSI-BLAST, IMPALA and MODELLER; MODLOOP, a web server for automated loop modeling that relies on MODELLER; MOULDER, a CPU intensive protocol of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure; MODVIEW, a Netscape plugin for Linux that integrates viewing of multiple sequences and structures; and SNPWEB, a web server for structure-based prediction of the functional impact of a single amino acid substitution.

  8. Comparative analysis of used car price evaluation models

    NASA Astrophysics Data System (ADS)

    Chen, Chuancan; Hao, Lulu; Xu, Cong

    2017-05-01

    An accurate used car price evaluation is a catalyst for the healthy development of used car market. Data mining has been applied to predict used car price in several articles. However, little is studied on the comparison of using different algorithms in used car price estimation. This paper collects more than 100,000 used car dealing records throughout China to do empirical analysis on a thorough comparison of two algorithms: linear regression and random forest. These two algorithms are used to predict used car price in three different models: model for a certain car make, model for a certain car series and universal model. Results show that random forest has a stable but not ideal effect in price evaluation model for a certain car make, but it shows great advantage in the universal model compared with linear regression. This indicates that random forest is an optimal algorithm when handling complex models with a large number of variables and samples, yet it shows no obvious advantage when coping with simple models with less variables.

  9. 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.

  10. Comparative analysis of existing models for power-grid synchronization

    NASA Astrophysics Data System (ADS)

    Nishikawa, Takashi; Motter, Adilson E.

    2015-01-01

    The dynamics of power-grid networks is becoming an increasingly active area of research within the physics and network science communities. The results from such studies are typically insightful and illustrative, but are often based on simplifying assumptions that can be either difficult to assess or not fully justified for realistic applications. Here we perform a comprehensive comparative analysis of three leading models recently used to study synchronization dynamics in power-grid networks—a fundamental problem of practical significance given that frequency synchronization of all power generators in the same interconnection is a necessary condition for a power grid to operate. We show that each of these models can be derived from first principles within a common framework based on the classical model of a generator, thereby clarifying all assumptions involved. This framework allows us to view power grids as complex networks of coupled second-order phase oscillators with both forcing and damping terms. Using simple illustrative examples, test systems, and real power-grid datasets, we study the inherent frequencies of the oscillators as well as their coupling structure, comparing across the different models. We demonstrate, in particular, that if the network structure is not homogeneous, generators with identical parameters need to be modeled as non-identical oscillators in general. We also discuss an approach to estimate the required (dynamical) system parameters that are unavailable in typical power-grid datasets, their use for computing the constants of each of the three models, and an open-source MATLAB toolbox that we provide for these computations.

  11. Comparative Proteomic Analysis of Two Uveitis Models in Lewis Rats

    PubMed Central

    Pepple, Kathryn L.; Rotkis, Lauren; Wilson, Leslie; Sandt, Angela; Van Gelder, Russell N.

    2015-01-01

    Purpose Inflammation generates changes in the protein constituents of the aqueous humor. Proteins that change in multiple models of uveitis may be good biomarkers of disease or targets for therapeutic intervention. The present study was conducted to identify differentially-expressed proteins in the inflamed aqueous humor. Methods Two models of uveitis were induced in Lewis rats: experimental autoimmune uveitis (EAU) and primed mycobacterial uveitis (PMU). Differential gel electrophoresis was used to compare naïve and inflamed aqueous humor. Differentially-expressed proteins were separated by using 2-D gel electrophoresis and excised for identification with matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF). Expression of select proteins was verified by Western blot analysis in both the aqueous and vitreous. Results The inflamed aqueous from both models demonstrated an increase in total protein concentration when compared to naïve aqueous. Calprotectin, a heterodimer of S100A8 and S100A9, was increased in the aqueous in both PMU and EAU. In the vitreous, S100A8 and S100A9 were preferentially elevated in PMU. Apolipoprotein E was elevated in the aqueous of both uveitis models but was preferentially elevated in EAU. Beta-B2–crystallin levels decreased in the aqueous and vitreous of EAU but not PMU. Conclusions The proinflammatory molecules S100A8 and S100A9 were elevated in both models of uveitis but may play a more significant role in PMU than EAU. The neuroprotective protein β-B2–crystallin was found to decline in EAU. Therapies to modulate these proteins in vivo may be good targets in the treatment of ocular inflammation. PMID:26747776

  12. 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.

  13. Model for Comparative Analysis of Antigen Receptor Repertoires

    PubMed Central

    Rempala, Grzegorz A.; Seweryn, Michał; Ignatowicz, Leszek

    2010-01-01

    In modern molecular biology one of the standard ways of analyzing a vertebrate immune system is to sequence and compare the counts of specific antigen receptor clones (either immunoglobulins or T-cell receptors) derived from various tissues under different experimental or clinical conditions. The resulting statistical challenges are difficult and do not fit readily into the standard statistical framework of contingency tables primarily due to the serious under-sampling of the receptor populations. This under-sampling is caused, on one hand, by the extreme diversity of antigen receptor repertoires maintained by the immune system and, on the other, by the high cost and labor intensity of the receptor data collection process. In most of the recent immunological literature the differences across antigen receptor populations are examined via non-parametric statistical measures of the species overlap and diversity borrowed from ecological studies. While this approach is robust in a wide range of situations, it seems to provide little insight into the underlying clonal size distribution and the overall mechanism differentiating the receptor populations. As a possible alternative, the current paper presents a parametric method that adjusts for the data under-sampling as well as provides a unifying approach to a simultaneous comparison of multiple receptor groups by means of the modern statistical tools of unsupervised learning. The parametric model is based on a flexible multivariate Poisson-lognormal distribution and is seen to be a natural generalization of the univariate Poisson-lognormal models used in the ecological studies of biodiversity patterns. The procedure for evaluating a model’s fit is described along with the public domain software developed to perform the necessary diagnostics. The model-driven analysis is seen to compare favorably vis a vis traditional methods when applied to the data from T-cell receptors in transgenic mice populations. PMID:20955715

  14. Comparative analysis of marine ecosystems: international production modelling workshop.

    PubMed

    Link, Jason S; Megrey, Bernard A; Miller, Thomas J; Essington, Tim; Boldt, Jennifer; Bundy, Alida; Moksness, Erlend; Drinkwater, Ken F; Perry, R Ian

    2010-12-23

    Understanding the drivers that dictate the productivity of marine ecosystems continues to be a globally important issue. A vast literature identifies three main processes that regulate the production dynamics of such ecosystems: biophysical, exploitative and trophodynamic. Exploring the prominence among this 'triad' of drivers, through a synthetic analysis, is critical for understanding how marine ecosystems function and subsequently produce fisheries resources of interest to humans. To explore this topic further, an international workshop was held on 10-14 May 2010, at the National Academy of Science's Jonsson Center in Woods Hole, MA, USA. The workshop compiled the data required to develop production models at different hierarchical levels (e.g. species, guild, ecosystem) for many of the major Northern Hemisphere marine ecosystems that have supported notable fisheries. Analyses focused on comparable total system biomass production, functionally equivalent species production, or simulation studies for 11 different marine fishery ecosystems. Workshop activities also led to new analytical tools. Preliminary results suggested common patterns driving overall fisheries production in these ecosystems, but also highlighted variation in the relative importance of each among ecosystems.

  15. Comparative analysis of four disease prediction models of Parkinson's disease.

    PubMed

    Kumudini, Nadella; Naushad, Shaik Mohammad; Alex Stanley, Balraj; Niveditha, Manoharan; Sharmila, Gunasekaran; Kumaraswami, Konda; Borghain, Rupam; Mridula, Rukmini; Kutala, Vijay Kumar

    2016-01-01

    Parkinson's disease (PD) is a multi-factorial disorder with high-penetrant mutations accounting for small percentage of PD. Our previous studies demonstrated individual association of genetic variants in folate, xenobiotic, and dopamine metabolic pathways with PD risk. The rational of the study was to develop a risk prediction model for PD using these genetic polymorphisms along with synuclein (SNCA) polymorphism. We have generated additive, multifactor dimensionality reduction (MDR), recursive partitioning (RP), and artificial neural network (ANN) models using 21 SNPs as inputs and disease outcome as output. The clinical utility of all these models was assessed by plotting receiver operating characteristics curves where in area under the curve (AUC) was used as an index of diagnostic utility of the model. The additive model was the simplest and exhibited an AUC of 0.72. The MDR model showed significant gene-gene interactions between SNCA, DRD4VNTR, and DRD2A polymorphisms. The RP model showed SHMT C1420T as important determinant of PD risk. This variant allele was found to be protective and this protection was nullified by MTRR A66G. Inheritance of SHMT wild allele and SNCA intronic polymorphism was shown to increase the risk of PD. The ANN model showed higher diagnostic utility (AUC = 0.86) compared to all the models and was able to explain 56.6% cases of sporadic PD. To conclude, the ANN model developed using SNPs in folate, xenobiotic, and dopamine pathways along with SNCA has higher clinical utility in predicting PD risk compared to other models.

  16. Comparative Analysis.

    DTIC Science & Technology

    1987-11-01

    Al" 56 COMPARATIVE ANALYSIS(U) MASSACJWSETTS INST OF TECH 1/1 CAMBRIDGE ARTIFICIAL INTELLIGENCE LAO 9 S MELD NOV B, RI-N-95i NMM4-85-K-0124...0 0 0 0 0 0 i. -~~ --- WU V1 2 fwx~, - - W-na alc F!LFI MASSACHUSETTS INSTITUTE OF TECHNOLOGY CO ARTIFICIAL INTELLIGENCE LABORATORY Lfl 0 Al/Memo...differential qualita- tive (DQ) analysis, which solves the task, providing explanations suitable for use by design systems, automated diagnosis, intelligent

  17. Comparative analysis of modeled nitrogen removal by shellfish farms.

    PubMed

    Rose, Julie M; Bricker, Suzanne B; Ferreira, Joao G

    2015-02-15

    The use of shellfish aquaculture for nutrient removal and reduction of coastal eutrophication has been proposed. Published literature has indicated that nitrogen contained in harvested shellfish can be accurately estimated from shell length:nitrogen content ratios. The range of nitrogen that could be removed by a typical farm in a specific estuarine or coastal setting is also of interest to regulators and planners. Farm Aquaculture Resource Management (FARM) model outputs of nitrogen removal at the shellfish farm scale have been summarized here, from 14 locations in 9 countries across 4 continents. Modeled nitrogen removal ranged from 105 lbs acre(-1) year(-1) (12 g m(-2) year(-1)) to 1356 lbs acre(-1) year(-1) (152 g m(-2) year(-1)). Mean nitrogen removal was 520 lbs acre(-1) year(-1) (58 g m(-2) year(-1)). These model results are site-specific in nature, but compare favorably to reported nitrogen removal effectiveness of agricultural best management practices and stormwater control measures. Published by Elsevier Ltd.

  18. A Comparative Analysis of Global Cropping Systems Models and Maps

    NASA Astrophysics Data System (ADS)

    Anderson, W. B.; You, L.; Wood, S.; Wood-Sichra, U.; Wu, W.

    2013-12-01

    Agricultural practices have dramatically altered the land cover of the Earth, but the spatial extent and intensity of these practices is often difficult to catalogue. Cropland accounts for nearly 15 million km2 of the Earth's land cover - amounting to 12% of the Earth's ice-free land surface - yet information on the distribution and performance of specific crops is often available only through national or sub-national statistics. While remote sensing products offer spatially disaggregated information, those currently available on a global scale are ill-suited for many applications due to the limited separation of crop types within the area classified as cropland. Recently, however, there have been multiple independent efforts to incorporate the detailed information available from statistical surveys with supplemental spatial information to produce a spatially explicit global dataset specific to individual cropss for the year 2000. While these datasets provide analysts and decision makers with improved information on global cropping systems, the final global cropping maps differ from one another substantially. This study aims to explore and quantify systematic similarities and differences between four major global cropping systems products: the monthly irrigated and rainfed crop areas around the year 2000 (MIRAC2000) dataset, the spatial production allocation model (SPAM), the global agro-ecological zone (GAEZ) dataset, and the dataset developed by Monfreda et al., 2008. The analysis explores not only the final cropping systems maps but also the interdependencies of each product, methodological differences and modeling assumptions, which will provide users with information vital for discerning between datasets in selecting a product appropriate for each intended application.

  19. A Comparative Analysis of Community Wind Power DevelopmentModels

    SciTech Connect

    Bolinger, Mark; Wiser, Ryan; Wind, Tom; Juhl, Dan; Grace, Robert; West, Peter

    2005-05-20

    For years, farmers in the United States have looked with envy on their European counterparts ability to profitably farm the wind through ownership of distributed, utility-scale wind projects. Only within the past few years, however, has farmer- or community-owned windpower development become a reality in the United States. The primary hurdle to this type of development in the United States has been devising and implementing suitable business and legal structures that enable such projects to take advantage of tax-based federal incentives for windpower. This article discusses the limitations of such incentives in supporting farmer- or community-owned wind projects, describes four ownership structures that potentially overcome such limitations, and finally conducts comparative financial analysis on those four structures, using as an example a hypothetical 1.5 MW farmer-owned project located in the state of Oregon. We find that material differences in the competitiveness of each structure do exist, but that choosing the best structure for a given project will largely depend on the conditions at hand; e.g., the ability of the farmer(s) to utilize tax credits, preference for individual versus cooperative ownership, and the state and utility service territory in which the project will be located.

  20. 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…

  1. 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…

  2. 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...

  3. 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...

  4. Comparative analysis of conceptual models with error correction, artificial neural networks and committee models

    NASA Astrophysics Data System (ADS)

    Corzo P, Gerald A.; Solomatine, Dimitri

    2014-05-01

    In operational flow forecasting conceptual or process-based hydrological models are typically used, and more and more in combination with precipitation forecasts complemented by corrected data assimilation or data-driven error corrector models. Alternatively, predictive data-driven models, alone or in ensembles, have been employed in different researches, claiming that they ensure high accuracy of flow forecasting; for this, an artificial neural network (ANN) seems to be the most developed in studies. In this paper a comparative analysis of different error correctors and ANN models is made to contribute on the selection of operational. For this we explore the performance of various model combinations forecasting single and multiple time steps. The HBV hydrological model with and without error correction, data-driven models (ANNs) and hybrid committee models integrating conceptual models and ANNs. The capabilities of a model at a single time step (simulation) as well as multiple forecast horizons are represented in comparative graphs. Limitations of the meteorological forecasts are not contemplated in the hydrological forecast scenarios, so precipitation hindcast information was used as input in all models. Single time step forecast simulation of the HBV has 30 percent higher error than a one day forecast ANN model. However, for forecast horizons higher than 3 days a high variability of models' accuracy is found, and the clear dominant performance of the HBV hydrological model with an ANN error corrector is observed. In the forecasts for up to two days the committee and error-corrected models were the best, followed by ANN, and the conceptual model without error correction. The conceptual HBV model alone shows to perform best on long term sequential or iterative forecasts.

  5. Comparative analysis of mathematical models of the matrix photodetector used in digital holography

    NASA Astrophysics Data System (ADS)

    Grebenyuk, K. A.

    2017-08-01

    It is established, that in modern works on digital holography, three fundamentally different mathematical models of a matrix photodetector are used. Comparative analysis of these models, including analysis of the formula of each model and test calculations, has been conducted. The possibility of using these models to account for the influence of geometrical parameters of a matrix photodetector on the properties of recorded digital holograms is considered.

  6. 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…

  7. 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…

  8. 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.

  9. A Comparative Evaluation of Mixed Dentition Analysis on Reliability of Cone Beam Computed Tomography Image Compared to Plaster Model

    PubMed Central

    Gowd, Snigdha; Shankar, T; Dash, Samarendra; Sahoo, Nivedita; Chatterjee, Suravi; Mohanty, Pritam

    2017-01-01

    Aims and Objective: The aim of the study was to evaluate the reliability of cone beam computed tomography (CBCT) obtained image over plaster model for the assessment of mixed dentition analysis. Materials and Methods: Thirty CBCT-derived images and thirty plaster models were derived from the dental archives, and Moyer's and Tanaka-Johnston analyses were performed. The data obtained were interpreted and analyzed statistically using SPSS 10.0/PC (SPSS Inc., Chicago, IL, USA). Descriptive and analytical analysis along with Student's t-test was performed to qualitatively evaluate the data and P < 0.05 was considered statistically significant. Results: Statistically, significant results were obtained on data comparison between CBCT-derived images and plaster model; the mean for Moyer's analysis in the left and right lower arch for CBCT and plaster model was 21.2 mm, 21.1 mm and 22.5 mm, 22.5 mm, respectively. Conclusion: CBCT-derived images were less reliable as compared to data obtained directly from plaster model for mixed dentition analysis. PMID:28852639

  10. A Comparative Evaluation of Mixed Dentition Analysis on Reliability of Cone Beam Computed Tomography Image Compared to Plaster Model.

    PubMed

    Gowd, Snigdha; Shankar, T; Dash, Samarendra; Sahoo, Nivedita; Chatterjee, Suravi; Mohanty, Pritam

    2017-01-01

    The aim of the study was to evaluate the reliability of cone beam computed tomography (CBCT) obtained image over plaster model for the assessment of mixed dentition analysis. Thirty CBCT-derived images and thirty plaster models were derived from the dental archives, and Moyer's and Tanaka-Johnston analyses were performed. The data obtained were interpreted and analyzed statistically using SPSS 10.0/PC (SPSS Inc., Chicago, IL, USA). Descriptive and analytical analysis along with Student's t-test was performed to qualitatively evaluate the data and P < 0.05 was considered statistically significant. Statistically, significant results were obtained on data comparison between CBCT-derived images and plaster model; the mean for Moyer's analysis in the left and right lower arch for CBCT and plaster model was 21.2 mm, 21.1 mm and 22.5 mm, 22.5 mm, respectively. CBCT-derived images were less reliable as compared to data obtained directly from plaster model for mixed dentition analysis.

  11. Fixed Target Comparative Analysis

    DTIC Science & Technology

    1991-12-01

    development was required to produce the 3D models to support evaluation of this 3D model -supported exploitation approach. The comparative analysis techniques...that were developed exploited the fact that the 3D site model data base was available during the automatic processing. This opened up a new range of...processing strategies during the automated image comparison function. In addition, the existence of the 3D site models allows for the development of an

  12. 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.

  13. Comparative analysis of zonal systems for macro-level crash modeling.

    PubMed

    Cai, Qing; Abdel-Aty, Mohamed; Lee, Jaeyoung; Eluru, Naveen

    2017-06-01

    Macro-level traffic safety analysis has been undertaken at different spatial configurations. However, clear guidelines for the appropriate zonal system selection for safety analysis are unavailable. In this study, a comparative analysis was conducted to determine the optimal zonal system for macroscopic crash modeling considering census tracts (CTs), state-wide traffic analysis zones (STAZs), and a newly developed traffic-related zone system labeled traffic analysis districts (TADs). Poisson lognormal models for three crash types (i.e., total, severe, and non-motorized mode crashes) are developed based on the three zonal systems without and with consideration of spatial autocorrelation. The study proposes a method to compare the modeling performance of the three types of geographic units at different spatial configurations through a grid based framework. Specifically, the study region is partitioned to grids of various sizes and the model prediction accuracy of the various macro models is considered within these grids of various sizes. These model comparison results for all crash types indicated that the models based on TADs consistently offer a better performance compared to the others. Besides, the models considering spatial autocorrelation outperform the ones that do not consider it. Based on the modeling results and motivation for developing the different zonal systems, it is recommended using CTs for socio-demographic data collection, employing TAZs for transportation demand forecasting, and adopting TADs for transportation safety planning. The findings from this study can help practitioners select appropriate zonal systems for traffic crash modeling, which leads to develop more efficient policies to enhance transportation safety. Copyright © 2017 Elsevier Ltd and National Safety Council. All rights reserved.

  14. 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

  15. Quantitative analysis of human-model agreement in visual saliency modeling: a comparative study.

    PubMed

    Borji, Ali; Sihite, Dicky N; Itti, Laurent

    2013-01-01

    Visual attention is a process that enables biological and machine vision systems to select the most relevant regions from a scene. Relevance is determined by two components: 1) top-down factors driven by task and 2) bottom-up factors that highlight image regions that are different from their surroundings. The latter are often referred to as "visual saliency." Modeling bottom-up visual saliency has been the subject of numerous research efforts during the past 20 years, with many successful applications in computer vision and robotics. Available models have been tested with different datasets (e.g., synthetic psychological search arrays, natural images or videos) using different evaluation scores (e.g., search slopes, comparison to human eye tracking) and parameter settings. This has made direct comparison of models difficult. Here, we perform an exhaustive comparison of 35 state-of-the-art saliency models over 54 challenging synthetic patterns, three natural image datasets, and two video datasets, using three evaluation scores. We find that although model rankings vary, some models consistently perform better. Analysis of datasets reveals that existing datasets are highly center-biased, which influences some of the evaluation scores. Computational complexity analysis shows that some models are very fast, yet yield competitive eye movement prediction accuracy. Different models often have common easy/difficult stimuli. Furthermore, several concerns in visual saliency modeling, eye movement datasets, and evaluation scores are discussed and insights for future work are provided. Our study allows one to assess the state-of-the-art, helps to organizing this rapidly growing field, and sets a unified comparison framework for gauging future efforts, similar to the PASCAL VOC challenge in the object recognition and detection domains.

  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. Predicting Air Permeability of Handloom Fabrics: A Comparative Analysis of Regression and Artificial Neural Network Models

    NASA Astrophysics Data System (ADS)

    Mitra, Ashis; Majumdar, Prabal Kumar; Bannerjee, Debamalya

    2013-03-01

    This paper presents a comparative analysis of two modeling methodologies for the prediction of air permeability of plain woven handloom cotton fabrics. Four basic fabric constructional parameters namely ends per inch, picks per inch, warp count and weft count have been used as inputs for artificial neural network (ANN) and regression models. Out of the four regression models tried, interaction model showed very good prediction performance with a meager mean absolute error of 2.017 %. However, ANN models demonstrated superiority over the regression models both in terms of correlation coefficient and mean absolute error. The ANN model with 10 nodes in the single hidden layer showed very good correlation coefficient of 0.982 and 0.929 and mean absolute error of only 0.923 and 2.043 % for training and testing data respectively.

  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. Copyright © 2012 Wiley Periodicals, Inc.

  19. Whole genome comparative analysis of channel catfish (Ictalurus punctatus) with four model fish species

    PubMed Central

    2013-01-01

    Background Comparative mapping is a powerful tool to study evolution of genomes. It allows transfer of genome information from the well-studied model species to non-model species. Catfish is an economically important aquaculture species in United States. A large amount of genome resources have been developed from catfish including genetic linkage maps, physical maps, BAC end sequences (BES), integrated linkage and physical maps using BES-derived markers, physical map contig-specific sequences, and draft genome sequences. Application of such genome resources should allow comparative analysis at the genome scale with several other model fish species. Results In this study, we conducted whole genome comparative analysis between channel catfish and four model fish species with fully sequenced genomes, zebrafish, medaka, stickleback and Tetraodon. A total of 517 Mb draft genome sequences of catfish were anchored to its genetic linkage map, which accounted for 62% of the total draft genome sequences. Based on the location of homologous genes, homologous chromosomes were determined among catfish and the four model fish species. A large number of conserved syntenic blocks were identified. Analysis of the syntenic relationships between catfish and the four model fishes supported that the catfish genome is most similar to the genome of zebrafish. Conclusion The organization of the catfish genome is similar to that of the four teleost species, zebrafish, medaka, stickleback, and Tetraodon such that homologous chromosomes can be identified. Within each chromosome, extended syntenic blocks were evident, but the conserved syntenies at the chromosome level involve extensive inter-chromosomal and intra-chromosomal rearrangements. This whole genome comparative map should facilitate the whole genome assembly and annotation in catfish, and will be useful for genomic studies of various other fish species. PMID:24215161

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

    SciTech Connect

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

    2016-06-08

    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 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.

  2. Comparative efficiency assessment of primary care service delivery models using data envelopment analysis.

    PubMed

    Milliken, Olga; Devlin, Rose Anne; Barham, Victoria; Hogg, William; Dahrouge, Simone; Russell, Grant

    2011-01-01

    This paper compares the relative productive efficiencies of four models of primary care service delivery using the data envelopment analysis method on 130 primary care practices in Ontario, Canada. A quality-controlled measure of output and two input scenarios are employed: one with full-time-equivalent labour inputs and the other with total expenditures. Regression analysis controls for the mix of patients in the practice population. Overall, we find that community health centres fare the worst when it comes to relative efficiency scores.

  3. Protein Dynamics from NMR: The Slowly Relaxing Local Structure Analysis Compared with Model-Free Analysis

    PubMed Central

    Meirovitch, Eva; Shapiro, Yury E.; Polimeno, Antonino; Freed, Jack H.

    2009-01-01

    15N-1H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multi-field data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the Slowly Relaxing Local Structure (SRLS) approach which accounts rigorously for mode-mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulae are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF force-fits the experimental data because mode-mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multi-field multi-temperature data analyzed by MF may lead to the detection of incorrect phenomena, while conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS densities comply with this requirement. PMID:16821820

  4. 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

  5. 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.

  6. Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics.

    PubMed

    Veneman, Wouter J; de Sonneville, Jan; van der Kolk, Kees-Jan; Ordas, Anita; Al-Ars, Zaid; Meijer, Annemarie H; Spaink, Herman P

    2015-03-01

    We present a RNA deep sequencing (RNAseq) analysis of a comparison of the transcriptome responses to infection of zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. We show how our developed GeneTiles software can improve RNAseq analysis approaches by more confidently identifying a large set of markers upon infection with these bacteria. For analysis of RNAseq data currently, software programs such as Bowtie2 and Samtools are indispensable. However, these programs that are designed for a LINUX environment require some dedicated programming skills and have no options for visualisation of the resulting mapped sequence reads. Especially with large data sets, this makes the analysis time consuming and difficult for non-expert users. We have applied the GeneTiles software to the analysis of previously published and newly obtained RNAseq datasets of our zebrafish infection model, and we have shown the applicability of this approach also to published RNAseq datasets of other organisms by comparing our data with a published mammalian infection study. In addition, we have implemented the DEXSeq module in the GeneTiles software to identify genes, such as glucagon A, that are differentially spliced under infection conditions. In the analysis of our RNAseq data, this has led to the possibility to improve the size of data sets that could be efficiently compared without using problem-dedicated programs, leading to a quick identification of marker sets. Therefore, this approach will also be highly useful for transcriptome analyses of other organisms for which well-characterised genomes are available.

  7. Comparative analysis of cognitive tasks for modeling mental workload with electroencephalogram.

    PubMed

    Hwang, Taeho; Kim, Miyoung; Hwangbo, Minsu; Oh, Eunmi

    2014-01-01

    Previous electroencephalogram (EEG) studies have shown that cognitive workload can be estimated by using several types of cognitive tasks. In this study, we attempted to characterize cognitive tasks that have been used to manipulate workload for generating classification models. We carried out a comparative analysis between two representative types of working memory tasks: the n-back task and the mental arithmetic task. Based on experiments with 7 healthy subjects using Emotiv EPOC, we compared the consistency, robustness, and efficiency of each task in determining cognitive workload in a short training session. The mental arithmetic task seems consistent and robust in manipulating clearly separable high and low levels of cognitive workload with less training. In addition, the mental arithmetic task shows consistency despite repeated usage over time and without notable task adaptation in users. The current study successfully quantifies the quality and efficiency of cognitive workload modeling depending on the type and configuration of training tasks.

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

    PubMed

    Butland, Barbara K; Armstrong, Ben; Atkinson, Richard W; Wilkinson, Paul; Heal, Mathew R; Doherty, Ruth M; Vieno, Massimo

    2013-11-13

    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. 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). 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). Even if correlations between

  9. Comparative analysis of bleeding risk by the location and shape of arachnoid cysts: a finite element model analysis.

    PubMed

    Lee, Chang-Hyun; Han, In Seok; Lee, Ji Yeoun; Phi, Ji Hoon; Kim, Seung-Ki; Kim, Young-Eun; Wang, Kyu-Chang

    2017-01-01

    Although arachnoid cysts (ACs) are observed in various locations, only sylvian ACs are mainly regarded to be associated with bleeding. The reason for this selective association of sylvian ACs with bleeding is not understood well. This study is to investigate the effect of the location and shape of ACs on the risk of bleeding. A developed finite element model of the head/brain was modified for models of sylvian, suprasellar, and posterior fossa ACs. A spherical AC was placed at each location to compare the effect of AC location. Bowl-shaped and oval-shaped AC models were developed to compare the effect by shape. The shear force on the spot-weld elements (SFSW) was measured between the dura and the outer wall of the ACs or the comparable arachnoid membrane in the normal model. All AC models revealed higher SFSW than comparable normal models. By location, sylvian AC displayed the highest SFSW for frontal and lateral impacts. By shape, small outer wall AC models showed higher SFSW than large wall models in sylvian area and lower SFSW than large ones in posterior fossa. In regression analysis, the presence of AC was the only independent risk of bleeding. The bleeding mechanism of ACs is very complex, and the risk quantification failed to show a significant role of location and shape of ACs. The presence of AC increases shear force on impact condition and may be a risk factor of bleeding, and sylvian location of AC may not have additive risks of AC bleeding.

  10. 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.

  11. Comparative Analysis between Profits of the Two Models of a CC Plant

    NASA Astrophysics Data System (ADS)

    Mathew, A. G.; Rizwan, S. M.; Majumder, M. C.; Ramachandran, K. P.; Taneja, G.

    2010-10-01

    This paper presents the comparative analysis between profits of the two models of a two-unit CC plant with same/different installed capacity combination. The analysis is useful in deciding the optimum plant equipment capacity combinations and particular model suitability over the other to the existing situation. In plant model I, the actual plant situation with four EOT cranes (unit I, II 200 ton each) is analyzed. But, it is observed that equipment combination in terms of installed capacities as specified above could be analyzed by varying the installed capacity and thereby achieving a significant difference in the plant performance. Hence, plant model II explores a situation by replacing the 200 ton unit II cranes with 100 ton cranes and operating both the units at full installed capacity with priority of repair and operation to unit I. Upon failure in either unit, an inspection is carried out to decide the type of maintenance task to be performed. The actual plant downtime data is used for achieving the optimized reliability indices and comparison among both the models. Essential graphs are plotted to demonstrate the results and related comparison.

  12. 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.

  13. 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).

  14. 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

  15. 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.

  16. 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.

  17. Comparative Analysis of InSAR Digital Surface Models for Test Area Bucharest

    NASA Astrophysics Data System (ADS)

    Dana, Iulia; Poncos, Valentin; Teleaga, Delia

    2010-03-01

    This paper presents the results of the interferometric processing of ERS Tandem, ENVISAT and TerraSAR- X for digital surface model (DSM) generation. The selected test site is Bucharest (Romania), a built-up area characterized by the usual urban complex pattern: mixture of buildings with different height levels, paved roads, vegetation, and water bodies. First, the DSMs were generated following the standard interferometric processing chain. Then, the accuracy of the DSMs was analyzed against the SPOT HRS model (30 m resolution at the equator). A DSM derived by optical stereoscopic processing of SPOT 5 HRG data and also the SRTM (3 arc seconds resolution at the equator) DSM have been included in the comparative analysis.

  18. Comparative mRNA analysis of behavioral and genetic mouse models of aggression.

    PubMed

    Malki, Karim; Tosto, Maria G; Pain, Oliver; Sluyter, Frans; Mineur, Yann S; Crusio, Wim E; de Boer, Sietse; Sandnabba, Kenneth N; Kesserwani, Jad; Robinson, Edward; Schalkwyk, Leonard C; Asherson, Philip

    2016-04-01

    Mouse models of aggression have traditionally compared strains, most notably BALB/cJ and C57BL/6. However, these strains were not designed to study aggression despite differences in aggression-related traits and distinct reactivity to stress. This study evaluated expression of genes differentially regulated in a stress (behavioral) mouse model of aggression with those from a recent genetic mouse model aggression. The study used a discovery-replication design using two independent mRNA studies from mouse brain tissue. The discovery study identified strain (BALB/cJ and C57BL/6J) × stress (chronic mild stress or control) interactions. Probe sets differentially regulated in the discovery set were intersected with those uncovered in the replication study, which evaluated differences between high and low aggressive animals from three strains specifically bred to study aggression. Network analysis was conducted on overlapping genes uncovered across both studies. A significant overlap was found with the genetic mouse study sharing 1,916 probe sets with the stress model. Fifty-one probe sets were found to be strongly dysregulated across both studies mapping to 50 known genes. Network analysis revealed two plausible pathways including one centered on the UBC gene hub which encodes ubiquitin, a protein well-known for protein degradation, and another on P38 MAPK. Findings from this study support the stress model of aggression, which showed remarkable molecular overlap with a genetic model. The study uncovered a set of candidate genes including the Erg2 gene, which has previously been implicated in different psychopathologies. The gene networks uncovered points at a Redox pathway as potentially being implicated in aggressive related behaviors.

  19. Comparative analysis of realistic CT-scan and simplified human airway models in airflow simulation.

    PubMed

    Johari, Nasrul Hadi; Osman, Kahar; Helmi, Nor Harris N; Abdul Kadir, Mohammed A Rafiq

    2015-01-01

    Efforts to model the human upper respiratory system have undergone many phases. Geometrical proximity to the realistic shape has been the subject of many research projects. In this study, three different geometries of the trachea and main bronchus were modelled, which were reconstructed from computed tomography (CT) scan images. The geometrical variations were named realistic, simplified and oversimplified. Realistic refers to the lifelike image taken from digital imaging and communications in medicine format CT scan images, simplified refers to the reconstructed image based on natural images without realistic details pertaining to the rough surfaces, and oversimplified describes the straight wall geometry of the airway. The characteristics of steady state flows with different flow rates were investigated, simulating three varied physical activities and passing through each model. The results agree with previous studies where simplified models are sufficient for providing comparable results for airflow in human airways. This work further suggests that, under most exercise conditions, the idealised oversimplified model is not favourable for simulating either airflow regimes or airflow with particle depositions. However, in terms of immediate analysis for the prediction of abnormalities of various dimensions of human airways, the oversimplified techniques may be used.

  20. Solving the forward problem in EEG source analysis by spherical and fdm head modeling: a comparative analysis - biomed 2009.

    PubMed

    Vatta, Federica; Meneghini, Fabio; Esposito, Fabrino; Mininel, Stefano; Di Salle, Francesca

    2009-01-01

    Neural source localization techniques based on electroencephalography (EEG) use scalp potential data to infer the location of underlying neural activity. This procedure entails modeling the sources of EEG activity and modeling the head volume conduction process to link the modeled sources to the EEG, solving the so called EEG forward problem, and reconstructing the brain electrical activity from recorded EEG data, solving the EEG inverse problem. Many factors affect the accuracy of the forward and hence of the inverse problem solution, one of them is the shape of the head model. Realistic head models can lead to more accurate forward problem solutions, but imply heavier computational burdens in comparison to spherical models. Conversely, inverse solutions require the forward model to be computationally efficient. The aim of this study is to investigate the different general potentialities, in terms of EEG source reconstruction, which can be achieved adopting realistic or spherical geometries in head modeling. Previous studies in the literature analyzed the effect of head model geometry presenting results for particular cases of head models. In this paper, we re-address the effect of realistic geometry in head modeling, seeking for more general results by adopting the Montreal Neurological Institute (MNI) phantom model to represent a whole family of realistic head models. This paper presents results of a computer simulation study in which the potentialities of two different four-shell head models are compared, the realistic MNI-based FDM and the corresponding sensor-fitted spherical-shaped model, by means of the Point Spread Function (PSF) correlation maps, with a quantitative analysis of the accuracy in EEG source reconstruction given by head modeling refinement from the spherical to the more complex realistic FDM head modeling.

  1. Comparative and Evolutionary Analysis of Grass Pollen Allergens Using Brachypodium distachyon as a Model System

    PubMed Central

    Sharma, Akanksha; Sharma, Niharika; Bhalla, Prem; Singh, Mohan

    2017-01-01

    Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses. Combining genomic data with the anther RNA-Seq dataset revealed 24 pollen allergen genes belonging to eight allergen groups mapping on the five chromosomes in B. distachyon. High levels of anther-specific expression profiles were observed for the 24 identified putative allergen-encoding genes in Brachypodium. The genomic evidence suggests that gene encoding the group 5 allergen, the most potent trigger of hay fever and allergic asthma originated as a pollen specific orphan gene in a common grass ancestor of Brachypodium and Triticiae clades. Gene structure analysis showed that the putative allergen-encoding genes in Brachypodium either lack or contain reduced number of introns. Promoter analysis of the identified Brachypodium genes revealed the presence of specific cis-regulatory sequences likely responsible for high anther/pollen-specific expression. With the identification of putative allergen-encoding genes in Brachypodium, this study has also described some important plant gene families (e.g. expansin superfamily, EF-Hand family, profilins etc) for the first time in the model plant Brachypodium. Altogether, the present study provides new insights into structural characterization and evolution of pollen allergens and will further serve as a base for their functional

  2. 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…

  3. 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

  4. Comparative analysis of modeling and experiments to study spalling process in Si wafers

    NASA Astrophysics Data System (ADS)

    Alhomoudi, Ibrahim A.

    2017-03-01

    A comparative analysis including modeling and experimental evaluation of a spalling process of silicon (Si) substrates was accomplished to define the optimum condition for uniform spalling. The residual stresses in Nickle (Ni) films on Si substrates have been evaluated. Different thicknesses of Ni films electroplated on Si(100) and Si(111) substrates have been used to predict the steady-state spalling depth and crack propagation direction. This study focuses on identifying the key variables; including the Ni film thickness (h) and critical stress needed to peel-off uniform thin layers from a Si substrate. The residual stresses (thermal and epitaxial) in the Ni films have been evaluated through experiment and modeling analysis to distinguish the sources of stress generation. Different thicknesses of spalled films from Si substrates were defined to investigate the influence of the stress intensity factors (KI, KII and KIII) and the energy release rate (J1) on the steady state spalling process. Finally, the critical normal stress (σII) versus h has been determined to predict the spalling depth with uniform thickness.

  5. 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.

  6. Stochastic segmentation models for array-based comparative genomic hybridization data analysis.

    PubMed

    Lai, Tze Leung; Xing, Haipeng; Zhang, Nancy

    2008-04-01

    Array-based comparative genomic hybridization (array-CGH) is a high throughput, high resolution technique for studying the genetics of cancer. Analysis of array-CGH data typically involves estimation of the underlying chromosome copy numbers from the log fluorescence ratios and segmenting the chromosome into regions with the same copy number at each location. We propose for the analysis of array-CGH data, a new stochastic segmentation model and an associated estimation procedure that has attractive statistical and computational properties. An important benefit of this Bayesian segmentation model is that it yields explicit formulas for posterior means, which can be used to estimate the signal directly without performing segmentation. Other quantities relating to the posterior distribution that are useful for providing confidence assessments of any given segmentation can also be estimated by using our method. We propose an approximation method whose computation time is linear in sequence length which makes our method practically applicable to the new higher density arrays. Simulation studies and applications to real array-CGH data illustrate the advantages of the proposed approach.

  7. 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.

  8. 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.

  9. A comparative modeling analysis of multiscale temporal variability of rainfall in Australia

    NASA Astrophysics Data System (ADS)

    Samuel, Jos M.; Sivapalan, Murugesu

    2008-07-01

    The effects of long-term natural climate variability and human-induced climate change on rainfall variability have become the focus of much concern and recent research efforts. In this paper, we present the results of a comparative analysis of observed multiscale temporal variability of rainfall in the Perth, Newcastle, and Darwin regions of Australia. This empirical and stochastic modeling analysis explores multiscale rainfall variability, i.e., ranging from short to long term, including within-storm patterns, and intra-annual, interannual, and interdecadal variabilities, using data taken from each of these regions. The analyses investigated how storm durations, interstorm periods, and average storm rainfall intensities differ for different climate states and demonstrated significant differences in this regard between the three selected regions. In Perth, the average storm intensity is stronger during La Niña years than during El Niño years, whereas in Newcastle and Darwin storm duration is longer during La Niña years. Increase of either storm duration or average storm intensity is the cause of higher average annual rainfall during La Niña years as compared to El Niño years. On the other hand, within-storm variability does not differ significantly between different ENSO states in all three locations. In the case of long-term rainfall variability, the statistical analyses indicated that in Newcastle the long-term rainfall pattern reflects the variability of the Interdecadal Pacific Oscillation (IPO) index, whereas in Perth and Darwin the long-term variability exhibits a step change in average annual rainfall (up in Darwin and down in Perth) which occurred around 1970. The step changes in Perth and Darwin and the switch in IPO states in Newcastle manifested differently in the three study regions in terms of changes in the annual number of rainy days or the average daily rainfall intensity or both. On the basis of these empirical data analyses, a stochastic

  10. Systems thinking, the Swiss Cheese Model and accident analysis: a comparative systemic analysis of the Grayrigg train derailment using the ATSB, AcciMap and STAMP models.

    PubMed

    Underwood, Peter; Waterson, Patrick

    2014-07-01

    The Swiss Cheese Model (SCM) is the most popular accident causation model and is widely used throughout various industries. A debate exists in the research literature over whether the SCM remains a viable tool for accident analysis. Critics of the model suggest that it provides a sequential, oversimplified view of accidents. Conversely, proponents suggest that it embodies the concepts of systems theory, as per the contemporary systemic analysis techniques. The aim of this paper was to consider whether the SCM can provide a systems thinking approach and remain a viable option for accident analysis. To achieve this, the train derailment at Grayrigg was analysed with an SCM-based model (the ATSB accident investigation model) and two systemic accident analysis methods (AcciMap and STAMP). The analysis outputs and usage of the techniques were compared. The findings of the study showed that each model applied the systems thinking approach. However, the ATSB model and AcciMap graphically presented their findings in a more succinct manner, whereas STAMP more clearly embodied the concepts of systems theory. The study suggests that, whilst the selection of an analysis method is subject to trade-offs that practitioners and researchers must make, the SCM remains a viable model for accident analysis.

  11. Regional disaster impact analysis: comparing Input-Output and Computable General Equilibrium models

    NASA Astrophysics Data System (ADS)

    Koks, E. E.; Carrera, L.; Jonkeren, O.; Aerts, J. C. J. H.; Husby, T. G.; Thissen, M.; Standardi, G.; Mysiak, J.

    2015-11-01

    A large variety of models has been developed 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 numbers of scholars has developed hybrid approaches; one that combines both or either of them in combination with non-economic 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 likely to vary with the chosen modelling approach (IO, CGE, or hybrid). Hence, regional disaster impact loss estimates resulting from a range of models facilitates better decisions and policy making. Therefore, in this study we analyze one specific case study, using three regional models: two hybrid IO models and a regionally calibrated version of a global 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 seven between the three models, depending on the type of recovery path. Total economic impact, comprising all Italian regions, is negative in all models though.

  12. 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.

  13. 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 ...

  14. 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 ...

  15. Adaptation to Climate Change: A Comparative Analysis of Modeling Methods for Heat-Related Mortality.

    PubMed

    Gosling, Simon N; Hondula, David M; Bunker, Aditi; Ibarreta, Dolores; Liu, Junguo; Zhang, Xinxin; Sauerborn, Rainer

    2017-08-16

    Multiple methods are employed for modeling adaptation when projecting the impact of climate change on heat-related mortality. The sensitivity of impacts to each is unknown because they have never been systematically compared. In addition, little is known about the relative sensitivity of impacts to "adaptation uncertainty" (i.e., the inclusion/exclusion of adaptation modeling) relative to using multiple climate models and emissions scenarios. This study had three aims: a) Compare the range in projected impacts that arises from using different adaptation modeling methods; b) compare the range in impacts that arises from adaptation uncertainty with ranges from using multiple climate models and emissions scenarios; c) recommend modeling method(s) to use in future impact assessments. We estimated impacts for 2070-2099 for 14 European cities, applying six different methods for modeling adaptation; we also estimated impacts with five climate models run under two emissions scenarios to explore the relative effects of climate modeling and emissions uncertainty. The range of the difference (percent) in impacts between including and excluding adaptation, irrespective of climate modeling and emissions uncertainty, can be as low as 28% with one method and up to 103% with another (mean across 14 cities). In 13 of 14 cities, the ranges in projected impacts due to adaptation uncertainty are larger than those associated with climate modeling and emissions uncertainty. Researchers should carefully consider how to model adaptation because it is a source of uncertainty that can be greater than the uncertainty in emissions and climate modeling. We recommend absolute threshold shifts and reductions in slope. https://doi.org/10.1289/EHP634.

  16. 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

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

    PubMed

    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

    2014-08-01

    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.

  18. Comparative gene expression profiling of normal and degenerative discs: analysis of a rabbit annular laceration model.

    PubMed

    Anderson, D Greg; Izzo, Marc W; Hall, David J; Vaccaro, Alexander R; Hilibrand, Alan; Arnold, William; Tuan, Rocky S; Albert, Todd J

    2002-06-15

    A rabbit annular laceration model was used to investigate intervertebral disc gene expression in normal and lacerated discs. To determine and compare the pattern of expression of potentially important genes in normal and lacerated discs and to determine if the changes in gene expression were similar to human degenerative discs. Little is known regarding gene expression in normal or degenerating disc tissue. Eighteen rabbits were subjected to annular laceration of the L1-L2 and L2-L3 discs while two rabbits served as sham controls. Control and lacerated discs were harvested 1 week, 3 weeks, and 6 weeks following surgery and subjected to histologic examination and gene expression analysis using the reverse transcription-polymerase chain reaction (RT-PCR). The genes studied included collagen Type I (Col I), collagen Type II (Col II), decorin, fibronectin (FN), interleukin-1a (IL-1alpha), bone morphogenetic protein 2 (BMP-2), Fas, matrix metalloproteinase 1 (MMP-1), matrix metalloproteinase 9 (MMP-9), matrix metalloproteinase 13 (MMP-13), and tumor necrosis factor (TNF). Expression levels of each gene were normalized to that of glyceraldehyde-3-phosphate dehydrogenase (GADPH), a constitutively expressed gene. Histology confirmed progressive degeneration of the discs over the 6-week study period. Different patterns of gene expression were observed in control and lesioned discs. Annular laceration caused a marked upregulation (two- to eightfold) of the expression of Col I, Col II, FN, MMP-1, MMP-9, MMP-13, and Fas genes, whereas that of BMP-2, IL-1alpha, and TNF genes was unaffected. Expression of the decorin gene was downregulated approximately sixfold after annular laceration. Annular laceration in this animal model resulted in marked changes in gene expression. Upregulation of gene expression was observed for some molecules found at high concentration in human degenerated discs, suggesting similarities to human disc degeneration at the molecular level. This supports

  19. Sensitivity analysis of PBL schemes by comparing WRF model and experimental data

    NASA Astrophysics Data System (ADS)

    Balzarini, A.; Angelini, F.; Ferrero, L.; Moscatelli, M.; Perrone, M. G.; Pirovano, G.; Riva, G. M.; Sangiorgi, G.; Toppetti, A. M.; Gobbi, G. P.; Bolzacchini, E.

    2014-09-01

    This work discusses the sources of model biases in reconstructing the Planetary Boundary Layer (PBL) height among five commonly used PBL parameterizations. The Weather Research and Forecasting (WRF) Model was applied over the critical area of Northern Italy with 5 km of horizontal resolution, and compared against a wide set of experimental data for February 2008. Three non-local closure PBL schemes (Asymmetrical Convective Model version 2, ACM2; Medium Range Forecast, MRF; Yonsei University, YSU) and two local closure parameterizations (Mellor Yamada Janjic, MYJ; University of Washington Moist Turbulence, UW) were selected for the analysis. Vertical profiles of aerosol number concentrations and Lidar backscatter profiles were collected in the metropolitan area of Milan in order to derive the PBL hourly evolution. Moreover, radio-soundings of Milano Linate airport as well as surface temperature, mixing ratio and wind speed of several meteorological stations were considered too. Results show that all five parameterizations produce similar performances in terms of temperature, mixing ratio and wind speed in the city of Milan, implying some systematic errors in all simulations. However, UW and ACM2 use the same local closure during nighttime conditions, allowing smaller mean biases (MB) of temperature (ACM2 MB = 0.606 K, UW MB = 0.209 K), and wind speed (ACM2 MB = 0.699 m s-1, UW MB = 0.918 m s-1). All schemes have the same variations of the diurnal PBL height, since over predictions of temperature and wind speed are found to cause a general overestimation of mixing during its development in winter. In particular, temperature estimates seem to impact the early evolution of the PBL height, while entrainment fluxes parameterizations have major influence on the afternoon development. MRF, MYJ and ACM2 use the same approach in reconstructing the entrainment process, producing the largest overestimations of PBL height (MB ranges from 85.51-179.10 m). On the contrary, the

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

    PubMed

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

    2007-09-01

    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. 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). 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 Indian epidemic, the disease

  1. 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

  2. Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

    PubMed Central

    Heavner, Benjamin D.; Price, Nathan D.

    2015-01-01

    We have compared 12 genome-scale models of the Saccharomyces cerevisiae metabolic network published since 2003 to evaluate progress in reconstruction of the yeast metabolic network. We compared the genomic coverage, overlap of annotated metabolites, predictive ability for single gene essentiality with a selection of model parameters, and biomass production predictions in simulated nutrient-limited conditions. We have also compared pairwise gene knockout essentiality predictions for 10 of these models. We found that varying approaches to model scope and annotation reflected the involvement of multiple research groups in model development; that single-gene essentiality predictions were affected by simulated medium, objective function, and the reference list of essential genes; and that predictive ability for single-gene essentiality did not correlate well with predictive ability for our reference list of synthetic lethal gene interactions (R = 0.159). We conclude that the reconstruction of the yeast metabolic network is indeed gradually improving through the iterative process of model development, and there remains great opportunity for advancing our understanding of biology through continued efforts to reconstruct the full biochemical reaction network that constitutes yeast metabolism. Additionally, we suggest that there is opportunity for refining the process of deriving a metabolic model from a metabolic network reconstruction to facilitate mechanistic investigation and discovery. This comparative study lays the groundwork for developing improved tools and formalized methods to quantitatively assess metabolic network reconstructions independently of any particular model application, which will facilitate ongoing efforts to advance our understanding of the relationship between genotype and cellular phenotype. PMID:26566239

  3. Comparative analysis of system identification techniques for nonlinear modeling of the neuron-microelectrode junction.

    PubMed

    Khan, Saad Ahmad; Thakore, Vaibhav; Behal, Aman; Bölöni, Ladislau; Hickman, James J

    2013-03-01

    Applications of non-invasive neuroelectronic interfacing in the fields of whole-cell biosensing, biological computation and neural prosthetic devices depend critically on an efficient decoding and processing of information retrieved from a neuron-electrode junction. This necessitates development of mathematical models of the neuron-electrode interface that realistically represent the extracellular signals recorded at the neuroelectronic junction without being computationally expensive. Extracellular signals recorded using planar microelectrode or field effect transistor arrays have, until now, primarily been represented using linear equivalent circuit models that fail to reproduce the correct amplitude and shape of the signals recorded at the neuron-microelectrode interface. In this paper, to explore viable alternatives for a computationally inexpensive and efficient modeling of the neuron-electrode junction, input-output data from the neuron-electrode junction is modeled using a parametric Wiener model and a Nonlinear Auto-Regressive network with eXogenous input trained using a dynamic Neural Network model (NARX-NN model). Results corresponding to a validation dataset from these models are then employed to compare and contrast the computational complexity and efficiency of the aforementioned modeling techniques with the Lee-Schetzen technique of cross-correlation for estimating a nonlinear dynamic model of the neuroelectronic junction.

  4. 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…

  5. 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…

  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. Required duration of mass ivermectin treatment for onchocerciasis elimination in Africa: a comparative modelling analysis.

    PubMed

    Stolk, Wilma A; Walker, Martin; Coffeng, Luc E; Basáñez, María-Gloria; de Vlas, Sake J

    2015-10-22

    The World Health Organization (WHO) has set ambitious targets for the elimination of onchocerciasis by 2020-2025 through mass ivermectin treatment. Two different mathematical models have assessed the feasibility of reaching this goal for different settings and treatment scenarios, namely the individual-based microsimulation model ONCHOSIM and the population-based deterministic model EPIONCHO. In this study, we harmonize some crucial assumptions and compare model predictions on common outputs. Using a range of initial endemicity levels and treatment scenarios, we compared the models with respect to the following outcomes: 1) model-predicted trends in microfilarial (mf) prevalence and mean mf intensity during 25 years of (annual or biannual) mass ivermectin treatment; 2) treatment duration needed to bring mf prevalence below a provisional operational threshold for treatment interruption (pOTTIS, i.e. 1.4 %), and 3) treatment duration needed to drive the parasite population to local elimination, even in the absence of further interventions. Local elimination was judged by stochastic fade-out in ONCHOSIM and by reaching transmission breakpoints in EPIONCHO. ONCHOSIM and EPIONCHO both predicted that in mesoendemic areas the pOTTIS can be reached with annual treatment, but that this strategy may be insufficient in very highly hyperendemic areas or would require prolonged continuation of treatment. For the lower endemicity levels explored, ONCHOSIM predicted that the time needed to reach the pOTTIS is longer than that needed to drive the parasite population to elimination, whereas for the higher endemicity levels the opposite was true. In EPIONCHO, the pOTTIS was reached consistently sooner than the breakpoint. The operational thresholds proposed by APOC may have to be adjusted to adequately reflect differences in pre-control endemicities. Further comparative modelling work will be conducted to better understand the main causes of differences in model-predicted trends

  8. A comparative analysis of three vector-borne diseases across Australia using seasonal and meteorological models

    PubMed Central

    Stratton, Margaret D.; Ehrlich, Hanna Y.; Mor, Siobhan M.; Naumova, Elena N.

    2017-01-01

    Ross River virus (RRV), Barmah Forest virus (BFV), and dengue are three common mosquito-borne diseases in Australia that display notable seasonal patterns. Although all three diseases have been modeled on localized scales, no previous study has used harmonic models to compare seasonality of mosquito-borne diseases on a continent-wide scale. We fit Poisson harmonic regression models to surveillance data on RRV, BFV, and dengue (from 1993, 1995 and 1991, respectively, through 2015) incorporating seasonal, trend, and climate (temperature and rainfall) parameters. The models captured an average of 50–65% variability of the data. Disease incidence for all three diseases generally peaked in January or February, but peak timing was most variable for dengue. The most significant predictor parameters were trend and inter-annual periodicity for BFV, intra-annual periodicity for RRV, and trend for dengue. We found that a Temperature Suitability Index (TSI), designed to reclassify climate data relative to optimal conditions for vector establishment, could be applied to this context. Finally, we extrapolated our models to estimate the impact of a false-positive BFV epidemic in 2013. Creating these models and comparing variations in periodicities may provide insight into historical outbreaks as well as future patterns of mosquito-borne diseases. PMID:28071683

  9. A comparative analysis of three vector-borne diseases across Australia using seasonal and meteorological models

    NASA Astrophysics Data System (ADS)

    Stratton, Margaret D.; Ehrlich, Hanna Y.; Mor, Siobhan M.; Naumova, Elena N.

    2017-01-01

    Ross River virus (RRV), Barmah Forest virus (BFV), and dengue are three common mosquito-borne diseases in Australia that display notable seasonal patterns. Although all three diseases have been modeled on localized scales, no previous study has used harmonic models to compare seasonality of mosquito-borne diseases on a continent-wide scale. We fit Poisson harmonic regression models to surveillance data on RRV, BFV, and dengue (from 1993, 1995 and 1991, respectively, through 2015) incorporating seasonal, trend, and climate (temperature and rainfall) parameters. The models captured an average of 50-65% variability of the data. Disease incidence for all three diseases generally peaked in January or February, but peak timing was most variable for dengue. The most significant predictor parameters were trend and inter-annual periodicity for BFV, intra-annual periodicity for RRV, and trend for dengue. We found that a Temperature Suitability Index (TSI), designed to reclassify climate data relative to optimal conditions for vector establishment, could be applied to this context. Finally, we extrapolated our models to estimate the impact of a false-positive BFV epidemic in 2013. Creating these models and comparing variations in periodicities may provide insight into historical outbreaks as well as future patterns of mosquito-borne diseases.

  10. 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. Copyright 2002 John Wiley & Sons, Ltd.

  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. Comparative analysis of regression and artificial neural network models for wind speed prediction

    NASA Astrophysics Data System (ADS)

    Bilgili, Mehmet; Sahin, Besir

    2010-11-01

    In this study, wind speed was modeled by linear regression (LR), nonlinear regression (NLR) and artificial neural network (ANN) methods. A three-layer feedforward artificial neural network structure was constructed and a backpropagation algorithm was used for the training of ANNs. To get a successful simulation, firstly, the correlation coefficients between all of the meteorological variables (wind speed, ambient temperature, atmospheric pressure, relative humidity and rainfall) were calculated taking two variables in turn for each calculation. All independent variables were added to the simple regression model. Then, the method of stepwise multiple regression was applied for the selection of the “best” regression equation (model). Thus, the best independent variables were selected for the LR and NLR models and also used in the input layer of the ANN. The results obtained by all methods were compared to each other. Finally, the ANN method was found to provide better performance than the LR and NLR methods.

  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. Interactions of proteins with immobilized metal ions: a comparative analysis using various isotherm models.

    PubMed

    Sharma, S; Agarwal, G P

    2001-01-15

    Immobilized metal ion affinity chromatography (IMAC) is now a widely accepted technique for the purification of natural and recombinant therapeutic products and is beginning to find industrial applications. The design, optimization, and scale-up of a chromatographic process using IMAC demands a thorough understanding to be developed regarding the fundamental factors governing the various interactions between immobilized metal ions and proteins. Consequently, there is an immediate need to find out a theory that is able to account for these interactions most efficiently in a qualitative as well as a quantitative manner. In view of this requirement, the interactions of several model proteins (lysozyme, ovalbumin, bovine serum albumin, conalbumin, and wheat germ agglutinin) with metal (Cu(II), Ni(II))-chelated IDA (iminodiacetate) and tris(2-aminoethyl)amine were investigated. The adsorption data were analyzed using four isotherm models, viz., the general affinity interaction theory/Langmuir model, the Freundlich model, the Temkin model, and the Langmuir-Freundlich model, and the sorption parameters were computed. Although the first three models were applicable to some protein-IMA-M(II) systems, the Langmuir-Freundlich model appeared to be the most efficient model for explaining the interactions of proteins with IMA-M(II) gels. Also, this model was able to explain cooperativity and binding heterogeneity in quantitative terms. It is envisaged that this analysis would be useful in developing an improved understanding of protein-immobilized metal ion interactions and providing guidelines for designing preparative-scale separations using IMAC. Copyright 2001 Academic Press.

  15. Comparative Analysis of Induced vs. Spontaneous Models of Autoimmune Uveitis Targeting the Interphotoreceptor Retinoid Binding Protein

    PubMed Central

    Chen, Jun; Qian, Haohua; Horai, Reiko; Chan, Chi-Chao; Falick, Yishay; Caspi, Rachel R.

    2013-01-01

    Animal models of autoimmunity to the retina mimic specific features of human uveitis, but no model by itself reproduces the full spectrum of human disease. We compared three mouse models of uveitis that target the interphotoreceptor retinoid binding protein (IRBP): (i) the “classical” model of experimental autoimmune uveitis (EAU) induced by immunization with IRBP; (ii) spontaneous uveitis in IRBP T cell receptor transgenic mice (R161H) and (iii) spontaneous uveitis in Autoimmune Regulator (AIRE)−/− mice. Disease course and severity, pathology and changes in visual function were studied using fundus imaging and histological examinations, optical coherence tomography and electroretinography. All models were on the B10.RIII background. Unlike previously reported, IRBP-induced EAU in B10.RIII mice exhibited two distinct patterns of disease depending on clinical scores developed after onset: severe monophasic with extensive destruction of the retina and rapid loss of visual signal, or lower grade with a prolonged chronic phase culminating after several months in retinal degeneration and loss of vision. R161H and AIRE−/− mice spontaneously developed chronic progressive inflammation; visual function declined gradually as retinal degeneration developed. Spontaneous uveitis in R161H mice was characterized by persistent cellular infiltrates and lymphoid aggregation, whereas AIRE−/− mice characteristically developed multi-focal infiltrates and severe choroidal inflammation. These data demonstrate variability and unique distinguishing features in the different models of uveitis, suggesting that each one can represent distinct aspects of uveitis in humans. PMID:24015215

  16. Realistic and Spherical Head Modeling for EEG Forward Problem Solution: A Comparative Cortex-Based Analysis

    PubMed Central

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

    2010-01-01

    The accuracy of forward models for electroencephalography (EEG) partly depends on head tissues geometry and strongly affects the reliability of the source reconstruction process, but it is not yet clear which brain regions are more sensitive to the choice of different model geometry. In this paper we compare different spherical and realistic head modeling techniques in estimating EEG forward solutions from current dipole sources distributed on a standard cortical space reconstructed from Montreal Neurological Institute (MNI) MRI data. Computer simulations are presented for three different four-shell head models, two with realistic geometry, either surface-based (BEM) or volume-based (FDM), and the corresponding sensor-fitted spherical-shaped model. Point Spread Function (PSF) and Lead Field (LF) cross-correlation analyses were performed for 26 symmetric dipole sources to quantitatively assess models' accuracy in EEG source reconstruction. Realistic geometry turns out to be a relevant factor of improvement, particularly important when considering sources placed in the temporal or in the occipital cortex. PMID:20169107

  17. Realistic and spherical head modeling for EEG forward problem solution: a comparative cortex-based analysis.

    PubMed

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

    2010-01-01

    The accuracy of forward models for electroencephalography (EEG) partly depends on head tissues geometry and strongly affects the reliability of the source reconstruction process, but it is not yet clear which brain regions are more sensitive to the choice of different model geometry. In this paper we compare different spherical and realistic head modeling techniques in estimating EEG forward solutions from current dipole sources distributed on a standard cortical space reconstructed from Montreal Neurological Institute (MNI) MRI data. Computer simulations are presented for three different four-shell head models, two with realistic geometry, either surface-based (BEM) or volume-based (FDM), and the corresponding sensor-fitted spherical-shaped model. Point Spread Function (PSF) and Lead Field (LF) cross-correlation analyses were performed for 26 symmetric dipole sources to quantitatively assess models' accuracy in EEG source reconstruction. Realistic geometry turns out to be a relevant factor of improvement, particularly important when considering sources placed in the temporal or in the occipital cortex.

  18. 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.

  19. Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC-Treated Mouse Strains

    PubMed Central

    Pandey, Vikash; Sultan, Marc; Kashofer, Karl; Ralser, Meryem; Amstislavskiy, Vyacheslav; Starmann, Julia; Osprian, Ingrid; Grimm, Christina; Hache, Hendrik; Yaspo, Marie-Laure; Sültmann, Holger; Trauner, Michael; Denk, Helmut; Zatloukal, Kurt; Lehrach, Hans; Wierling, Christoph

    2014-01-01

    Background Non-alcoholic fatty liver disease (NAFLD) has a broad spectrum of disease states ranging from mild steatosis characterized by an abnormal retention of lipids within liver cells to steatohepatitis (NASH) showing fat accumulation, inflammation, ballooning and degradation of hepatocytes, and fibrosis. Ultimately, steatohepatitis can result in liver cirrhosis and hepatocellular carcinoma. Methodology and Results In this study we have analyzed three different mouse strains, A/J, C57BL/6J, and PWD/PhJ, that show different degrees of steatohepatitis when administered a 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) containing diet. RNA-Seq gene expression analysis, protein analysis and metabolic profiling were applied to identify differentially expressed genes/proteins and perturbed metabolite levels of mouse liver samples upon DDC-treatment. Pathway analysis revealed alteration of arachidonic acid (AA) and S-adenosylmethionine (SAMe) metabolism upon other pathways. To understand metabolic changes of arachidonic acid metabolism in the light of disease expression profiles a kinetic model of this pathway was developed and optimized according to metabolite levels. Subsequently, the model was used to study in silico effects of potential drug targets for steatohepatitis. Conclusions We identified AA/eicosanoid metabolism as highly perturbed in DDC-induced mice using a combination of an experimental and in silico approach. Our analysis of the AA/eicosanoid metabolic pathway suggests that 5-hydroxyeicosatetraenoic acid (5-HETE), 15-hydroxyeicosatetraenoic acid (15-HETE) and prostaglandin D2 (PGD2) are perturbed in DDC mice. We further demonstrate that a dynamic model can be used for qualitative prediction of metabolic changes based on transcriptomics data in a disease-related context. Furthermore, SAMe metabolism was identified as being perturbed due to DDC treatment. Several genes as well as some metabolites of this module show differences between A/J and C57BL/6J

  20. 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

    2011-10-09

    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. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. 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

  2. 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

  3. A comparative model and techno-economic analysis of next generation AON ethernet and TDM PON

    NASA Astrophysics Data System (ADS)

    Wang, Kun; Larsen, Claus Popp; Gavler, Anders; Lannoo, Bart; Chiaroni, Dominique; Popov, Mikhail

    2010-12-01

    A global reference model covering next generation active and passive networks has been developed for techno-economic evaluations, and an extensive techno-economic analysis with a focus on CAPEX has been performed for 10G TDM PON and 1G AON - both capable of delivering 1Gbit/s to end-users. Two major cases have been considered: urban and rural at green field deployment. The results show that AON is less expensive than PON solution in urban case while in rural case 10G TDM PON is more competitive.

  4. 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.

  5. Biomechanical analysis comparing natural and alloplastic temporomandibular joint replacement using a finite element model.

    PubMed

    Mesnard, Michel; Ramos, Antonio; Ballu, Alex; Morlier, Julien; Cid, M; Simoes, J A

    2011-04-01

    Prosthetic materials and bone present quite different mechanical properties. Consequently, mandible reconstruction with metallic materials (or a mandible condyle implant) modifies the physiologic behavior of the mandible (stress, strain patterns, and condyle displacements). The changing of bone strain distribution results in an adaptation of the temporomandibular joint, including articular contacts. Using a validated finite element model, the natural mandible strains and condyle displacements were evaluated. Modifications of strains and displacements were then assessed for 2 different temporomandibular joint implants. Because materials and geometry play important key roles, mechanical properties of cortical bone were taken into account in models used in finite element analysis. The finite element model allowed verification of the worst loading configuration of the mandibular condyle. Replacing the natural condyle by 1 of the 2 tested implants, the results also show the importance of the implant geometry concerning biomechanical mandibular behavior. The implant geometry and stiffness influenced mainly strain distribution. The different forces applied to the mandible by the elevator muscles, teeth, and joint loads indicate that the finite element model is a relevant tool to optimize implant geometry or, in a subsequent study, to choose a more suitable distribution of the screws. Bone screws (number and position) have a significant influence on mandibular behavior and on implant stress pattern. Stress concentration and implant fracture must be avoided. Copyright © 2011 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

  6. Key Process Uncertainties in Soil Carbon Dynamics: Comparing Multiple Model Structures and Observational Meta-analysis

    NASA Astrophysics Data System (ADS)

    Sulman, B. N.; Moore, J.; Averill, C.; Abramoff, R. Z.; Bradford, M.; Classen, A. T.; Hartman, M. D.; Kivlin, S. N.; Luo, Y.; Mayes, M. A.; Morrison, E. W.; Riley, W. J.; Salazar, A.; Schimel, J.; Sridhar, B.; Tang, J.; Wang, G.; Wieder, W. R.

    2016-12-01

    Soil carbon (C) dynamics are crucial to understanding and predicting C cycle responses to global change and soil C modeling is a key tool for understanding these dynamics. While first order model structures have historically dominated this area, a recent proliferation of alternative model structures representing different assumptions about microbial activity and mineral protection is providing new opportunities to explore process uncertainties related to soil C dynamics. We conducted idealized simulations of soil C responses to warming and litter addition using models from five research groups that incorporated different sets of assumptions about processes governing soil C decomposition and stabilization. We conducted a meta-analysis of published warming and C addition experiments for comparison with simulations. Assumptions related to mineral protection and microbial dynamics drove strong differences among models. In response to C additions, some models predicted long-term C accumulation while others predicted transient increases that were counteracted by accelerating decomposition. In experimental manipulations, doubling litter addition did not change soil C stocks in studies spanning as long as two decades. This result agreed with simulations from models with strong microbial growth responses and limited mineral sorption capacity. In observations, warming initially drove soil C loss via increased CO2 production, but in some studies soil C rebounded and increased over decadal time scales. In contrast, all models predicted sustained C losses under warming. The disagreement with experimental results could be explained by physiological or community-level acclimation, or by warming-related changes in plant growth. In addition to the role of microbial activity, assumptions related to mineral sorption and protected C played a key role in driving long-term model responses. In general, simulations were similar in their initial responses to perturbations but diverged over

  7. Comparing model-based adaptive LMS filters and a model-free hysteresis loop analysis method for structural health monitoring

    NASA Astrophysics Data System (ADS)

    Zhou, Cong; Chase, J. Geoffrey; Rodgers, Geoffrey W.; Xu, Chao

    2017-02-01

    The model-free hysteresis loop analysis (HLA) method for structural health monitoring (SHM) has significant advantages over the traditional model-based SHM methods that require a suitable baseline model to represent the actual system response. This paper provides a unique validation against both an experimental reinforced concrete (RC) building and a calibrated numerical model to delineate the capability of the model-free HLA method and the adaptive least mean squares (LMS) model-based method in detecting, localizing and quantifying damage that may not be visible, observable in overall structural response. Results clearly show the model-free HLA method is capable of adapting to changes in how structures transfer load or demand across structural elements over time and multiple events of different size. However, the adaptive LMS model-based method presented an image of greater spread of lesser damage over time and story when the baseline model is not well defined. Finally, the two algorithms are tested over a simpler hysteretic behaviour typical steel structure to quantify the impact of model mismatch between the baseline model used for identification and the actual response. The overall results highlight the need for model-based methods to have an appropriate model that can capture the observed response, in order to yield accurate results, even in small events where the structure remains linear.

  8. 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

  9. Comparing Strategies for Lipid Lowering in Argentina: An Analysis from the CVD Policy Model-Argentina.

    PubMed

    Konfino, Jonatan; Fernandez, Alicia; Penko, Joanne; Mason, Antoinette; Martinez, Eugenio; Coxson, Pamela; Heller, David; Moran, Andrew; Bibbins-Domingo, Kirsten; Pérez-Stable, Eliseo J; Mejía, Raul

    2017-05-01

    In Argentina, the national guidelines for lipid control emphasize the use of relatively inexpensive low- or moderate-potency statins by patients at high risk (>20 %) of a cardiovascular event. The objective of this study was to compare the impact and costs of the current national CVD prevention guidelines with regard to morbidity and mortality in Argentina with the impact and costs of three strategies that incorporate high-potency statins. We used the CVD Policy Model-Argentina to model the proposed interventions. This model is a national-scale, state-transition (Markov) computer simulation model of the CVD incidence, prevalence, mortality, and costs in adults 35-84 years of age. We modeled three scenarios: scenario 1 lowers the risk threshold for treatment to >10 % according the Framingham Risk Score (FRS); scenario 2 intensifies statin potency under current treatment thresholds; and scenario 3 combines both scenarios by lowering the treatment threshold to ≥10 % FRS and intensifying statin potency. Scenario 1 would translate into 1400 fewer MIs and 500 fewer CHD deaths every year, a 3 % and 2 % reduction, respectively. Scenario 2 would lead to 2000 fewer MIs and 1000 fewer CHD deaths every year. Scenario 3 would result in the greatest reduction in MIs and CHD deaths, with 3400 fewer MIs and 1400 fewer CHD deaths every year, which translates to a 7 % and 6 % reduction, respectively. All scenarios were cost-effective if the cost of a high-potency statin pill was under US$0.25. Incorporating those individuals with greater than 10 % cardiovascular risk and the use of high-potency statins into Argentina's national lipid guidelines could result in fewer CHD deaths and events at a reasonable cost.

  10. 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.

  11. Comparative proteome analysis of serum from acute pulmonary embolism rat model for biomarker discovery.

    PubMed

    Li, Sheng-qing; Yun, Jun; Xue, Fu-bo; Bai, Chang-qing; Yang, Shu-guang; Que, Hai-ping; Zhao, Xin; Wu, Zhe; Wang, Yu; Liu, Shao-jun

    2007-01-01

    Pulmonary embolism (PE) is a common, potentially fatal disease and its diagnosis is challenging because clinical signs and symptoms are nonspecific. In this study, to investigate protein alterations of a rat PE model, total serum proteins collected at different time points were separated by two-dimensional electrophoresis (2-DE) and identified using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Bioinformatics analysis of 24 differentially expressed proteins showed that 20 had corresponding protein candidates in the database. According to their properties and obvious alterations after PE, changes of serum concentrations of Hp, Fn, DBP, RBP, and TTR were selected to be reidentified by western blot analysis. Semiquantitative RT-PCR showed DBP, RBP, and TTR to be down-regulated at mRNA levels in livers but not in lung tissues. The low serum concentrations of DBP, RBP, and TTR resulted in the up-regulation of 25(OH)D3, vitamin A, and FT4 (ligands of DBP, RBP, and TTR) after acute PE in rat models. The serum levels of Hp and Fn were detected in patients with DVT/PE and controls to explore their diagnostic prospects in acute PE because the mRNA levels of Hp and Fn were found to be up-regulated both in lung tissues and in livers after acute PE. Our data suggested that the concentration of serum Fn in controls was 79.42 +/- 31.57 microg/L, whereas that of PE/DVT patients was 554.43 +/- 136.18 microg/L (P < 0.001), and that the concentration of serum Hp in controls was 824.37 +/- 235.24 mg/L, whereas that of PE/DVT patients was 2063.48 +/- 425.38 mg/L (P < 0.001). The experimental PE rat model selected in this study was more similar to the clinical process than the other existing PE animal models, and the findings indicated instant changes of serum proteins within 48 h after acute PE. The exploration of these differentially expressed proteins or their combination with existent markers such as D-dimer may greatly improve the

  12. Cost-effectiveness analysis of a randomized trial comparing care models for chronic kidney disease.

    PubMed

    Hopkins, Robert B; Garg, Amit X; Levin, Adeera; Molzahn, Anita; Rigatto, Claudio; Singer, Joel; Soltys, George; Soroka, Steven; Parfrey, Patrick S; Barrett, Brendan J; Goeree, Ron

    2011-06-01

    Potential cost and effectiveness of a nephrologist/nurse-based multifaceted intervention for stage 3 to 4 chronic kidney disease are not known. This study examines the cost-effectiveness of a chronic disease management model for chronic kidney disease. Cost and cost-effectiveness were prospectively gathered alongside a multicenter trial. The Canadian Prevention of Renal and Cardiovascular Endpoints Trial (CanPREVENT) randomized 236 patients to receive usual care (controls) and another 238 patients to multifaceted nurse/nephrologist-supported care that targeted factors associated with development of kidney and cardiovascular disease (intervention). Cost and outcomes over 2 years were examined to determine the incremental cost-effectiveness of the intervention. Base-case analysis included disease-related costs, and sensitivity analysis included all costs. Consideration of all costs produced statistically significant differences. A lower number of days in hospital explained most of the cost difference. For both base-case and sensitivity analyses with all costs included, the intervention group required fewer resources and had higher quality of life. The direction of the results was unchanged to inclusion of various types of costs, consideration of payer or societal perspective, changes to the discount rate, and levels of GFR. The nephrologist/nurse-based multifaceted intervention represents good value for money because it reduces costs without reducing quality of life for patients with chronic kidney disease.

  13. A Network Epidemic Model with Preventive Rewiring: Comparative Analysis of the Initial Phase.

    PubMed

    Britton, Tom; Juher, David; Saldaña, Joan

    2016-12-01

    This paper is concerned with stochastic SIR and SEIR epidemic models on random networks in which individuals may rewire away from infected neighbors at some rate [Formula: see text] (and reconnect to non-infectious individuals with probability [Formula: see text] or else simply drop the edge if [Formula: see text]), so-called preventive rewiring. The models are denoted SIR-[Formula: see text] and SEIR-[Formula: see text], and we focus attention on the early stages of an outbreak, where we derive the expressions for the basic reproduction number [Formula: see text] and the expected degree of the infectious nodes [Formula: see text] using two different approximation approaches. The first approach approximates the early spread of an epidemic by a branching process, whereas the second one uses pair approximation. The expressions are compared with the corresponding empirical means obtained from stochastic simulations of SIR-[Formula: see text] and SEIR-[Formula: see text] epidemics on Poisson and scale-free networks. Without rewiring of exposed nodes, the two approaches predict the same epidemic threshold and the same [Formula: see text] for both types of epidemics, the latter being very close to the mean degree obtained from simulated epidemics over Poisson networks. Above the epidemic threshold, pairwise models overestimate the value of [Formula: see text] computed from simulations, which turns out to be very close to the one predicted by the branching process approximation. When exposed individuals also rewire with [Formula: see text] (perhaps unaware of being infected), the two approaches give different epidemic thresholds, with the branching process approximation being more in agreement with simulations.

  14. A comparative analysis of nonlinear models in short reach optical transmissions

    NASA Astrophysics Data System (ADS)

    Tao, Li; Tan, Hui; Liu, Qifeng; Chi, Nan

    2017-10-01

    In this paper, we present Wiener model (W-model), Hammerstein model (H-model), and parallel Hammerstein model (PH-model) based equalization schemes, which are the reduction of general Volterra series model, for the nonlinear distortions compensation in short reach optical transmission. The principle of each model is presented and the performance of these Volterra-class models based NLEs are investigated through pulse amplitude modulation (PAM) and carriless amplitude and phase modulation (CAP) simulation system. A 28 Gb/s CAP16 experiment system over 15 km fiber link is also demonstrated using the proposed NLEs. Finally, a comparison of performance and complexity using different NLEs is conducted.

  15. Comparing the Performance of Three Land Models in Global C Cycle Simulations: A Detailed Structural Analysis: Structural Analysis of Land Models

    SciTech Connect

    Rafique, Rashid; Xia, Jianyang; Hararuk, Oleksandra; Leng, Guoyong; Asrar, Ghassem; Luo, Yiqi

    2016-04-01

    Land models are valuable tools to understand the dynamics of global carbon (C) cycle. Various models have been developed and used for predictions of future C dynamics but uncertainties still exist. Diagnosing the models’ behaviors in terms of structures can help to narrow down the uncertainties in prediction of C dynamics. In this study three widely used land surface models, namely CSIRO’s Atmosphere Biosphere Land Exchange (CABLE) with 9 C pools, Community Land Model (version 3.5) combined with Carnegie-Ames-Stanford Approach (CLM-CASA) with 12 C pools and Community Land Model (version 4) (CLM4) with 26 C pools were driven by the observed meteorological forcing. The simulated C storage and residence time were used for analysis. The C storage and residence time were computed globally for all individual soil and plant pools, as well as net primary productivity (NPP) and its allocation to different plant components’ based on these models. Remotely sensed NPP and statistically derived HWSD, and GLC2000 datasets were used as a reference to evaluate the performance of these models. Results showed that CABLE exhibited better agreement with referenced C storage and residence time for plant and soil pools, as compared with CLM-CASA and CLM4. CABLE had longer bulk residence time for soil C pools and stored more C in roots, whereas, CLM-CASA and CLM4 stored more C in woody pools due to differential NPP allocation. Overall, these results indicate that the differences in C storage and residence times in three models are largely due to the differences in their fundamental structures (number of C pools), NPP allocation and C transfer rates. Our results have implications in model development and provide a general framework to explain the bias/uncertainties in simulation of C storage and residence times from the perspectives of model structures.

  16. Comparative Analysis of Context-Dependent Mutagenesis Using Human and Mouse Models

    PubMed Central

    Medvedeva, Sofya A.; Panchin, Alexander Y.; Alexeevski, Andrey V.; Spirin, Sergey A.; Panchin, Yuri V.

    2013-01-01

    Substitution rates strongly depend on their nucleotide context. One of the most studied examples is the excess of C > T mutations in the CG context in various groups of organisms, including vertebrates. Studies on the molecular mechanisms underlying this mutation regularity have provided insights into evolution, mutagenesis, and cancer development. Recently several other hypermutable motifs were identified in the human genome. There is an increased frequency of T > C mutations in the second position of the words ATTG and ATAG and an increased frequency of A > C mutations in the first position of the word ACAA. For a better understanding of evolution, it is of interest whether these mutation regularities are human specific or present in other vertebrates, as their presence might affect the validity of currently used substitution models and molecular clocks. A comprehensive analysis of mutagenesis in 4 bp mutation contexts requires a vast amount of mutation data. Such data may be derived from the comparisons of individual genomes or from single nucleotide polymorphism (SNP) databases. Using this approach, we performed a systematical comparison of mutation regularities within 2–4 bp contexts in Mus musculus and Homo sapiens and uncovered that even closely related organisms may have notable differences in context-dependent mutation regularities. PMID:24058920

  17. [Comparative analysis of spatial EEG organization on models of non-verbal divergent and convergent thinking].

    PubMed

    Sviderskaia, N E; Antonov, A G; Butneva, L S

    2007-01-01

    Features of neurophysiological organization of two main thinking types playing different roles in creative processes, i.e., divergent and convergent were studied with participation of 30 right-handed male subjects at the age from 30 to 50 years. Two tests were presented: (1) creation of many visual images on the basis of two simple geometrical figures (the model of divergent thinking) and (2) classification of a figure element with one of the offered standard samples (convergent thinking). The number of created images or correctly classified elements for five minutes served a criterion of performance productivity. It was found that performance of the divergent test with high productivity (as compared to low productivity) was characterized by a greater increase in non-linear interactions between the cortical potentials, especially in the axis right frontal--left occipital areas. At the same time, under conditions of high productivity, the number of active narrow-frequency spectral-coherent EEG bands increased. The data confirm the notion of neurophysiological organization of creative processes, according to which creative processes require the intensification of retrieval operations (both conscious and unconscious), based on extensive interhemispheric interaction and involvement of a system of EEG coherent structures oscillating with different frequencies.

  18. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Estimating Time to Disease Progression Comparing Transition Models and Survival Methods - an Analysis of Multiple Sclerosis Data

    PubMed Central

    Mandel, Micha; Mercier, Francois; Eckert, Benjamin; Chin, Peter; Betensky, Rebecca A.

    2014-01-01

    Summary This paper reports an analysis that aims to quantify the effect of fingolimod, an oral treatment for relapsing remitting multiple sclerosis (MS), on disability progression. The standard approach utilizes survival analysis methods, which may be problematic for MS studies that assess disability at only a few time points and include as a cardinal feature both relapses and remissions. Instead, a Markov transition model, originally developed in the framework of longitudinal data, is fit, and its special probabilistic properties are used to estimate survival curves for time to disability progression. The transition approach models the whole disability process and uses all available transition data for inference, while survival methods concentrate on a single event of interest and use only time to event data. This paper compares the transition model approach to survival analysis methods, and discusses the differences in the interpretations of the estimated parameters. It applies both models to data obtained from two phase 3 clinical trials and finds that both yield positive effects for the new treatment compared to placebo, and provide similar estimates for the probability of disability progression over time. The transition model enables calculation of covariate-specific transition matrices that describe the short-term effect of treatment and other covariates on the disability process. PMID:23410536

  20. Comparative Logic Modeling for Policy Analysis: The Case of HIV Testing Policy Change at the Department of Veterans Affairs

    PubMed Central

    Langer, Erika M; Gifford, Allen L; Chan, Kee

    2011-01-01

    Objective Logic models have been used to evaluate policy programs, plan projects, and allocate resources. Logic Modeling for policy analysis has been used rarely in health services research but can be helpful in evaluating the content and rationale of health policies. Comparative Logic Modeling is used here on human immunodeficiency virus (HIV) policy statements from the Department of Veterans Affairs (VA) and Centers for Disease Control and Prevention (CDC). We created visual representations of proposed HIV screening policy components in order to evaluate their structural logic and research-based justifications. Data Sources and Study Design We performed content analysis of VA and CDC HIV testing policy documents in a retrospective case study. Data Collection Using comparative Logic Modeling, we examined the content and primary sources of policy statements by the VA and CDC. We then quantified evidence-based causal inferences within each statement. Principal Findings VA HIV testing policy structure largely replicated that of the CDC guidelines. Despite similar design choices, chosen research citations did not overlap. The agencies used evidence to emphasize different components of the policies. Conclusion Comparative Logic Modeling can be used by health services researchers and policy analysts more generally to evaluate structural differences in health policies and to analyze research-based rationales used by policy makers. PMID:21689094

  1. A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi

    PubMed Central

    2013-01-01

    Background Fungal pathogens cause devastating losses in economically important cereal crops by utilising pathogen proteins to infect host plants. Secreted pathogen proteins are referred to as effectors and have thus far been identified by selecting small, cysteine-rich peptides from the secretome despite increasing evidence that not all effectors share these attributes. Results We take advantage of the availability of sequenced fungal genomes and present an unbiased method for finding putative pathogen proteins and secreted effectors in a query genome via comparative hidden Markov model analyses followed by unsupervised protein clustering. Our method returns experimentally validated fungal effectors in Stagonospora nodorum and Fusarium oxysporum as well as the N-terminal Y/F/WxC-motif from the barley powdery mildew pathogen. Application to the cereal pathogen Fusarium graminearum reveals a secreted phosphorylcholine phosphatase that is characteristic of hemibiotrophic and necrotrophic cereal pathogens and shares an ancient selection process with bacterial plant pathogens. Three F. graminearum protein clusters are found with an enriched secretion signal. One of these putative effector clusters contains proteins that share a [SG]-P-C-[KR]-P sequence motif in the N-terminal and show features not commonly associated with fungal effectors. This motif is conserved in secreted pathogenic Fusarium proteins and a prime candidate for functional testing. Conclusions Our pipeline has successfully uncovered conservation patterns, putative effectors and motifs of fungal pathogens that would have been overlooked by existing approaches that identify effectors as small, secreted, cysteine-rich peptides. It can be applied to any pathogenic proteome data, such as microbial pathogen data of plants and other organisms. PMID:24252298

  2. A Model for Carbohydrate Metabolism in the Diatom Phaeodactylum tricornutum Deduced from Comparative Whole Genome Analysis

    PubMed Central

    Kaplan, Aaron; Caron, Lise; Weber, Till; Maheswari, Uma; Armbrust, E. Virginia; Bowler, Chris

    2008-01-01

    Background Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids. Methodology/Principal Findings The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO2 fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a β-1,3-glucan) outside of the plastids. We identified various β-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes. Conclusions/Significance Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel

  3. Validation of the Modes of Transmission Model as a Tool to Prioritize HIV Prevention Targets: A Comparative Modelling Analysis

    PubMed Central

    Mishra, Sharmistha; Pickles, Michael; Blanchard, James F.; Moses, Stephen; Shubber, Zara; Boily, Marie-Claude

    2014-01-01

    Background The static Modes of Transmission (MOT) model predicts the annual fraction of new HIV infections acquired across subgroups (MOT metric), and is used to focus HIV prevention. Using synthetic epidemics via a dynamical model, we assessed the validity of the MOT metric for identifying epidemic drivers (behaviours or subgroups that are sufficient and necessary for HIV to establish and persist), and the potential consequence of MOT-guided policies. Methods and Findings To generate benchmark MOT metrics for comparison, we simulated three synthetic epidemics (concentrated, mixed, and generalized) with different epidemic drivers using a dynamical model of heterosexual HIV transmission. MOT metrics from generic and complex MOT models were compared against the benchmark, and to the contribution of epidemic drivers to overall HIV transmission (cumulative population attributable fraction over t years, PAFt). The complex MOT metric was similar to the benchmark, but the generic MOT underestimated the fraction of infections in epidemic drivers. The benchmark MOT metric identified epidemic drivers early in the epidemics. Over time, the MOT metric did not identify epidemic drivers. This was not due to simplified MOT models or biased parameters but occurred because the MOT metric (irrespective of the model used to generate it) underestimates the contribution of epidemic drivers to HIV transmission over time (PAF5–30). MOT-directed policies that fail to reach epidemic drivers could undermine long-term impact on HIV incidence, and achieve a similar impact as random allocation of additional resources. Conclusions Irrespective of how it is obtained, the MOT metric is not a valid stand-alone tool to identify epidemic drivers, and has limited additional value in guiding the prioritization of HIV prevention targets. Policy-makers should use the MOT model judiciously, in combination with other approaches, to identify epidemic drivers. PMID:25014543

  4. Computer simulation environment for comparative analysis of models for investment portfolio management

    NASA Astrophysics Data System (ADS)

    Marchev, Angel, Jr.; Marchev, Angel

    2013-12-01

    Building on the notion of systematically analyzing investment portfolio as a feedback system, there is a need of experimentation system. In this paper such system for experimenting with various traditional, classical, advanced, etc. models for portfolio management is described. The main objective is to have the ability to compete the models systematically on a unified data track.

  5. A Comparative Analysis of Leadership Development Models in Post-Baccalaureate Theological Education

    ERIC Educational Resources Information Center

    Kiedis, Thomas Lee

    2009-01-01

    This research study was concerned with higher education, leadership development, and understanding and examining the training models that are employed to prepare men and women for Christian ministry. The study combines qualitative and quantitative research elements to examine the growing number of leadership development training models in…

  6. Sound propagation in woods. Comparative analysis between in situ measurements, laboratory measurements and the values predicted by a theoretical model

    NASA Astrophysics Data System (ADS)

    Tarrero Fernandez, Ana Isabel

    This PhD Thesis studies sound propagation outdoors and the potential effect of trees on such propagation. In the first part of the thesis, seven different types of grounds (sand, grass, concrete...) are characterised from an acoustical point of view. In order to determine the ground impedance of each type of ground, it was necessary to determine the flow resistivity by means of an indirect method. In this method the flow resistivity values are chosen so as to give the best fit between experimental values and the values given by a theoretical propagation model. This first part includes a comparative analysis of sound attenuation over two very similar types of grounds, one with trees and the other one without trees. It is observed that at high frequencies sound attenuation in the case of ground with trees (wood) is higher. In the second part of this work, the theoretical outdoor sound propagation model NORD 2000, which has been developed by a group of scientists in the Scandinavian countries, is described and then validated. This model takes into account the source characteristics, the geometric divergence, atmospheric absorption, ground effects and the scattering produced by obstacles such as trees, houses... In order to validate this theoretical model, we have compared the predictions given by the model under many different circumstances with the values measured in situ in different types of woods and also with the values measured in a scaled model in laboratory, using different trees density, trunk diameters... From a deep analysis of all the set of comparisons it was concluded that the theoretical model NORD 2000 agrees very well with the experimental values both measured in situ and in laboratory (scale model) at low and medium frequencies. At high frequencies there are some discrepancies between the model and the experimental values.

  7. A global analysis of the comparability of winter chill models for fruit and nut trees

    NASA Astrophysics Data System (ADS)

    Luedeling, Eike; Brown, Patrick H.

    2011-05-01

    Many fruit and nut trees must fulfill a chilling requirement to break their winter dormancy and resume normal growth in spring. Several models exist for quantifying winter chill, and growers and researchers often tacitly assume that the choice of model is not important and estimates of species chilling requirements are valid across growing regions. To test this assumption, Safe Winter Chill (the amount of winter chill that is exceeded in 90% of years) was calculated for 5,078 weather stations around the world, using the Dynamic Model [in Chill Portions (CP)], the Chilling Hours (CH) Model and the Utah Model [Utah Chill Units (UCU)]. Distributions of the ratios between different winter chill metrics were mapped on a global scale. These ratios should be constant if the models were strictly proportional. Ratios between winter chill metrics varied substantially, with the CH/CP ratio ranging between 0 and 34, the UCU/CP ratio between -155 and +20 and the UCU/CH ratio between -10 and +5. The models are thus not proportional, and chilling requirements determined in a given location may not be valid elsewhere. The Utah Model produced negative winter chill totals in many Subtropical regions, where it does not seem to be useful. Mean annual temperature and daily temperature range influenced all winter chill ratios, but explained only between 12 and 27% of the variation. Data on chilling requirements should always be amended with information on the location and experimental conditions of the study in which they were determined, ideally including site-specific conversion factors between winter chill models. This would greatly facilitate the transfer of such information across growing regions, and help prepare growers for the impact of climate change.

  8. A global analysis of the comparability of winter chill models for fruit and nut trees.

    PubMed

    Luedeling, Eike; Brown, Patrick H

    2011-05-01

    Many fruit and nut trees must fulfill a chilling requirement to break their winter dormancy and resume normal growth in spring. Several models exist for quantifying winter chill, and growers and researchers often tacitly assume that the choice of model is not important and estimates of species chilling requirements are valid across growing regions. To test this assumption, Safe Winter Chill (the amount of winter chill that is exceeded in 90% of years) was calculated for 5,078 weather stations around the world, using the Dynamic Model [in Chill Portions (CP)], the Chilling Hours (CH) Model and the Utah Model [Utah Chill Units (UCU)]. Distributions of the ratios between different winter chill metrics were mapped on a global scale. These ratios should be constant if the models were strictly proportional. Ratios between winter chill metrics varied substantially, with the CH/CP ratio ranging between 0 and 34, the UCU/CP ratio between -155 and +20 and the UCU/CH ratio between -10 and +5. The models are thus not proportional, and chilling requirements determined in a given location may not be valid elsewhere. The Utah Model produced negative winter chill totals in many Subtropical regions, where it does not seem to be useful. Mean annual temperature and daily temperature range influenced all winter chill ratios, but explained only between 12 and 27% of the variation. Data on chilling requirements should always be amended with information on the location and experimental conditions of the study in which they were determined, ideally including site-specific conversion factors between winter chill models. This would greatly facilitate the transfer of such information across growing regions, and help prepare growers for the impact of climate change.

  9. Comparative analysis of data collection methods for individualized modeling of radiologists' visual similarity judgments in mammograms.

    PubMed

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

    2013-11-01

    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. Six observers of varying 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. The average accuracy of the user models derived from data collected with the hybrid method was 55.5 ± 1.5%. The models were significantly more accurate (P < .0005) than those derived from the rating (45.3 ± 3.5%) and the preference (40.8 ± 5%) methods. On average, the rating data collection method was significantly faster than the other two methods (P < .0001). No time advantage was observed between the preference and the hybrid methods. 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. Copyright © 2013 AUR. Published by Elsevier Inc. All rights reserved.

  10. 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.

  11. 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

  12. Comparing root architectural models

    NASA Astrophysics Data System (ADS)

    Schnepf, Andrea; Javaux, Mathieu; Vanderborght, Jan

    2017-04-01

    Plant roots play an important role in several soil processes (Gregory 2006). Root architecture development determines the sites in soil where roots provide input of carbon and energy and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architectural models have been widely used and been further developed into functional-structural models that are able to simulate the fate of water and solutes in the soil-root system (Dunbabin et al. 2013). Still, a systematic comparison of the different root architectural models is missing. In this work, we focus on discrete root architecture models where roots are described by connected line segments. These models differ (a) in their model concepts, such as the description of distance between branches based on a prescribed distance (inter-nodal distance) or based on a prescribed time interval. Furthermore, these models differ (b) in the implementation of the same concept, such as the time step size, the spatial discretization along the root axes or the way stochasticity of parameters such as root growth direction, growth rate, branch spacing, branching angles are treated. Based on the example of two such different root models, the root growth module of R-SWMS and RootBox, we show the impact of these differences on simulated root architecture and aggregated information computed from this detailed simulation results, taking into account the stochastic nature of those models. References Dunbabin, V.M., Postma, J.A., Schnepf, A., Pagès, L., Javaux, M., Wu, L., Leitner, D., Chen, Y.L., Rengel, Z., Diggle, A.J. Modelling root-soil interactions using three-dimensional models of root growth, architecture and function (2013) Plant and Soil, 372 (1-2), pp. 93 - 124. Gregory (2006) Roots, rhizosphere and soil: the route to a better understanding of soil science? European Journal of Soil Science 57: 2-12.

  13. 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.

  14. 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.

  15. Population Education in the School Curriculum: A Comparative Analysis of the American and Asian Models.

    ERIC Educational Resources Information Center

    Okobiah, Omamurhomu Solomon

    1981-01-01

    A content analysis of two selected population education curriculum materials, one representative of advanced nations, the other of developing nations: "Population, Environmental-Ecological Education Project" (Missouri State Department of Education, 1973) and "Population and Family Education" (Unesco Regional Office for Asia,…

  16. Experiencing the Portfolio Process during the Internship: A Comparative Analysis of Two PETE Portfolio Models.

    ERIC Educational Resources Information Center

    Senne, Terry A.; Rikard, G. Linda

    2002-01-01

    Analyzed two physical education teacher education portfolio models regarding the impact on intern perceptions of the value of portfolios, intern professional growth, and portfolio representation in single and dual internship site placements. Data from surveys and reflection logs indicated that although interns showed no change in moral judgement…

  17. 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…

  18. 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…

  19. A Comparative Analysis of MMPI-2 Malingering Detection Models among Inmates

    ERIC Educational Resources Information Center

    Steffan, Jarrod S.; Morgan, Robert D.; Lee, Jeahoon; Sellbom, Martin

    2010-01-01

    There are several strategies, or models, for combining the Minnesota Multiphasic Personality Inventory-2 (MMPI-2) validity indicators to detect malingered psychiatric symptoms. Some scholars have recommended that an elevated F (Infrequency) score should be followed by the inspection of Fp (Infrequency-Psychopathology), whereas a recent…

  20. 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…

  1. A Comparative Analysis of MMPI-2 Malingering Detection Models among Inmates

    ERIC Educational Resources Information Center

    Steffan, Jarrod S.; Morgan, Robert D.; Lee, Jeahoon; Sellbom, Martin

    2010-01-01

    There are several strategies, or models, for combining the Minnesota Multiphasic Personality Inventory-2 (MMPI-2) validity indicators to detect malingered psychiatric symptoms. Some scholars have recommended that an elevated F (Infrequency) score should be followed by the inspection of Fp (Infrequency-Psychopathology), whereas a recent…

  2. Sports Medicine and Rehabilitation Team Clinic: Comparative Model Analysis of Navy and Marine Corps Options

    DTIC Science & Technology

    2003-05-01

    30-09-2003 Final Report July 2002 to July 2003 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Sports Medicine and Rehabilitation Team Clinic: Comparative 5b...distribution is unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT The purpose of this project was to examine the suitabibity of several Sports Medicine...for musculoskeletal injuries or illnesses. 15. SUBJECT TERMS Sport Medicine, Athletic Trainers, Rehabilitation Team, SMART, Musculoskeletal Injuries

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

    PubMed

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

    2015-01-01

    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. 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. 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. By following a stepwise approach, a minimally invasive, effective, and reproducible rabbit model of catheter-induced myocardial

  4. A Comparative Analysis of Commercial Off-The-Shelf Naval Simulations and Classic Operations Research Models

    DTIC Science & Technology

    2009-09-01

    provides the information necessary to produce realistic models. Built upon the two original formulas developed by Larry Bond to first, determine a ship’s...graciously agreed to be my Second Reader. His advice and guidance were the keys to defining the original problem and overcoming those that arose... originally created by Mr. Larry Bond. Harpoon is the name of a comprehensive series of naval warfare games developed initially in miniatures by Larry

  5. A comparative analysis of the density distributions and the structure models of 9Li

    NASA Astrophysics Data System (ADS)

    Aygun, M.

    2017-03-01

    In the present study, we have analysed the elastic scattering cross-section data of 9Li + 12C system at E lab = 540 MeV and 9Li + 208Pb system at E c.m. = 28.3 MeV for some cluster models and various density distributions of the 9Li nucleus. First, we have obtained five different density distributions of the 9Li nucleus to generate real potentials with the help of double-folding model. For these densities, we have calculated the elastic scattering angular distributions. Secondly, using a simple approach, we have investigated some cluster models of the 9Li nucleus consisting of 6He + 3H and 8Li + n systems. We have presented the comparison of elastic scattering angular distributions for each system with each other as well as with the experimental data. Finally, we have given the cross-section values obtained from the theoretical calculations for all the systems studied in this paper.

  6. Comparative empirical analysis of flow-weighted transit route networks in R-space and evolution modeling

    NASA Astrophysics Data System (ADS)

    Huang, Ailing; Zang, Guangzhi; He, Zhengbing; Guan, Wei

    2017-05-01

    Urban public transit system is a typical mixed complex network with dynamic flow, and its evolution should be a process coupling topological structure with flow dynamics, which has received little attention. This paper presents the R-space to make a comparative empirical analysis on Beijing’s flow-weighted transit route network (TRN) and we found that both the Beijing’s TRNs in the year of 2011 and 2015 exhibit the scale-free properties. As such, we propose an evolution model driven by flow to simulate the development of TRNs with consideration of the passengers’ dynamical behaviors triggered by topological change. The model simulates that the evolution of TRN is an iterative process. At each time step, a certain number of new routes are generated driven by travel demands, which leads to dynamical evolution of new routes’ flow and triggers perturbation in nearby routes that will further impact the next round of opening new routes. We present the theoretical analysis based on the mean-field theory, as well as the numerical simulation for this model. The results obtained agree well with our empirical analysis results, which indicate that our model can simulate the TRN evolution with scale-free properties for distributions of node’s strength and degree. The purpose of this paper is to illustrate the global evolutional mechanism of transit network that will be used to exploit planning and design strategies for real TRNs.

  7. Comparative Analysis of Calcium Silicate-based Root Filling Materials Using an Open Apex Model.

    PubMed

    Tran, Dennis; He, Jianing; Glickman, Gerald N; Woodmansey, Karl F

    2016-04-01

    Many new calcium silicate-based root filling materials have emerged in the market; however, their performance in the orthograde obturation of an open apex has not been evaluated. The purpose of this study was to compare the marginal adaptation of ProRoot MTA (Dentsply Tulsa Dental, Tulsa, OK), NeoMTA Plus (Avalon Biomed Inc, Bradenton, FL), and Endosequence BC RRM-Fast Set Putty (BC RRM-FS; Brasseler USA, Savannah, GA) after orthograde placement in roots with open apices. Palatal roots of maxillary molars were instrumented to create divergent open apices and divided into 4 groups for orthograde obturation: ProRoot MTA, NeoMTA Plus, BC RRM-FS, and BC RRM-FS + BC Sealer. Using a scanning electron microscope, the quality of material adaptation at the anatomic apex was evaluated by 5 blinded examiners; 3 mm of the root end was sectioned, and gap distance was measured at the material-dentin interface. Statistical analyses were performed using the Kruskal-Wallis test. There were no significant differences in marginal adaptation among the 4 groups at the level of the anatomic apex (P = .175). BC RRM-FS + BC Sealer had a significantly smaller gap size after 3-mm root end resection compared with the other 3 groups (P < .01). No differences were observed among the other 3 materials. All materials showed comparable marginal adaptation at the anatomic apex when used for orthograde obturation of open apices. Application of BC Sealer before the delivery of BC RRM-FS Putty enhanced the quality of adaptation coronal to the apex. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  8. 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…

  9. 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.

  10. Comparative analysis of 2D and 3D model of a PEMFC in COMSOL

    NASA Astrophysics Data System (ADS)

    Lakshmi, R. Bakiya; Harikrishnan, N. P.; Juliet, A. Vimala

    2017-10-01

    In this article, 2D and 3D model of a PEMFC has been simulated in order to study their performance when subjected to similar operating conditions. The comparison reveals interesting phenomena of performance enhancement of the fuel cell. Design of fuel cell channel and stationary studies were done in COMSOL. Variations in current density and electrolyte potential from simulation results were observed when operated at a temperature of 120 °C. The electrolyte potential was found to have increased from 1 to 2.5 V and the surface pressure due to fluid flow was found to have increased from 3 to 9.58 Pa.

  11. 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.

  12. Inhibitors of Trypanosoma brucei trypanothione reductase: comparative molecular field analysis modeling and structural basis for selective inhibition.

    PubMed

    Ferreira, Leonardo G; Andricopulo, Adriano D

    2013-10-01

    Sleeping sickness is a major cause of death in Africa. Since no secure treatment is available, the development of novel therapeutic agents is urgent. In this context, the enzyme trypanothione reductase (TR) is a prominent molecular target that has been investigated in drug design for sleeping sickness. In this study, comparative molecular field analysis models were generated for a series of Trypanosoma brucei TR inhibitors. Statistically significant results were obtained and the models were applied to predict the activity of external test sets, with good correlation between predicted and experimental results. We have also investigated the structural requirements for the selective inhibition of the parasite's enzyme over the human glutathione reductase. The quantitative structure-activity relationship models provided valuable information regarding the essential molecular requirements for the inhibitory activity upon the target protein, providing important insights into the design of more potent and selective TR inhibitors.

  13. 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.

  14. Comparative analysis of numerical integration schemes of density equation for a computational model of bone remodelling.

    PubMed

    Garzón-Alvarado, D A; Linero, D

    2012-01-01

    In this study, a computational model of bone remodelling problem as proposed by Weinans et al. (1992) is described and solved by other temporal integration techniques different from the Euler scheme. This model considers three types of numerical integration schemes of the evolution of the material density during the remodelling: Euler, Heun and Runge-Kutta methods. Also the strain and the density field are obtained inside each element, at Gauss points or at the nodes of the mesh. A square plate with 1.00 m of side subjected to non-uniform pressure is simulated with two meshes of quadrilateral element with size [Formula: see text] and [Formula: see text] m. Two increments time size: [Formula: see text] and [Formula: see text] days are used. The results show that Euler, Heun and Runge-Kutta's methods correctly approached the problem of bone remodelling and that there were no appreciable differences in the patterns obtained by the mesh and time step used. In contrast, using an element-based approach and node-based approach, substantial differences were produced in bone remodelling density pattern. 'Chess board' type discontinuities were found in the element approach near the applied pressure area, as were well-defined columns away from this. The node-based approach showed continuity in density distribution. These patterns were well represented by the methods for resolving the density equation. This study concluded that any method of time integration could be used for these meshes and time steps size.

  15. Peer cluster theory and adolescent alcohol use: an explanation of alcohol use and a comparative analysis between two causal models.

    PubMed

    Rose, C D

    1999-01-01

    This study tests the premise of peer cluster theory as it applies to individual alcohol use, and makes a comparative analysis between its ability to explain alcohol use and marijuana use. Using the results of a 1996 drug and alcohol survey of 1312 Western Kentucky University students, path analysis was used to measure the influence of six of peer cluster theory's psychosocial characteristics on the percentage of the respondent's college friends who use alcohol. All of these variables were then regressed on the respondent's alcohol use. The results of the causal models did show some support for peer cluster theory. The direct effect of the student's association with alcohol-using peers on individual alcohol use was shown to have the strongest direct influence on this outcome variable. However, a few limitations of this theoretical perspective were identified. The causal model for alcohol use showed that the indirect influence of two of these psychosocial characteristics (parental attitudes on alcohol use and success in school) was weaker than their direct influence on individual alcohol use. And, the comparative analysis showed that peer cluster theory is better suited to explain the use of marijuana than the use of alcohol.

  16. 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.

  17. 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.

  18. Accuracy of Bolton analysis measured in laser scanned digital models compared with plaster models (gold standard) and cone-beam computer tomography images

    PubMed Central

    Kim, Jooseong

    2016-01-01

    Objective The aim of this study was to compare the accuracy of Bolton analysis obtained from digital models scanned with the Ortho Insight three-dimensional (3D) laser scanner system to those obtained from cone-beam computed tomography (CBCT) images and traditional plaster models. Methods CBCT scans and plaster models were obtained from 50 patients. Plaster models were scanned using the Ortho Insight 3D laser scanner; Bolton ratios were calculated with its software. CBCT scans were imported and analyzed using AVIZO software. Plaster models were measured with a digital caliper. Data were analyzed with descriptive statistics and the intraclass correlation coefficient (ICC). Results Anterior and overall Bolton ratios obtained by the three different modalities exhibited excellent agreement (> 0.970). The mean differences between the scanned digital models and physical models and between the CBCT images and scanned digital models for overall Bolton ratios were 0.41 ± 0.305% and 0.45 ± 0.456%, respectively; for anterior Bolton ratios, 0.59 ± 0.520% and 1.01 ± 0.780%, respectively. ICC results showed that intraexaminer error reliability was generally excellent (> 0.858 for all three diagnostic modalities), with < 1.45% discrepancy in the Bolton analysis. Conclusions Laser scanned digital models are highly accurate compared to physical models and CBCT scans for assessing the spatial relationships of dental arches for orthodontic diagnosis. PMID:26877978

  19. Accuracy of Bolton analysis measured in laser scanned digital models compared with plaster models (gold standard) and cone-beam computer tomography images.

    PubMed

    Kim, Jooseong; Lagravére, Manuel O

    2016-01-01

    The aim of this study was to compare the accuracy of Bolton analysis obtained from digital models scanned with the Ortho Insight three-dimensional (3D) laser scanner system to those obtained from cone-beam computed tomography (CBCT) images and traditional plaster models. CBCT scans and plaster models were obtained from 50 patients. Plaster models were scanned using the Ortho Insight 3D laser scanner; Bolton ratios were calculated with its software. CBCT scans were imported and analyzed using AVIZO software. Plaster models were measured with a digital caliper. Data were analyzed with descriptive statistics and the intraclass correlation coefficient (ICC). Anterior and overall Bolton ratios obtained by the three different modalities exhibited excellent agreement (> 0.970). The mean differences between the scanned digital models and physical models and between the CBCT images and scanned digital models for overall Bolton ratios were 0.41 ± 0.305% and 0.45 ± 0.456%, respectively; for anterior Bolton ratios, 0.59 ± 0.520% and 1.01 ± 0.780%, respectively. ICC results showed that intraexaminer error reliability was generally excellent (> 0.858 for all three diagnostic modalities), with < 1.45% discrepancy in the Bolton analysis. Laser scanned digital models are highly accurate compared to physical models and CBCT scans for assessing the spatial relationships of dental arches for orthodontic diagnosis.

  20. 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

  1. 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.

  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. Replacing an academic internal medicine residency program with a physician assistant--hospitalist model: a comparative analysis study.

    PubMed

    Dhuper, Sunil; Choksi, Sonia

    2009-01-01

    This study describes a comparative analysis of replacing medical residents with physician assistants and hospitalists on patient outcomes in a community hospital. Prospective data during the physician assistants-hospitalists service for 2 years was compared with 2 years of retrospective data of the medical residents model. Outcome measures included mortality, adverse events, readmissions, and patient satisfaction. For physician assistants- hospitalists versus medical residents models, all-cause and case mix index-adjusted mortality was 107/5508 (1.94%) and 0.019 versus 156/5458 (2.85%) and 0.029, respectively (P < or = .001). The adverse event cases were 9 versus 5 ( P = .29), and the readmission rate within 30 days was 64 versus 69 (P = .34). Patient satisfaction was 95% versus 96% (P = .33). Quality of care provided by the physician assistants-hospitalists model was equivalent. All-cause and case mix index- adjusted mortality was significantly lower during the physician assistants-hospitalists period.Although the application of these findings to other institutions requires further study, the authors found no intrinsic barriers that would impede implementation elsewhere.

  4. 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

  5. Comparative Protein Structure Modeling Using MODELLER

    PubMed Central

    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. PMID:27322406

  6. Diagnostic analysis of water balance variability: A comparative modeling study of catchments in Perth, Newcastle, and Darwin, Australia

    NASA Astrophysics Data System (ADS)

    Samuel, Jos M.; Sivapalan, Murugesu; Struthers, Iain

    2008-06-01

    A comparative study is performed to explore interactions between climate variability and landscape factors that control water balance variability in three diverse regions of Australia: Perth (temperate with distinct dry summers); Newcastle (temperate with no distinct dry season); and Darwin (tropical region affected by monsoons). This comparative analysis is carried out through adoption of a common conceptual model. The similarity and differences between the three catchments are explored through evaluation of signatures of streamflow and soil moisture variability, and systematic sensitivity analysis with respect to parameters representing various landscape characteristics. The results of the analysis show that the biggest contributor to the differences between the catchments is the distribution of soil depth and the soil's drainage characteristics. The second factor is climate, as exemplified by the (annual) climatic dryness index and the intra-annual (seasonal) variability of both rainfall and potential evaporation, and associated rainfall intensity patterns, and their interactions with the soil properties (i.e., soil depth and the soil's drainage characteristics). In Perth and Darwin, climate seasonality is responsible for a seasonal switching on/off of subsurface stormflow at the start/end of the wet season, respectively. In Newcastle, where soil moisture contents hover near the field capacity value throughout the year, subsurface stormflow occurs frequently throughout the year, with event-based switching on/off in response to individual storms of moderate magnitude and temporal clustering of small storms. In addition, in rare circumstance, surface runoff is triggered in response to extreme storm events and temporal clustering of moderate to large storm events.

  7. The use of modelling to predict levels of estrogens in a river catchment: how does modelled data compare with chemical analysis and in vitro yeast assay results?

    PubMed

    Balaam, Jan L; Grover, Darren; Johnson, Andrew C; Jürgens, Monika; Readman, James; Smith, Andy J; White, Stefan; Williams, Richard; Zhou, John L

    2010-09-15

    Effluent discharges at Rodbourne sewage treatment works (STWs) were assessed using chemical and in vitro biological analysis as well as modelling predictions. Results showed that Rodbourne STW discharged less estrone (E1) than expected, but similar 17beta-estradiol (E2) and 17alpha-ethinyl estradiol (EE2) to those predicted by a widely cited effluent prediction model. The Exposure Analysis Modelling System (EXAMS) model was set up using measured effluent concentrations as its starting point to predict estrogen concentrations along a 10 km length of the receiving water of the River Ray. The model adequately simulated estrogen concentrations along the river when compared to July 2007 measured data. The model predicted combined estrogen equivalents in reasonable agreement with estrogenicity as measured by passive sampler (POCIS) extracts using the yeast estrogen screen. Using gauged mean flow values for 2007 the model indicated that the most important determinand for estrogen exposure in the Ray was not season, but proximity to the Rodbourne effluent. Thus, fish in the first 3 km downstream of Rodbourne were typically exposed to two or even three times more estrogens than those living 7-10 km further downstream. The modelling indicated that, assuming the effluent estrogen concentrations measured in February 2008 were typical, throughout the year the whole length of the Ray downstream of Rodbourne would be estrogenic, i.e. exceeding the 1 ng/L E2 equivalent threshold for endocrine disruption. Crown Copyright 2010. Published by Elsevier B.V. All rights reserved.

  8. A comparative analysis of projected impacts of climate change on river runoff from global and catchment-scale hydrological models

    NASA Astrophysics Data System (ADS)

    Gosling, S. N.; Taylor, R. G.; Arnell, N. W.; Todd, M. C.

    2011-01-01

    We present a comparative analysis of projected impacts of climate change on river runoff from two types of distributed hydrological model, a global hydrological model (GHM) and catchment-scale hydrological models (CHM). Analyses are conducted for six catchments that are global in coverage and feature strong contrasts in spatial scale as well as climatic and developmental conditions. These include the Liard (Canada), Mekong (SE Asia), Okavango (SW Africa), Rio Grande (Brazil), Xiangxi (China) and Harper's Brook (UK). A single GHM (Mac-PDM.09) is applied to all catchments whilst different CHMs are applied for each catchment. The CHMs include SLURP v. 12.2 (Liard), SLURP v. 12.7 (Mekong), Pitman (Okavango), MGB-IPH (Rio Grande), AV-SWAT-X 2005 (Xiangxi) and Cat-PDM (Harper's Brook). The CHMs typically simulate water resource impacts based on a more explicit representation of catchment water resources than that available from the GHM and the CHMs include river routing, whereas the GHM does not. Simulations of mean annual runoff, mean monthly runoff and high (Q5) and low (Q95) monthly runoff under baseline (1961-1990) and climate change scenarios are presented. We compare the simulated runoff response of each hydrological model to (1) prescribed increases in global-mean air temperature of 1.0, 2.0, 3.0, 4.0, 5.0 and 6.0 °C relative to baseline from the UKMO HadCM3 Global Climate Model (GCM) to explore response to different amounts of climate forcing, and (2) a prescribed increase in global-mean air temperature of 2.0 °C relative to baseline for seven GCMs to explore response to climate model structural uncertainty. We find that the differences in projected changes of mean annual runoff between the two types of hydrological model can be substantial for a given GCM (e.g. an absolute GHM-CHM difference in mean annual runoff percentage change for UKMO HadCM3 2 °C warming of up to 25%), and they are generally larger for indicators of high and low monthly runoff. However

  9. A comparative analysis of projected impacts of climate change on river runoff from global and catchment-scale hydrological models

    NASA Astrophysics Data System (ADS)

    Gosling, S. N.; Taylor, R. G.; Arnell, N. W.; Todd, M. C.

    2010-09-01

    We present a comparative analysis of projected impacts of climate change on river runoff from two types of distributed hydrological model, a global hydrological model (GHM) and catchment-scale hydrological models (CHM). Analyses are conducted for six catchments that are global in coverage and feature strong contrasts in spatial scale as well as climatic and developmental conditions. These include the Liard (Canada), Mekong (SE Asia), Okavango (SW Africa), Rio Grande (Brazil), Xiangxi (China) and Harper's Brook (UK). A single GHM (Mac-PDM.09) is applied to all catchments whilst different CHMs are applied for each catchment. The CHMs include SLURP v. 12.2 (Liard), SLURP v. 12.7 (Mekong), Pitman (Okavango), MGB-IPH (Rio Grande), AV-SWAT-X 2005 (Xiangxi) and Cat-PDM (Harper's Brook). Simulations of mean annual runoff, mean monthly runoff and high (Q5) and low (Q95) monthly runoff under baseline (1961-1990) and climate change scenarios are presented. We compare the simulated runoff response of each hydrological model to (1) prescribed increases in global-mean air temperature of 1.0, 2.0, 3.0, 4.0, 5.0 and 6.0 °C relative to baseline from the UKMO HadCM3 Global Climate Model (GCM) to explore response to different amounts of climate forcing, and (2) a prescribed increase in global-mean air temperature of 2.0 °C relative to baseline for seven GCMs to explore response to climate model structural uncertainty. We find that the differences in projected changes of mean annual runoff between the two types of hydrological model can be substantial for a given GCM, and they are generally larger for indicators of high and low monthly runoff. However, they are relatively small in comparison to the range of projections across the seven GCMs. Hence, for the six catchments and seven GCMs we considered, climate model structural uncertainty is greater than the uncertainty associated with the type of hydrological model applied. Moreover, shifts in the seasonal cycle of runoff with

  10. 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.

  11. Beta-triketone inhibitors of plant p-hydroxyphenylpyruvate dioxygenase: modeling and comparative molecular field analysis of their interactions.

    PubMed

    Dayan, Franck E; Singh, Nidhi; McCurdy, Christopher R; Godfrey, Colette A; Larsen, Lesley; Weavers, Rex T; Van Klink, John W; Perry, Nigel B

    2009-06-24

    p-Hydroxyphenylpyruvate dioxygenase (HPPD) is the target site of beta-triketone herbicides in current use. Nineteen beta-triketones and analogues, including the naturally occurring leptospermone and grandiflorone, were synthesized and tested as inhibitors of purified Arabidopsis thaliana HPPD. The most active compound was a beta-triketone with a C(9) alkyl side chain, not reported as natural, which inhibited HPPD with an I(50) of 19 +/- 1 nM. This is significantly more active than sulcotrione, which had an I(50) of 250 +/- 21 nM in this assay system. The most active naturally occurring beta-triketone was grandiflorone, which had an I(50) of 750 +/- 70 nM. This compound is of potential interest as a natural herbicide because it can be extracted with good yield and purity from some Leptospermum shrubs. Analogues without the 1,3-diketone group needed to interact with Fe(2+) at the HPPD active site were inactive (I(50)s > 50 microM), as were analogues with prenyl or ethyl groups on the triketone ring. Modeling of the binding of the triketones to HPPD, three-dimensional QSAR analysis using CoMFA (comparative molecular field analysis), and evaluation of the hydrophobic contribution with HINT (hydropathic interactions) provided a structural basis to describe the ligand/receptor interactions.

  12. The Indecision Model of Psychophysical Performance in Dual-Presentation Tasks: Parameter Estimation and Comparative Analysis of Response Formats.

    PubMed

    García-Pérez, Miguel A; Alcalá-Quintana, Rocío

    2017-01-01

    Psychophysical data from dual-presentation tasks are often collected with the two-alternative forced-choice (2AFC) response format, asking observers to guess when uncertain. For an analytical description of performance, psychometric functions are then fitted to data aggregated across the two orders/positions in which stimuli were presented. Yet, order effects make aggregated data uninterpretable, and the bias with which observers guess when uncertain precludes separating sensory from decisional components of performance. A ternary response format in which observers are also allowed to report indecision should fix these problems, but a comparative analysis with the 2AFC format has never been conducted. In addition, fitting ternary data separated by presentation order poses serious challenges. To address these issues, we extended the indecision model of psychophysical performance to accommodate the ternary, 2AFC, and same-different response formats in detection and discrimination tasks. Relevant issues for parameter estimation are also discussed along with simulation results that document the superiority of the ternary format. These advantages are demonstrated by fitting the indecision model to published detection and discrimination data collected with the ternary, 2AFC, or same-different formats, which had been analyzed differently in the sources. These examples also show that 2AFC data are unsuitable for testing certain types of hypotheses. matlab and R routines written for our purposes are available as Supplementary Material, which should help spread the use of the ternary format for dependable collection and interpretation of psychophysical data.

  13. The Indecision Model of Psychophysical Performance in Dual-Presentation Tasks: Parameter Estimation and Comparative Analysis of Response Formats

    PubMed Central

    García-Pérez, Miguel A.; Alcalá-Quintana, Rocío

    2017-01-01

    Psychophysical data from dual-presentation tasks are often collected with the two-alternative forced-choice (2AFC) response format, asking observers to guess when uncertain. For an analytical description of performance, psychometric functions are then fitted to data aggregated across the two orders/positions in which stimuli were presented. Yet, order effects make aggregated data uninterpretable, and the bias with which observers guess when uncertain precludes separating sensory from decisional components of performance. A ternary response format in which observers are also allowed to report indecision should fix these problems, but a comparative analysis with the 2AFC format has never been conducted. In addition, fitting ternary data separated by presentation order poses serious challenges. To address these issues, we extended the indecision model of psychophysical performance to accommodate the ternary, 2AFC, and same–different response formats in detection and discrimination tasks. Relevant issues for parameter estimation are also discussed along with simulation results that document the superiority of the ternary format. These advantages are demonstrated by fitting the indecision model to published detection and discrimination data collected with the ternary, 2AFC, or same–different formats, which had been analyzed differently in the sources. These examples also show that 2AFC data are unsuitable for testing certain types of hypotheses. matlab and R routines written for our purposes are available as Supplementary Material, which should help spread the use of the ternary format for dependable collection and interpretation of psychophysical data. PMID:28747893

  14. Autologous Stem Cell Transplantation in Patients With Multiple Myeloma: An Activity-based Costing Analysis, Comparing a Total Inpatient Model Versus an Early Discharge Model.

    PubMed

    Martino, Massimo; Console, Giuseppe; Russo, Letteria; Meliado', Antonella; Meliambro, Nicola; Moscato, Tiziana; Irrera, Giuseppe; Messina, Giuseppe; Pontari, Antonella; Morabito, Fortunato

    2017-08-01

    Activity-based costing (ABC) was developed and advocated as a means of overcoming the systematic distortions of traditional cost accounting. We calculated the cost of high-dose chemotherapy and autologous stem cell transplantation (ASCT) in patients with multiple myeloma using the ABC method, through 2 different care models: the total inpatient model (TIM) and the early-discharge outpatient model (EDOM) and compared this with the approved diagnosis related-groups (DRG) Italian tariffs. The TIM and EDOM models involved a total cost of €28,615.15 and €16,499.43, respectively. In the TIM model, the phase with the greatest economic impact was the posttransplant (recovery and hematologic engraftment) with 36.4% of the total cost, whereas in the EDOM model, the phase with the greatest economic impact was the pretransplant (chemo-mobilization, apheresis procedure, cryopreservation, and storage) phase, with 60.4% of total expenses. In an analysis of each episode, the TIM model comprised a higher absorption than the EDOM. In particular, the posttransplant represented 36.4% of the total costs in the TIM and 17.7% in EDOM model, respectively. The estimated reduction in cost per patient using an EDOM model was over €12,115.72. The repayment of the DRG in Calabrian Region for the ASCT procedure is €59,806. Given the real cost of the transplant, the estimated cost saving per patient is €31,190.85 in the TIM model and €43,306.57 in the EDOM model. In conclusion, the actual repayment of the DRG does not correspond to the real cost of the ASCT procedure in Italy. Moreover, using the EDOM, the cost of ASCT is approximately the half of the TIM model. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Comparative analysis of computational models of solar wind interaction with Venus based on Pioneer-Venus experimental data.

    NASA Astrophysics Data System (ADS)

    Breus, T. K.; Krymskij, A. M.; Mitnitskij, V. Ya.

    1995-02-01

    Results from a gas-dynamic model of solar wind interaction with Venus are compared with those from hybrid models. Contradictions between the hybrid model of Moor et al. (1991) (MTM) and the (BKM) gas-dynamic model (Breus et al., 1992) are demonstrated. They can be explained by too large computational grid cells used in the MTM model. For the same reason, in the MTM model the effect of a magnetic barrier on the bowshock standoff distance is overestimated, as was shown in the hybrid model of Brecht and Ferrante (1991). The effect of the solar wind mass-loading phenomenon on the bowshock location, taken into account in the BKM model, makes it possible to simulate the location of the bowshock observed by the Pioneer-Venus spacecraft.

  16. Comparative analysis of computational models of solar wind interaction with Venus based on Pioneer-Venus experimental data.

    NASA Astrophysics Data System (ADS)

    Breus, T. K.; Krymskij, A. M.; Mitnitskij, V. Ya.

    1995-02-01

    Results from the gas-dynamic model of Breus et al. (1992, BKM) of solar wind interaction with Venus are compared with those from hybrid models. Contradictions between the hybrid model of Moor et al. (1991, MTM) and the BKM model are demonstrated. They can be explained by too large computational grid cells used in the MTM model. For the same reason, in the MTM model the effect of a magnetic barrier on the bowshock standoff distance is overestimated, as was shown in the hybrid model of Brecht and Ferrante (1991). The effect of the solar wind mass-loading phenomenon on the bowshock location, taken into account in the BKM model, makes it possible to simulate the location of the bowshock observed by the Pioneer-Venus spacecraft.

  17. In vitro comparative optical bench analysis of a spherical and aspheric optic design of the same IOL model.

    PubMed

    Tandogan, Tamer; Auffarth, Gerd U; Choi, Chul Y; Liebing, Stephanie; Mayer, Christian; Khoramnia, Ramin

    2017-02-08

    To analyse objective optical properties of the spherical and aspheric design of the same intraocular lens (IOL) model using optical bench analysis. This study entailed a comparative analysis of 10 spherical C-flex 570 C and 10 aspheric C-flex 970 C IOLs (Rayner Intraocular Lenses Ltd., Hove, UK) of 26 diopters [D] using an optical bench (OptiSpheric, Trioptics, Germany). In all lenses, we evaluated the modulation transfer function (MTF) at 50 lp/mm and 100 lp/mm and the Strehl Ratio using a 3-mm (photopic) and 4.5-mm (mesopic) aperture. At 50 lp/mm, the MTF values were 0.713/0.805 (C-flex 570 C/C-flex 970 C) for a 3-mm aperture and 0.294/0.591 for a 4.5-mm aperture. At 100 lp/mm, the MTF values were 0.524/0.634 for a 3-mm aperture and 0.198/0.344 for a 4.5-mm aperture. The Strehl Ratio was 0.806/0.925 and 0.237/0.479 for a 3-mm and 4.5-mm aperture respectively. A Mann-Whitney U test revealed all intergroup differences to be statistically significant (p < 0.01). The aspheric IOL design achieved higher MTF values than the spherical design of the same IOL for both apertures. Moreover, the differences between the two designs of the IOL were more prominent for larger apertures. This suggests that the evaluated IOL provides enhanced optical quality to patients with larger pupils or working under mesopic conditions.

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

    NASA Astrophysics Data System (ADS)

    Brunner, Dominik; Savage, Nicholas; Jorba, Oriol; Eder, Brian; Giordano, Lea; Badia, Alba; Balzarini, Alessandra; Baró, Rocío; Bianconi, Roberto; Chemel, Charles; Curci, Gabriele; Forkel, Renate; Jiménez-Guerrero, Pedro; Hirtl, Marcus; Hodzic, Alma; Honzak, Luka; Im, Ulas; Knote, Christoph; Makar, Paul; Manders-Groot, Astrid; van Meijgaard, Erik; Neal, Lucy; Pérez, Juan L.; Pirovano, Guido; San Jose, Roberto; Schröder, Wolfram; Sokhi, Ranjeet S.; Syrakov, Dimiter; Torian, Alfreida; Tuccella, Paolo; Werhahn, Johannes; Wolke, Ralf; Yahya, Khairunnisa; Zabkar, Rahela; Zhang, Yang; Hogrefe, Christian; Galmarini, Stefano

    2015-08-01

    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 coupled chemistry and meteorology models participated in a coordinated model evaluation exercise. Each group simulated the year 2010 for a domain covering either Europe or North America or both. Here were present an operational analysis of model performance with respect to key meteorological variables relevant for atmospheric chemistry processes and air quality. These parameters include temperature and wind speed at the surface and in the vertical profile, incoming solar radiation at the ground, precipitation, and planetary boundary layer heights. A similar analysis was performed during AQMEII phase 1 (Vautard et al., 2012) for offline air quality models not directly coupled to the meteorological model core as the model systems investigated here. Similar to phase 1, we found significant overpredictions of 10-m wind speeds by most models, more pronounced during night than during daytime. The seasonal evolution of temperature was well captured with monthly mean biases below 2 K over all domains. Solar incoming radiation, precipitation and PBL heights, on the other hand, showed significant spread between models and observations suggesting that major challenges still remain in the simulation of meteorological parameters relevant for air quality and for chemistry-climate interactions at the regional scale.

  19. Comparing the effectiveness of pharmacist-managed warfarin anticoagulation with other models: a systematic review and meta-analysis.

    PubMed

    Zhou, S; Sheng, X Y; Xiang, Q; Wang, Z N; Zhou, Y; Cui, Y M

    2016-12-01

    Anticoagulation management services are well known to improve the quality of patient care and to reduce the rates of hospitalization and emergency department visits following adverse events related to anticoagulation therapy. The complexity of managing warfarin has led to the development of a variety of specialized models managed by pharmacists, physicians, nurses, and self-managed care. The aim of the study is to compare the effectiveness of pharmacist-managed anticoagulation control of warfarin with other models. We performed a systematic literature search of the PubMed, Medline@Web of Knowledge, EMBASE, Cochrane Library and Cumulative Index to Nursing and Allied Health Literature to identify randomized controlled trials (RCTs) from database inception up to July 2015. The search terms used for the study were 'warfarin', 'pharmacists', 'Vitamin K antagonist', 'anticoagulation' and 'management model.' We used the Cochrane Collaboration's tool from the Cochrane Handbook to assess the risk of bias of RCTs. We performed statistical analyses using RevMan 5.3 and used the Grading of Recommendations, Assessment, Development, and Evaluations profiler to rate the quality of evidence of the outcomes. The anticoagulation control outcomes were the percentage of time within the standard and expanded therapeutic range and thrombosis events; the safety outcomes were bleeding events and mortality, and patients' satisfaction of anticoagulation service. Eight RCTs from 981 potentially relevant publications with a total of 1493 patients were included. Meta-analysis of the RCTs showed that a significant difference existed between pharmacist-managed care and other models for satisfaction (mean difference (MD) = 0·41, 95% CI, 0·01-0·81, P = 0·04, low-quality evidence) with heterogeneity, and the percentage of time within the standard therapeutic range (MD = 3·66, 95% CI 2·20-5·11, P < 0·00001, high-quality evidence) without heterogeneity. However, the pharmacist

  20. Comparative analysis of insect succession data from Victoria (Australia) using summary statistics versus preceding mean ambient temperature models.

    PubMed

    Archer, Mel

    2014-03-01

    Minimum postmortem interval (mPMI) can be estimated with preceding mean ambient temperature models that predict carrion taxon pre-appearance interval. But accuracy has not been compared with using summary statistics (mean ± SD of taxon arrival/departure day, range, 95% CI). This study collected succession data from ten experimental and five control (infrequently sampled) pig carcasses over two summers (n = 2 experimental, n = 1 control per placement date). Linear and exponential preceding mean ambient temperature models for appearance and departure times were constructed for 17 taxa/developmental stages. There was minimal difference in linear or exponential model success, although arrival models were more often significant: 65% of linear arrival (r2 = 0.09–0.79) and exponential arrival models (r2 = 0.05–81.0) were significant, and 35% of linear departure (r2 = 0.0–0.71) and exponential departure models (r2 = 0.0–0.72) were significant. Performance of models and summary statistics for estimating mPMI was compared in two forensic cases. Only summary statistics produced accurate mPMI estimates.

  1. A Comparative Analysis of the CABAS Model of Education at the Fred S. Keller School: A Twenty-Year Review

    ERIC Educational Resources Information Center

    Singer-Dudek, Jessica; Speckman, JeanneMarie; Nuzzolo, Robin

    2010-01-01

    The Comprehensive Application of Behavior Analysis to Schooling or CABAS[R] model is characterized by an organizational system of teacher training and mentoring by those with more expertise in the science of behavior analytic teaching. At the center of the system are the students, whose data drive the system. Decades of research support the…

  2. 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.

  3. Comparative protein structure modeling using MODELLER.

    PubMed

    Eswar, Narayanan; Webb, Ben; Marti-Renom, Marc A; Madhusudhan, M S; Eramian, David; Shen, Min-Yi; Pieper, Ursula; Sali, Andrej

    2007-11-01

    Functional characterization of a protein sequence is a common goal in biology, and is usually facilitated by having an 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. (c) 2007 by John Wiley & Sons, Inc.

  4. 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.

  5. 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.

  6. 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

    2016-07-01

    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.

  7. 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

  8. A comparative research of different ensemble surrogate models based on set pair analysis for the DNAPL-contaminated aquifer remediation strategy optimization

    NASA Astrophysics Data System (ADS)

    Hou, Zeyu; Lu, Wenxi; Xue, Haibo; Lin, Jin

    2017-08-01

    Surrogate-based simulation-optimization technique is an effective approach for optimizing the surfactant enhanced aquifer remediation (SEAR) strategy for clearing DNAPLs. The performance of the surrogate model, which is used to replace the simulation model for the aim of reducing computation burden, is the key of corresponding researches. However, previous researches are generally based on a stand-alone surrogate model, and rarely make efforts to improve the approximation accuracy of the surrogate model to the simulation model sufficiently by combining various methods. In this regard, we present set pair analysis (SPA) as a new method to build ensemble surrogate (ES) model, and conducted a comparative research to select a better ES modeling pattern for the SEAR strategy optimization problems. Surrogate models were developed using radial basis function artificial neural network (RBFANN), support vector regression (SVR), and Kriging. One ES model is assembling RBFANN model, SVR model, and Kriging model using set pair weights according their performance, and the other is assembling several Kriging (the best surrogate modeling method of three) models built with different training sample datasets. Finally, an optimization model, in which the ES model was embedded, was established to obtain the optimal remediation strategy. The results showed the residuals of the outputs between the best ES model and simulation model for 100 testing samples were lower than 1.5%. Using an ES model instead of the simulation model was critical for considerably reducing the computation time of simulation-optimization process and maintaining high computation accuracy simultaneously.

  9. Model-based meta-analysis for comparing Vitamin D2 and D3 parent-metabolite pharmacokinetics.

    PubMed

    Ocampo-Pelland, Alanna S; Gastonguay, Marc R; Riggs, Matthew M

    2017-08-01

    Association of Vitamin D (D3 & D2) and its 25OHD metabolite (25OHD3 & 25OHD2) exposures with various diseases is an active research area. D3 and D2 dose-equivalency and each form's ability to raise 25OHD concentrations are not well-defined. The current work describes a population pharmacokinetic (PK) model for D2 and 25OHD2 and the use of a previously developed D3-25OHD3 PK model [1] for comparing D3 and D2-related exposures. Public-source D2 and 25OHD2 PK data in healthy or osteoporotic populations, including 17 studies representing 278 individuals (15 individual-level and 18 arm-level units), were selected using search criteria in PUBMED. Data included oral, single and multiple D2 doses (400-100,000 IU/d). Nonlinear mixed effects models were developed simultaneously for D2 and 25OHD2 PK (NONMEM v7.2) by considering 1- and 2-compartment models with linear or nonlinear clearance. Unit-level random effects and residual errors were weighted by arm sample size. Model simulations compared 25OHD exposures, following repeated D2 and D3 oral administration across typical dosing and baseline ranges. D2 parent and metabolite were each described by 2-compartment models with numerous parameter estimates shared with the D3-25OHD3 model [1]. Notably, parent D2 was eliminated (converted to 25OHD) through a first-order clearance whereas the previously published D3 model [1] included a saturable non-linear clearance. Similar to 25OHD3 PK model results [1], 25OHD2 was eliminated by a first-order clearance, which was almost twice as fast as the former. Simulations at lower baselines, following lower equivalent doses, indicated that D3 was more effective than D2 at raising 25OHD concentrations. Due to saturation of D3 clearance, however, at higher doses or baselines, the probability of D2 surpassing D3's ability to raise 25OHD concentrations increased substantially. Since 25OHD concentrations generally surpassed 75 nmol/L at these higher baselines by 3 months, there would be no

  10. Timed pentylenetetrazol infusion test: a comparative analysis with s.c.PTZ and MES models of anticonvulsant screening in mice.

    PubMed

    Mandhane, Sanjay N; Aavula, Keerthikumar; Rajamannar, T

    2007-10-01

    The intravenous pentylenetetrazol (i.v.PTZ) seizure test provides threshold dose for induction of seizures in individual animals. In the present study, the i.v. and s.c.PTZ seizure models in mice were compared for seizure pattern, intra- and interanimal variability. Anticonvulsant activities of several antiepileptic drugs (AEDs) at non-ataxic dose levels were evaluated in the PTZ and maximal electroshock (MES) seizure tests. In the i.v.PTZ test, at 0.5 ml/min rate of administration, the mean threshold PTZ doses for induction of clonus and tonic extensor were 44.17 and 99.59 mg/kg, respectively. The intra- and interanimal variabilities in the seizure response were low in the i.v.PTZ as compared to the s.c.PTZ model. Phenobarbital sodium, ethosuximide, sodium valproate, diazepam, tiagabine, oxcarbazepine and zonisamide enhanced threshold or onset latency for clonus in the i.v. and s.c.PTZ tests, respectively. Levetiracetam and pregabalin were active in the i.v.PTZ test, but had no effect in the s.c.PTZ test. Ability of AEDs to protect from tonic extensor was compared in the MES and i.v.PTZ tests. For this effect, phenobarbital sodium, phenytoin, carbamazepine, sodium valproate, gabapentin, oxcarbazepine, zonisamide and pregabalin were effective in the i.v.PTZ and MES tests. Ethosuximide, diazepam and levetiracetam were effective in the i.v.PTZ test, but not the MES test. On the contrary, lamotrigine and topiramate were active in the MES, but not the i.v.PTZ test. These results indicate that it is advantageous to use i.v.PTZ test as an acute seizure model for screening of antiepileptic drugs. This model can identify molecules with varied mechanism of action and broad clinical utility in the treatment of epilepsy.

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

    DOE PAGES

    Harper, Bryan; Thomas, Dennis G.; Chikkagoudar, Satish; ...

    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

  12. 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.

  13. Grassland and cropland net ecosystem production of the U.S. Great Plains: Regression tree model development and comparative analysis

    USGS Publications Warehouse

    Wylie, Bruce K.; Howard, Daniel; Dahal, Devendra; Gilmanov, Tagir; Ji, Lei; Zhang, Li; Smith, Kelcy

    2016-01-01

    This paper presents the methodology and results of two ecological-based net ecosystem production (NEP) regression tree models capable of up scaling measurements made at various flux tower sites throughout the U.S. Great Plains. Separate grassland and cropland NEP regression tree models were trained using various remote sensing data and other biogeophysical data, along with 15 flux towers contributing to the grassland model and 15 flux towers for the cropland model. The models yielded weekly mean daily grassland and cropland NEP maps of the U.S. Great Plains at 250 m resolution for 2000–2008. The grassland and cropland NEP maps were spatially summarized and statistically compared. The results of this study indicate that grassland and cropland ecosystems generally performed as weak net carbon (C) sinks, absorbing more C from the atmosphere than they released from 2000 to 2008. Grasslands demonstrated higher carbon sink potential (139 g C·m−2·year−1) than non-irrigated croplands. A closer look into the weekly time series reveals the C fluctuation through time and space for each land cover type.

  14. Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and Panicoid crop species.

    PubMed

    Petti, Carloalberto; Shearer, Andrew; Tateno, Mizuki; Ruwaya, Matthew; Nokes, Sue; Brutnell, Tom; Debolt, Seth

    2013-01-01

    Second generation feedstocks for bioethanol will likely include a sizable proportion of perennial C4 grasses, principally in the Panicoideae clade. The Panicoideae contain agronomically important annual grasses including Zea mays L. (maize), Sorghum bicolor (L.) Moench (sorghum), and Saccharum officinarum L. (sugar cane) as well as promising second generation perennial feedstocks including Miscanthus×giganteus and Panicum virgatum L. (switchgrass). The underlying complexity of these polyploid grass genomes is a major limitation for their direct manipulation and thus driving a need for rapidly cycling comparative model. Setaria viridis (green millet) is a rapid cycling C4 panicoid grass with a relatively small and sequenced diploid genome and abundant seed production. Stable, transient, and protoplast transformation technologies have also been developed for Setaria viridis making it a potentially excellent model for other C4 bioenergy grasses. Here, the lignocellulosic feedstock composition, cellulose biosynthesis inhibitor response and saccharification dynamics of Setaria viridis are compared with the annual sorghum and maize and the perennial switchgrass bioenergy crops as a baseline study into the applicability for translational research. A genome-wide systematic investigation of the cellulose synthase-A genes was performed identifying eight candidate sequences. Two developmental stages; (a) metabolically active young tissue and (b) metabolically plateaued (mature) material are examined to compare biomass performance metrics.

  15. Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and Panicoid crop species

    PubMed Central

    Petti, Carloalberto; Shearer, Andrew; Tateno, Mizuki; Ruwaya, Matthew; Nokes, Sue; Brutnell, Tom; DeBolt, Seth

    2013-01-01

    Second generation feedstocks for bioethanol will likely include a sizable proportion of perennial C4 grasses, principally in the Panicoideae clade. The Panicoideae contain agronomically important annual grasses including Zea mays L. (maize), Sorghum bicolor (L.) Moench (sorghum), and Saccharum officinarum L. (sugar cane) as well as promising second generation perennial feedstocks including Miscanthus×giganteus and Panicum virgatum L. (switchgrass). The underlying complexity of these polyploid grass genomes is a major limitation for their direct manipulation and thus driving a need for rapidly cycling comparative model. Setaria viridis (green millet) is a rapid cycling C4 panicoid grass with a relatively small and sequenced diploid genome and abundant seed production. Stable, transient, and protoplast transformation technologies have also been developed for Setaria viridis making it a potentially excellent model for other C4 bioenergy grasses. Here, the lignocellulosic feedstock composition, cellulose biosynthesis inhibitor response and saccharification dynamics of Setaria viridis are compared with the annual sorghum and maize and the perennial switchgrass bioenergy crops as a baseline study into the applicability for translational research. A genome-wide systematic investigation of the cellulose synthase-A genes was performed identifying eight candidate sequences. Two developmental stages; (a) metabolically active young tissue and (b) metabolically plateaued (mature) material are examined to compare biomass performance metrics. PMID:23802002

  16. Insights into the Evolution of the CSP Gene Family through the Integration of Evolutionary Analysis and Comparative Protein Modeling

    PubMed Central

    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

  17. 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)

  18. 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.

  19. 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

  20. 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…

  1. 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…

  2. Comparative transcriptomic analysis of mice liver treated with different AMPK activators in a mice model of atherosclerosis.

    PubMed

    Ma, Ang; Wang, Dongmei; An, Yuanyuan; Fang, Wei; Zhu, Haibo

    2017-02-02

    Atherosclerosis is known to be the primary underlying factor responsible for the development of cardiovascular diseases. Suppression of AMP-activated protein kinase stimulates arterial deposition of excess lipids, resulting in the development of atherosclerotic lesions. In this study we successfully developed the disease model of mice and mimicked the therapeutic effect, for that we chose three different AMP-activated protein kinase activators (IMM-H007, A-769662 and Metformin) to identify which one has a superior effect in the atherosclerosis model. We combined the transcriptomes of four groups of mice liver including high-fat diet group and the experimental groups treated with different AMP-activated protein kinase activators. We analyzed the increased genes to candidate metabolic and disease pathways. Compared to the high-fat diet group, a total of 799 differentially expressed genes were identified in treatment groups. There were 291, 473, and 323 differentially expressed genes in H007, Metformin, and A-769662 group respectively. And seven statistically significant pathways were observed in both H007 and Metformin groups. We expect that gene expression profiling in the mice model would extend our understanding of atherosclerosis in the molecular level. This study provides a fundamental framework for future clinical research on human atherosclerosis and new clues for developing novel drugs for the treatment of atherosclerosis.

  3. Comparative analysis of some representative models of viscosity versus pressure in the case of various hydrocarbons and their mixtures

    NASA Astrophysics Data System (ADS)

    Boned, C.; Et-Tahir, A.; Lagourette, B.; Xans, P.; Gao, Guanghua

    1996-01-01

    A critical study of some representative models has been conducted with the experimental determinations of the viscosity of ten pure substances and three binary systems measured as a function of temperature T (25°C, 40°C, 60°C, 80°C, 90°C) and pressure P(≤ 100 MPa). The pure substances were: toluene, p-xylene, m-xylene, o-xylene, methylcyclohexane, methylnaphtalene, decahydronaphtalene, phenyldodecane, heptamethylnonane and tetramethylpentadecane (pristane). The three binaries were: toluene + tetramethylpentadecane, toluene + methylnaphtalene and toluene + heptamethylnonane, for molar fractions x of toluene ranging between 0 and 1. The three binaries are highly “contrasted” systems, i.e. systems in which the viscosities of the pure components are very different for each P, T pair. In all, 547 experimental determinations were carried out, the 279 experimental data for viscosity of the pure substances and 268 data concerning the mixtures ( x ≠ 0 and 1) were used to make a critical analysis of the various representative models, These included an empirical representation of variations of versus T on each isobar, a self-referencing model developed in our laboratory, a corresponding states model with one reference, various mixing rules with or without adjustable parameters, a combination of the self-referencing model and mixing rules, a method based on the Bloomfield and Dewan excess viscosity, and a group contribution method, comparison of the results showed the self-referencing method to be of particular interest, Moreover when coupled with mixing rules without adjustable parameters it was able to account satisfactorily for the variations η( P, T, x) of the mixtures, on the simple basis of knowledge if the viscosity of the components of the system, at 25°C and at atmospheric pressure, For all the binaries an average absolute deviation of 9.5% was observed. Finally it appears that the introduction of the pressure parameter does not alter the usual

  4. 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.

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

    PubMed

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

    The integration of rapid assays, large datasets, 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 in developing embryonic zebrafish, were established at realistic exposure levels and used to develop a hazard ranking of diverse nanomaterial toxicity. Hazard ranking and clustering analysis of 68 diverse nanomaterials revealed distinct patterns of toxicity related to both the core composition and outermost surface chemistry of nanomaterials. The resulting clusters guided the development of a surface chemistry-based model of gold nanoparticle toxicity. 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. Research should continue to focus on methodologies for determining nanomaterial hazard based on multiple sub-lethal responses following realistic, low-dose exposures, thus increasing the availability of quantitative measures of nanomaterial hazard to support the development of nanoparticle structure-activity relationships.

  6. 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.

  7. 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

  8. 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.

  9. Comparative analysis of collaboration networks

    NASA Astrophysics Data System (ADS)

    Progulova, Tatiana; Gadjiev, Bahruz

    2011-03-01

    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.

  10. Comparative analysis of the beneficial effects of treadmill training and electroacupuncture in a rat model of neonatal hypoxia-ischemia

    PubMed Central

    Kim, Ha Neui; Pak, Malk Eun; Shin, Myung Jun; Kim, Soo Yeon; Shin, Yong Beom; Yun, Young Ju; Shin, Hwa Kyoung; Choi, Byung Tae

    2017-01-01

    In the present study, we investigated whether treadmill training and electroacupuncture (EA) have autonomous or synergistic beneficial effects on deficits caused by neonatal hypoxia-ischemia in Sprague-Dawley rats. For this purpose, rats subjected to hypoxia-ischemia underwent treadmill training and EA stimulation from 4 to 8 weeks of age. Conventional EA (CEA) and scalp EA (SEA) were delivered by electrical stimulation (2 Hz, 1 mA) at traditional acupoints and at the scalp to the primary motor area, respectively. In the behavioral examination, markedly improved performances in the rotarod test were observed in the rats that underwent treadmill exercise, and in the rats that underwent treadmill exercise and CEA compared to the untreated rats subjected to hypoxia-ischemia. An improvement was also observed in the passive avoidance test in the rats that underwent treadmill training and EA. As shown by western blot analysis, the expression levels of neuronal nuclei (NeuN), 2′,3′-cyclic-nucleotide 3′-phosphodiesterase and myelin basic protein (MBP) exhibited a significant decrease in the contralateral subventricular zone (SVZ) of the rats subjected to hypoxia-ischemia compared to the controls; however, these expression levels increased following treadmill exercise and EA stimulation. As shown by immunohistochemical analyses, the thickness of the corpus callosum and the integrated optical density (IOD) of MBP were significantly increased in the rats subjected to treadmill exercise and EA compared to the untreated rats subjected to hypoxiaa-ischemia. The synergistic effects of treadmill training and EA were also observed in the protein levels and IOD of MBP. A marked increase in the number of bromodeoxyuridine (BrdU)- and BrdU/NeuN-positive cells in the contralateral SVZ was also observed in the rats that underwent treadmill training and EA; the number of BrdU-positive cells was synergistically affected by treadmill training and EA. These results suggest that

  11. Comparative analysis of the beneficial effects of treadmill training and electroacupuncture in a rat model of neonatal hypoxia-ischemia.

    PubMed

    Kim, Ha Neui; Pak, Malk Eun; Shin, Myung Jun; Kim, Soo Yeon; Shin, Yong Beom; Yun, Young Ju; Shin, Hwa Kyoung; Choi, Byung Tae

    2017-06-01

    In the present study, we investigated whether treadmill training and electroacupuncture (EA) have autonomous or synergistic beneficial effects on deficits caused by neonatal hypoxia‑ischemia in Sprague-Dawley rats. For this purpose, rats subjected to hypoxia-ischemia underwent treadmill training and EA stimulation from 4 to 8 weeks of age. Conventional EA (CEA) and scalp EA (SEA) were delivered by electrical stimulation (2 Hz, 1 mA) at traditional acupoints and at the scalp to the primary motor area, respectively. In the behavioral examination, markedly improved performances in the rotarod test were observed in the rats that underwent treadmill exercise, and in the rats that underwent treadmill exercise and CEA compared to the untreated rats subjected to hypoxia-ischemia. An improvement was also observed in the passive avoidance test in the rats that underwent treadmill training and EA. As shown by western blot analysis, the expression levels of neuronal nuclei (NeuN), 2',3'-cyclic-nucleotide 3'-phosphodiesterase and myelin basic protein (MBP) exhibited a significant decrease in the contralateral subventricular zone (SVZ) of the rats subjected to hypoxia‑ischemia compared to the controls; however, these expression levels increased following treadmill exercise and EA stimulation. As shown by immunohistochemical analyses, the thickness of the corpus callosum and the integrated optical density (IOD) of MBP were significantly increased in the rats subjected to treadmill exercise and EA compared to the untreated rats subjected to hypoxiaa-ischemia. The synergistic effects of treadmill training and EA were also observed in the protein levels and IOD of MBP. A marked increase in the number of bromodeoxyuridine (BrdU)- and BrdU/NeuN-positive cells in the contralateral SVZ was also observed in the rats that underwent treadmill training and EA; the number of BrdU-positive cells was synergistically affected by treadmill training and EA. These results

  12. Genetic network models: a comparative study

    NASA Astrophysics Data System (ADS)

    van Someren, Eugene P.; Wessels, Lodewyk F. A.; Reinders, Marcel J. T.

    2001-06-01

    Currently, the need arises for tools capable of unraveling the functionality of genes based on the analysis of microarray measurements. Modeling genetic interactions by means of genetic network models provides a methodology to infer functional relationships between genes. Although a wide variety of different models have been introduced so far, it remains, in general, unclear what the strengths and weaknesses of each of these approaches are and where these models overlap and differ. This paper compares different genetic modeling approaches that attempt to extract the gene regulation matrix from expression data. A taxonomy of continuous genetic network models is proposed and the following important characteristics are suggested and employed to compare the models: inferential power; predictive power; robustness; consistency; stability and computational cost. Where possible, synthetic time series data are employed to investigate some of these properties. The comparison shows that although genetic network modeling might provide valuable information regarding genetic interactions, current models show disappointing results on simple artificial problems. For now, the simplest models are favored because they generalize better, but more complex models will probably prevail once their bias is more thoroughly understood and their variance is better controlled.

  13. Comparative Sensitivity Analysis of Muscle Activation Dynamics

    PubMed Central

    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

  14. 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.

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

    PubMed Central

    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. PMID:26636071

  16. 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

  17. Comparing flood loss models of different complexity

    NASA Astrophysics Data System (ADS)

    Schröter, Kai; Kreibich, Heidi; Vogel, Kristin; Riggelsen, Carsten; Scherbaum, Frank; Merz, Bruno

    2013-04-01

    Any deliberation on flood risk requires the consideration of potential flood losses. In particular, reliable flood loss models are needed to evaluate cost-effectiveness of mitigation measures, to assess vulnerability, for comparative risk analysis and financial appraisal during and after floods. In recent years, considerable improvements have been made both concerning the data basis and the methodological approaches used for the development of flood loss models. Despite of that, flood loss models remain an important source of uncertainty. Likewise the temporal and spatial transferability of flood loss models is still limited. This contribution investigates the predictive capability of different flood loss models in a split sample cross regional validation approach. For this purpose, flood loss models of different complexity, i.e. based on different numbers of explaining variables, are learned from a set of damage records that was obtained from a survey after the Elbe flood in 2002. The validation of model predictions is carried out for different flood events in the Elbe and Danube river basins in 2002, 2005 and 2006 for which damage records are available from surveys after the flood events. The models investigated are a stage-damage model, the rule based model FLEMOps+r as well as novel model approaches which are derived using data mining techniques of regression trees and Bayesian networks. The Bayesian network approach to flood loss modelling provides attractive additional information concerning the probability distribution of both model predictions and explaining variables.

  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.

  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. 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

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

    PubMed

    Zhang, Fan; Suh, Kyung-Jin; Lee, Kyung-Min

    2016-01-01

    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. 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. 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. 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.

  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. 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...

  4. Comparative analysis of the secretome from a model filarial nematode (Litomosoides sigmodontis) reveals maximal diversity in gravid female parasites.

    PubMed

    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

    2014-10-01

    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 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

  6. Emergent structures and understanding from a comparative uncertainty analysis of the FUSE rainfall-runoff modelling platform for >1,100 catchments

    NASA Astrophysics Data System (ADS)

    Freer, J. E.; Odoni, N. A.; Coxon, G.; Bloomfield, J.; Clark, M. P.; Greene, S.; Johnes, P.; Macleod, C.; Reaney, S. M.

    2013-12-01

    If we are to learn about catchments and their hydrological function then a range of analysis techniques can be proposed from analysing observations to building complex physically based models using detailed attributes of catchment characteristics. Decisions regarding which technique is fit for a specific purpose will depend on the data available, computing resources, and the underlying reasons for the study. Here we explore defining catchment function in a relatively general sense expressed via a comparison of multiple model structures within an uncertainty analysis framework. We use the FUSE (Framework for Understanding Structural Errors - Clark et al., 2008) rainfall-runoff modelling platform and the GLUE (Generalised Likelihood Uncertainty Estimation - Beven and Freer, 2001) uncertainty analysis framework. Using these techniques we assess two main outcomes: 1) Benchmarking our predictive capability using discharge performance metrics for a diverse range of catchments across the UK 2) evaluating emergent behaviour for each catchment and/or region expressed as ';best performing' model structures that may be equally plausible representations of catchment behaviour. We shall show how such comparative hydrological modelling studies show patterns of emergent behaviour linked both to seasonal responses and to different geoclimatic regions. These results have implications for the hydrological community regarding how models can help us learn about places as hypothesis testing tools. Furthermore we explore what the limits are to such an analysis when dealing with differing data quality and information content from ';pristine' to less well characterised and highly modified catchment domains. This research has been piloted in the UK as part of the Environmental Virtual Observatory programme (EVOp), funded by NERC to demonstrate the use of cyber-infrastructure and cloud computing resources to develop better methods of linking data and models and to support scenario analysis

  7. Transitions in state public health law: comparative analysis of state public health law reform following the Turning Point Model State Public Health Act.

    PubMed

    Meier, Benjamin Mason; Hodge, James G; Gebbie, Kristine M

    2009-03-01

    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.

  8. 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…

  9. 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.

  10. A comparative analysis of three habitat suitability models for commercial yield estimation of Tapes philippinarum in a North Adriatic coastal lagoon (Sacca di Goro, Italy).

    PubMed

    Vincenzi, Simone; Caramori, Graziano; Rossi, Remigio; De Leo, Giulio A

    2007-01-01

    Habitat Suitability (HS) models have been extensively used by conservation planners to estimate the spatial distribution of threatened species and of species of commercial interest. In this work we compare three HS models for the estimation of commercial yield potential and the identification of suitable sites for Tapes philippinarum rearing in the Sacca di Goro lagoon (Italy) on the basis of six environmental factors. The habitat suitability index (HSI) is based on expert opinion while the habitat suitability conditional (HSC) is calibrated on observational data. The habitat suitability mixed (HSM) model is a two-part model combining expert knowledge and regression analysis: the first component of the model uses logistic regression to identify the areas in which clams are likely to be present; the second part applies the same parameter-specific suitability functions of the HSI model only in the areas previously identified as productive by the logistic component. The HS models were validated on an independent data set and estimates of potential yield of the Goro lagoon were compared. The effectiveness of the three approaches is then discussed in terms of predicted yield and identification of suitable sites for farming.

  11. 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…

  12. An analysis of controls on fire activity in boreal Canada: comparing models built with different temporal resolutions

    Treesearch

    Marc-Andre Parisien; Sean A. Parks; Meg A. Krawchuk; John M. Little; Mike D. Flannigan; Lynn M. Gowman; Max A. Moritz

    2014-01-01

    Fire regimes of the Canadian boreal forest are driven by certain environmental factors that are highly variable from year to year (e.g., temperature, precipitation) and others that are relatively stable (e.g., land cover, topography). Studies examining the relative influence of these environmental drivers on fire activity suggest that models making explicit use of...

  13. A Causal-Comparative Analysis of the Effects of a Student Support Team (SST) Intervention Model at a Secondary School

    ERIC Educational Resources Information Center

    Johnson, Mid D.

    2010-01-01

    The purpose of this research was to identify and examine the effectiveness of a "Student Support Team" (SST) intervention model designed to increase the performance of struggling secondary students and to help them achieve prescribed state standards on the mathematics "Texas Assessment of Knowledge and Skills (TAKS)"…

  14. A Causal-Comparative Analysis of the Effects of a Student Support Team (SST) Intervention Model at a Secondary School

    ERIC Educational Resources Information Center

    Johnson, Mid D.

    2010-01-01

    The purpose of this research was to identify and examine the effectiveness of a "Student Support Team" (SST) intervention model designed to increase the performance of struggling secondary students and to help them achieve prescribed state standards on the mathematics "Texas Assessment of Knowledge and Skills (TAKS)"…

  15. 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.

  16. A comparative analysis of models used to evaluate the cost-effectiveness of dabigatran versus warfarin for the prevention of stroke in atrial fibrillation.

    PubMed

    Sorensen, Sonja V; Peng, Siyang; Monz, Brigitta U; Bradley-Kennedy, Carole; Kansal, Anuraag R

    2013-07-01

    A number of models exploring the cost-effectiveness of dabigatran versus warfarin for stroke prevention in atrial fibrillation have been published. These studies found dabigatran was generally cost-effective, considering well-accepted willingness-to-pay thresholds, but estimates of the incremental cost-effectiveness ratios (ICERs) varied, even in the same setting. The objective of this study was to compare the findings of the published economic models and identify key model features accounting for differences. All aspects of the economic evaluations were reviewed: model approach, inputs, and assumptions. A previously published model served as the reference model for comparisons of the selected studies in the US and UK settings. The reference model was adapted, wherever possible, using the inputs and key assumptions from each of the other published studies to determine if results could be reproduced in the reference model. Incremental total costs, incremental quality-adjusted life years (QALYs), and ICERs (cost per QALY) were compared between each study and the corresponding adapted reference model. The impact of each modified variable or assumption was tracked separately. The selected studies were in the US setting (2), the Canadian setting (1), and the UK setting (2). All models used the Randomized Evaluation of Long-Term Anticoagulation study (RE-LY) as the main source for clinical inputs, and all used a Markov modelling approach, except one that used discrete event simulation. The reference model had been published in the Canadian and UK settings. In the UK setting, the reference model reported an ICER of UK£4,831, whereas the other UK-based analysis reported an ICER of UK£23,082. When the reference model was modified to use the same population characteristics, cost inputs, and utility inputs, it reproduced the results of the other model (ICER UK£25,518) reasonably well. Key reasons for the different results between the two models were the assumptions on the

  17. 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.

  18. Comparative Analysis of Novel Noninvasive Renal Biomarkers and Metabonomic Changes in a Rat Model of Gentamicin Nephrotoxicity

    PubMed Central

    Sieber, Max; Hoffmann, Dana; Adler, Melanie; Vaidya, Vishal S.; Clement, Matthew; Bonventre, Joseph V.; Zidek, Nadine; Rached, Eva; Amberg, Alexander; Callanan, John J.; Dekant, Wolfgang; Mally, Angela

    2009-01-01

    Although early detection of toxicant induced kidney injury during drug development and chemical safety testing is still limited by the lack of sensitive and reliable biomarkers of nephrotoxicity, omics technologies have brought enormous opportunities for improved detection of toxicity and biomarker discovery. Thus, transcription profiling has led to the identification of several candidate kidney biomarkers such as kidney injury molecule (Kim-1), clusterin, lipocalin-2, and tissue inhibitor of metalloproteinase 1 (Timp-1), and metabonomic analysis of urine is increasingly used to indicate biochemical perturbations due to renal toxicity. This study was designed to assess the value of a combined 1H-NMR and gas chromatography–mass spectrometry (GC-MS) metabonomics approach and a set of novel urinary protein markers for early detection of nephrotoxicity following treatment of male Wistar rats with gentamicin (60 and 120 mg/kg bw, sc) for 7 days. Time- and dose-dependent separation of gentamicin-treated animals from controls was observed by principal component analysis of 1H-NMR and GC-MS data. The major metabolic alterations responsible for group separation were linked to the gut microflora, thus related to the pharmacology of the drug, and increased glucose in urine of gentamicin-treated animals, consistent with damage to the S1 and S2 proximal tubules, the primary sites for glucose reabsorption. Altered excretion of urinary protein biomarkers Kim-1 and lipocalin-2, but not Timp-1 and clusterin, was detected before marked changes in clinical chemistry parameters were evident. The early increase in urine, which correlated with enhanced gene and protein expression at the site of injury, provides further support for lipocalin-2 and Kim-1 as sensitive, noninvasive biomarkers of nephrotoxicity. PMID:19349640

  19. A Comparative Analysis of Prognostic Factor Models for Follicular Lymphoma based on a Phase III Trial of CHOP-Rituximab vs CHOP + 131Iodine-Tositumomab

    PubMed Central

    Press, Oliver W.; Unger, Joseph M.; Rimsza, Lisa M.; Friedberg, Jonathan W.; LeBlanc, Michael; Czuczman, Myron S.; Kaminski, Mark; Braziel, Rita M.; Spier, Catherine; Gopal, Ajay K.; Maloney, David G.; Cheson, Bruce D.; Dakhil, Shaker R.; Miller, Thomas P.; Fisher, Richard I.

    2013-01-01

    Purpose There is currently no consensus on optimal front-line therapy for patients with follicular lymphomas (FL). We analyzed a Phase III randomized intergroup trial comparing 6 cycles of CHOP-R with six cycles of CHOP followed by iodine I-131 tositumomab radioimmunotherapy (RIT) to assess whether any subsets benefitted more from one treatment or the other, and to compare three prognostic models. Experimental Design We conducted univariate and multivariate Cox regression analyses of 532 patients enrolled on this trial and compared the prognostic value of the FLIPI, FLIPI2, and LDH + β2M models. Results Outcomes were excellent, but not statistically different between the two study arms (5 year PFS of 60% with CHOP-R and 66% with CHOP-RIT [p =0.11]; 5-yr OS of 92% with CHOP-R and 86% with CHOP-RIT [p=0.08]; overall response rate of 84% for both arms). The only factor found to potentially predict the impact of treatment was serum β2 microglobulin (β2M); among patients with normal β2M, CHOP-RIT patients had better PFS compared to CHOP-R patients, whereas among patients with high serum β2M, PFS by arm was similar (interaction p-value=.02). Conclusions All three prognostic models (FLIPI, FLIPI2, LDH + β2M) predicted both PFS and OS well, though the LDH + β2M model is easiest to apply and identified an especially poor risk subset. In an exploratory analysis using the latter model, there was a statistically significant trend suggesting that low risk patients had superior observed PFS if treated with CHOP-RIT, whereas high risk patients had a better PFS with CHOP-R. PMID:24130072

  20. miRNA expression and function in thyroid carcinomas: a comparative and critical analysis and a model for other cancers

    PubMed Central

    Saiselet, Manuel; Pita, Jaime M.; Augenlicht, Alice; Dom, Geneviève; Tarabichi, Maxime; Fimereli, Danai; Dumont, Jacques E.; Detours, Vincent; Maenhaut, Carine

    2016-01-01

    As in many cancer types, miRNA expression profiles and functions have become an important field of research on non-medullary thyroid carcinomas, the most common endocrine cancers. This could lead to the establishment of new diagnostic tests and new cancer therapies. However, different studies showed important variations in their research strategies and results. In addition, the action of miRNAs is poorly considered as a whole because of the use of underlying dogmatic truncated concepts. These lead to discrepancies and limits rarely considered. Recently, this field has been enlarged by new miRNA functional and expression studies. Moreover, studies using next generation sequencing give a new view of general miRNA differential expression profiles of papillary thyroid carcinoma. We analyzed in detail this literature from both physiological and differential expression points of view. Based on explicit examples, we reviewed the progresses but also the discrepancies and limits trying to provide a critical approach of where this literature may lead. We also provide recommendations for future studies. The conclusions of this systematic analysis could be extended to other cancer types. PMID:27248468

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

    PubMed

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

    2014-03-01

    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.

  2. 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

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

    PubMed Central

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

    2015-01-01

    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

  4. 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. © 2016 American Society of Plant Biologists. All rights reserved.

  5. 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.

  6. 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.

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

    PubMed Central

    Chen, Chunhong; Newell, Kim; Lawrence, Gregory J.; 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

  8. 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

    2016-06-06

    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.

  9. Support vector regression and artificial neural network models for stability indicating analysis of mebeverine hydrochloride and sulpiride mixtures in pharmaceutical preparation: A comparative study

    NASA Astrophysics Data System (ADS)

    Naguib, Ibrahim A.; Darwish, Hany W.

    2012-02-01

    A comparison between support vector regression (SVR) and Artificial Neural Networks (ANNs) multivariate regression methods is established showing the underlying algorithm for each and making a comparison between them to indicate the inherent advantages and limitations. In this paper we compare SVR to ANN with and without variable selection procedure (genetic algorithm (GA)). To project the comparison in a sensible way, the methods are used for the stability indicating quantitative analysis of mixtures of mebeverine hydrochloride and sulpiride in binary mixtures as a case study in presence of their reported impurities and degradation products (summing up to 6 components) in raw materials and pharmaceutical dosage form via handling the UV spectral data. For proper analysis, a 6 factor 5 level experimental design was established resulting in a training set of 25 mixtures containing different ratios of the interfering species. An independent test set consisting of 5 mixtures was used to validate the prediction ability of the suggested models. The proposed methods (linear SVR (without GA) and linear GA-ANN) were successfully applied to the analysis of pharmaceutical tablets containing mebeverine hydrochloride and sulpiride mixtures. The results manifest the problem of nonlinearity and how models like the SVR and ANN can handle it. The methods indicate the ability of the mentioned multivariate calibration models to deconvolute the highly overlapped UV spectra of the 6 components' mixtures, yet using cheap and easy to handle instruments like the UV spectrophotometer.

  10. Comparative Analysis of the Cardioprotective Properties of Opioid Receptor Agonists in a Rat Model of Myocardial Infarction

    PubMed Central

    Maslov, Leonid N.; Lishmanov, Yury B.; Oeltgen, Peter R.; Barzakh, Eva I.; Krylatov, Andrey V.; Naryzhnaya, Natalia V.; Pei, Jian-Ming; Brown, Stephen A.

    2010-01-01

    Objectives This study was conducted to test the hypothesis that opioid receptor (OR) mediated cardioprotection is agonist-specific when administered prior to coronary artery occlusion and reperfusion in a rat model. Methods Anesthetized open-chest male Wistar rats were subjected to 45 minutes of left coronary artery occlusion and 2 hours of reperfusion. Opioid agonists were infused 15 minutes prior to coronary artery occlusion. Two control groups and 15 opioid treated groups were studied. Controls were infused with either saline alone (n = 16) or dimethyl sulfoxide (DMSO) plus hydroxypropyl-β-cyclodextrin in saline (n = 19). The μ selective agonist DAMGO was infused at either 150 nmol/kg (n = 15) or 1500 nmol/kg (n = 14), and Dermorphin-H was infused at 150 nmol/kg (n = 14). The δ1 selective agonist D-Pen2,5 Enkephalin (DPDPE) was infused at 150 nmol/kg (n = 16) or 1500 nmol/kg (n = 14). The δ2 selective agonists Deltorphin II (n = 16), Deltorphin-Dvariant (n = 15) and Deltorphin-E (n = 14) were infused at 150 nmol/kg. The selective κ1 opioid agonist U-50488 was infused at 240 nmol/kg (n = 14), 1500 nmol/kg (n = 14), and 2,400 nmol/kg (n = 14). The selective κ2 opioid agonist GR-89696 was infused at 150 nmol/kg (n = 14) and 1500 nmol/kg (n = 15). Orphinan FQ (Nociceptin), also referred to as OR Ligand1 (ORL1), was infused at 220 nmol/kg (n = 15) and 1500 nmol/kg (n = 15). The infarct size/area at risk (IS/AAR) ratio was determined after reperfusion by negative staining with patent blue violet dye. Hemodynamic parameters including heart rate, mean arterial blood pressure (MAP), and rate pressure product (RPP) were determined. Results Pretreatment with the δ2 OR agonist Deltorphin II (150 nmol/kg) significantly reduced the IS/AAR ratio, while Deltorphin-Dvariant and Deltorphin-E did not exhibit an infarct sparing effect at that treatment dose. Activation of δ1 OR by DPDPE, κ1 OR by U-50488, κ2 OR by U-50488, μ OR by DAMGO, Dermophin-H, and Nociceptin had

  11. 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

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

    2013-03-01

    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. 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. 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. We failed to establish a rat spinal cord stimulation model. However, sacral neuromodulation have a therapeutic potential to improve neurogenic bladder and muscle atrophy.

  12. Meta-Analysis Comparing Established Risk Prediction Models (EuroSCORE II, STS Score, and ACEF Score) for Perioperative Mortality During Cardiac Surgery.

    PubMed

    Sullivan, Patrick G; Wallach, Joshua D; Ioannidis, John P A

    2016-11-15

    A wide variety of multivariable risk models have been developed to predict mortality in the setting of cardiac surgery; however, the relative utility of these models is unknown. This study investigated the literature related to comparisons made between established risk prediction models for perioperative mortality used in the setting of cardiac surgery. A systematic review was conducted to capture studies in cardiac surgery comparing the relative performance of at least 2 prediction models cited in recent guidelines (European System for Cardiac Operative Risk Evaluation [EuroSCORE II], Society for Thoracic Surgeons 2008 Cardiac Surgery Risk Models [STS] score, and Age, Creatinine, Ejection Fraction [ACEF] score) for the outcomes of 1-month or inhospital mortality. For articles that met inclusion criteria, we extracted information on study design, predictive performance of risk models, and potential for bias. Meta-analyses were conducted to calculate a summary estimate of the difference in AUCs between models. We identified 22 eligible studies that contained 33 comparisons among the above models. Meta-analysis of differences in AUCs revealed that the EuroSCORE II and STS score performed similarly (with a summary difference in AUC = 0.00), while outperforming the ACEF score (with summary differences in AUC of 0.10 and 0.08, respectively, p <0.05). Other metrics of discrimination and calibration were presented less consistently, and no study presented any metric of reclassification. Small sample size and absent descriptions of missing data were common in these studies. In conclusion, the EuroSCORE II and STS score outperform the ACEF score on discrimination. Copyright © 2016. Published by Elsevier Inc.

  13. [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.

  14. Secondary structure model for mouse beta Maj globin mRNA derived from enzymatic digestion data, comparative sequence and computer analysis.

    PubMed Central

    Lockard, R E; Currey, K; Browner, M; Lawrence, C; Maizel, J

    1986-01-01

    A model for the secondary structure of mouse beta Maj globin messenger RNA is presented based on enzymatic digestion data, comparative sequence and computer analysis. Using 5'-32P-end-labeled beta globin mRNA as a substrate, single-stranded regions were determined with S1 and T1 nucleases and double-stranded regions with V1 ribonuclease from cobra venom. The structure data obtained for ca. 75% of the molecule was introduced into a computer algorithm which predicts secondary structures of minimum free energy consistent with the enzymatic data. Two prominent base paired regions independently derived by phylogenetic analysis were also present in the computer generated structure lending support for the model. An interesting feature of the model is the presence of long-range base pairing interactions which permit the beta globin mRNA to fold back on itself, thereby bringing the 5'- and 3'-noncoding regions within close proximity. This feature is consistent with data from other laboratories suggesting an interaction of the 5'- and 3'-domains in the mammalian globin mRNAs. Images PMID:3737415

  15. Primary screening for human papillomavirus compared with cytology screening for cervical cancer in European settings: cost effectiveness analysis based on a Dutch microsimulation model

    PubMed Central

    van Rosmalen, Joost; Dillner, Joakim; Arbyn, Marc; Sasieni, Peter; Iftner, Thomas; van Ballegooijen, Marjolein

    2012-01-01

    Objectives To investigate, using a Dutch model, whether and under what variables framed for other European countries screening for human papillomavirus (HPV) is preferred over cytology screening for cervical cancer, and to calculate the preferred number of examinations over a woman’s lifetime. Design Cost effectiveness analysis based on a Dutch simulation model. Base case analyses investigated the cost effectiveness of more than 1500 different screening policies using the microsimulation model. Subsequently, the policies were compared for five different scenarios that represent different possible scenarios (risk of cervical cancer, previous screening, quality associated test characteristics, costs of testing, and prevalence of HPV). Setting Various European countries. Population Unvaccinated women born between 1939 and 1992. Main outcome measures Optimal screening strategy in terms of incremental cost effectiveness ratios (costs per quality adjusted life years gained) compared with different cost effectiveness thresholds, for two levels of sensitivity and costs of the HPV test. Results Primary HPV screening was the preferred primary test over the age of 30 in many considered scenarios. Primary cytology screening was preferred only in scenarios with low costs of cytology and in scenarios with a high prevalence of HPV in combination with high costs of HPV testing. Conclusions Most European countries should consider switching from primary cytology to HPV screening for cervical cancer. HPV screening must, however, only be implemented in situations where screening is well controlled. PMID:22391612

  16. Comparative cost-benefit analysis of tele-homecare for community-dwelling elderly in Japan: Non-Government versus Government Supported Funding Models.

    PubMed

    Akiyama, Miki; Abraham, Chon

    2017-08-01

    Tele-homecare is gaining prominence as a viable care alternative, as evidenced by the increase in financial support from international governments to fund initiatives in their respective countries. The primary reason for the funding is to support efforts to reduce lags and increase capacity in access to care as well as to promote preventive measures that can avert costly emergent issues from arising. These efforts are especially important to super-aged and aging societies such as in Japan, many European countries, and the United States (US). However, to date and to our knowledge, a direct comparison of non-government vs. government-supported funding models for tele-homecare is particularly lacking in Japan. The aim of this study is to compare these operational models (i.e., non-government vs. government-supported funding) from a cost-benefit perspective. This simulation study applies to a Japanese hypothetical cohort with implications for other super-aged and aging societies abroad. We performed a cost-benefit analysis (CBA) on two operational models for enabling tele-homecare for elderly community-dwelling cohorts based on a decision tree model, which we created with parameters from published literature. The two models examined are (a) Model 1-non-government-supported funding that includes monthly fixed charges paid by users for a portion of the operating costs, and (b) Model 2-government-supported funding that includes startup and installation costs only (i.e., no operating costs) and no monthly user charges. We performed base case cost-benefit analysis and probabilistic cost-benefit analysis with a Monte Carlo simulation. We calculated net benefit and benefit-to-cost ratios (BCRs) from the societal perspective with a five-year time horizon applying a 3% discount rate for both cost and benefit values. The cost of tele-homecare included (a) the startup system expense, averaged over a five-year depreciation period, and (b) operation expenses (i.e., labor and non

  17. Enhanced Precision of the New Hologic Horizon Model Compared With the Old Discovery Model Is Less Evident When Fewer Vertebrae Are Included in the Analysis.

    PubMed

    McNamara, Elizabeth A; Kilim, Holly P; Malabanan, Alan O; Whittaker, LaTarsha G; Rosen, Harold N

    2016-07-12

    The International Society for Clinical Densitometry guidelines recommend using locally derived precision data for spine bone mineral densities (BMDs), but do not specify whether data derived from L1-L4 spines correctly reflect the precision for spines reporting fewer than 4 vertebrae. Our experience suggested that the decrease in precision with successively fewer vertebrae is progressive as more vertebrae are excluded and that the precision for the newer Horizon Hologic model might be better than that for the previous model, and we sought to quantify. Precision studies were performed on Hologic densitometers by acquiring spine BMD in fast array mode twice on 30 patients, according to International Society for Clinical Densitometry guidelines. This was done 10 different times on various Discovery densitometers, and once on a Horizon densitometer. When 1 vertebral body was excluded from analysis, there was no significant deterioration in precision. When 2 vertebrae were excluded, there was a nonsignificant trend to poorer precision, and when 3 vertebrae were excluded, there was significantly worse precision. When 3 or 4 vertebrae were reported, the precision of the spine BMD measurement was significantly better on the Hologic Horizon than on the Discovery, but the difference in precision between densitometers narrowed and was no longer significant when 1 or 2 vertebrae were reported. The results suggest that (1) the measurement of in vivo spine BMD on the new Hologic Horizon densitometer is significantly more precise than on the older Discovery model; (2) the difference in precision between the Horizon and Discovery models decreases as fewer vertebrae are included; (3) the measurement of spine BMD is less precise as more vertebrae are excluded, but still quite reasonable even when only 1 vertebral body is included; and (4) when 3 vertebrae are reported, L1-L4 precision data can reasonably be used to report significance of changes in BMD. When 1 or 2 vertebrae are

  18. 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

  19. Comparative analysis of the influence of turbulence models on the description of the nitrogen oxides formation during the combustion of swirling pulverized coal flow

    NASA Astrophysics Data System (ADS)

    Kuznetsov, V.; Chernetskaya, N.; Chernetskiy, M.

    2016-10-01

    The paper presents the results of numerical research on the influence of the two- parametric k-ε, and k-ω SST turbulence models as well as Reynolds stress model (RSM) on the description of the nitrogen oxides formation during the combustion of pulverized coal in swirling flow. For the numerical simulation of turbulent flow of an incompressible liquid, we used the Reynolds equation taking into account the interfacial interactions. To solve the equation of thermal radiation transfer, the P1 approximation of spherical harmonics method was employed. The optical properties of gases were described based on the sum of gray gases model. To describe the motion of coal particles we used the method of Lagrange multipliers. Burning of coke residue was considered based on diffusion - kinetic approximation. Comparative analysis has shown that the choice of turbulence model has a significant impact on the root mean square (RMS) values of the velocity and temperature pulsation components. This leads to significant differences in the calculation of the nitrogen oxides formation process during the combustion of pulverized coal.

  20. Cost effectiveness of a lidocaine 5% medicated plaster compared with pregabalin for the treatment of postherpetic neuralgia in the UK: a Markov model analysis.

    PubMed

    Ritchie, Mark; Liedgens, Hiltrud; Nuijten, Mark

    2010-01-01

    Published analyses have demonstrated that the lidocaine (lignocaine) plaster is a cost-effective treatment for postherpetic neuralgia (PHN) relative to gabapentin or pregabalin. However, these analyses have been based on indirect comparisons from placebo-controlled trials, and there is evidence of a discrepancy between the outcomes of direct and indirect analyses. Fortunately, recent publication of the results of a head-to-head trial comparing the lidocaine plaster and pregabalin in patients with PHN or diabetic polyneuropathy allows customization of the existing model to more accurately reflect the relative cost effectiveness of these two products. To assess the cost-effectiveness of the lidocaine 5% medicated plaster compared with pregabalin for the treatment of PHN in the UK primary-care setting. A Markov model has been developed to assess the costs and benefits of the lidocaine plaster and pregabalin over a 6-month time horizon for the treatment of patients with PHN who are intolerant to tricyclic antidepressants and in whom analgesics are ineffective or contraindicated. The model structure allows for differences in costs, utilities (derived from published data and from the head-to-head trial) and transition probabilities between the initial 30-day run-in period and maintenance therapy, and also takes account of add-in medication and drugs received by patients discontinuing therapy. The calculation was based on data from the recent head-to-head trial described above. Additional data sources included published literature, discussions with a Delphi panel, official price/tariff lists and national population statistics. The study was conducted from the perspective of the UK National Health Service (NHS). The base-case analysis (1.71 lidocaine plasters per day used in the head-to-head trial for the PHN population) indicated that the total cost of treating PHN patients for 6 months with the lidocaine plaster was pound 980 per patient treated, compared with pound 784

  1. One Method for Comparing Different Nursing Models.

    ERIC Educational Resources Information Center

    Sohn, Kum Sook

    1991-01-01

    Discusses a simple method for comparing nursing models, using a four-step framework: assessment, diagnosis plan, implementation, and evaluation. Uses four nursing models as illustrations--Henderson, Orem, Neuman, and Roy. (JOW)

  2. 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.)

  3. 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.)

  4. 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.

  5. Comparative assessment of differential network analysis methods.

    PubMed

    Lichtblau, Yvonne; Zimmermann, Karin; Haldemann, Berit; Lenze, Dido; Hummel, Michael; Leser, Ulf

    2017-09-01

    Differential network analysis (DiNA) denotes a recent class of network-based Bioinformatics algorithms which focus on the differences in network topologies between two states of a cell, such as healthy and disease, to identify key players in the discriminating biological processes. In contrast to conventional differential analysis, DiNA identifies changes in the interplay between molecules, rather than changes in single molecules. This ability is especially important in cases where effectors are changed, e.g. mutated, but their expression is not. A number of different DiNA approaches have been proposed, yet a comparative assessment of their performance in different settings is still lacking. In this paper, we evaluate 10 different DiNA algorithms regarding their ability to recover genetic key players from transcriptome data. We construct high-quality regulatory networks and enrich them with co-expression data from four different types of cancer. Next, we assess the results of applying DiNA algorithms on these data sets using a gold standard list (GSL). We find that local DiNA algorithms are generally superior to global algorithms, and that all DiNA algorithms outperform conventional differential expression analysis. We also assess the ability of DiNA methods to exploit additional knowledge in the underlying cellular networks. To this end, we enrich the cancer-type specific networks with known regulatory miRNAs and compare the algorithms performance in networks with and without miRNA. We find that including miRNAs consistently and considerably improves the performance of almost all tested algorithms. Our results underline the advantages of comprehensive cell models for the analysis of -omics data. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. 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.

  7. 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

  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. A mathematical model of Clostridium difficile transmission in medical wards and a cost-effectiveness analysis comparing different strategies for laboratory diagnosis and patient isolation

    PubMed Central

    Carmeli, Yehuda; Leshno, Moshe

    2017-01-01

    Background Clostridium difficile infection (CDI) is a common and potentially fatal healthcare-associated infection. Improving diagnostic tests and infection control measures may prevent transmission. We aimed to determine, in resource-limited settings, whether it is more effective and cost-effective to allocate resources to isolation or to diagnostics. Methods We constructed a mathematical model of CDI transmission based on hospital data (9 medical wards, 350 beds) between March 2010 and February 2013. The model consisted of three compartments: susceptible patients, asymptomatic carriers and CDI patients. We used our model results to perform a cost-effectiveness analysis, comparing four strategies that were different combinations of 2 test methods (the two-step test and uniform PCR) and 2 infection control measures (contact isolation in multiple-bed rooms or single-bed rooms/cohorting). For each strategy, we calculated the annual cost (of CDI diagnosis and isolation) for a decrease of 1 in the average daily number of CDI patients; the strategy of the two-step test and contact isolation in multiple-bed rooms was the reference strategy. Results Our model showed that the average number of CDI patients increased exponentially as the transmission rate increased. Improving diagnosis by adopting uniform PCR assay reduced the average number of CDI cases per day per 350 beds from 9.4 to 8.5, while improving isolation by using single-bed rooms reduced the number to about 1; the latter was cost saving. Conclusions CDI can be decreased by better isolation and more sensitive laboratory methods. From the hospital perspective, improving isolation is more cost-effective than improving diagnostics. PMID:28187144

  10. 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

  11. Comparative molecular field analysis and molecular modeling studies of 20-(S)- camptothecin analogs as inhibitors of DNA topoisomerase I and anticancer/antitumor agents

    NASA Astrophysics Data System (ADS)

    Carrigan, Sean W.; Fox, Peter C.; Wall, Monroe E.; Wani, Mansukh C.; Bowen, J. Phillip

    1997-01-01

    Conformational studies and comparative molecular field analysis (CoMFA) were undertakenfor a series of camptothecin (CPT) analogs to correlate topoisomerase I inhibition with thesteric and electrostatic properties of 32 known compounds. The resulting CoMFA modelshave been used to make predictions on novel CPT derivatives. Using the newly derived MM3parameters, a molecular database of the 32 CPT analogs was created. Various point atomiccharges were generated and assigned to the MM3 minimized structures, which were used inpartial least-squares analyses. Overall, CoMFA models with the greatest predictive validitywere obtained when both the R- and S-isomers were included in the data set, andsemiempirical charges were calculated for MM3 minimized low-energy lactone structures. Across-validated R2 of 0.758 and a non-cross-validated R2 of 0.916 were obtained for MM3minimized structures with PM3 ESP charges for the 32 CPT analogs. The derived QSARequations were used to assign topoisomerase I inhibition values for compounds in this studyand compounds not included in the original data set. Prior to its appearance in the literature,an IC50 of 103 nM was predicted for the 10,11-oxazole derivative. This CoMFA predictedvalue compared favorably with the recently reported value of 150 nM. The CoMFA modelwas also evaluated by predicting the activities of recently reported 11-aza CPT and trionederivatives. The predicted activity (IC50 = 249 nM) for 11-aza CPT compared well with thereported value of 383 nM.

  12. 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,…

  13. 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,…

  14. A comparative analysis of extended water cloud model and backscatter modelling for above-ground biomass assessment in Corbett Tiger Reserve

    NASA Astrophysics Data System (ADS)

    Kumar, Yogesh; Singh, Sarnam; Chatterjee, R. S.; Trivedi, Mukul

    2016-04-01

    Forest biomass acts as a backbone in regulating the climate by storing carbon within itself. Thus the assessment of forest biomass is crucial in understanding the dynamics of the environment. Traditionally the destructive methods were adopted for the assessment of biomass which were further advanced to the non-destructive methods. The allometric equations developed by destructive methods were further used in non-destructive methods for the assessment, but they were mostly applied for woody/commercial timber species. However now days Remote Sensing data are primarily used for the biomass geospatial pattern assessment. The Optical Remote Sensing data (Landsat8, LISS III, etc.) are being used very successfully for the estimation of above ground biomass (AGB). However optical data is not suitable for all atmospheric/environmental conditions, because it can't penetrate through clouds and haze. Thus Radar data is one of the alternate possible ways to acquire data in all-weather conditions irrespective of weather and light. The paper examines the potential of ALOS PALSAR L-band dual polarisation data for the estimation of AGB in the Corbett Tiger Reserve (CTR) covering an area of 889 km2. The main focus of this study is to explore the accuracy of Polarimetric Scattering Model (Extended Water Cloud Model (EWCM) with respect to Backscatter model in the assessment of AGB. The parameters of the EWCM were estimated using the decomposition components (Raney Decomposition) and the plot level information. The above ground biomass in the CTR ranges from 9.6 t/ha to 322.6 t/ha.

  15. 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.

  16. Comparing methods for single paragraph similarity analysis.

    PubMed

    Stone, Benjamin; Dennis, Simon; Kwantes, Peter J

    2011-01-01

    The focus of this paper is two-fold. First, similarities generated from six semantic models were compared to human ratings of paragraph similarity on two datasets-23 World Entertainment News Network paragraphs and 50 ABC newswire paragraphs. Contrary to findings on smaller textual units such as word associations (Griffiths, Tenenbaum, & Steyvers, 2007), our results suggest that when single paragraphs are compared, simple nonreductive models (word overlap and vector space) can provide better similarity estimates than more complex models (LSA, Topic Model, SpNMF, and CSM). Second, various methods of corpus creation were explored to facilitate the semantic models' similarity estimates. Removing numeric and single characters, and also truncating document length improved performance. Automated construction of smaller Wikipedia-based corpora proved to be very effective, even improving upon the performance of corpora that had been chosen for the domain. Model performance was further improved by augmenting corpora with dataset paragraphs. Copyright © 2010 Cognitive Science Society, Inc.

  17. Prasugrel compared to clopidogrel in patients with acute coronary syndrome undergoing percutenaous coronary intervention: a Spanish model-based cost effectiveness analysis.

    PubMed

    Davies, A; Sculpher, M; Barrett, A; Huete, T; Sacristán, J A; Dilla, T

    2013-01-01

    To assess the long-term cost-effectiveness of 12 months treatment of prasugrel compared to clopidogrel in patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI) in the Spanish health care system. A Markov state transition model was developed to estimate health outcomes, quality adjusted life years (QALYs), life years (LY), and costs over patients' lifetimes. Clinical inputs were based on an analysis of the TRITON-TIMI 38 clinical trial. Hospital readmissions captured during the trial in a sub-study of patients from eight countries (and subsequent re-hospitalisations modelled to accrue beyond the time horizon of the trial), were assigned to Spanish diagnosis-related group payment schedules to estimate hospitalisation costs. Mean total treatment costs were ?11,427 and ?10,910 for prasugrel and clopidogrel respectively. The mean cost of the study drug was ?538 higher for prasugrel vs. clopidogrel, but rehospitalisation costs at 12 months were ?79 lower for prasugrel due to reduced rates of revascularisation. Hospitalisation costs beyond 12 months were higher with prasugrel by ?55, due to longer life expectancy (+0.071 LY and +0.054 QALYs) associated with the decreased nonfatal myocardial infarction rate in the prasugrel group. The incremental cost per life year and QALY gained with prasugrel was ?7,198, and ?9,489, respectively. Considering a willingness-to-pay threshold of ?30,000/QALY gained in the Spanish setting, prasugrel represents a cost-effective option in comparison with clopidogrel among patients with ACS undergoing PCI. Copyright © 2013 SEFH. Published by AULA MEDICA. All rights reserved.

  18. Comparative morphometric analysis of microglia in the spinal cord of SOD1(G93A) transgenic mouse model of amyotrophic lateral sclerosis.

    PubMed

    Ohgomori, Tomohiro; Yamada, Jun; Takeuchi, Hideyuki; Kadomatsu, Kenji; Jinno, Shozo

    2016-05-01

    It has long been recognized that reactive microglia undergo a series of phenotypic changes accompanying morphological transformation. However, the morphological classification of microglia has not yet been achieved. To address this issue, here we morphometrically analysed three-dimensionally reconstructed ionized calcium binding adaptor molecule 1-immunoreactive (Iba1(+) ) microglia in the ventral horn of the lumbar spinal cord of SOD1(G93A) transgenic mice, a model of amyotrophic lateral sclerosis. The hierarchical cluster analysis revealed that microglia were objectively divided into four groups: type S (named after surveillant microglia) and types R1, R2 and R3 (named after reactive microglia). For the purpose of comparative morphometry, we also analysed two pharmacological disease models using wild-type mice: 3,3'-iminodipropionitrile (IDPN)-induced axonopathy and lipopolysaccharide (LPS)-induced neuroinflammation. Type S microglia showed a typical ramified morphology of surveillant microglia, and were mostly observed in wild-type controls. Type R1 microglia were seen at the early stage of disease in SOD1(G93A) mice, and also frequently occurred in IDPN-treated mice. They exhibited small cell bodies with shorter and simple processes. Type R2 microglia were morphologically similar to type R1 microglia, but only transiently occurred in the middle stage of disease in SOD1(G93A) mice and in IDPN-treated mice. Type R3 microglia exhibited a bushy shape, and were observed in the end stage of disease in SOD1(G93A) mice and in LPS-treated mice. These findings indicate that microglia of SOD1(G93A) mice can be classified into four types, and also suggest that the phenotypic changes may be induced by the events related to axonopathy and neuroinflammation. © 2016 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

  19. 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.

  20. Fold assessment for comparative protein structure modeling

    PubMed Central

    Melo, Francisco; Sali, Andrej

    2007-01-01

    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. PMID:17905832

  1. 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.

  2. Analysis of the Eyjafjallajökull Eruption using the WRF-Chem Model compared to Satellite-Based Ash Retrieval Algorithms

    NASA Astrophysics Data System (ADS)

    Steensen, T. S.; Stuefer, M.; Webley, P.; Grell, G. A.; de Freitas, S. R.

    2010-12-01

    On April 14th, 2010, the long-dormant ice-capped volcano Eyjafjallajökull in southern Iceland exhibited a black ash-rich plume that quickly developed into an upper-tropospheric ash-cloud covering large parts of Europe grounding the majority of European air traffic for days. The emission of the ash-cloud continued for three days before the eruption turned more magmatic on April 18th. Due to a strong jet stream the plume initially drifted towards the United Kingdom and Norway with ash-fall occurring in many cities in both countries. Over the course of a week, most countries in Europe were affected by the dispersing cloud resulting in numbers of closed airports never seen before, grounded planes and confused passengers. This eruption, although small on the international scale, drew volcanic hazards into the public eye and called for better understanding of evolving volcanic plumes and their ash content. The Weather Research and Forecast model (WRF) coupled with Chemistry (Chem) has been utilized to use wind fields and chemical compositions to forecast the drift and chemical alteration of dispersed substances such as forest fires and volcanic ash and, in this study, was used to simulate the developing plume in time, based on physical input parameters of the initial plume as well as the wind patterns over Europe during April 2010. The results of this model have been compared to satellite-based ash retrieval algorithms like the Reverse Absorption Method and the Principal Component Analysis using Advanced Very High Resolution Radiometer (AVHRR) the Moderate-Resolution Imaging Spectroradiometer (MODIS) data. This comparison allows both, the ratification of the model as a forecasting tool and of the satellites as an in-situ measurement. Both parts are essential components to be able to predict and analyze airborne volcanic ash and to constantly improve the hazard assessment of ash cloud forecasting to minimize the burden on the aviation community while maximizing the

  3. Comparing and Using Occupation-Focused Models.

    PubMed

    Wong, Su Ren; Fisher, Gail

    2015-01-01

    As health care moves toward understanding the importance of function, participation and occupation, occupational therapists would be well served to use occupation-focused theories to guide intervention. Most therapists understand that applying occupation-focused models supports best practice, but many do not routinely use these models. Barriers to application of theory include lack of understanding of the models and limited strategies to select and apply them for maximum client benefit. The aim of this article is to compare occupation-focused models and provide recommendations on how to choose and combine these models in practice; and to provide a systematic approach for integrating occupation-focused models with frames of reference to guide assessment and intervention.

  4. Comparative biology of cystic fibrosis animal models.

    PubMed

    Fisher, John T; Zhang, Yulong; Engelhardt, John F

    2011-01-01

    Animal models of human diseases are critical for dissecting mechanisms of pathophysiology and developing therapies. In the context of cystic fibrosis (CF), mouse models have been the dominant species by which to study CF disease processes in vivo for the past two decades. Although much has been learned through these CF mouse models, limitations in the ability of this species to recapitulate spontaneous lung disease and several other organ abnormalities seen in CF humans have created a need for additional species on which to study CF. To this end, pig and ferret CF models have been generated by somatic cell nuclear transfer and are currently being characterized. These new larger animal models have phenotypes that appear to closely resemble human CF disease seen in newborns, and efforts to characterize their adult phenotypes are ongoing. This chapter will review current knowledge about comparative lung cell biology and cystic fibrosis transmembrane conductance regulator (CFTR) biology among mice, pigs, and ferrets that has implications for CF disease modeling in these species. We will focus on methods used to compare the biology and function of CFTR between these species and their relevance to phenotypes seen in the animal models. These cross-species comparisons and the development of both the pig and the ferret CF models may help elucidate pathophysiologic mechanisms of CF lung disease and lead to new therapeutic approaches.

  5. A Comparative Analysis of Models of Bachelors of Arts' Professional Training in Applied Linguistics at the Universities of Ukraine and the USA

    ERIC Educational Resources Information Center

    Korniienko, Vita

    2014-01-01

    The analysis of scientists' researches from different countries dealing with different aspects of training in the educational systems of developed countries was carried out. The models of Bachelors of Arts in Applied Linguistics professional training in Ukraine were considered. It was analyzed a professional training of Bachelor of Arts in Applied…

  6. A Comparative Analysis of Models of Bachelors of Arts' Professional Training in Applied Linguistics at the Universities of Ukraine and the USA

    ERIC Educational Resources Information Center

    Korniienko, Vita

    2014-01-01

    The analysis of scientists' researches from different countries dealing with different aspects of training in the educational systems of developed countries was carried out. The models of Bachelors of Arts in Applied Linguistics professional training in Ukraine were considered. It was analyzed a professional training of Bachelor of Arts in Applied…

  7. Comparative proteome analysis of Bifidobacterium longum subsp. infantis grown on β-glucans from different sources and a model for their utilization.

    PubMed

    Zhao, Jinyang; Cheung, Peter C K

    2013-05-08

    Recent studies have demonstrated that β-glucans from different sources, which are considered as potential prebiotics, could enhance growth of bifidobacteria. To elucidate the metabolic pathway of β-glucans in the widely used probiotic B. longum subsp. infantis, a comparative proteomic analysis was carried out along with two-dimensional difference gel electrophoresis (2D-DIGE), real-time RT-PCR, and enzyme activity assay on samples obtained from cultures grown on β-glucans derived from barley, seaweed, and mushroom. Results showed that 77 spots were found to be differentially expressed among different cultures, and 17 of them were predicted to play a role in β-glucan catabolism, including ABC transporter for sugars, enolase, and phosphotransferase system protein. Among them, 6 genes encoding for 6 proteins were shown to be induced by β-glucans at the transcriptional level and had higher abundance. The enzyme activity assay detected intracellular glucanase activity present in the cultures grown on the β-glucans from seaweed and mushroom. On the basis of the above results, a model for catabolism of β-glucans in B. infantis is proposed as follows: β-glucan molecules in the medium are transported into the cell through the ABC (ATP-binding cassette) transport system and PTS (phosphotransferase system) proteins followed by hydrolysis through action of intracellular glucanase to glucose, which is subsequently incorporated into the central fermentative pathway 'bifid shunt'. This study for the first time reveals the possible degradation pathway of β-glucans by B. infantis, which has implications for potential use of these β-glucans as novel prebiotics in development of synbiotic application.

  8. 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.

  9. 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,…

  10. Howard University: A Comparative Fiscal Analysis.

    ERIC Educational Resources Information Center

    Inman, Deborah; And Others

    This report presents a fiscal analysis of Howard University (District of Columbia) including: (1) general education revenues; (2) education and general expenditures; and (3) faculty salaries. The study compared Howard University to four different groups of higher education institutions: similar private institutions with hospitals; public…

  11. 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…

  12. Comparative genomic analysis of esophageal cancers.

    PubMed

    Caygill, Christine P J; Gatenby, Piers A C; Herceg, Zdenko; Lima, Sheila C S; Pinto, Luis F R; Watson, Anthony; Wu, Ming-Shiang

    2014-09-01

    The following, from the 12th OESO World Conference: Cancers of the Esophagus, includes commentaries on comparative genomic analysis of esophageal cancers: genomic polymorphisms, the genetic and epigenetic drivers in esophageal cancers, and the collection of data in the UK Barrett's Oesophagus Registry.

  13. A Comparative Analysis and Taxonomy of Comets

    NASA Astrophysics Data System (ADS)

    Osip, David James

    1995-01-01

    A comparative analysis of narrowband photometry observations of 85 comets yields a wealth of information about the nature of comets. The data set consists of 2020 observations obtained over 429 nights between 1976 and 1992 that are fully reduced in a consistent manner to molecular production rates of 5 emission species (OH, NH, CN, C _3, and C_2) as well as a comparative measure of the dust production rate. Ratios of these production rates serve as a means of exploring compositional variation between comets. Vaporization models are used to estimate the active surface area for each comet, which is indicative of intrinsic differences in activity level among comets. Orbital parameters distinguish comets by dynamical age and separate the database into several dynamical classes. The current investigation confirms a number of results from earlier studies. There are no significant or systematic variations of the various abundance ratios with heliocentric distance. Neither the cometary dust -to-gas ratio nor the activity level vary systematically with dynamical age or with heliocentric distance. There is no conclusive evidence suggesting changes in composition based on dynamical evolution of the comet. Also, this investigation finds for many comets the strong degree of homogeneity in abundance ratios suggested by other studies, particularly among the carbon bearing species. Results unique to the present database include a significant correlation between the cometary dust-to -gas ratio and perihelion distance of a comet, suggesting mantling effects on the nucleus. Additional evidence for mantling is provided by the large number of comets with very low levels of activity as measured by the surface active area and the low fractional active areas calculated for those comets with nucleus size estimates available. The most important result from this study, however, is a taxonomic classification of comets separating chemically distinct compositional groupings most likely due to

  14. 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.

  15. 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.

  16. 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)

  17. 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.

  18. 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.

  19. 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

  20. A Comparative Analysis of Reynolds-Averaged Navier-Stokes Model Predictions for Rayleigh-Taylor Instability and Mixing with Constant and Complex Accelerations

    NASA Astrophysics Data System (ADS)

    Schilling, Oleg

    2016-11-01

    Two-, three- and four-equation, single-velocity, multicomponent Reynolds-averaged Navier-Stokes (RANS) models, based on the turbulent kinetic energy dissipation rate or lengthscale, are used to simulate At = 0 . 5 Rayleigh-Taylor turbulent mixing with constant and complex accelerations. The constant acceleration case is inspired by the Cabot and Cook (2006) DNS, and the complex acceleration cases are inspired by the unstable/stable and unstable/neutral cases simulated using DNS (Livescu, Wei & Petersen 2011) and the unstable/stable/unstable case simulated using ILES (Ramaprabhu, Karkhanis & Lawrie 2013). The four-equation models couple equations for the mass flux a and negative density-specific volume correlation b to the K- ɛ or K- L equations, while the three-equation models use a two-fluid algebraic closure for b. The lengthscale-based models are also applied with no buoyancy production in the L equation to explore the consequences of neglecting this term. Predicted mixing widths, turbulence statistics, fields, and turbulent transport equation budgets are compared among these models to identify similarities and differences in the turbulence production, dissipation and diffusion physics represented by the closures used in these models. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  1. 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

  2. Embedded Hyperchaotic Generators: A Comparative Analysis

    NASA Astrophysics Data System (ADS)

    Sadoudi, Said; Tanougast, Camel; Azzaz, Mohamad Salah; Dandache, Abbas

    In this paper, we present a comparative analysis of FPGA implementation performances, in terms of throughput and resources cost, of five well known autonomous continuous hyperchaotic systems. The goal of this analysis is to identify the embedded hyperchaotic generator which leads to designs with small logic area cost, satisfactory throughput rates, low power consumption and low latency required for embedded applications such as secure digital communications between embedded systems. To implement the four-dimensional (4D) chaotic systems, we use a new structural hardware architecture based on direct VHDL description of the forth order Runge-Kutta method (RK-4). The comparative analysis shows that the hyperchaotic Lorenz generator provides attractive performances compared to that of others. In fact, its hardware implementation requires only 2067 CLB-slices, 36 multipliers and no block RAMs, and achieves a throughput rate of 101.6 Mbps, at the output of the FPGA circuit, at a clock frequency of 25.315 MHz with a low latency time of 316 ns. Consequently, these good implementation performances offer to the embedded hyperchaotic Lorenz generator the advantage of being the best candidate for embedded communications applications.

  3. 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.

  4. Comparative Analysis of Ralstonia solanacearum Methylomes.

    PubMed

    Erill, Ivan; Puigvert, Marina; Legrand, Ludovic; Guarischi-Sousa, Rodrigo; Vandecasteele, Céline; Setubal, João C; Genin, Stephane; Guidot, Alice; Valls, Marc

    2017-01-01

    Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants.

  5. Comparative Analysis of Ralstonia solanacearum Methylomes

    PubMed Central

    Erill, Ivan; Puigvert, Marina; Legrand, Ludovic; Guarischi-Sousa, Rodrigo; Vandecasteele, Céline; Setubal, João C.; Genin, Stephane; Guidot, Alice; Valls, Marc

    2017-01-01

    Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants. PMID:28450872

  6. A comparative analysis of frog early development

    PubMed Central

    del Pino, Eugenia M.; Venegas-Ferrín, Michael; Romero-Carvajal, Andrés; Montenegro-Larrea, Paola; Sáenz-Ponce, Natalia; Moya, Iván M.; Alarcón, Ingrid; Sudou, Norihiro; Yamamoto, Shinji; Taira, Masanori

    2007-01-01

    The current understanding of Xenopus laevis development provides a comparative background for the analysis of frog developmental modes. Our analysis of development in various frogs reveals that the mode of gastrulation is associated with developmental rate and is unrelated to egg size. In the gastrula of the rapidly developing embryos of the foam-nesting frogs Engystomops coloradorum and Engystomops randi, archenteron and notochord elongation overlapped with involution at the blastopore lip, as in X. laevis embryos. In embryos of dendrobatid frogs and in the frog without tadpoles Eleutherodactylus coqui, which develop somewhat more slowly than X. laevis, involution and archenteron elongation concomitantly occurred during gastrulation; whereas elongation of the notochord and, therefore, dorsal convergence and extension, occurred in the postgastrula. In contrast, in the slow developing embryos of the marsupial frog Gastrotheca riobambae, only involution occurred during gastrulation. The processes of archenteron and notochord elongation and convergence and extension were postgastrulation events. We produced an Ab against the homeodomain protein Lim1 from X. laevis as a tool for the comparative analysis of development. By the expression of Lim1, we were able to identify the dorsal side of the G. riobambae early gastrula, which otherwise was difficult to detect. Moreover, the Lim1 expression in the dorsal lip of the blastopore and notochord differed among the studied frogs, indicating variation in the timing of developmental events. The variation encountered gives evidence of the modular character of frog gastrulation. PMID:17606898

  7. 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

  8. Conflicts versus analytical redundancy relations: a comparative analysis of the model based diagnosis approach from the artificial intelligence and automatic control perspectives.

    PubMed

    Cordier, Marie-Odile; Dague, Philippe; Lévy, François; Montmain, Jacky; Staroswiecki, Marcel; Travé-Massuyès, Louise

    2004-10-01

    Two distinct and parallel research communities have been working along the lines of the model-based diagnosis approach: the fault detection and isolation (FDI) community and the diagnostic (DX) community that have evolved in the fields of automatic control and artificial intelligence, respectively. This paper clarifies and links the concepts and assumptions that underlie the FDI analytical redundancy approach and the DX consistency-based logical approach. A formal framework is proposed in order to compare the two approaches and the theoretical proof of their equivalence together with the necessary and sufficient conditions is provided.

  9. A comparative analysis of models of Na+ channel gating for mammalian and invertebrate nonmyelinated axons: relationship to energy efficient action potentials.

    PubMed

    Clay, John R

    2013-01-01

    The rapidly activating, voltage gated Na(+) current, INa, has recently been measured in mammalian nonmyelinated axons. Those results have been incorporated in simulations of the action potential, results that demonstrate a significant separation in time during the spike between INa and the repolarizing K(+) current, IK. The original Hodgkin and Huxley (1952) model of Na(+) channel gating, m(3)h, where m and h are channel activation and inactivation, respectively, has been used in this analysis. This model was originally developed for invertebrate nonmyelinated axons, squid giant axons in particular. The model has not survived challenges based on results from invertebrate preparations using a double-step voltage clamp protocol and measurements of gating currents, results that demonstrate a kinetic link between activation and inactivation leading to a delayed onset of inactivation following a voltage step. These processes are independent of each other in the Hodgkin and Huxley (1952) model. Application of the double-step protocol to the m(3)h model for mammalian INa results reveals a surprising prediction, an apparent delay in onset of inactivation even though activation and inactivation are uncoupled in the model. Other results, most notably gating currents, will be required to demonstrate such a link, if indeed it exists for mammalian Na(+) channels. The information obtained will be significant in determining the way in which the Na(+) channel is sequestered away from its open state during repolarization, thereby allowing for a separation in time between INa and IK during a spike, an energetically efficient mechanism of neuronal signaling in the mammalian brain. Published by Elsevier Ltd.

  10. Comparative modelling of cytochromes P450.

    PubMed

    Kirton, Stewart B; Baxter, Carol A; Sutcliffe, Michael J

    2002-03-31

    The superfamily of enzymes known as the cytochromes P450 (P450s) comprises a wide-ranging class of proteins with diverse functions. They are known, amongst other things, to be involved in the hormonal regulation of metabolism and reproduction, as well as having a major clinical significance through their association with diseases such as cancer, diabetes and hepatitis. Knowledge of the three-dimensional (3D) structure of a protein gives insight into its function. The 3D structures of P450s are therefore of considerable scientific interest. A number of high-resolution structures of P450s have been determined by X-ray crystallography and studies of these structures have provided valuable insights into the mechanism of these enzymes. Only one of these structures is mammalian and as yet there is no structural information on human P450s in the public domain. Until such a structure is solved it is necessary to employ alternative methods to gain structural insight into how human P450s perform their biological function. Here we report on the use of comparative modelling to predict the structure of human P450s based on knowledge of their amino acid sequences plus the 3D structures of other (not human) P450s. As an illustrative example of these techniques we have modelled the structure of P450 2C5 using five bacterial P450 structures as templates. We examine the importance of selecting suitable templates, obtaining a good amino acid sequence alignment, and evaluating the models generated. To improve the quality of the models an iterative cycle of sequence alignment, model building, and model evaluation is employed. The result is a model with excellent stereochemistry, good amino acid side chain environment properties, and a Calpha trace similar to the crystal structure.

  11. Value of Organoids from Comparative Epithelia Models

    PubMed Central

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

    2015-01-01

    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

  12. Comparative analysis of black carbon in soils

    NASA Astrophysics Data System (ADS)

    Schmidt, Michael W. I.; Skjemstad, Jan O.; Czimczik, Claudia I.; Glaser, Bruno; Prentice, Ken M.; Gelinas, Yves; Kuhlbusch, Thomas A. J.

    2001-03-01

    Black carbon (BC), produced by incomplete combustion of fossil fuels and vegetation, occurs ubiquitously in soils and sediments. BC exists as a continuum from partly charred material to highly graphitized soot particles, with no general agreement on clear-cut boundaries of definition or analysis. In a comparative analysis, we measured BC forms in eight soil samples by six established methods. All methods involved removal of the non-BC components from the sample by thermal or chemical means or a combination of both. The remaining carbon, operationally defined as BC, was quantified via mass balance, elemental composition or by exploiting benzenecarboxylic acids as molecular markers or applying 13C MAS NMR (magic angle spinning nuclear magnetic resonance) spectroscopy. BC concentrations measured for individual samples vary over 2 orders of magnitude (up to a factor of 571). One possible explanation for this wide range of results is that the individual BC methods rely on operational definitions with clear-cut but different boundaries and developed for specific scientific questions, whereas BC represents a continuum of materials with widely contrasting physicochemical properties. Thus the methods are inherently designed to analytically determine different parts of the continuum, and it is crucial to know how measurements made by different techniques relate to each other. It is clear from this preliminary comparative analysis that a collection of BC reference materials should be established as soon as possible 1 ) to ensure long-term intralaboratory and interlaboratory data quality and 2) to facilitate comparative analyses between different analytical techniques and scientific approaches

  13. 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

  14. 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

  15. Stock index dynamics worldwide: a comparative analysis

    NASA Astrophysics Data System (ADS)

    Cortines, A. A. G.; Anteneodo, C.; Riera, R.

    2008-09-01

    We perform a comparative analysis of twenty-four daily stock indices across the world, encompassing developed and emerging markets. We compute, directly from the return empirical time series, the Kramers-Moyal (KM) expansion coefficients that govern the evolution of the probability density function of returns throughout timelags. Our study discloses universal patterns of the KM coefficients, which can be described in terms of a few microscopic parameters. These parameters allow to quantify features such as deviations from Gaussianity or from efficiency, providing a tool to discriminate market dynamics.

  16. Fundus camera systems: a comparative analysis.

    PubMed

    DeHoog, Edward; Schwiegerling, James

    2009-01-10

    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.

  17. Accuracy of stereolithographically printed digital models compared to plaster models.

    PubMed

    Camardella, Leonardo Tavares; Vilella, Oswaldo V; van Hezel, Marleen M; Breuning, Karel H

    2017-03-30

    This study compared the accuracy of plaster models from alginate impressions and printed models from intraoral scanning. A total of 28 volunteers were selected and alginate impressions and intraoral scans were used to make plaster models and digital models of their dentition, respectively. The digital models were printed using a stereolithographic (SLA) 3D printer with a horseshoe-shaped design. Two calibrated examiners measured distances on the plaster and printed models with a digital caliper. The paired t test was used to determine intraobserver error and compare the measurements. The Pearson correlation coefficient was used to evaluate the reliability of measurements for each model type. The measurements on plaster models and printed models show some significant differences in tooth dimensions and interarch parameters, but these differences were not clinically relevant, except for the transversal measurements. The upper and lower intermolar distances on the printed models were statistically significant and clinically relevant smaller. Printed digital models with the SLA 3D printer studied, with a horseshoe-shaped base made from intraoral scans cannot replace conventional plaster models from alginate impressions in orthodontics for diagnosis and treatment planning because of their clinically relevant transversal contraction.

  18. Comparative analysis of solar photovoltaic monitoring systems

    NASA Astrophysics Data System (ADS)

    Madeti, Siva Ramakrishna; Singh, S. N.

    2017-07-01

    This paper is focused on comparative analysis of photovoltaic (PV) monitoring system for observing the performance and stability of the system. The cost and complexity of existing PV monitoring systems restricted their use to large scale PV plants. Over the past decade, different aspects of the PV monitoring systems were reported in the wide range of literature. In this paper, a comparative analysis of various PV monitoring systems is presented for the first time. It is based on analyzing six main characteristics of PV monitoring system, such as data transfer mechanism, controller, monitoring parameters, sampling interval, program development software and monitoring methods. The comparison of methodologies and the description of implementation process are discussed in this context. The key findings of this study will contribute to the development of a new PV monitoring system. The acquaintance of all these aspects is crucial for the development of effective, low cost, and viable PV monitoring systems for the small and medium scale PV plants without compromising on the desired performance.

  19. 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…

  20. 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…

  1. 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.

  2. Comparative transcriptome analysis of muscular dystrophy models Large(myd), Dmd(mdx)/Large(myd) and Dmd(mdx): what makes them different?

    PubMed

    Almeida, Camila F; Martins, Poliana Cm; Vainzof, Mariz

    2016-08-01

    Muscular dystrophies (MD) are a clinically and genetically heterogeneous group of Mendelian diseases. The underlying pathophysiology and phenotypic variability in each form are much more complex, suggesting the involvement of many other genes. Thus, here we studied the whole genome expression profile in muscles from three mice models for MD, at different time points: Dmd(mdx) (mutation in dystrophin gene), Large(myd-/-) (mutation in Large) and Dmd(mdx)/Large(myd-/-) (both mutations). The identification of altered biological functions can contribute to understand diseases and to find prognostic biomarkers and points for therapeutic intervention. We identified a substantial number of differentially expressed genes (DEGs) in each model, reflecting diseases' complexity. The main biological process affected in the three strains was immune system, accounting for the majority of enriched functional categories, followed by degeneration/regeneration and extracellular matrix remodeling processes. The most notable differences were in 21-day-old Dmd(mdx), with a high proportion of DEGs related to its regenerative capacity. A higher number of positive embryonic myosin heavy chain (eMyHC) fibers confirmed this. The new Dmd(mdx)/Large(myd-/-) model did not show a highly different transcriptome from the parental lineages, with a profile closer to Large(myd-/-), but not bearing the same regenerative potential as Dmd(mdx). This is the first report about transcriptome profile of a mouse model for congenital MD and Dmd(mdx)/Large(myd). By comparing the studied profiles, we conclude that alterations in biological functions due to the dystrophic process are very similar, and that the intense regeneration in Dmd(mdx) involves a large number of activated genes, not differentially expressed in the other two strains.

  3. Comparative analysis of mediastinal fat-associated lymphoid cluster development and lung cellular infiltration in murine autoimmune disease models and the corresponding normal control strains.

    PubMed

    Elewa, Yaser Hosny Ali; Ichii, Osamu; Kon, Yasuhiro

    2016-01-01

    We previously discovered mediastinal fat-associated lymphoid clusters (MFALCs) as novel lymphoid clusters associated with mediastinal fat tissue in healthy mice. However, no data about their morphology in immune-associated disease conditions, and their relationship with lung infiltration, is available to date. In the present study, we compared the morphological features of MFALCs in 4-month-old male murine autoimmune disease models (MRL/MpJ-lpr mice and BXSB/MpJ-Yaa mice) with those of the corresponding control strains (MRL/MpJ and BXSB/MpJ, respectively). In addition, we analysed their correlation with lung infiltration. Furthermore, immunohistochemistry for CD3, B220, Iba1, Gr1 and BrdU was performed to detect T cells and B cells, macrophages, granulocytes and proliferating cells, respectively. The spleen weight to body weight ratios and anti-double-stranded DNA autoantibody titres were found to be significantly higher in the autoimmune models than in the control strains. Furthermore, the autoimmune model presented prominent MFALCs, with a significantly greater ratio of lymphoid cluster area to total mediastinal fat tissue area, and more apparent diffused cellular infiltration into the lung lobes than the other studied strains. Higher numbers of T and B cells, macrophages and proliferating cells, but fewer granulocytes, were observed in the autoimmune models than in the control strains. Interestingly, a significant positive Pearson's correlation between the size of the MFALCs and the density of CD3-, B220- and Iba1-positive cells in the lung was observed. Therefore, our data suggest a potentially important role for MFALCs in the progression of lung disease. However, further investigation is required to clarify the pathological role of MFALCs in lung disease, especially in inflammatory disorders.

  4. 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

  5. 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

  6. 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.

  7. The doubly vergent inverted structures in the Mesozoic basins of northern Chile (28°S): A comparative analysis from field data and analogue modeling

    NASA Astrophysics Data System (ADS)

    Martínez, Fernando; Cristallini, Ernesto

    2017-08-01

    Doubly vergent contractional structures are common features in many regions of the Central Andes. They represent the first-order structural style observed in the inverted Mesozoic basins located along the flat-slab subduction segment of northern Chile. Here, we present a comparative analyses based on geological data previously published and a series of analogue models that were applied to understand the geometry and kinematics of doubly vergent structures related to tectonic inversion, similar to those exposed along the Chanarcillo and Lautaro basins located in northern Chile at 28°S. Our experiments consisted of orthogonal shortening of sand-microbead mixture models located over two pre-existing antithetic master normal faults separated by a structural high to reproduce their tectonic inversion. During the tests, we evaluated the influence of the distance between the master normal faults and synorogenic sedimentation on the final configuration of the doubly vergent structures. The results showed that: a) the tectonic inversion of antithetic normal faults separated by structural highs geometrically reproduce the doubly vergent structures confined to the edge of the Chañarcillo and Lautaro basins. This pre-shortening initial configuration is required to create doubly vergent systems composed of opposite-dipping inverted faults; b) the initial separation distance between the antithetic normal faults strongly influenced the final configuration of the doubly vergent structures during their tectonic inversion. Narrow separations can produce more complex tectonic scenarios; c) the synorogenic sedimentation between the inverted faults can modify the final geometry of the doubly vergent inverted structures, since it allows the shortening to be preferentially accumulated by inversion anticlines. Finally we conclude that although these results can be comparable with the main structures present in the Mesozoic inverted basins of northern Chile, some geological features

  8. Comparative molecular modelling of biologically active sterols

    NASA Astrophysics Data System (ADS)

    Baran, Mariusz; Mazerski, Jan

    2015-04-01

    Membrane sterols are targets for a clinically important antifungal agent - amphotericin B. The relatively specific antifungal action of the drug is based on a stronger interaction of amphotericin B with fungal ergosterol than with mammalian cholesterol. Conformational space occupied by six sterols has been defined using the molecular dynamics method to establish if the conformational features correspond to the preferential interaction of amphotericin B with ergosterol as compared with cholesterol. The compounds studied were chosen on the basis of structural features characteristic for cholesterol and ergosterol and on available experimental data on the ability to form complexes with the antibiotic. Statistical analysis of the data obtained has been performed. The results show similarity of the conformational spaces occupied by all the sterols tested. This suggests that the conformational differences of sterol molecules are not the major feature responsible for the differential sterol - drug affinity.

  9. 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.

  10. Ring current dynamics in moderate and strong storms: Comparative analysis of TWINS and IMAGE/HENA data with the Comprehensive Ring Current Model

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    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.

  11. 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.

  12. 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.

  13. Comparative modeling of UDP-N-acetylmuramoyl-glycyl-D-glutamate-2, 6-diaminopimelate ligase from Mycobacterium leprae and analysis of its binding features through molecular docking studies.

    PubMed

    Shanmugam, Anusuya; Natarajan, Jeyakumar

    2012-01-01

    Leprosy is an infectious disease caused by Mycobacterium leprae. The increasing drug and multi-drug resistance of M. leprae enforce the importance of finding new drug targets. Mycobacterium has unusually impermeable cell wall that contributes to considerable resistance to many drugs. Peptidoglycan is an important component of the cell wall of M. leprae. UDP-N-acetylmuramoyl-glycyl-D-glutamate-2, 6-diaminopimelate ligase (MurE) plays a crucial role in the peptidoglycan biosynthesis and hence it could be considered as a potential drug target for leprosy. Structure of this enzyme for M. leprae has not yet been elucidated. We modeled the three-dimensional structure of MurE from M. leprae using comparative modeling methods based on the X-ray crystal structure of MurE from E. coli and validated. The 3D-structure of M. leprae MurE enzyme was docked with its substrates meso-diaminopimelic acid (A2pm) and UDP-N-acetyl muramoyl-glycyl-D- glutamate (UMGG) and its product UDP-N-acetyl muramoyl-glycyl-D-glu-meso-A(2)pm (UTP) and also with ATP. The docked complexes reveal the amino acids responsible for binding the substrates. Superposition of these complex structures suggests that carboxylic acid group of UMGG is positioned in proximity to γ-phosphate of the ATP to facilitate the formation of acylphosphate intermediate. The orientation of an amino group of A(2)pm facilitates the nucleophilic attack to form the product. Overall, the proposed model together with its binding features gained from docking studies could help to design a truly selective ligand inhibitor specific to MurE for the treatment of leprosy.

  14. 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.

  15. Hawaiian propolis: comparative analysis and botanical origin.

    PubMed

    Inui, Saori; Hosoya, Takahiro; Kumazaw, Shigenori

    2014-02-01

    Propolis is a resinous mixture of substances collected and processed from various botanical sources by honeybees (Apis mellifera). We recently obtained Hawaiian propolis, the study of which, to our knowledge, has not been reported. The purpose of this study was to analyze the composition of Hawaiian propolis and to identify its botanical origin. A comparative analysis of Hawaiian and Okinawan propolis and of the glandular trichomes on Macaranga tanarius fruit (the botanical origin of Okinawan propolis) was performed using reversed-phase high-performance liquid chromatography coupled with high resolution-electrospray mass spectrometry. Hawaiian propolis contained nine prenylflavonoids that were also isolated from Okinawan propolis. In conclusion, we suggest that the botanical origin of Hawaiian propolis is M. tanarius, the same as that of Okinawan propolis.

  16. Comparative Modal Analysis of Sieve Hardware Designs

    NASA Technical Reports Server (NTRS)

    Thompson, Nathaniel

    2012-01-01

    The CMTB Thwacker hardware operates as a testbed analogue for the Flight Thwacker and Sieve components of CHIMRA, a device on the Curiosity Rover. The sieve separates particles with a diameter smaller than 150 microns for delivery to onboard science instruments. The sieving behavior of the testbed hardware should be similar to the Flight hardware for the results to be meaningful. The elastodynamic behavior of both sieves was studied analytically using the Rayleigh Ritz method in conjunction with classical plate theory. Finite element models were used to determine the mode shapes of both designs, and comparisons between the natural frequencies and mode shapes were made. The analysis predicts that the performance of the CMTB Thwacker will closely resemble the performance of the Flight Thwacker within the expected steady state operating regime. Excitations of the testbed hardware that will mimic the flight hardware were recommended, as were those that will improve the efficiency of the sieving process.

  17. 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.

  18. 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.

  19. Drug design using comparative molecular surface analysis.

    PubMed

    Polanski, Jaroslaw

    2006-12-01

    Chemists have eagerly extended a concept of shape into the molecular scale in an attempt to explain molecular effects. Although the molecular surface that shapes a molecule is a fuzzy category, which makes important theoretical problems with its precise interpretation, shape analysis appears to be an efficient method providing an explanation for a variety of effects. Comparative molecular surface analysis (CoMSA) is a three-dimensional quantitative structure-activity relationship (3D QSAR) method used for the comparison of molecular surfaces and shapes. In this review, the authors demonstrate that 3D QSAR basically works as a visualisation tool that investigates molecular similarity and indicates pharmacophoric sites. In this context, CoMSA that is based on the Kohonen self-organising maps that allow the projection of three-dimensional molecular data into two-dimensional maps without topological distortion has an important advantage over the traditional 3D QSAR methods. However, It should be remembered that the majority of the 3D QSAR limitations are still important for this technique and consequently a strategy to use the molecular data to produce drugs in this way still maps a 'far and bumpy road'.

  20. Comparative analysis of the feline immunoglobulin repertoire.

    PubMed

    Steiniger, Sebastian C J; Glanville, Jacob; Harris, Douglas W; Wilson, Thomas L; Ippolito, Gregory C; Dunham, Steven A

    2017-01-25

    Next-Generation Sequencing combined with bioinformatics is a powerful tool for analyzing the large number of DNA sequences present in the expressed antibody repertoire and these data sets can be used to advance a number of research areas including antibody discovery and engineering. The accurate measurement of the immune repertoire sequence composition, diversity and abundance is important for understanding the repertoire response in infections, vaccinations and cancer immunology and could also be useful for elucidating novel molecular targets. In this study 4 individual domestic cats (Felis catus) were subjected to antibody repertoire sequencing with total number of sequences generated 1079863 for VH for IgG, 1050824 VH for IgM, 569518 for VK and 450195 for VL. Our analysis suggests that a similar VDJ expression patterns exists across all cats. Similar to the canine repertoire, the feline repertoire is dominated by a single subgroup, namely VH3. The antibody paratope of felines showed similar amino acid variation when compared to human, mouse and canine counterparts. All animals show a similarly skewed VH CDR-H3 profile and, when compared to canine, human and mouse, distinct differences are observed. Our study represents the first attempt to characterize sequence diversity in the expressed feline antibody repertoire and this demonstrates the utility of using NGS to elucidate entire antibody repertoires from individual animals. These data provide significant insight into understanding the feline immune system function.

  1. 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.

  2. A Comparative Analysis of Biomarker Selection Techniques

    PubMed Central

    Dessì, Nicoletta

    2013-01-01

    Feature selection has become the essential step in biomarker discovery from high-dimensional genomics data. It is recognized that different feature selection techniques may result in different set of biomarkers, that is, different groups of genes highly correlated to a given pathological condition, but few direct comparisons exist which quantify these differences in a systematic way. In this paper, we propose a general methodology for comparing the outcomes of different selection techniques in the context of biomarker discovery. The comparison is carried out along two dimensions: (i) measuring the similarity/dissimilarity of selected gene sets; (ii) evaluating the implications of these differences in terms of both predictive performance and stability of selected gene sets. As a case study, we considered three benchmarks deriving from DNA microarray experiments and conducted a comparative analysis among eight selection methods, representatives of different classes of feature selection techniques. Our results show that the proposed approach can provide useful insight about the pattern of agreement of biomarker discovery techniques. PMID:24324960

  3. 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

  4. 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.

  5. An Orthology-Based Analysis of Pathogenic Protozoa Impacting Global Health: An Improved Comparative Genomics Approach with Prokaryotes and Model Eukaryote Orthologs

    PubMed Central

    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

    2014-01-01

    Abstract A key focus in 21st 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

  6. Diffusion of Innovations model helps interpret the comparative uptake of two methodological innovations: co-authorship network analysis and recommendations for the integration of novel methods in practice.

    PubMed

    Cadarette, Suzanne M; Ban, Joann K; Consiglio, Giulia P; Black, Cody D; Dubins, David; Marin, Alexandra; Tadrous, Mina

    2017-04-01

    The objective of this study was to characterize the diffusion of methodological innovation. Comparative case study analysis of the diffusion of two methods that summarize confounder information into a single score: disease risk score (DRS) and high-dimensional propensity score (hdPS). We completed systematic searches to identify DRS and hdPS papers in the field of pharmacoepidemiology through to the end of 2013, plotted the number of papers and unique authors over time, and created sociograms and animations to visualize co-authorship networks. First and last author affiliations were used to ascribe institutional contributions to each paper and network. We identified 43 DRS papers by 153 authors since 1981, reflecting slow uptake during initial periods of uncertainty and broader diffusion since 2001 linked to early adopters from Vanderbilt. We identified 44 hdPS papers by 147 authors since 2009, reflecting rapid and integrated diffusion, likely facilitated by opinion leaders, early presentation at conferences, easily accessible statistical code, and improvement in funding. Most contributions (87% DRS, 96% hdPS) were from North America. When proposing new methods, authors are encouraged to consider innovation attributes and early evaluation to improve knowledge translation of their innovations for integration into practice, and we provide recommendations for consideration. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  7. 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. Copyright © 2016. Published by Elsevier Ireland Ltd.

  8. 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.

  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. Comparative characterization of the infarcted and reperfused ventricular wall muscles by finite element analysis and a myocardial muscle-blood composite model.

    PubMed

    Pao, Y C; Ritman, E L

    1998-02-01

    Two methods of characterizing the myocardial fiber bundles' property in the left ventricular wall are reviewed: (1) a myocardial muscle-blood composite model which assumes the myocardial muscle bundles to be incompressible but allows the intramural blood volume fraction to be taken into account, and (2) a two-dimensional finite element method for inverse determination of the myocardial Young's modulus during diastole by matching the computed and tomographically imaged cross-sectional areas near the mid-ventricular, short axis of the left ventricle at the end of diastole. The first method requires the measurements of ventricular wall thickness and the intramural blood volume fraction while the second method requires the image cross-sectional shapes and the corresponding left ventricular chamber pressures. This paper gives greater details of these two methods than in the previously presented progress reports and also presents a scheme for comparative characterization of the myocardial properties for an initial coronary artery occlusion and subsequent reperfusion study of the recently infarcted, left-ventricular wall regions. Furthermore, an attempt is made to correlate the data computed by the two methods. This may eventually lead to a reduction in the number of the required measurements needed for the two methods.

  11. Comparative transcriptome analysis of isogenic cell line models and primary cancers links capicua (CIC) loss to activation of the MAPK signalling cascade.

    PubMed

    LeBlanc, Veronique G; Firme, Marlo; Song, Jungeun; Chan, Susanna Y; Lee, Min Hye; Yip, Stephen; Chittaranjan, Suganthi; Marra, Marco A

    2017-06-01

    CIC encodes a transcriptional repressor, capicua (CIC), whose disrupted activity appears to be involved in several cancer types, including type I low-grade gliomas (LGGs) and stomach adenocarcinomas (STADs). To explore human CIC's transcriptional network in an isogenic background, we developed novel isogenic CIC knockout cell lines as model systems, and used these in transcriptome analyses to study the consequences of CIC loss. We also compared our results with analyses of transcriptome data from TCGA for type I LGGs and STADs. We identified 39 candidate targets of CIC transcriptional regulation, and confirmed seven of these as direct targets. We showed that, although many CIC targets appear to be context-specific, the effects of CIC loss converge on the dysregulation of similar biological processes in different cancer types. For example, we found that CIC deficiency was associated with disruptions in the expression of genes involved in cell-cell adhesion, and in the development of several cell and tissue types. We also showed that loss of CIC leads to overexpression of downstream members of the mitogen-activated protein kinase (MAPK) signalling cascade, indicating that CIC deficiency may present a novel mechanism for activation of this oncogenic pathway. © 2017 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland. © 2017 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

  12. Construction of a Seasonal Difference-Geographically and Temporally Weighted Regression (SD-GTWR) Model and Comparative Analysis with GWR-Based Models for Hemorrhagic Fever with Renal Syndrome (HFRS) in Hubei Province (China)

    PubMed Central

    Ge, Liang; Zhao, Youlin; Sheng, Zhongjie; Wang, Ning; Zhou, Kui; Mu, Xiangming; Guo, Liqiang; Wang, Teng; Yang, Zhanqiu; Huo, Xixiang

    2016-01-01

    Hemorrhagic fever with renal syndrome (HFRS) is considered a globally distributed infectious disease which results in many deaths annually in Hubei Province, China. In order to conduct a better analysis and accurately predict HFRS incidence in Hubei Province, a new model named Seasonal Difference-Geographically and Temporally Weighted Regression (SD-GTWR) was constructed. The SD-GTWR model, which integrates the analysis and relationship of seasonal difference, spatial and temporal characteristics of HFRS (HFRS was characterized by spatiotemporal heterogeneity and it is seasonally distributed), was designed to illustrate the latent relationships between the spatio-temporal pattern of the HFRS epidemic and its influencing factors. Experiments from the study demonstrated that SD-GTWR model is superior to traditional models such as GWR- based models in terms of the efficiency and the ability of providing influencing factor analysis. PMID:27801870

  13. Predictive and comparative analysis of Ebolavirus proteins

    PubMed Central

    Cong, Qian; Pei, Jimin; Grishin, Nick V

    2015-01-01

    Ebolavirus is the pathogen for Ebola Hemorrhagic Fever (EHF). This disease exhibits a high fatality rate and has recently reached a historically epidemic proportion in West Africa. Out of the 5 known Ebolavirus species, only Reston ebolavirus has lost human pathogenicity, while retaining the ability to cause EHF in long-tailed macaque. Significant efforts have been spent to determine the three-dimensional (3D) structures of Ebolavirus proteins, to study their interaction with host proteins, and to identify the functional motifs in these viral proteins. Here, in light of these experimental results, we apply computational analysis to predict the 3D structures and functional sites for Ebolavirus protein domains with unknown structure, including a zinc-finger domain of VP30, the RNA-dependent RNA polymerase catalytic domain and a methyltransferase domain of protein L. In addition, we compare sequences of proteins that interact with Ebolavirus proteins from RESTV-resistant primates with those from RESTV-susceptible monkeys. The host proteins that interact with GP and VP35 show an elevated level of sequence divergence between the RESTV-resistant and RESTV-susceptible species, suggesting that they may be responsible for host specificity. Meanwhile, we detect variable positions in protein sequences that are likely associated with the loss of human pathogenicity in RESTV, map them onto the 3D structures and compare their positions to known functional sites. VP35 and VP30 are significantly enriched in these potential pathogenicity determinants and the clustering of such positions on the surfaces of VP35 and GP suggests possible uncharacterized interaction sites with host proteins that contribute to the virulence of Ebolavirus. PMID:26158395

  14. Comparative genomic analysis of the genus Enterococcus.

    PubMed

    Zhong, Zhi; Zhang, Wenyi; Song, Yuqin; Liu, Wenjun; Xu, Haiyan; Xi, Xiaoxia; Menghe, Bilige; Zhang, Heping; Sun, Zhihong

    2017-03-01

    As important lactic acid bacteria, Enterococcus species are widely used in the production of fermented food. However, as some strains of Enterococcus are opportunistic pathogens, their safety has not been generally accepted. In recent years, a large number of new species have been described and classified within the genus Enterococcus, so a better understanding of the genetic relationships and evolution of Enterococcus species is needed. In this study, the genomes of 29 type strains of Enterococcus species were sequenced. In combination with eight complete genome sequences from the Genbank database, the whole genomes of 37 strains of Enterococcus were comparatively analyzed. The average length of Enterococcus genomes was 3.20Mb and the average GC content was 37.99%. The core- and pan- genomes were defined based on the genomes of the 37 strains of Enterococcus. The core-genome contained 605 genes, a large proportion of which were associated with carbohydrate metabolism, protein metabolism, DNA and RNA metabolism. The phylogenetic tree showed that habitat is very important in the evolution of Enterococcus. The genetic relationships were closer in strains that come from similar habitats. According to the topology of the time tree, we found that humans and mammals may be the original hosts of Enterococcus, and then species from humans and mammals made a host-shift to plants, birds, food and other environments. However, it was just an evolutionary scenario, and more data and efforts were needed to prove this postulation. The comparative genomic analysis provided a snapshot of the evolution and genetic diversity of the genus Enterococcus, which paves the way for follow-up studies on its taxonomy and functional genomics. Copyright © 2017 Elsevier GmbH. All rights reserved.

  15. 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.

  16. Comparative genomic analysis of prion genes

    PubMed Central

    Premzl, Marko; Gamulin, Vera

    2007-01-01

    Background The homologues of human disease genes are expected to contribute to better understanding of physiological and pathogenic processes. We made use of the present availability of vertebrate genomic sequences, and we have conducted the most comprehensive comparative genomic analysis of the prion protein gene PRNP and its homologues, shadow of prion protein gene SPRN and doppel gene PRND, and prion testis-specific gene PRNT so far. Results While the SPRN and PRNP homologues are present in all vertebrates, PRND is known in tetrapods, and PRNT is present in primates. PRNT could be viewed as a TE-associated gene. Using human as the base sequence for genomic sequence comparisons (VISTA), we annotated numerous potential cis-elements. The conserved regions in SPRNs harbour the potential Sp1 sites in promoters (mammals, birds), C-rich intron splicing enhancers and PTB intron splicing silencers in introns (mammals, birds), and hsa-miR-34a sites in 3'-UTRs (eutherians). We showed the conserved PRNP upstream regions, which may be potential enhancers or silencers (primates, dog). In the PRNP 3'-UTRs, there are conserved cytoplasmic polyadenylation element sites (mammals, birds). The PRND core promoters include highly conserved CCAAT, CArG and TATA boxes (mammals). We deduced 42 new protein primary structures, and performed the first phylogenetic analysis of all vertebrate prion genes. Using the protein alignment which included 122 sequences, we constructed the neighbour-joining tree which showed four major clusters, including shadoos, shadoo2s and prion protein-likes (cluster 1), fish prion proteins (cluster 2), tetrapode prion proteins (cluster 3) and doppels (cluster 4). We showed that the entire prion protein conformationally plastic region is well conserved between eutherian prion proteins and shadoos (18–25% identity and 28–34% similarity), and there could be a potential structural compatibility between shadoos and the left-handed parallel beta-helical fold

  17. Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species.

    PubMed

    Bräutigam, Andrea; Schliesky, Simon; Külahoglu, Canan; Osborne, Colin P; Weber, Andreas P M

    2014-07-01

    C4 photosynthesis affords higher photosynthetic carbon conversion efficiency than C3 photosynthesis and it therefore represents an attractive target for engineering efforts aiming to improve crop productivity. To this end, blueprints are required that reflect C4 metabolism as closely as possible. Such blueprints have been derived from comparative transcriptome analyses of C3 species with related C4 species belonging to the NAD-malic enzyme (NAD-ME) and NADP-ME subgroups of C4 photosynthesis. However, a comparison between C3 and the phosphoenolpyruvate carboxykinase (PEP-CK) subtype of C4 photosynthesis is still missing. An integrative analysis of all three C4 subtypes has also not been possible to date, since no comparison has been available for closely related C3 and PEP-CK C4 species. To generate the data, the guinea grass Megathyrsus maximus, which represents a PEP-CK species, was analysed in comparison with a closely related C3 sister species, Dichanthelium clandestinum, and with publicly available sets of RNA-Seq data from C4 species belonging to the NAD-ME and NADP-ME subgroups. The data indicate that the core C4 cycle of the PEP-CK grass M. maximus is quite similar to that of NAD-ME species with only a few exceptions, such as the subcellular location of transfer acid production and the degree and pattern of up-regulation of genes encoding C4 enzymes. One additional mitochondrial transporter protein was associated with the core cycle. The broad comparison identified sucrose and starch synthesis, as well as the prevention of leakage of C4 cycle intermediates to other metabolic pathways, as critical components of C4 metabolism. Estimation of intercellular transport fluxes indicated that flux between cells is increased by at least two orders of magnitude in C4 species compared with C3 species. In contrast to NAD-ME and NADP-ME species, the transcription of photosynthetic electron transfer proteins was unchanged in PEP-CK. In summary, the PEP-CK blueprint of M

  18. Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species

    PubMed Central

    Bräutigam, Andrea; Schliesky, Simon; Külahoglu, Canan; Osborne, Colin P.; Weber, Andreas P.M.

    2014-01-01

    C4 photosynthesis affords higher photosynthetic carbon conversion efficiency than C3 photosynthesis and it therefore represents an attractive target for engineering efforts aiming to improve crop productivity. To this end, blueprints are required that reflect C4 metabolism as closely as possible. Such blueprints have been derived from comparative transcriptome analyses of C3 species with related C4 species belonging to the NAD-malic enzyme (NAD-ME) and NADP-ME subgroups of C4 photosynthesis. However, a comparison between C3 and the phosphoenolpyruvate carboxykinase (PEP-CK) subtype of C4 photosynthesis is still missing. An integrative analysis of all three C4 subtypes has also not been possible to date, since no comparison has been available for closely related C3 and PEP-CK C4 species. To generate the data, the guinea grass Megathyrsus maximus, which represents a PEP-CK species, was analysed in comparison with a closely related C3 sister species, Dichanthelium clandestinum, and with publicly available sets of RNA-Seq data from C4 species belonging to the NAD-ME and NADP-ME subgroups. The data indicate that the core C4 cycle of the PEP-CK grass M. maximus is quite similar to that of NAD-ME species with only a few exceptions, such as the subcellular location of transfer acid production and the degree and pattern of up-regulation of genes encoding C4 enzymes. One additional mitochondrial transporter protein was associated with the core cycle. The broad comparison identified sucrose and starch synthesis, as well as the prevention of leakage of C4 cycle intermediates to other metabolic pathways, as critical components of C4 metabolism. Estimation of intercellular transport fluxes indicated that flux between cells is increased by at least two orders of magnitude in C4 species compared with C3 species. In contrast to NAD-ME and NADP-ME species, the transcription of photosynthetic electron transfer proteins was unchanged in PEP-CK. In summary, the PEP-CK blueprint of M

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. Modeller's attitude in catchment modelling: a comparative study

    NASA Astrophysics Data System (ADS)

    Battista Chirico, Giovanni

    2010-05-01

    Ten modellers have been invited to predict, independently from each other, the discharge of the artificial Chicken Creek catchment in North-East Germany for simulation period of three years, providing them only soil texture, terrain and meteorological data. No data concerning the discharge or other sources of state variables and fluxes within the catchment have been provided. Modellers had however the opportunity to visit the experimental catchment and inspect areal photos of the catchments since its initial development stage. This study has been a unique comparative study focussing on how different modellers deal with the key issues in predicting the discharge in ungauged catchments: 1) choice of the model structure; 2) identification of model parameters; 3) identification of model initial and boundary conditions. The first general lesson learned during this study was that the modeller is just part of the entire modelling process and has a major bearing on the model results, particularly in ungauged catchments where there are more degrees of freedom in making modelling decisions. Modellers' attitudes during the stages of the model implementation and parameterisation have been deeply influenced by their own experience from previous modelling studies. A common outcome was that modellers have been mainly oriented to apply process-based models able to exploit the available data concerning the physical properties of the catchment and therefore could be more suitable to cope with the lack of data concerning state variables or fluxes. The second general lesson learned during this study was the role of dominant processes. We believed that the modelling task would have been much easier in an artificial catchment, where heterogeneity were expected to be negligible and processes simpler, than in catchments that have evolved over a longer time period. The results of the models were expected to converge, and this would have been a good starting point to proceed for a model

  4. Allograft materials in phalloplasty: a comparative analysis.

    PubMed

    Solomon, Mark P; Komlo, Caroline; Defrain, Molly

    2013-09-01

    Allograft use has increased recently with the rising use of allograft materials in breast surgery. There are few data that compare the performance of the various allograft materials in this application, despite marketing efforts by the manufacturers to present one allograft material as superior to another. Phalloplasty is a procedure that uses allografts for penis girth augmentation. Preparation of these grafts differs with each manufacturer. We report our experience with 3 different types of allografts for this procedure. This allows for the comparison of these materials in their performance with a single model. Forty-seven patients who underwent penis girth enhancement with allograft material were reviewed. All patients underwent circumferential grafting to the shaft of the penis at the level of Buck's fascia. Graft materials included AlloDerm (n = 9), Belladerm (n = 20), and Repriza (n = 21). Charts were reviewed for material type, presence and type of infection, wound exposure, and graft loss with attention to the type of allograft material that was used. Follow-up ranged from 1 to 120 months with an average of 11.25 months. Infection, defined as an open wound with graft exposure, occurred in 20 (42%) of 47 patients. Of these, graft exposure only occurred in 17 (36%) patients, whereas 3 (6%) patients sustained total graft loss. Graft exposure or loss occurred in 3 patients who had AlloDerm, 9 patients with Belladerm, and 8 patients with Repriza. No patients with AlloDerm sustained graft loss, whereas 2 patients with Belladerm and 1 patient with Repriza sustained graft loss. There were no statistical differences among these graft types with regard to infection or graft loss. Three different brands of allograft material were used in 1 surgical procedure and followed up for their performance with regard to exposure and infection. In this model, there is no difference in the rate of infection in these materials despite their different methods of preparation

  5. [Comparative analysis of 3D data visibility of the prepared tooth finishing line on a synthetic jaw model, captured by international scanners in a laboratory conditions].

    PubMed

    Ryakhovsky, A N; Kostyukova, V V

    The aim of the study was to compare accuracy of digital impression's finishing line and the zone under it taken by different intraoral scanning systems. Parameters of comparison were: different level of the finishing line to the gingiva and width of sulcus after retraction. For this purpose two synthetic jaw models with prepared teeth were scanned using intraoral scanning systems: 3D Progress (MHT S.P.A., IT - MHT Optic Research AG, CH); True Definition (3M ESPE, USA); Trios (3Shape A/S, DNK); CEREC AC Bluecam, CEREC Omnicam (Sirona Dental System GmbH, DE); Planscan (Planmeca, FIN) (each n=10). Reference-scanning was done by ATOS Core (GOM mbH, DE). The resulting digital impressions were superimposed with the master-scan. The lowest measured deviations (trueness) for intraoral scanners, where the finishing line was 0.5 mm above gingiva were with scanner True Definition - 18.8±6.63 (on the finishing line) and 51.0±14.33 µm (0.3 mm under the finishing line). In conditions where finishing line was on the same level with gingiva, scanner Trios showed the best results: 17.0±3.96 and 52.7±6.52 µm. When the finishing line was 0.5 mm under gingiva, none of the testing scanners could visualize the zone 0.3 mm lower the finishing line. The best results for accuracy o the finishing line in that circumstances showed Trios: 15.1±5.05 µm. The optimum visualization of the finishing line and the zone under it was reached when the sulcus was 0.3 mm after retraction. Thus, the best accuracy was obtained with Trios: 10.3±2.69 (on the finishing line) and 57.2±13.58 µm (0.3 mm under finishing line). The results show that intraoral scanners also provide enough accuracy for indicating finishing line and the zone under it in different conditions of preparation and gingiva retraction. However, not all of the testing scanners can properly indicate finishing line and the zone under it when shoulder is below gingiva and the width of sulcus is less than 0.2 mm.

  6. Antibodies as a model system for comparative model refinement

    PubMed Central

    Sellers, Benjamin D.; Nilmeier, Jerome P.; Jacobson, Matthew P.

    2010-01-01

    Predicting the conformations of loops is a critical aspect of protein comparative (“homology”) modeling. Despite considerable advances in developing loop prediction algorithms, refining loops in homology models remains challenging. In this work, we use antibodies as a model system to investigate strategies for more robustly predicting loop conformations when the protein model contains errors in the conformations of side chains and protein backbone surrounding the loop in question. Specifically, our test system consists of partial models of antibodies in which the “scaffold” (i.e., the portion other than the complementarity determining region, CDR, loops) retains native backbone conformation, while the CDR loops are predicted using a combination of knowledge-based modeling (H1, H2, L1, L2, and L3) and ab initio loop prediction (H3). H3 is the most variable of the CDRs. Using a previously published method, a test set of 10 shorter H3 loops (5–7 residues) are predicted to an average backbone (N-Cα-C-O) RMSD of 2.7 Å while 11 longer loops (8-9 residues) are predicted to 5.1 Å, thus recapitulating the difficulties in refining loops in models. By contrast, in control calculations predicting the same loops in crystal structures, the same method reconstructs the loops to an average of 0.5 Å and 1.4 Å for the shorter and longer loops, respectively. We modify the loop prediction method to improve the ability to sample near-native loop conformations in the models, primarily by reducing the sensitivity of the sampling to the loop surroundings, and allowing the other CDR loops to optimize with the H3 loop. The new method improves the average accuracy significantly to 1.3 Å RMSD and 3.1 Å RMSD for the shorter and longer loops, respectively. Finally, we present results predicting 8-10 residue loops within complete comparative models of five non-antibody proteins. While anecdotal, these mixed, full-model results suggest our approach is a promising step towards

  7. 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.; hide

    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.

  8. Image Analysis and Modeling

    DTIC Science & Technology

    1976-03-01

    This report summarizes the results of the research program on Image Analysis and Modeling supported by the Defense Advanced Research Projects Agency...The objective is to achieve a better understanding of image structure and to use this knowledge to develop improved image models for use in image ... analysis and processing tasks such as information extraction, image enhancement and restoration, and coding. The ultimate objective of this research is

  9. Comparative Analysis of Hepatic CD14 Expression between Two Different Endotoxin Shock Model Mice: Relation between Hepatic Injury and CD14 Expression

    PubMed Central

    Hozumi, Hiroyasu; Tada, Rui; Murakami, Taisuke; Adachi, Yoshiyuki; Ohno, Naohito

    2013-01-01

    CD14 is a glycoprotein that recognizes gram-negative bacterial lipopolysaccharide (LPS) and exists in both membrane-bound and soluble forms. Infectious and/or inflammatory diseases induce CD14 expression, which may be involved in the pathology of endotoxin shock. We previously found that the expression of CD14 protein differs among the endotoxin shock models used, although the reasons for these differences are unclear. We hypothesized that the differences in CD14 expression might be due to liver injury, because the hepatic tissue produces CD14 protein. We investigated CD14 expression in the plasma and liver in the carrageenan (CAR)-primed and D-galN-primed mouse models of endotoxin shock. Our results showed that severe liver injury was not induced in CAR-primed endotoxin shock model mice. In this CAR-primed model, the higher mRNA and protein expression of CD14 was observed in the liver, especially in the interlobular bile duct in contrast to D-galN-primed-endotoxin shock model mice. Our findings indicated that the molecular mechanism(s) underlying septic shock in CAR-primed and D-galN-primed endotoxin shock models are quite different. Because CD14 expression is correlated with clinical observations, the CAR-primed endotoxin shock model might be useful for studying the functions of CD14 during septic shock in vivo. PMID:23308276

  10. 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.

  11. 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…

  12. 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…

  13. 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…

  14. 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…

  15. 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...

  16. 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...

  17. 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…

  18. 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.

  19. Comparative 3-D modeling of tmRNA.

    PubMed

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

    2005-06-15

    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. 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. 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.

  20. Question analysis for Indonesian comparative question

    NASA Astrophysics Data System (ADS)

    Saelan, A.; Purwarianti, A.; Widyantoro, D. H.

    2017-01-01

    Information seeking is one of human needs today. Comparing things using search engine surely take more times than search only one thing. In this paper, we analyzed comparative questions for comparative question answering system. Comparative question is a question that comparing two or more entities. We grouped comparative questions into 5 types: selection between mentioned entities, selection between unmentioned entities, selection between any entity, comparison, and yes or no question. Then we extracted 4 types of information from comparative questions: entity, aspect, comparison, and constraint. We built classifiers for classification task and information extraction task. Features used for classification task are bag of words, whether for information extraction, we used lexical, 2 previous and following words lexical, and previous label as features. We tried 2 scenarios: classification first and extraction first. For classification first, we used classification result as a feature for extraction. Otherwise, for extraction first, we used extraction result as features for classification. We found that the result would be better if we do extraction first before classification. For the extraction task, classification using SMO gave the best result (88.78%), while for classification, it is better to use naïve bayes (82.35%).

  1. Comparative analysis and visualization of multiple collinear genomes

    PubMed Central

    2012-01-01

    Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

  2. 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.

  3. Comparative analysis for evaluating the traceability of interventional devices using blood vessel phantom models made of PVA-H or silicone.

    PubMed

    Yu, Chang-Ho; Kwon, Tae-Kyu; Park, Chan Hee; Ohta, Makoto; Kim, Sung Hoon

    2015-01-01

    In this paper, we investigated the parameters with effective traceability to assess the mechanical properties of interventional devices. In our evaluation system, a box-shaped poly (vinyl alcohol) hydrogel (PVA-H) and silicone were prepared with realistic geometry, and the measurement and evaluation of traceability were carried out on devices using load hand force. The phantom models had a total of five curve pathways to reach the aneurysm sac. Traceability depends on the performance of the interventional devices in order to pass through the curved part of the model simulation track. The traceability of the guide wire was found to be much better than that of the balloon and stent loading catheter, as it reached the aneurysm sac in both phantom models. Observation using the video record is another advantage of our system, because the high transparency of the materials with silicone and PVA-H can allow visualization of the inside of an artery.

  4. 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

  5. Spontaneous remission from the problematic use of substances: an inductive model derived from a comparative analysis of the alcohol, opiate, tobacco, and food/obesity literatures.

    PubMed

    Stall, R; Biernacki, P

    1986-01-01

    Despite obvious theoretical and treatment implications, the study of how individuals end the "compulsive" use of substances without formal treatment ("spontaneous remission") remains a relatively neglected topic. This paper reviews the literature germane to spontaneous remission from four substances (opiates, alcohol, food/obesity, and tobacco) selected for their widely variant meanings within the mainstream North American culture. Common processes important to spontaneous remission from these four substances are identified and form the basis of an inductively derived model of spontaneous remission behavior. This model, relevant to interactionist theory, is offered for further, empirical testing.

  6. 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.

  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. 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 ...

  9. 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 ...

  10. Performance of several Saccharomyces strains for the alcoholic fermentation of sugar-sweetened high-strength wastewaters: Comparative analysis and kinetic modelling.

    PubMed

    Comelli, Raúl N; Seluy, Lisandro G; Isla, Miguel A

    2016-12-25

    This work focuses on the performance of ten commercial Saccharomyces yeast strains in the batch alcoholic fermentation of sugars contained in selected industrial wastewaters from the soft drink industry. Fermentation has been applied successfully to treat these effluents prior to their disposal. Although many strains were investigated, similar behaviour was observed between all of the Saccharomyces strains tested. When media were inoculated with 2gL(-1) of yeast, all strains were able to completely consume the available sugars in less than 14h. Thus, any of the strains studied in this work could be used in non-conventional wastewater treatment processes based on alcoholic fermentation. However, ethanol production varied between strains, and these differences could be significant from a production point of view. Saccharomyces bayanus produced the most ethanol, with a mean yield of 0.44gethanolgsugarconsumed(-1) and an ethanol specific production rate of 5.96gethanol (Lh)(-1). As the assayed soft drinks wastewaters contain about 105gsugar/L of fermentable sugars, the concentration of ethanol achieved after the fermentations process was 46.2gethanol/L. A rigorous kinetic modelling methodology was used to model the Saccharomyces bayanus fermentation process. The kinetic model included coupled mass balances and a minimal number of parameters. A simple unstructured model based on the Andrews equation (substrate inhibition) was developed. This model satisfactorily described biomass growth, sugar consumption and bioethanol production. In addition to providing insights into the fermentative performance of potentially relevant strains, this work can facilitate the design of large-scale ethanol production processes that use wastewaters from the sugar-sweetened beverage industry as feedstock.

  11. Impact of a Novel, Anti-microbial Dressing on In Vivo, Pseudomonas aeruginosa Wound Biofilm: Quantitative Comparative Analysis using a Rabbit Ear Model

    DTIC Science & Technology

    2014-12-01

    Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China, and 3. Microbiology Branch, US Army Dental and...planktonic S. aureus within the wounds. Dressing materials Wounds were subject to one of three dressings during the study (Table 1). Telfa AMD was...quantification of epithelial and granulation gaps, and total epithelial and granulation areas, using a digital analysis system (NIS-Elements Basic Research, Nikon

  12. 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…

  13. Comparative QSAR analysis of cyclo-oxygenase2 inhibiting drugs.

    PubMed

    Mohanapriya, Arumugam; Achuthan, Dayalan

    2012-01-01

    Cyclo-oxygenase 2 (COX2) inhibiting drugs were subjected to comparative quantitative structure activity relationship (QSAR) analysis with an attempt to derive and to understand the relationship between the biological activity and molecular descriptors by multiple regression analysis. The different drugs that inhibit cyclo-oxygenase 2 enzyme were compared instead of subjecting one drug and its derivatives to QSAR analysis. The study was conducted to look for the common structural features between the drugs which confer to a good biological activity. Based on the regression analysis the following descriptors were finalized as the components fitting best in the regression equations: Ss, SCBO, RBN, nN, SIC0, IC1, and H-055. These descriptors belong to constitution (Ss, SCBO, RBN, nN), information indices (SIC0, IC1) and atom centered fragments (H-055) category. Based on these descriptors QSAR models were generated and evaluated for best structure-activity correlation. The model generated from constitution and information indices descriptors corresponds to the essential structural features of the drugs and are found to have significant correlation with COX2 inhibiting activity. This study shall help in rational drug design and synthesis of new selective cyclo-oxygenase 2 inhibitors with predetermined affinity and activity.

  14. A comparative study of mixture cure models with covariate

    NASA Astrophysics Data System (ADS)

    Leng, Oh Yit; Khalid, Zarina Mohd

    2017-05-01

    In survival analysis, the survival time is assumed to follow a non-negative distribution, such as the exponential, Weibull, and log-normal distributions. In some cases, the survival time is influenced by some observed factors. The absence of these observed factors may cause an inaccurate estimation in the survival function. Therefore, a survival model which incorporates the influences of observed factors is more appropriate to be used in such cases. These observed factors are included in the survival model as covariates. Besides that, there are cases where a group of individuals who are cured, that is, not experiencing the event of interest. Ignoring the cure fraction may lead to overestimate in estimating the survival function. Thus, a mixture cure model is more suitable to be employed in modelling survival data with the presence of a cure fraction. In this study, three mixture cure survival models are used to analyse survival data with a covariate and a cure fraction. The first model includes covariate in the parameterization of the susceptible individuals survival function, the second model allows the cure fraction to depend on covariate, and the third model incorporates covariate in both cure fraction and survival function of susceptible individuals. This study aims to compare the performance of these models via a simulation approach. Therefore, in this study, survival data with varying sample sizes and cure fractions are simulated and the survival time is assumed to follow the Weibull distribution. The simulated data are then modelled using the three mixture cure survival models. The results show that the three mixture cure models are more appropriate to be used in modelling survival data with the presence of cure fraction and an observed factor.

  15. 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…

  16. 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.

  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. 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

  19. Comparative Analysis of Monographic Collections in Nursing.

    ERIC Educational Resources Information Center

    Bowden, Virginia M.; And Others

    The results of a project comparing the nursing monograph collections of academic health science center libraries in the Southwest are reported. Records for nursing monographs from the TALON (South Central Regional Medical Library Program) Union Catalog of Monographs from 1977-1983 were analyzed to reveal the distribution by year, publisher, and…

  20. A Comparative Analysis of Teacher Ethnotheories.

    ERIC Educational Resources Information Center

    Akkari, Abdeljalil; Serpell, Robert; Baker, Linda; Sonnenschein, Susan

    1998-01-01

    Compared the beliefs of African-American (AA) and European-American (EA) elementary teachers about teaching and literacy development. Teacher interviews found no differences in child development perceptions and approaches to literacy. AA teachers placed more emphasis on the themes of universal educability and teacher responsibility, while EA…

  1. Comparative Naval Architecture Analysis of Diesel Submarines

    DTIC Science & Technology

    2005-06-01

    mission, cost, or other factors affect the architecture? This study examines and compares the naval architecture of selected diesel submarines from...79 A ppendix E : Subm arine Shape Factors ................................................................................... 90 5 List of...country. Do factors such as mission, cost, or tradition 10 affect submarine naval architecture? An in depth comparison is performed of six diesel

  2. 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.

  3. 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.

  4. A multi-template combination algorithm for protein comparative modeling

    PubMed Central

    Cheng, Jianlin

    2008-01-01

    Background Multiple protein templates are commonly used in manual protein structure prediction. However, few automated algorithms of selecting and combining multiple templates are available. Results Here we develop an effective multi-template combination algorithm for protein comparative modeling. The algorithm selects templates according to the similarity significance of the alignments between template and target proteins. It combines the whole template-target alignments whose similarity significance score is close to that of the top template-target alignment within a threshold, whereas it only takes alignment fragments from a less similar template-target alignment that align with a sizable uncovered region of the target. We compare the algorithm with the traditional method of using a single top template on the 45 comparative modeling targets (i.e. easy template-based modeling targets) used in the seventh edition of Critical Assessment of Techniques for Protein Structure Prediction (CASP7). The multi-template combination algorithm improves the GDT-TS scores of predicted models by 6.8% on average. The statistical analysis shows that the improvement is significant (p-value < 10-4). Compared with the ideal approach that always uses the best template, the multi-template approach yields only slightly better performance. During the CASP7 experiment, the preliminary implementation of the multi-template combination algorithm (FOLDpro) was ranked second among 67 servers in the category of high-accuracy structure prediction in terms of GDT-TS measure. Conclusion We have developed a novel multi-template algorithm to improve protein comparative modeling. PMID:18366648

  5. Comparative analysis of the spatial analysis methods for hotspot identification.

    PubMed

    Yu, Hao; Liu, Pan; Chen, Jun; Wang, Hao

    2014-05-01

    Spatial analysis technique has been introduced as an innovative approach for hazardous road segments identification (HRSI). In this study, the performance of two spatial analysis methods and four conventional methods for HRSI was compared against three quantitative evaluation criteria. The spatial analysis methods considered in this study include the local spatial autocorrelation method and the kernel density estimation (KDE) method. It was found that the empirical Bayesian (EB) method and the KDE method outperformed other HRSI approaches. By transferring the kernel density function into a form that was analogous to the form of the EB function, we further proved that the KDE method can eventually be considered a simplified version of the EB method in which crashes reported at neighboring spatial units are used as the reference population for estimating the EB-adjusted crashes. Theoretically, the KDE method may outperform the EB method in HRSI when the neighboring spatial units provide more useful information on the expected crash frequency than a safety performance function does. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Comparative analysis of binding affinities to epidermal growth factor receptor of monoclonal antibodies nimotuzumab and cetuximab using different experimental animal models.

    PubMed

    Ledón, N; Casacó, A; Casanova, E; Beausoleil, I

    2011-07-01

    Although pharmaco/toxicological studies have always been conducted in pharmacologically relevant species in which the test material is pharmacologically active, the very specificity of many biopharmaceuticals could present challenges in the identification of a relevant species for pharmaco/toxicological studies. Alternative approaches may improve the predictive value of preclinical assessments of species-specific biopharmaceuticals. This could lead to improved decision-making, reduce the number of experimental animals by eliminating non-relevant studies, and decrease the time and cost involved in the drug development process. As an alternative to utilizing traditional animal models, this study investigated the activity of human EGF and the anti-EGF receptor monoclonal antibodies nimotuzumab and cetuximab using the placenta microsomal fraction of different experimental animals. Ligand-receptor binding curves were obtained from the different experimental animal models, and binding constants were calculated based on the Scatchard plots. The constants for human and monkey EGF receptor expressed on the placental extract showed a K(a)<10(-8)M, while rabbits, mice and rats showed a K(a)>10(-8)M. The K(a) values obtained from animal placentas show that Macaca fascicularis and Cercopitecus aethiops monkeys are relevant species for studying the pharmaco/toxicological properties of nimotuzumab and cetuximab.

  7. A comparative study of two statistical approaches for the analysis of real seismicity sequences and synthetic seismicity generated by a stick-slip experimental model

    NASA Astrophysics Data System (ADS)

    Flores-Marquez, Leticia Elsa; Ramirez Rojaz, Alejandro; Telesca, Luciano

    2015-04-01

    The study of two statistical approaches is analyzed for two different types of data sets, one is the seismicity generated by the subduction processes occurred at south Pacific coast of Mexico between 2005 and 2012, and the other corresponds to the synthetic seismic data generated by a stick-slip experimental model. The statistical methods used for the present study are the visibility graph in order to investigate the time dynamics of the series and the scaled probability density function in the natural time domain to investigate the critical order of the system. This comparison has the purpose to show the similarities between the dynamical behaviors of both types of data sets, from the point of view of critical systems. The observed behaviors allow us to conclude that the experimental set up globally reproduces the behavior observed in the statistical approaches used to analyses the seismicity of the subduction zone. The present study was supported by the Bilateral Project Italy-Mexico Experimental Stick-slip models of tectonic faults: innovative statistical approaches applied to synthetic seismic sequences, jointly funded by MAECI (Italy) and AMEXCID (Mexico) in the framework of the Bilateral Agreement for Scientific and Technological Cooperation PE 2014-2016.

  8. Comparative Analysis of Treatment Costs in EUROHOPE.

    PubMed

    Iversen, Tor; Aas, Eline; Rosenqvist, Gunnar; Häkkinen, Unto

    2015-12-01

    This study examines the challenges of estimating risk-adjusted treatment costs in international comparative research, specifically in the European Health Care Outcomes, Performance, and Efficiency (EuroHOPE) project. We describe the diverse format of resource data and challenges of converting these data into resource use indicators that allow meaningful cross-country comparisons. The three cost indicators developed in EuroHOPE are then described, discussed, and applied. We compare the risk-adjusted mean treatment costs of acute myocardial infarction for four of the seven countries in the EuroHOPE project, namely, Finland, Hungary, Norway, and Sweden. The outcome of the comparison depends on the time perspective as well as on the particular resource use indicator. We argue that these complementary indicators add to our understanding of the variation in resource use across countries.

  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. A Comparative Analysis of Reinforcement Learning Methods

    DTIC Science & Technology

    1991-10-01

    reinforcement learning for both programming and adapting situated agents. In the first part of the paper we discuss two specific reinforcement learning algorithms: Q-learning and the Bucket Brigade. We introduce a special case of the Bucket Brigade, and analyze and compare its performance to Q-learning in a number of experiments. The second part of the paper discusses the key problems of reinforcement learning : time and space complexity, input generalization, sensitivity to parameter values, and selection of the reinforcement

  11. STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION.

    PubMed

    Hansen, Thomas F

    1997-10-01

    Comparative studies tend to differ from optimality and functionality studies in how they treat adaptation. While the comparative approach focuses on the origin and change of traits, optimality studies assume that adaptations are maintained at an optimum by stabilizing selection. This paper presents a model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force. Interspecific variation is treated as variation in the position of adaptive optima. The model illustrates how phylogenetic constraints not only lead to correlations between phylogenetically related species, but also to imperfect adaptations. From this model, a statistical comparative method is derived that can be used to estimate the effect of a selective factor on adaptive optima in a way that would be consistent with an optimality study of adaptation to this factor. The method is illustrated with an analysis of dental evolution in fossil horses. The use of comparative methods to study evolutionary trends is also discussed. © 1997 The Society for the Study of Evolution.

  12. 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.

  13. 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)

  14. Comparing prediction models for radiographic exposures

    NASA Astrophysics Data System (ADS)

    Ching, W.; Robinson, J.; McEntee, M. F.

    2015-03-01

    During radiographic exposures the milliampere-seconds (mAs), kilovoltage peak (kVp) and source-to-image distance can be adjusted for variations in patient thicknesses. Several exposure adjustment systems have been developed to assist with this selection. This study compares the accuracy of four systems to predict the required mAs for pelvic radiographs taken on a direct digital radiography system (DDR). Sixty radiographs were obtained by adjusting mAs to compensate for varying combinations of source-to-image distance (SID), kVp and patient thicknesses. The 25% rule, the DuPont Bit System and the DigiBit system were compared to determine which of these three most accurately predicted the mAs required for an increase in patient thickness. Similarly, the 15% rule, the DuPont Bit System and the DigiBit system were compared for an increase in kVp. The exposure index (EI) was used as an indication of exposure to the DDR. For each exposure combination the mAs was adjusted until an EI of 1500+/-2% was achieved. The 25% rule was the most accurate at predicting the mAs required for an increase in patient thickness, with 53% of the mAs predictions correct. The DigiBit system was the most accurate at predicting mAs needed for changes in kVp, with 33% of predictions correct. This study demonstrated that the 25% rule and DigiBit system were the most accurate predictors of mAs required for an increase in patient thickness and kVp respectively. The DigiBit system worked well in both scenarios as it is a single exposure adjustment system that considers a variety of exposure factors.

  15. Comparative Analysis of National Legislation in Support of the Revised International Health Regulations: Potential Models for Implementation in the United States

    PubMed Central

    Kornblet, Sarah

    2010-01-01

    In 2005, the World Health Organization adopted the revised International Health Regulations, or IHR (2005), to establish obligations for detecting and responding to public health emergencies of international concern. The success of the IHR (2005) rests on the ability of states to implement the objectives and to execute the regulations in a legal and politically acceptable manner. Implementation of the IHR (2005) may be challenging for federalist nations, where most public health regulatory power lies in local rather than in national governments. We examine the implementation strategies of 4 nations: Australia, Canada, Germany, and India. The methods currently being considered by these nations for executing the IHR (2005) are potentially applicable models for the United States to consider. PMID:20966376

  16. Fos and pERK immunoreactivity in spinal cord slices: Comparative analysis of in vitro models for testing putative antinociceptive molecules.

    PubMed

    Ferrini, Francesco; Russo, Arianna; Salio, Chiara

    2014-07-01

    To detect central neuron activation, expression of the transcription factor Fos and phosphorylation of the protein kinase ERK (pERK) can be visualized by immunocytochemistry. These approaches have been extensively used to quantify the activation of nociceptive neurons in the spinal dorsal horn (DH) following peripheral stimulation in vivo. Here we propose an alternative and simplified in vitro model to investigate Fos and pERK expression based on the stimulation of acutely dissected spinal cord slices to mimic acute inflammatory changes in DH. Transverse slices were obtained from postnatal (P8-P12) CD1 mice and were treated for 5 min with capsaicin (CAP, 2 μM). CAP induces a strong release of glutamate from primary afferent terminals which, in turn, excites spinal DH neurons. Since ERK phosphorylation and Fos expression occur following different time frames, two distinct protocols were used to detect their activation. Thus, for studying Fos immunoreactivity CAP-treated slices were left for 3h in Krebs solution after stimulation. Instead, for studying pERK immunoreactivity slices were maintained in Krebs solution for only 15 min after stimulation. Both Fos and pERK were significantly up-regulated following CAP challenge. To validate our model we tested the efficacy of octreotide (OCT, 1 μM) in preventing the CAP effect on Fos and pERK expression. OCT is a synthetic antinociceptive analog of somatostatin, one of the neuropeptides involved in the negative modulation of pain signals in DH. After CAP, OCT reduced the response to both Fos and pERK. Our data validate the use of Fos and pERK immunoreactivity in vitro to investigate the activation of spinal nociceptive pathways and testing potentially antinociceptive molecules.

  17. [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.

  18. 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

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

    DOE PAGES

    Faria, José P.; Edirisinghe, Janaka N.; Davis, James J.; ...

    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

  20. Cost-effectiveness of insulin detemir compared to NPH insulin for type 1 and type 2 diabetes mellitus in the Canadian payer setting: modeling analysis.

    PubMed

    Tunis, Sandra L; Minshall, Michael E; Conner, Christopher; McCormick, John I; Kapor, Jovana; Yale, Jean-François; Groleau, Danielle

    2009-05-01

    This study was conducted to quantify the long-term cost-effectiveness of insulin detemir (Levemir) versus intermediate-acting neutral protamine Hagedorn (NPH) insulin for the treatment of type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM) in Canada, and to assess the sensitivity of results to dis-utilities for hypoglycemic events. dagger Levemir is a trade name of Novo Nordisk, Princeton, NJ, USA RESEARCH DESIGN AND METHODS: The web-based IMS-CORE diabetes model has a menu-driven interface programmed in hypertext markup language (HTML). It was used to project lifetime (60 years for T1DM and 35 years for T2DM) clinical and economic outcomes for patients on detemir vs. NPH. Cohort characteristics, utilities, and costs were derived from published literature. For T1DM, clinical trial data for HbA(1c) improvement (detemir -0.94% +/- 1.07; NPH -0.82% +/- 1.01) from baseline, and rates of hypoglycemic events (major events: 0.20 vs. 0.80 per patient-year for detemir vs. NPH, respectively) were modeled. For T2DM, observational study data for HbA(1c) improvement (detemir -0.18%) from baseline, and reductions in hypoglycemic events (major events: 0.0995 vs. 1.33 per patient-year for detemir vs. NPH, respectively) were modeled. Base-case hypoglycemia dis-utilities were -0.0118 for major and -0.0035 for minor events. Sensitivity analyses were conducted on discount rate and hypoglycemia dis-utility. Outcomes included costs of treatment/management and costs (and incidence) of diabetes-related complications. Incremental cost-effectiveness ratios (ICERs) were calculated from differences in total costs and quality-adjusted life-years (QALYs). Average total costs for T1DM were $CAN 83 622 +/- 4585 for detemir and $CAN 72 016 +/- 4593 for NPH. QALYs increased by 0.475 years with detemir, with an ICER of $CAN 24 389/QALY. Average direct costs for T2DM were $CAN 74 919 +/- 6391 (detemir) and $CAN 69 230 +/- 6840 (NPH). QALYs increased by 0.305 years. The ICER was $CAN

  1. De novo transcriptome sequencing and comparative analysis of midgut tissues of four non-model insects pertaining to Hemiptera, Coleoptera, Diptera and Lepidoptera.

    PubMed

    Gazara, Rajesh K; Cardoso, Christiane; Bellieny-Rabelo, Daniel; Ferreira, Clélia; Terra, Walter R; Venancio, Thiago M

    2017-09-05

    Despite the great morphological diversity of insects, there is a regularity in their digestive functions, which is apparently related to their physiology. In the present work we report the de novo midgut transcriptomes of four non-model insects from four distinct orders: Spodoptera frugiperda (Lepidoptera), Musca domestica (Diptera), Tenebrio molitor (Coleoptera) and Dysdercus peruvianus (Hemiptera). We employed a computational strategy to merge assemblies obtained with two different algorithms, which substantially increased the quality of the final transcriptomes. Unigenes were annotated and analyzed using the eggNOG database, which allowed us to assign some level of functional and evolutionary information to 79.7% to 93.1% of the transcriptomes. We found interesting transcriptional patterns, such as: i) the intense use of lysozymes in digestive functions of M. domestica larvae, which are streamlined and adapted to feed on bacteria; ii) the up-regulation of orthologous UDP-glycosyl transferase and cytochrome P450 genes in the whole midguts different species, supporting the existence of an ancient defense frontline to counter xenobiotics; iii) evidence supporting roles for juvenile hormone binding proteins in the midgut physiology, probably as a way to activate genes that help fight anti-nutritional substances (e.g. protease inhibitors). The results presented here shed light on the digestive and structural properties of the digestive systems of these distantly related species. Furthermore, the produced datasets will also be useful for scientists studying these insects. Copyright © 2017. Published by Elsevier B.V.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Nutrient profiling schemes: overview and comparative analysis.

    PubMed

    Garsetti, Marcella; de Vries, Jan; Smith, Maurice; Amosse, Amélie; Rolf-Pedersen, Nathalie

    2007-12-01

    Nutrient profiling is a discipline aimed at classifying foods based on their nutritional composition. So far, several profiling schemes have been proposed for varied purposes world-wide. Primary aim to inventory the main profiling schemes that have been developed so far (both applied and not) and to summarise their main aspects. Secondary aim to critically review a selection of them, to test their "performance" and to evaluate their strengths and weaknesses. Scientific and popular search engines were used for identifying profiling schemes. Schemes were described concisely by providing details on four main "Building Blocks" or factors: (1) Food category declination: category-wise or "across the board"; (2) Reference amount: 100 g, 100 kcal; serving; (3) Cut-off use: thresholds or scores; (4) Nutrients Selection: balance between positive and negative nutrients and number of them. The "performance" analysis was done by testing how the selected schemes classify a sample of food. Profiling schemes display considerable variation based on the underlying approach, format and content. Moreover, the rationale of the schemes largely varies and seems to be inspired by either nutrient recommendations or regulations figures. When tested for "performance", the five selected schemes classify in the same way foods having either a very "positive" or a very "negative" nutrient profile, whereas they give inconsistent results for food products with intermediate characteristics. Strengths and weaknesses analysis shows the difficulty of finding schemes combining qualities such as simplicity, scientific relevance, ability to cope with changes in nutrient recommendations. Current proposed profiling schemes exhibit a wide range of differences both in terms of approaches and "performance". Nutrition scientists have now the challenge to develop the "ideal scheme" that, in our view, will have to be strict enough to ensure consumer protection but also flexible enough to encourage food industry

  9. Comparative analysis of Debrecen sunspot catalogues

    NASA Astrophysics Data System (ADS)

    Győri, L.; Ludmány, A.; Baranyi, T.

    2017-02-01

    Sunspot area data are important for studying solar activity and its long-term variations. At the Debrecen Heliophysical Observatory, we compiled three sunspot catalogues: the Debrecen Photoheliographic Data (DPD), the SDO/HMI Debrecen Data (HMIDD) and the SOHO/MDI Debrecen Data. For comparison, we also compiled an additional sunspot catalogue, the Greenwich Photoheliographic Data, from the digitized Royal Greenwich Observatory images for 1974-76. By comparing these catalogues when they overlap in time, we can investigate how various factors influence the measured area of sunspots, and, in addition, we can derive area cross-calibration factors for these catalogues. The main findings are as follows. Poorer seeing increases the individual corrected spot areas and decreases the number of small spots. Interestingly, the net result of these two effects for the total corrected spot area is zero. DPD daily total corrected sunspot areas are 5 per cent smaller than the HMIDD ones. Revised DPD daily total corrected umbra areas are 9 per cent smaller than those of HMIDD. The Greenwich photoheliographic areas are only a few per cent smaller than DPD areas. A 0.2° difference between the north directions of the DPD and MDI images is found. This value is nearly the same as was found (0.22°) by us in a previous paper comparing HMI and MDI images. The area measurement practice (spots smaller than 10 mh were not directly measured but an area of 2 mh was assigned to each) of the Solar Observing Optical Network cannot explain the large area deficit of the Solar Observing Optical Network.

  10. Domain analysis of 3 Keto Acyl-CoA synthase for structural variations in Vitis vinifera and Oryza brachyantha using comparative modelling.

    PubMed

    Sagar, Mamta; Pandey, Neetesh; Qamar, Naseha; Singh, Brijendra; Shukla, Akanksha

    2015-03-01

    The long chain fatty acids incorporated into plant lipids are derived from the iterative addition of C2 units which is provided by malonyl-CoA to an acyl-CoA after interactions with 3-ketoacyl-CoA synthase (KCS), found in several plants. This study provides functional characterization of three 3 ketoacyl CoA synthase like proteins in Vitis vinifera (one) and Oryza brachyantha (two proteins). Sequence analysis reveals that protein of Oryza brachyantha shows 96% similarity to a hypothetical protein in Sorghum bicolor; total 11 homologs were predicted in Sorghum bicolor. Conserved domain prediction confirm the presence of FAE1/Type III polyketide synthase-like protein, Thiolase-like, subgroup; Thiolase-like and 3-Oxoacyl-ACP synthase III, C-terminal and chalcone synthase like domain but very long chain 3-keto acyl CoA domain is absent. All three proteins were found to have Chalcone and stilbene synthases C terminal domain which is similar to domain of thiolase and β keto acyl synthase. Its N terminal domain is absent in J3M9Z7 protein of Oryza brachyantha and F6HH63 protein of Vitis vinifera. Differences in N-terminal domain is responsible for distinguish activity. The J3MF16 protein of Oryza brachyantha contains N terminal domain and C terminal domain and characterized using annotation of these domains. Domains Gcs (streptomyces coelicolor) and Chalcone-stilbene synthases (KAS) in 2-pyrone synthase (Gerbera hybrid) and chalcone synthase 2 (Medicago sativa) were found to be present in three proteins. This similarity points toward anthocyanin biosynthetic process. Similarity to chalcone synthase 2 reveals its possible role in Naringenine and Chalcone synthase like activity. In 3 keto acyl CoA synthase of Oryza brachyantha. Active site residues C-240, H-407, N-447 are present in J3MF16 protein that are common in these three protein at different positions. Structural variations among dimer interface, product binding site, malonyl-CoA binding sites, were predicted in

  11. 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.

  12. Community detection algorithms: a comparative analysis.

    PubMed

    Lancichinetti, Andrea; Fortunato, Santo

    2009-11-01

    Uncovering the community structure exhibited by real networks is a crucial step toward an understanding of complex systems that goes beyond the local organization of their constituents. Many algorithms have been proposed so far, but none of them has been subjected to strict tests to evaluate their performance. Most of the sporadic tests performed so far involved small networks with known community structure and/or artificial graphs with a simplified structure, which is very uncommon in real systems. Here we test several methods against a recently introduced class of benchmark graphs, with heterogeneous distributions of degree and community size. The methods are also tested against the benchmark by Girvan and Newman [Proc. Natl. Acad. Sci. U.S.A. 99, 7821 (2002)] and on random graphs. As a result of our analysis, three recent algorithms introduced by Rosvall and Bergstrom [Proc. Natl. Acad. Sci. U.S.A. 104, 7327 (2007); Proc. Natl. Acad. Sci. U.S.A. 105, 1118 (2008)], Blondel [J. Stat. Mech.: Theory Exp. (2008), P10008], and Ronhovde and Nussinov [Phys. Rev. E 80, 016109 (2009)] have an excellent performance, with the additional advantage of low computational complexity, which enables one to analyze large systems.

  13. 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.

  14. Vestibular migraine: comparative analysis between diagnostic criteria.

    PubMed

    Salmito, Márcio Cavalcante; Morganti, Lígia Oliveira Gonçalves; Nakao, Bruno Higa; Simões, Juliana Caminha; Duarte, Juliana Antoniolli; Ganança, Fernando Freitas

    2015-01-01

    There is a strong association between vertigo and migraine. Vestibular migraine (VM) was described in 1999, and diagnostic criteria were proposed in 2001 and revised in 2012. To compare the diagnostic criteria for VM proposed in 2001 with 2012 criteria with respect to their diagnostic power and therapeutic effect of VM prophylaxis. Clinical chart review of patients attended to in a VM clinic. The 2012 criteria made the diagnosis more specific, restricting the diagnosis of VM to a smaller number of patients, such that 87.7% of patients met 2001 criteria and 77.8% met 2012 criteria. Prophylaxis for VM was effective both for patients diagnosed by either set of criteria and for those who did not meet any of the criteria. The 2012 diagnostic criteria for VM limited the diagnosis of the disease to a smaller number of patients, mainly because of the type, intensity, and duration of dizziness. Patients diagnosed with migraine and associated dizziness demonstrated improvement after prophylactic treatment of VM, even when they did not meet diagnostic criteria. Copyright © 2015 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

  15. Recognizing chemicals in patents: a comparative analysis.

    PubMed

    Habibi, Maryam; Wiegandt, David Luis; Schmedding, Florian; Leser, Ulf

    2016-01-01

    Recently, methods for Chemical Named Entity Recognition (NER) have gained substantial interest, driven by the need for automatically analyzing todays ever growing collections of biomedical text. Chemical NER for patents is particularly essential due to the high economic importance of pharmaceutical findings. However, NER on patents has essentially been neglected by the research community for long, mostly because of the lack of enough annotated corpora. A recent international competition specifically targeted this task, but evaluated tools only on gold standard patent abstracts instead of full patents; furthermore, results from such competitions are often difficult to extrapolate to real-life settings due to the relatively high homogeneity of training and test data. Here, we evaluate the two state-of-the-art chemical NER tools, tmChem and ChemSpot, on four different annotated patent corpora, two of which consist of full texts. We study the overall performance of the tools, compare their results at the instance level, report on high-recall and high-precision ensembles, and perform cross-corpus and intra-corpus evaluations. Our findings indicate that full patents are considerably harder to analyze than patent abstracts and clearly confirm the common wisdom that using the same text genre (patent vs. scientific) and text type (abstract vs. full text) for training and testing is a pre-requisite for achieving high quality text mining results.

  16. Comparative and demographic analysis of orangutan genomes

    PubMed Central

    Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; Mitreva, Makedonka; Cook, Lisa; Delehaunty, Kim D.; Fronick, Catrina; Schmidt, Heather; Fulton, Lucinda A.; Fulton, Robert S.; Nelson, Joanne O.; Magrini, Vincent; Pohl, Craig; Graves, Tina A.; Markovic, Chris; Cree, Andy; Dinh, Huyen H.; Hume, Jennifer; Kovar, Christie L.; Fowler, Gerald R.; Lunter, Gerton; Meader, Stephen; Heger, Andreas; Ponting, Chris P.; Marques-Bonet, Tomas; Alkan, Can; Chen, Lin; Cheng, Ze; Kidd, Jeffrey M.; Eichler, Evan E.; White, Simon; Searle, Stephen; Vilella, Albert J.; Chen, Yuan; Flicek, Paul; Ma, Jian; Raney, Brian; Suh, Bernard; Burhans, Richard; Herrero, Javier; Haussler, David; Faria, Rui; Fernando, Olga; Darré, Fleur; Farré, Domènec; Gazave, Elodie; Oliva, Meritxell; Navarro, Arcadi; Roberto, Roberta; Capozzi, Oronzo; Archidiacono, Nicoletta; Valle, Giuliano Della; Purgato, Stefania; Rocchi, Mariano; Konkel, Miriam K.; Walker, Jerilyn A.; Ullmer, Brygg; Batzer, Mark A.; Smit, Arian F. A.; Hubley, Robert; Casola, Claudio; Schrider, Daniel R.; Hahn, Matthew W.; Quesada, Victor; Puente, Xose S.; Ordoñez, Gonzalo R.; López-Otín, Carlos; Vinar, Tomas; Brejova, Brona; Ratan, Aakrosh; Harris, Robert S.; Miller, Webb; Kosiol, Carolin; Lawson, Heather A.; Taliwal, Vikas; Martins, André L.; Siepel, Adam; RoyChoudhury, Arindam; Ma, Xin; Degenhardt, Jeremiah; Bustamante, Carlos D.; Gutenkunst, Ryan N.; Mailund, Thomas; Dutheil, Julien Y.; Hobolth, Asger; Schierup, Mikkel H.; Chemnick, Leona; Ryder, Oliver A.; Yoshinaga, Yuko; de Jong, Pieter J.; Weinstock, George M.; Rogers, Jeffrey; Mardis, Elaine R.; Gibbs, Richard A.; Wilson, Richard K.

    2011-01-01

    “Orangutan” is derived from the Malay term “man of the forest” and aptly describes the Southeast Asian great apes native to Sumatra and Borneo. The orangutan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orangutan draft genome assembly and short read sequence data from five Sumatran and five Bornean orangutan genomes. Our analyses reveal that, compared to other primates, the orangutan genome has many unique features. Structural evolution of the orangutan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe the first primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orangutan genome structure. Orangutans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400k years ago (ya), is more recent than most previous studies and underscores the complexity of the orangutan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities

  17. Comparative flood damage model assessment: Towards a European approach

    NASA Astrophysics Data System (ADS)

    Jongman, B.; Kreibich, H.; Bates, P. D.; de Roo, A. P. J.; Barredo, J. I.; Gericke, A.; Apel, H.; Neal, J.; Aerts, J. C. J. H.; Ward, P. J.

    2012-04-01

    There is a wide variety of flood damage assessment models in use across countries and institutions, with large variations in their approaches and assumptions. In this study we compare seven established methodologies qualitatively and quantitatively, in order to identify key factors that should be taken into consideration in the development of a pan-European flood damage model. In the comparison, we included seven different flood damage models: FLEMO (Germany), Damage Scanner (The Netherlands), Rhine Atlas (Rhine basin), the Flemish method (Belgium), Multi-Coloured Manual (United Kingdom), HAZUS-MH (United States) and the aggregated EC-JRC approach (European Commission). The study is based on two case-studies of historical flood events, for which both hydrological and land-use data are available, as well as data on observed economic damages. One case-study is based on a 2002 flood event in Eilenburg, Germany. The second case-study covers the 2005 flooding in Carlisle, United Kingdom. We found that the models designed for the specific regions come very close to estimating the observed economic damage. A sensitivity analysis shows that the model results are most sensitive to variation in assumed maximum damage values, and almost as much to variation in the applied depth-damage functions. On the basis of these results, we propose the development of a Europe-wide flood damage model that is based on disaggregated land-use data, local asset values and a variable set of depth-damage functions.

  18. A cost-effectiveness analysis of celecoxib compared with diclofenac in the treatment of pain in osteoarthritis (OA) within the Swedish health system using an adaptation of the NICE OA model.

    PubMed

    Brereton, Nicholas; Pennington, Becky; Ekelund, Mats; Akehurst, Ronald

    2014-09-01

    Celecoxib for the treatment of pain resulting from osteoarthritis (OA) was reviewed by the Tandvårds- och läkemedelsförmånsverket-Dental and Pharmaceutical Benefits Board (TLV) in Sweden in late 2010. This study aimed to evaluate the incremental cost-effectiveness ratio (ICER) of celecoxib plus a proton pump inhibitor (PPI) compared to diclofenac plus a PPI in a Swedish setting. The National Institute for Health and Care Excellence (NICE) in the UK developed a health economic model as part of their 2008 assessment of treatments for OA. In this analysis, the model was reconstructed and adapted to a Swedish perspective. Drug costs were updated using the TLV database. Adverse event costs were calculated using the regional price list of Southern Sweden and the standard treatment guidelines from the county council of Stockholm. Costs for treating cardiovascular (CV) events were taken from the Swedish DRG codes and the literature. Over a patient's lifetime treatment with celecoxib plus a PPI was associated with a quality-adjusted life year (QALY) gain of 0.006 per patient when compared to diclofenac plus a PPI. There was an increase in discounted costs of 529 kr per patient, which resulted in an incremental cost-effectiveness ratio (ICER) of 82,313 kr ($12,141). Sensitivity analysis showed that treatment was more cost effective in patients with an increased risk of bleeding or gastrointestinal (GI) complications. The results suggest that celecoxib plus a PPI is a cost effective treatment for OA when compared to diclofenac plus a PPI. Treatment is shown to be more cost effective in Sweden for patients with a high risk of bleeding or GI complications. It was in this population that the TLV gave a positive recommendation. There are known limitations on efficacy in the original NICE model.

  19. 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

  20. 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

  1. Bayesian analysis of CCDM models

    NASA Astrophysics Data System (ADS)

    Jesus, J. F.; Valentim, R.; Andrade-Oliveira, F.

    2017-09-01

    Creation of Cold Dark Matter (CCDM), in the context of Einstein Field Equations, produces a negative pressure term which can be used to explain the accelerated expansion of the Universe. In this work we tested six different spatially flat models for matter creation using statistical criteria, in light of SNe Ia data: Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) and Bayesian Evidence (BE). These criteria allow to compare models considering goodness of fit and number of free parameters, penalizing excess of complexity. We find that JO model is slightly favoured over LJO/ΛCDM model, however, neither of these, nor Γ = 3αH0 model can be discarded from the current analysis. Three other scenarios are discarded either because poor fitting or because of the excess of free parameters. A method of increasing Bayesian evidence through reparameterization in order to reducing parameter degeneracy is also developed.

  2. Comparative Statistical Analysis of Auroral Models

    DTIC Science & Technology

    2012-03-22

    3 . This accounts for the characteristic shape of the Interplanetary Magnetic Field (IMF), which permeates the entire solar system...boundary of the oval changes requires knowledge of the solar wind and the Interplanetary Magnetic Field (IMF), the individual and coupled dynamics of the...this point occurs: 3 | | ( 3 ) 14 where is the kinetic energy perpendicular to the magnetic field and is the convective electric field

  3. A comparative analysis of Media Lengua and Quichua vowel production.

    PubMed

    Stewart, Jesse

    2014-01-01

    This study presents a comparative analysis of F1 and F2 vowel frequencies from Pijal Media Lengua (PML) and Imbabura Quichua. Mixed-effects models are used to test Spanish-derived high and low vowels against their Quichua-derived counterparts for statistical significance. Spanish-derived and Quichua-derived high vowels are also tested against Spanish-derived mid vowels. This analysis suggests that PML may be manipulating as many as eight vowels where Spanishderived high and low vowels coexist as near-mergers with their Quichua-derived counterparts, while high and mid vowels coexist with partial overlap. Quichua, traditionally viewed as a three-vowel system, shows similar results and may be manipulating as many as six vowels. © 2015 S. Karger AG, Basel.

  4. [Cost-effectiveness Analysis of Panitumumab Plus mFOLFOX6 Compared to Bevacizumab Plus mFOLFOX6 for First-line Treatment of Patients with Wild-type RAS Metastatic Colorectal Cancer--Czech Republic Model Adaptation].

    PubMed

    Fínek, J; Skoupá, J; Jandová, P

    2015-01-01

    Pharmacoeconomic assessments are a part of the decision process not only during reimbursement setting, but in clinical practice as well. The presented cost-effectiveness analysis assesses panitumumab+mFOLFOX6 vs. bevacizumab+mFOLFOX6 in 1st line treatment of patients with wildtype RAS metastatic colorectal cancer (mCRC) in the Czech environment. The adaptation of a Markov model considers the healthcare perspective; clinical data (efficacy, healthcare utilization and adverse events) are derived from a head-to-head comparison (PEAK study). Health states included in the model: progression free on treatment, progression (with/ without active treatment), resection of metastases, disease-free after successful resection and death. Actual reimbursement levels were used to estimate costs, published literature to estimate duration of 2nd line treatment. The analysis assumes a lifetime horizon; uncertainty was limited by performing one-way and probabilistic sensitivity analyses. Analysis outcomes are life-years gained (LYG) and quality-adjusted life-years (QALYs). Panitumumab+mFOLFOX6 is more effective and more costly in 1st line patients with wildtype RAS mCRC. Incremental costs per QALY are 837,270 CZK, per LYG 615,022 CZK; however, below the willingness-to-pay threshold applied in the Czech Republic. Panitumumab+mFOLFOX6 is cost-effective in 1st line treatment of patients with wildtype RAS mCRC compared to bevacizumab+mFOLFOX6 in the Czech setting.

  5. Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes

    PubMed Central

    Boyle, Greg; Richter, Kerstin; Priest, Henry D.; Traver, David; Mockler, Todd C.; Chang, Jeffrey T.; Kay, Steve A.

    2017-01-01

    From photosynthetic bacteria to mammals, the circadian clock evolved to track diurnal rhythms and enable organisms to anticipate daily recurring changes such as temperature and light. It orchestrates a broad spectrum of physiology such as the sleep/wake and eating/fasting cycles. While we have made tremendous advances in our understanding of the molecular details of the circadian clock mechanism and how it is synchronized with the environment, we still have rudimentary knowledge regarding its connection to help regulate diurnal physiology. One potential reason is the sheer size of the output network. Diurnal/circadian transcriptomic studies are reporting that around 10% of the expressed genome is rhythmically controlled. Zebrafish is an important model system for the study of the core circadian mechanism in vertebrate. As Zebrafish share more than 70% of its genes with human, it could also be an additional model in addition to rodent for exploring the diurnal/circadian output with potential for translational relevance. Here we performed comparative diurnal/circadian transcriptome analysis with established mouse liver and other tissue datasets. First, by combining liver tissue sampling in a 48h time series, transcription profiling using oligonucleotide arrays and bioinformatics analysis, we profiled rhythmic transcripts and identified 2609 rhythmic genes. The comparative analysis revealed interesting features of the output network regarding number of rhythmic genes, proportion of tissue specific genes and the extent of transcription factor family expression. Undoubtedly, the Zebrafish model system will help identify new vertebrate outputs and their regulators and provides leads for further characterization of the diurnal cis-regulatory network. PMID:28076377

  6. 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.

  7. 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.

  8. Virtual ligand screening against comparative protein structure models.

    PubMed

    Fan, Hao; Irwin, John J; Sali, Andrej

    2012-01-01

    Virtual ligand screening uses computation to discover new ligands of a protein by screening one or more of its structural models against a database of potential ligands. Comparative protein structure modeling extends the applicability of virtual screening beyond the atomic structures determined by X-ray crystallography or NMR spectroscopy. Here, we describe an integrated modeling and docking protocol, combining comparative modeling by MODELLER and virtual ligand screening by DOCK.

  9. Noncoding RNA gene detection using comparative sequence analysis

    PubMed Central

    Rivas, Elena; Eddy, Sean R

    2001-01-01

    Background Noncoding RNA genes produce transcripts that exert their function without ever producing proteins. Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes. A reliable general purpose computational genefinder for noncoding RNA genes has been elusive. Results We describe a comparative sequence analysis algorithm for detecting novel structural RNA genes. The key idea is to test the pattern of substitutions observed in a pairwise alignment of two homologous sequences. A conserved coding region tends to show a pattern of synonymous substitutions, whereas a conserved structural RNA tends to show a pattern of compensatory mutations consistent with some base-paired secondary structure. We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution. Given an input pairwise sequence alignment (e.g. from a BLASTN comparison of two related genomes) we classify the alignment into the coding, RNA, or null class according to the posterior probability of each class. Conclusions We have implemented this approach as a program, QRNA, which we consider to be a prototype structural noncoding RNA genefinder. Tests suggest that this approach detects noncoding RNA genes with a fair degree of reliability. PMID:11801179

  10. 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.

  11. 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.

  12. Comparing Poisson Sigma Model with A-model

    NASA Astrophysics Data System (ADS)

    Bonechi, F.; Cattaneo, A. S.; Iraso, R.

    2016-10-01

    We discuss the A-model as a gauge fixing of the Poisson Sigma Model with target a symplectic structure. We complete the discussion in [4], where a gauge fixing defined by a compatible complex structure was introduced, by showing how to recover the A-model hierarchy of observables in terms of the AKSZ observables. Moreover, we discuss the off-shell supersymmetry of the A-model as a residual BV symmetry of the gauge fixed PSM action.

  13. Comparative transcriptome analysis of the metal hyperaccumulator Noccaea caerulescens

    PubMed Central

    Halimaa, Pauliina; Blande, Daniel; Aarts, Mark G. M.; Tuomainen, Marjo; Tervahauta, Arja; Kärenlampi, Sirpa

    2014-01-01

    The metal hyperaccumulator Noccaea caerulescens is an established model to study the adaptation of plants to metalliferous soils. Various comparators have been used in these studies. The choice of suitable comparators is important and depends on the hypothesis to be tested and methods to be used. In high-throughput analyses such as microarray, N. caerulescens has been compared to non-tolerant, non-accumulator plants like Arabidopsis thaliana or Thlaspi arvense rather than to the related hypertolerant or hyperaccumulator plants. An underutilized source is N. caerulescens populations with considerable variation in their capacity to accumulate and tolerate metals. Whole transcriptome sequencing (RNA-Seq) is revealing interesting variation in their gene expression profiles. Combining physiological characteristics of N. caerulescens accessions with their RNA-Seq has a great potential to provide detailed insight into the underlying molecular mechanisms, including entirely new gene products. In this review we will critically consider comparative transcriptome analyses carried out to explore metal hyperaccumulation and hypertolerance of N. caerulescens, and demonstrate the potential of RNA-Seq analysis as a tool in evolutionary genomics. PMID:24904610

  14. In silico comparative genomic analysis of GABAA receptor transcriptional regulation.

    PubMed

    Joyce, Christopher J

    2007-06-30

    Subtypes of the GABAA receptor subunit exhibit diverse temporal and spatial expression patterns. In silico comparative analysis was used to predict transcriptional regulatory features in individual mammalian GABAA receptor subunit genes, and to identify potential transcriptional regulatory components involved in the coordinate regulation of the GABAA receptor gene clusters. Previously unreported putative promoters were identified for the beta2, gamma1, gamma3, epsilon, theta and pi subunit genes. Putative core elements and proximal transcriptional factors were identified within these predicted promoters, and within the experimentally determined promoters of other subunit genes. Conserved intergenic regions of sequence in the mammalian GABAA receptor gene cluster comprising the alpha1, beta2, gamma2 and alpha6 subunits were identified as potential long range transcriptional regulatory components involved in the coordinate regulation of these genes. A region of predicted DNase I hypersensitive sites within the cluster may contain transcriptional regulatory features coordinating gene expression. A novel model is proposed for the coordinate control of the gene cluster and parallel expression of the alpha1 and beta2 subunits, based upon the selective action of putative Scaffold/Matrix Attachment Regions (S/MARs). The putative regulatory features identified by genomic analysis of GABAA receptor genes were substantiated by cross-species comparative analysis and now require experimental verification. The proposed model for the coordinate regulation of genes in the cluster accounts for the head-to-head orientation and parallel expression of the alpha1 and beta2 subunit genes, and for the disruption of transcription caused by insertion of a neomycin gene in the close vicinity of the alpha6 gene, which is proximal to a putative critical S/MAR.

  15. Ionospheric topside models compared with experimental electron density profiles

    NASA Astrophysics Data System (ADS)

    Coisson, P.; Radicella, S. M.

    2003-04-01

    In the last couple of years an increasing number of topside electron density profiles has been made available through the Internet to the scientific community. This kind of data is particularly important for ionospheric modeling purposes, since the experimental information on the electron density above the ionosphere maximum of ionization is very scarce. The present work analyses the behavior of the NeQuick and IRI models, adopted by the ITU-R recommendation P.531-5, with respect to the topside electron density profiles available in the databases of ISIS2, IK19 and Cosmos-1809 satellites. Experimental total electron content (TEC) from the F2 peak up to satellite height and electron densities at fixed heights above that peak have been compared with values computed with the models. A wide range of different conditions (solar activity, local time, geographical and geomagnetic position has been considered). The analysis done allows to point out the behavior of the models and the improvement needed to allow a better reproduction of the experimental results.

  16. Comparative expression pathway analysis of human and canine mammary tumors

    PubMed Central

    Uva, Paolo; Aurisicchio, Luigi; Watters, James; Loboda, Andrey; Kulkarni, Amit; Castle, John; Palombo, Fabio; Viti, Valentina; Mesiti, Giuseppe; Zappulli, Valentina; Marconato, Laura; Abramo, Francesca; Ciliberto, Gennaro; Lahm, Armin; La Monica, Nicola; de Rinaldis, Emanuele

    2009-01-01

    Background Spontaneous tumors in dog have been demonstrated to share many features with their human counterparts, including relevant molecular targets, histological appearance, genetics, biological behavior and response to conventional treatments. Mammary tumors in dog therefore provide an attractive alternative to more classical mouse models, such as transgenics or xenografts, where the tumour is artificially induced. To assess the extent to which dog tumors represent clinically significant human phenotypes, we performed the first genome-wide comparative analysis of transcriptional changes occurring in mammary tumors of the two species, with particular focus on the molecular pathways involved. Results We analyzed human and dog gene expression data derived from both tumor and normal mammary samples. By analyzing the expression levels of about ten thousand dog/human orthologous genes we observed a significant overlap of genes deregulated in the mammary tumor samples, as compared to their normal counterparts. Pathway analysis of gene expression data revealed a great degree of similarity in the perturbation of many cancer-related pathways, including the 'PI3K/AKT', 'KRAS', 'PTEN', 'WNT-beta catenin' and 'MAPK cascade'. Moreover, we show that the transcriptional relationships between different gene signatures observed in human breast cancer are largely maintained in the canine model, suggesting a close interspecies similarity in the network of cancer signalling circuitries. Conclusion Our data confirm and further strengthen the value of the canine mammary cancer model and open up new perspectives for the evaluation of novel cancer therapeutics and the development of prognostic and diagnostic biomarkers to be used in clinical studies. PMID:19327144

  17. Fumonisin B1 toxicity in grower-finisher pigs: a comparative analysis of genetically engineered Bt corn and non-Bt corn by using quantitative dietary exposure assessment modeling.

    PubMed

    Delgado, James E; Wolt, Jeffrey D

    2011-08-01

    In this study, we investigate the long-term exposure (20 weeks) to fumonisin B(1) (FB(1)) in grower-finisher pigs by conducting a quantitative exposure assessment (QEA). Our analytical approach involved both deterministic and semi-stochastic modeling for dietary comparative analyses of FB(1) exposures originating from genetically engineered Bacillus thuringiensis (Bt)-corn, conventional non-Bt corn and distiller's dried grains with solubles (DDGS) derived from Bt and/or non-Bt corn. Results from both deterministic and semi-stochastic demonstrated a distinct difference of FB(1) toxicity in feed between Bt corn and non-Bt corn. Semi-stochastic results predicted the lowest FB(1) exposure for Bt grain with a mean of 1.5 mg FB(1)/kg diet and the highest FB(1) exposure for a diet consisting of non-Bt grain and non-Bt DDGS with a mean of 7.87 mg FB(1)/kg diet; the chronic toxicological incipient level of concern is 1.0 mg of FB(1)/kg of diet. Deterministic results closely mirrored but tended to slightly under predict the mean result for the semi-stochastic analysis. This novel comparative QEA model reveals that diet scenarios where the source of grain is derived from Bt corn presents less potential to induce FB(1) toxicity than diets containing non-Bt corn.

  18. 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.

  19. 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

  20. Comparative Analysis of Bracket Slot Dimensions Evaluating Different Manufacturing Techniques</