Science.gov

Sample records for cfd-based mechanistic deposit

  1. A CFD-Based Study of the Feasibility of Adapting an Erosion Burner Rig for Examining the Effect of CMAS Deposition Corrosion on Environmental Barrier Coatings

    NASA Technical Reports Server (NTRS)

    Miller, Robert A.; Kuczmarski, Maria A.

    2015-01-01

    Thermodynamic and computational fluid dynamics modeling has been conducted to examine the feasibility of adapting the NASA-Glenn erosion burner rigs for use in studies of corrosion of environmental barrier coatings by the deposition of molten CMAS. The effect of burner temperature, Mach number, particle preheat, duct heating, particle size, and particle phase (crystalline vs. glass) were analyzed. Detailed strategies for achieving complete melting of CMAS particles were developed, thereby greatly improving the probability of future successful experimental outcomes.

  2. A supportive architecture for CFD-based design optimisation

    NASA Astrophysics Data System (ADS)

    Li, Ni; Su, Zeya; Bi, Zhuming; Tian, Chao; Ren, Zhiming; Gong, Guanghong

    2014-03-01

    Multi-disciplinary design optimisation (MDO) is one of critical methodologies to the implementation of enterprise systems (ES). MDO requiring the analysis of fluid dynamics raises a special challenge due to its extremely intensive computation. The rapid development of computational fluid dynamic (CFD) technique has caused a rise of its applications in various fields. Especially for the exterior designs of vehicles, CFD has become one of the three main design tools comparable to analytical approaches and wind tunnel experiments. CFD-based design optimisation is an effective way to achieve the desired performance under the given constraints. However, due to the complexity of CFD, integrating with CFD analysis in an intelligent optimisation algorithm is not straightforward. It is a challenge to solve a CFD-based design problem, which is usually with high dimensions, and multiple objectives and constraints. It is desirable to have an integrated architecture for CFD-based design optimisation. However, our review on existing works has found that very few researchers have studied on the assistive tools to facilitate CFD-based design optimisation. In the paper, a multi-layer architecture and a general procedure are proposed to integrate different CFD toolsets with intelligent optimisation algorithms, parallel computing technique and other techniques for efficient computation. In the proposed architecture, the integration is performed either at the code level or data level to fully utilise the capabilities of different assistive tools. Two intelligent algorithms are developed and embedded with parallel computing. These algorithms, together with the supportive architecture, lay a solid foundation for various applications of CFD-based design optimisation. To illustrate the effectiveness of the proposed architecture and algorithms, the case studies on aerodynamic shape design of a hypersonic cruising vehicle are provided, and the result has shown that the proposed architecture

  3. Deposition, characterization, patterning and mechanistic study of inorganic resists for next-generation nanolithography

    NASA Astrophysics Data System (ADS)

    Luo, Feixiang

    The semiconductor industry has witnessed a continuous decrease in the size of logic, memory and other computer chip components since its birth over half a century ago. The shrinking (scaling) of components has to a large extent been enabled by the development of micro- and now nano-lithographic techniques. This thesis focuses on one central component of lithography, the resist, which is essentially a thin film that when appropriately exposed enables a pattern to be printed onto a surface. Smaller features require an ever more precisely focused photon, electron or ion beam with which to expose the resist. The likely next generation source of radiation that will enable sub-20nm features to be written will employ extreme ultraviolet radiation (EUV), 92eV (13.5nm). The work discussed here involves a novel class of inorganic resists (including a solution processed Hf-based resist called HafSOx), as the organic resists that have dominated the microlithography industry for the past few decades have approached fundamental scaling limits. In order to maintain the high throughput required by high volume semiconductor manufacturing, metal oxide resists have been proposed and developed to meet the resolution and sensitivity in EUV lithography. One can think of our resists as the nano-lithographic analog to the silver halide film that dominated the photographic print industry for a century. In this thesis, we mainly describe our work on HafSOx, a "first generation" metal oxide EUV resist system. HafSOx thin films can be deposited by spin-coating a mixed solution of HfOCl2, H2O 2, and H2SO4. Various materials characterization techniques have been employed to achieve a comprehensive understanding of film composition and structure at both surface and bulk level, as well as a mechanistic understanding of the film radiation chemistry. Taking advantage of the high energy x-rays used in the XPS experiment, we developed an experiment to dynamically monitor the photochemistry within the

  4. Mechanistic Study on the Degradation of Thermal Barrier Coatings Induced by Volcanic Ash Deposition

    NASA Astrophysics Data System (ADS)

    Arai, Masayuki

    2017-08-01

    Thermal stress generated on thermal barrier coatings (TBCs) by volcanic ash (VA) deposition was assessed measuring the tip deflection of a multilayered beam structure as a function of temperature. The TBC in this study was deposited onto the surface of a blade utilized in a land-based gas turbine which is composed of 8 wt.%Y2O3-ZrO2/CoNiCrAlY on a Ni-based superalloy. The VA-deposited TBC sample was heated at 1453 K, and the effect of VA deposition on TBC delamination was examined in comparison with a TBC sample without VA deposition as a reference. On the basis of the VA attack damage mechanism which was investigated via the tip deflection measurement and a comprehensive microstructure examination, a damage-coupled constitutive model was proposed. The proposed model was based on the infiltration of the molten VA inside pores and phase transformations of yttria -tabilized zirconia in the TBC system. The numerical analysis results, which were simulated utilizing the finite element code installing the developed constitutive model, showed us that VA attack on the TBC sample induced near-interfacial cracks because of a significant increasing in the coating stress.

  5. Mechanistic modeling study on process optimization and precursor utilization with atmospheric spatial atomic layer deposition

    SciTech Connect

    Deng, Zhang; He, Wenjie; Duan, Chenlong; Chen, Rong; Shan, Bin

    2016-01-15

    Spatial atomic layer deposition (SALD) is a promising technology with the aim of combining the advantages of excellent uniformity and conformity of temporal atomic layer deposition (ALD), and an industrial scalable and continuous process. In this manuscript, an experimental and numerical combined model of atmospheric SALD system is presented. To establish the connection between the process parameters and the growth efficiency, a quantitative model on reactant isolation, throughput, and precursor utilization is performed based on the separation gas flow rate, carrier gas flow rate, and precursor mass fraction. The simulation results based on this model show an inverse relation between the precursor usage and the carrier gas flow rate. With the constant carrier gas flow, the relationship of precursor usage and precursor mass fraction follows monotonic function. The precursor concentration, regardless of gas velocity, is the determinant factor of the minimal residual time. The narrow gap between precursor injecting heads and the substrate surface in general SALD system leads to a low Péclet number. In this situation, the gas diffusion act as a leading role in the precursor transport in the small gap rather than the convection. Fluid kinetics from the numerical model is independent of the specific structure, which is instructive for the SALD geometry design as well as its process optimization.

  6. Disintegration of nano-embedded microparticles after deposition on mucus: A mechanistic study.

    PubMed

    Ruge, Christian A; Bohr, Adam; Beck-Broichsitter, Moritz; Nicolas, Valérie; Tsapis, Nicolas; Fattal, Elias

    2016-03-01

    The conversion of colloidal drug carriers/polymeric nanoparticles into dry microparticulate powders (e.g., by spray-drying) is a prominent approach to overcome the aerodynamic limitations of these formulations for delivery via inhalation. However, to what extent such nano-embedded microparticles disintegrate into individual/intact nanoparticles after contacting relevant physiological media has so far not been addressed. Polymeric nanoparticles were spray-dried into nano-embedded microparticles (NEMs) using different amounts of trehalose as embedding matrix excipient. Formulations were characterized and then evaluated for their disintegration behavior after aerosolization onto model mucus. Although a rapid and complete aqueous redispersion was observed for specific excipient/nanoparticle weight ratios (i.e., greater than 1/1), the same formulations revealed no disintegration after deposition onto a static mucus layer. Double-labeled NEMs powders (i.e., dual color staining of polymeric nanoparticles and trehalose) demonstrated rapid matrix dissolution, while the nanoparticle aggregates persisted. When deposited onto agitated mucus, however, sufficient disintegration of NEMs into individual polymeric nanoparticles was observed. These findings indicate that mechanical forces are necessary to overcome the attraction between individual nanoparticles found within the NEMs. Thus, it remains questionable whether the lung mechanics (e.g., breathing, mucociliary clearance) acting on these formulations will contribute to the overall disintegration process. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. New Flutter Analysis Technique for CFD-based Unsteady Aeroelasticity

    NASA Technical Reports Server (NTRS)

    Pak, Chan-gi; Jutte, Christine V.

    2009-01-01

    This paper presents a flutter analysis technique for the transonic flight regime. The technique uses an iterative approach to determine the critical dynamic pressure for a given mach number. Unlike other CFD-based flutter analysis methods, each iteration solves for the critical dynamic pressure and uses this value in subsequent iterations until the value converges. This process reduces the iterations required to determine the critical dynamic pressure. To improve the accuracy of the analysis, the technique employs a known structural model, leaving only the aerodynamic model as the unknown. The aerodynamic model is estimated using unsteady aeroelastic CFD analysis combined with a parameter estimation routine. The technique executes as follows. The known structural model is represented as a finite element model. Modal analysis determines the frequencies and mode shapes for the structural model. At a given mach number and dynamic pressure, the unsteady CFD analysis is performed. The output time history of the surface pressure is converted to a nodal aerodynamic force vector. The forces are then normalized by the given dynamic pressure. A multi-input multi-output parameter estimation software, ERA, estimates the aerodynamic model through the use of time histories of nodal aerodynamic forces and structural deformations. The critical dynamic pressure is then calculated using the known structural model and the estimated aerodynamic model. This output is used as the dynamic pressure in subsequent iterations until the critical dynamic pressure is determined. This technique is demonstrated on the Aerostructures Test Wing-2 model at NASA's Dryden Flight Research Center.

  8. New Flutter Analysis Technique for CFD-based Unsteady Aeroelasticity

    NASA Technical Reports Server (NTRS)

    Pak, Chan-gi; Jutte, Christine V.

    2009-01-01

    This paper presents a flutter analysis technique for the transonic flight regime. The technique uses an iterative approach to determine the critical dynamic pressure for a given mach number. Unlike other CFD-based flutter analysis methods, each iteration solves for the critical dynamic pressure and uses this value in subsequent iterations until the value converges. This process reduces the iterations required to determine the critical dynamic pressure. To improve the accuracy of the analysis, the technique employs a known structural model, leaving only the aerodynamic model as the unknown. The aerodynamic model is estimated using unsteady aeroelastic CFD analysis combined with a parameter estimation routine. The technique executes as follows. The known structural model is represented as a finite element model. Modal analysis determines the frequencies and mode shapes for the structural model. At a given mach number and dynamic pressure, the unsteady CFD analysis is performed. The output time history of the surface pressure is converted to a nodal aerodynamic force vector. The forces are then normalized by the given dynamic pressure. A multi-input multi-output parameter estimation software, ERA, estimates the aerodynamic model through the use of time histories of nodal aerodynamic forces and structural deformations. The critical dynamic pressure is then calculated using the known structural model and the estimated aerodynamic model. This output is used as the dynamic pressure in subsequent iterations until the critical dynamic pressure is determined. This technique is demonstrated on the Aerostructures Test Wing-2 model at NASA's Dryden Flight Research Center.

  9. Electrophoretic deposition and mechanistic studies of nano-Al/CuO thermites

    NASA Astrophysics Data System (ADS)

    Sullivan, K. T.; Kuntz, J. D.; Gash, A. E.

    2012-07-01

    Electrophoretic deposition was used to deposit thin films (˜10-200 μm) of nano-aluminum/copper oxide thermites, with a density of 29% the theoretical maximum. The reaction propagation velocity was examined using fine-patterned electrodes (0.25 × 20 mm), and the optimum velocity was found to correspond to a fuel-rich equivalence ratio of 1.7. This value did not correlate with the calculated maximum in gas production or temperature, and it is suggested that it is a result of enhanced condensed-phase transport, which is speculated to increase for fuel-rich conditions. A ˜25% drop in propagation velocity occurred above an equivalence ratio of 2.0, where Al2O3 is predicted to undergo a phase change from liquid to solid. This is expected to hinder the kinetics by decreasing the mobility of condensed-phase reacting species. The effect of film thickness on propagation velocity was investigated, using the optimum equivalence ratio. The velocity was seen to exhibit a two-plateau behavior, with one plateau between 13 and 50 μm film thickness, and the other above ˜120 μm. The latter had nearly an order of magnitude faster velocity than the former, 36 m/s vs. 4 m/s, respectively. For film thicknesses in the 50-120 μm range, a linear transitional regime was observed. Images from the combustion studies showed an increase in forward-transported particles as the film thickness increased, along with more turbulent behavior of the flame. It was suggested that the two-plateau behavior indicated a shift in the energy transport mechanism. While nanocomposite thermites have been traditionally thought to exhibit convective energy transport, we find in this work that particle advection may also be important. The velocity of particles ejected through a thin slit mounted above a thermite strip was measured, and was found to be even faster (˜2-3×) than the flame propagation velocity. The morphology of captured particles was examined with an electron microscope, and indicated that

  10. Generalized Mechanistic Model for the Chemical Vapor Deposition of 2D Transition Metal Dichalcogenide Monolayers.

    PubMed

    Govind Rajan, Ananth; Warner, Jamie H; Blankschtein, Daniel; Strano, Michael S

    2016-04-26

    Transition metal dichalcogenides (TMDs) like molybdenum disulfide (MoS2) and tungsten disulfide (WS2) are layered materials capable of growth to one monolayer thickness via chemical vapor deposition (CVD). Such CVD methods, while powerful, are notoriously difficult to extend across different reactor types and conditions, with subtle variations often confounding reproducibility, particularly for 2D TMD growth. In this work, we formulate the first generalized TMD synthetic theory by constructing a thermodynamic and kinetic growth mechanism linked to CVD reactor parameters that is predictive of specific geometric shape, size, and aspect ratio from triangular to hexagonal growth, depending on specific CVD reactor conditions. We validate our model using experimental data from Wang et al. (Chem. Mater. 2014, 26, 6371-6379) that demonstrate the systemic evolution of MoS2 morphology down the length of a flow CVD reactor where variations in gas phase concentrations can be accurately estimated using a transport model (CSulfur = 9-965 μmol/m(3); CMoO3 = 15-16 mmol/m(3)) under otherwise isothermal conditions (700 °C). A stochastic model which utilizes a site-dependent activation energy barrier based on the intrinsic TMD bond energies and a series of Evans-Polanyi relations leads to remarkable, quantitative agreement with both shape and size evolution along the reactor. The model is shown to extend to the growth of WS2 at 800 °C and MoS2 under varied process conditions. Finally, a simplified theory is developed to translate the model into a "kinetic phase diagram" of the growth process. The predictive capability of this model and its extension to other TMD systems promise to significantly increase the controlled synthesis of such materials.

  11. Mechanistic considerations of the pyrolytic formation of metal boride thin films by chemical vapor deposition from borane precursors

    SciTech Connect

    Tan, Y.; Kher, S.S.; Spencer, J.T.

    1995-12-31

    The formation of metal boride thin films by CVD is an area of potentially significant technological consequence. Interest in these materials is primarily due to their breadth of unique physical properties and to their wide structural diversity. Recently, we have explored the use of a number of boron-containing CVC precursors to prepare a wide variety of both pure metal and metal boride thin film materials. The highly efficient formation of polycrystalline transition metal and lanthanide metal boride thin films from borane precursors has now been well demonstrated through this CVD chemistry. The fundamentally important chemical processes and reactions in the CVD of boranes in forming metal boride films has, however, remained mostly a mystery. In order to rationally design new precursors and tailor the deposited solid state materials, an understanding of these fundamental processes is critical. In our recent work, which will be reported here, we have begun detailed mechanistic studies into the CVD of metal borides. These reactions have been found to occur both in the gas phase and on the surface of the reactor. A variety of studies have provided valuable insights into these complexes chemical reactions including labeling, thermal, product distribution, surface analysis, kinetic and other investigations.

  12. Simultaneous Excitation of Multiple-Input Multiple-Output CFD-Based Unsteady Aerodynamic Systems

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.

    2008-01-01

    A significant improvement to the development of CFD-based unsteady aerodynamic reduced-order models (ROMs) is presented. This improvement involves the simultaneous excitation of the structural modes of the CFD-based unsteady aerodynamic system that enables the computation of the unsteady aerodynamic state-space model using a single CFD execution, independent of the number of structural modes. Four different types of inputs are presented that can be used for the simultaneous excitation of the structural modes. Results are presented for a flexible, supersonic semi-span configuration using the CFL3Dv6.4 code.

  13. Simultaneous Excitation of Multiple-Input Multiple-Output CFD-Based Unsteady Aerodynamic Systems

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.

    2007-01-01

    A significant improvement to the development of CFD-based unsteady aerodynamic reduced-order models (ROMs) is presented. This improvement involves the simultaneous excitation of the structural modes of the CFD-based unsteady aerodynamic system that enables the computation of the unsteady aerodynamic state-space model using a single CFD execution, independent of the number of structural modes. Four different types of inputs are presented that can be used for the simultaneous excitation of the structural modes. Results are presented for a flexible, supersonic semi-span configuration using the CFL3Dv6.4 code.

  14. Flight Behaviors of a Complex Projectile Using a Coupled Computational Fluid Dynamics (CFD)-based Simulation Technique: Free Motion

    DTIC Science & Technology

    2015-09-01

    extended for computation of free-flight aerodynamics and flight dynamics of a finned projectile with pulse jet control21 and is being extended for...Dynamics ( CFD )-based Simulation Technique: Free Motion by Jubaraj Sahu and Frank Fresconi Approved for public release...US Army Research Laboratory Flight Behaviors of a Complex Projectile Using a Coupled Computational Fluid Dynamics ( CFD )-based Simulation

  15. REVIEW OF EXPERIMENTAL CAPABILITIES AND HYDRODYNAMIC DATA FOR VALIDATION OF CFD BASED PREDICTIONS FOR SLURRY BUBBLE COLUMN REACTORS

    SciTech Connect

    Donna Post Guillen; Daniel S. Wendt

    2007-11-01

    The purpose of this paper is to document the review of several open-literature sources of both experimental capabilities and published hydrodynamic data to aid in the validation of a Computational Fluid Dynamics (CFD) based model of a slurry bubble column (SBC). The review included searching the Web of Science, ISI Proceedings, and Inspec databases, internet searches as well as other open literature sources. The goal of this study was to identify available experimental facilities and relevant data. Integral (i.e., pertaining to the SBC system), as well as fundamental (i.e., separate effects are considered), data are included in the scope of this effort. The fundamental data is needed to validate the individual mechanistic models or closure laws used in a Computational Multiphase Fluid Dynamics (CMFD) simulation of a SBC. The fundamental data is generally focused on simple geometries (i.e., flow between parallel plates or cylindrical pipes) or custom-designed tests to focus on selected interfacial phenomena. Integral data covers the operation of a SBC as a system with coupled effects. This work highlights selected experimental capabilities and data for the purpose of SBC model validation, and is not meant to be an exhaustive summary.

  16. REVIEW OF EXPERIMENTAL CAPABILITIES AND HYDRODYNAMIC DATA FOR VALIDATION OF CFD-BASED PREDICTIONS FOR SLURRY BUBBLE COLUMN REACTORS

    SciTech Connect

    Donna Post Guillen; Daniel S. Wendt; Steven P. Antal; Michael Z. Podowski

    2007-11-01

    The purpose of this paper is to document the review of several open-literature sources of both experimental capabilities and published hydrodynamic data to aid in the validation of a Computational Fluid Dynamics (CFD) based model of a slurry bubble column (SBC). The review included searching the Web of Science, ISI Proceedings, and Inspec databases, internet searches as well as other open literature sources. The goal of this study was to identify available experimental facilities and relevant data. Integral (i.e., pertaining to the SBC system), as well as fundamental (i.e., separate effects are considered), data are included in the scope of this effort. The fundamental data is needed to validate the individual mechanistic models or closure laws used in a Computational Multiphase Fluid Dynamics (CMFD) simulation of a SBC. The fundamental data is generally focused on simple geometries (i.e., flow between parallel plates or cylindrical pipes) or custom-designed tests to focus on selected interfacial phenomena. Integral data covers the operation of a SBC as a system with coupled effects. This work highlights selected experimental capabilities and data for the purpose of SBC model validation, and is not meant to be an exhaustive summary.

  17. Assessment of CFD-based Response Surface Model for Ares I Supersonic Ascent Aerodynamics

    NASA Technical Reports Server (NTRS)

    Hanke, Jeremy L.

    2011-01-01

    The Ascent Force and Moment Aerodynamic (AFMA) Databases (DBs) for the Ares I Crew Launch Vehicle (CLV) were typically based on wind tunnel (WT) data, with increments provided by computational fluid dynamics (CFD) simulations for aspects of the vehicle that could not be tested in the WT tests. During the Design Analysis Cycle 3 analysis for the outer mold line (OML) geometry designated A106, a major tunnel mishap delayed the WT test for supersonic Mach numbers (M) greater than 1.6 in the Unitary Plan Wind Tunnel at NASA Langley Research Center, and the test delay pushed the final delivery of the A106 AFMA DB back by several months. The aero team developed an interim database based entirely on the already completed CFD simulations to mitigate the impact of the delay. This CFD-based database used a response surface methodology based on radial basis functions to predict the aerodynamic coefficients for M > 1.6 based on only the CFD data from both WT and flight Reynolds number conditions. The aero team used extensive knowledge of the previous AFMA DB for the A103 OML to guide the development of the CFD-based A106 AFMA DB. This report details the development of the CFD-based A106 Supersonic AFMA DB, constructs a prediction of the database uncertainty using data available at the time of development, and assesses the overall quality of the CFD-based DB both qualitatively and quantitatively. This assessment confirms that a reasonable aerodynamic database can be constructed for launch vehicles at supersonic conditions using only CFD data if sufficient knowledge of the physics and expected behavior is available. This report also demonstrates the applicability of non-parametric response surface modeling using radial basis functions for development of aerodynamic databases that exhibit both linear and non-linear behavior throughout a large data space.

  18. Classification of processes for the atomic layer deposition of metals based on mechanistic information from density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Elliott, S. D.; Dey, G.; Maimaiti, Y.

    2017-02-01

    Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.

  19. Classification of processes for the atomic layer deposition of metals based on mechanistic information from density functional theory calculations.

    PubMed

    Elliott, S D; Dey, G; Maimaiti, Y

    2017-02-07

    Reaction cycles for the atomic layer deposition (ALD) of metals are presented, based on the incomplete data that exist about their chemical mechanisms, particularly from density functional theory (DFT) calculations. ALD requires self-limiting adsorption of each precursor, which results from exhaustion of adsorbates from previous ALD pulses and possibly from inactivation of the substrate through adsorption itself. Where the latter reaction does not take place, an "abbreviated cycle" still gives self-limiting ALD, but at a much reduced rate of deposition. Here, for example, ALD growth rates are estimated for abbreviated cycles in H2-based ALD of metals. A wide variety of other processes for the ALD of metals are also outlined and then classified according to which a reagent supplies electrons for reduction of the metal. Detailed results on computing the mechanism of copper ALD by transmetallation are summarized and shown to be consistent with experimental growth rates. Potential routes to the ALD of other transition metals by using complexes of non-innocent diazadienyl ligands as metal sources are also evaluated using DFT.

  20. Directing the deposition of ferromagnetic cobalt onto Pt-tipped CdSe@CdS nanorods: synthetic and mechanistic insights.

    PubMed

    Hill, Lawrence J; Bull, Mathew M; Sung, Younghun; Simmonds, Adam G; Dirlam, Philip T; Richey, Nathaniel E; DeRosa, Sean E; Shim, In-Bo; Guin, Debanjan; Costanzo, Philip J; Pinna, Nicola; Willinger, Marc-Georg; Vogel, Walter; Char, Kookheon; Pyun, Jeffrey

    2012-10-23

    A methodology providing access to dumbbell-tipped, metal-semiconductor and metal oxide-semiconductor heterostructured nanorods has been developed. The synthesis and characterization of CdSe@CdS nanorods incorporating ferromagnetic cobalt nanoinclusions at both nanorod termini (i.e., dumbbell morphology) are presented. The key step in the synthesis of these heterostructured nanorods was the decoration of CdSe@CdS nanorods with platinum nanoparticle tips, which promoted the deposition of metallic CoNPs onto Pt-tipped CdSe@CdS nanorods. Cobalt nanoparticle tips were then selectively oxidized to afford CdSe@CdS nanorods with cobalt oxide domains at both termini. In the case of longer cobalt-tipped nanorods, heterostructured nanorods were observed to self-organize into complex dipolar assemblies, which formed as a consequence of magnetic associations of terminal CoNP tips. Colloidal polymerization of these cobalt-tipped nanorods afforded fused nanorod assemblies from the oxidation of cobalt nanoparticle tips at the ends of nanorods via the nanoscale Kirkendall effect. Wurtzite CdS nanorods survived both the deposition of metallic CoNP tips and conversion into cobalt oxide phases, as confirmed by both XRD and HRTEM analysis. A series of CdSe@CdS nanorods of four different lengths ranging from 40 to 174 nm and comparable diameters (6-7 nm) were prepared and modified with both cobalt and cobalt oxide tips. The total synthesis of these heterostructured nanorods required five steps from commercially available reagents. Key synthetic considerations are discussed, with particular emphasis on reporting isolated yields of all intermediates and products from scale up of intermediate precursors.

  1. Recent Enhancements to the Development of CFD-Based Aeroelastic Reduced-Order Models

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.

    2007-01-01

    Recent enhancements to the development of CFD-based unsteady aerodynamic and aeroelastic reduced-order models (ROMs) are presented. These enhancements include the simultaneous application of structural modes as CFD input, static aeroelastic analysis using a ROM, and matched-point solutions using a ROM. The simultaneous application of structural modes as CFD input enables the computation of the unsteady aerodynamic state-space matrices with a single CFD execution, independent of the number of structural modes. The responses obtained from a simultaneous excitation of the CFD-based unsteady aerodynamic system are processed using system identification techniques in order to generate an unsteady aerodynamic state-space ROM. Once the unsteady aerodynamic state-space ROM is generated, a method for computing the static aeroelastic response using this unsteady aerodynamic ROM and a state-space model of the structure, is presented. Finally, a method is presented that enables the computation of matchedpoint solutions using a single ROM that is applicable over a range of dynamic pressures and velocities for a given Mach number. These enhancements represent a significant advancement of unsteady aerodynamic and aeroelastic ROM technology.

  2. TADS: A CFD-based turbomachinery and analysis design system with GUI. Volume 2: User's manual

    NASA Technical Reports Server (NTRS)

    Myers, R. A.; Topp, D. A.; Delaney, R. A.

    1995-01-01

    The primary objective of this study was the development of a computational fluid dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a graphical user interface (GUI). The computer codes resulting from this effort are referred to as the Turbomachinery Analysis and Design System (TADS). This document is intended to serve as a user's manual for the computer programs which comprise the TADS system. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of various programs was done in a way that alternative solvers or grid generators could be easily incorporated into the TADS framework.

  3. Development of Unsteady Aerodynamic State-Space Models from CFD-Based Pulse Responses

    NASA Technical Reports Server (NTRS)

    Silva, Walter A.; Raveh, Daniella E.

    2001-01-01

    A method for computing discrete-time state-space models of linearized unsteady aerodynamic behavior directly from aeroelastic CFD codes is presented. The method involves the treatment of CFD-based pulse responses as Markov parameters for use in a system identification /realization algorithm. Results are presented for the AGARD 445.6 Aeroelastic Wing with four aeroelastic modes at a Mach number of 0.96 using the EZNSS Euler/Navier-Stokes flow solver with aeroelastic capability. The System/Observer/Controller Identification Toolbox (SOCIT) algorithm, based on the Ho-Kalman realization algorithm, is used to generate 15th- and 32nd-order discrete-time state-space models of the unsteady aerodynamic response of the wing over the entire frequency range of interest.

  4. CFD-based method of determining form factor k for different ship types and different drafts

    NASA Astrophysics Data System (ADS)

    Wang, Jinbao; Yu, Hai; Zhang, Yuefeng; Xiong, Xiaoqing

    2016-09-01

    The value of form factor k at different drafts is important in predicting full-scale total resistance and speed for different types of ships. In the ITTC community, most organizations predict form factor k using a low-speed model test. However, this method is problematic for ships with bulbous bows and transom. In this article, a Computational Fluid Dynamics (CFD)-based method is introduced to obtain k for different type of ships at different drafts, and a comparison is made between the CFD method and the model test. The results show that the CFD method produces reasonable k values. A grid generating method and turbulence model are briefly discussed in the context of obtaining a consistent k using CFD.

  5. Developing an Accurate CFD Based Gust Model for the Truss Braced Wing Aircraft

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.

    2013-01-01

    The increased flexibility of long endurance aircraft having high aspect ratio wings necessitates attention to gust response and perhaps the incorporation of gust load alleviation. The design of civil transport aircraft with a strut or truss-braced high aspect ratio wing furthermore requires gust response analysis in the transonic cruise range. This requirement motivates the use of high fidelity nonlinear computational fluid dynamics (CFD) for gust response analysis. This paper presents the development of a CFD based gust model for the truss braced wing aircraft. A sharp-edged gust provides the gust system identification. The result of the system identification is several thousand time steps of instantaneous pressure coefficients over the entire vehicle. This data is filtered and downsampled to provide the snapshot data set from which a reduced order model is developed. A stochastic singular value decomposition algorithm is used to obtain a proper orthogonal decomposition (POD). The POD model is combined with a convolution integral to predict the time varying pressure coefficient distribution due to a novel gust profile. Finally the unsteady surface pressure response of the truss braced wing vehicle to a one-minus-cosine gust, simulated using the reduced order model, is compared with the full CFD.

  6. CFD-based multi-objective optimization method for ship design

    NASA Astrophysics Data System (ADS)

    Tahara, Yusuke; Tohyama, Satoshi; Katsui, Tokihiro

    2006-10-01

    This paper concerns development and demonstration of a computational fluid dynamics (CFD)-based multi-objective optimization method for ship design. Three main components of the method, i.e. computer-aided design (CAD), CFD, and optimizer modules are functionally independent and replaceable. The CAD used in the present study is NAPA system, which is one of the leading CAD systems in ship design. The CFD method is FLOWPACK version 2004d, a Reynolds-averaged Navier-Stokes (RaNS) solver developed by the present authors. The CFD method is implemented into a self-propulsion simulator, where the RaNS solver is coupled with a propeller-performance program. In addition, a maneuvering simulation model is developed and applied to predict ship maneuverability performance. Two nonlinear optimization algorithms are used in the present study, i.e. the successive quadratic programming and the multi-objective genetic algorithm, while the former is mainly used to verify the results from the latter. For demonstration of the present method, a multi-objective optimization problem is formulated where ship propulsion and maneuverability performances are considered. That is, the aim is to simultaneously minimize opposite hydrodynamic performances in design tradeoff. In the following, an overview of the present method is given, and results are presented and discussed for tanker stern optimization problem including detailed verification work on the present numerical schemes.

  7. An automatic CFD-based flow diverter optimization principle for patient-specific intracranial aneurysms.

    PubMed

    Janiga, Gábor; Daróczy, László; Berg, Philipp; Thévenin, Dominique; Skalej, Martin; Beuing, Oliver

    2015-11-05

    The optimal treatment of intracranial aneurysms using flow diverting devices is a fundamental issue for neuroradiologists as well as neurosurgeons. Due to highly irregular manifold aneurysm shapes and locations, the choice of the stent and the patient-specific deployment strategy can be a very difficult decision. To support the therapy planning, a new method is introduced that combines a three-dimensional CFD-based optimization with a realistic deployment of a virtual flow diverting stent for a given aneurysm. To demonstrate the feasibility of this method, it was applied to a patient-specific intracranial giant aneurysm that was successfully treated using a commercial flow diverter. Eight treatment scenarios with different local compressions were considered in a fully automated simulation loop. The impact on the corresponding blood flow behavior was evaluated qualitatively as well as quantitatively, and the optimal configuration for this specific case was identified. The virtual deployment of an uncompressed flow diverter reduced the inflow into the aneurysm by 24.4% compared to the untreated case. Depending on the positioning of the local stent compression below the ostium, blood flow reduction could vary between 27.3% and 33.4%. Therefore, a broad range of potential treatment outcomes was identified, illustrating the variability of a given flow diverter deployment in general. This method represents a proof of concept to automatically identify the optimal treatment for a patient in a virtual study under certain assumptions. Hence, it contributes to the improvement of virtual stenting for intracranial aneurysms and can support physicians during therapy planning in the future. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Multiphase CFD-based models for chemical looping combustion process: Fuel reactor modeling

    SciTech Connect

    Jung, Jonghwun; Gamwo, I.K.

    2008-04-21

    Chemical looping combustion (CLC) is a flameless two-step fuel combustion that produces a pure CO2 stream, ready for compression and sequestration. The process is composed of two interconnected fluidized bed reactors. The air reactor which is a conventional circulating fluidized bed and the fuel reactor which is a bubbling fluidized bed. The basic principle is to avoid the direct contact of air and fuel during the combustion by introducing a highly-reactive metal particle, referred to as oxygen carrier, to transport oxygen from the air to the fuel. In the process, the products from combustion are kept separated from the rest of the flue gases namely nitrogen and excess oxygen. This process eliminates the energy intensive step to separate the CO2 from nitrogen-rich flue gas that reduce the thermal efficiency. Fundamental knowledge of multiphase reactive fluid dynamic behavior of the gas–solid flow is essential for the optimization and operation of a chemical looping combustor. Our recent thorough literature review shows that multiphase CFD-based models have not been adapted to chemical looping combustion processes in the open literature. In this study, we have developed the reaction kinetics model of the fuel reactor and implemented the kinetic model into a multiphase hydrodynamic model, MFIX, developed earlier at the National Energy Technology Laboratory. Simulated fuel reactor flows revealed high weight fraction of unburned methane fuel in the flue gas along with CO2 and H2O. This behavior implies high fuel loss at the exit of the reactor and indicates the necessity to increase the residence time, say by decreasing the fuel flow rate, or to recirculate the unburned methane after condensing and removing CO2.

  9. Mechanistic study of atomic layer deposition of Al{sub x}Si{sub y}O thin film via in-situ FTIR spectroscopy

    SciTech Connect

    Cho, Jea; Kim, Taeseung; Seegmiller, Trevor; Chang, Jane P.

    2015-09-15

    A study of surface reaction mechanism on atomic layer deposition (ALD) of aluminum silicate (Al{sub x}Si{sub y}O) was conducted with trimethylaluminum (TMA) and tetraethoxysilane (TEOS) as precursors and H{sub 2}O as the oxidant. In-situ Fourier transform infrared spectroscopy (FTIR) was utilized to elucidate the underlying surface mechanism that enables the deposition of Al{sub x}Si{sub y}O by ALD. In-situ FTIR study revealed that ineffective hydroxylation of the surface ethoxy (–OCH{sub 2}CH{sub 3}) groups prohibits ALD of SiO{sub 2} by TEOS/H{sub 2}O. In contrast, effective desorption of the surface ethoxy group was observed in TEOS/H{sub 2}O/TMA/H{sub 2}O chemistry. The presence of Al-OH* group in vicinity of partially hydroxylated ethoxy (–OCH{sub 2}CH{sub 3}) group was found to propagate disproportionation reaction, which results in ALD of Al{sub x}Si{sub y}O. The maximum thickness from incorporation of SiO{sub x} from alternating exposures of TEOS/H{sub 2}O chemistry in Al{sub x}Si{sub y}O was found to be ∼2 Å, confirmed by high resolution transmission electron microscopy measurements.

  10. TADS: A CFD-based turbomachinery and analysis design system with GUI. Volume 1: Method and results

    NASA Technical Reports Server (NTRS)

    Topp, D. A.; Myers, R. A.; Delaney, R. A.

    1995-01-01

    The primary objective of this study was the development of a computational fluid dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a graphical user interface (GUI). The computer codes resulting from this effort are referred to as the Turbomachinery Analysis and Design System (TADS). This document describes the theoretical basis and analytical results from the TADS system. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of various programs was done in a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a highly loaded fan, a compressor stator, a low-speed turbine blade, and a transonic turbine vane.

  11. TADS--A CFD-Based Turbomachinery Analysis and Design System with GUI: User's Manual. 2.0

    NASA Technical Reports Server (NTRS)

    Koiro, M. J.; Myers, R. A.; Delaney, R. A.

    1999-01-01

    The primary objective of this study was the development of a Computational Fluid Dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a Graphical User Interface (GUI). The computer codes resulting from this effort are referred to as TADS (Turbomachinery Analysis and Design System). This document is intended to serve as a User's Manual for the computer programs which comprise the TADS system, developed under Task 18 of NASA Contract NAS3-27350, ADPAC System Coupling to Blade Analysis & Design System GUI and Task 10 of NASA Contract NAS3-27394, ADPAC System Coupling to Blade Analysis & Design System GUI, Phase II-Loss, Design and, Multi-stage Analysis. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) in an interactive package. Throughflow analysis and design capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of the various programs was done in such a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a highly loaded fan, a compressor stator, a low speed turbine blade and a transonic turbine vane.

  12. Development of CFD-Based Simulation Tools for In-Situ Thermal Processing of Oil Shale/Sands

    SciTech Connect

    None, None

    2012-02-01

    In our research, we are taking the novel approach of developing and applying high performance computing, computational fluid dynamics (CFD)-based simulation tools to a modified in-situ process for production of oil from oil shale. The simulation tools being developed capture the relevant physical processes and data from a large-scale system. The modified in-situ application is a pilot-scale heat transfer process inside Red Leaf Resources EcoShale capsule. We demonstrate the need to understand fluid flow behavior in the convective channels of the rubblized shale bed as convective heating greatly decreases the time required to heat the oil shale to the production temperature when compared with conductive heating alone. We have developed and implemented a geometry creation strategy for a representative section of the EcoShale capsule, developed a meshing approach to deal with the complicated geometry and produce a well-behaved mesh, analyzed the effects of boundary conditions on the simulation results, and devised a new operator splitting solution algorithm that reduces computational costs by taking advantage of the differing convective and conductive time scales occurring in the simulation. These simulation tools can be applied to a wide range of processes involving convective fluid flow heating in rubblized beds.

  13. TADS: A CFD-Based Turbomachinery Analysis and Design System with GUI: Methods and Results. 2.0

    NASA Technical Reports Server (NTRS)

    Koiro, M. J.; Myers, R. A.; Delaney, R. A.

    1999-01-01

    The primary objective of this study was the development of a Computational Fluid Dynamics (CFD) based turbomachinery airfoil analysis and design system, controlled by a Graphical User Interface (GUI). The computer codes resulting from this effort are referred to as TADS (Turbomachinery Analysis and Design System). This document is the Final Report describing the theoretical basis and analytical results from the TADS system developed under Task 10 of NASA Contract NAS3-27394, ADPAC System Coupling to Blade Analysis & Design System GUI, Phase II-Loss, Design and. Multi-stage Analysis. TADS couples a throughflow solver (ADPAC) with a quasi-3D blade-to-blade solver (RVCQ3D) or a 3-D solver with slip condition on the end walls (B2BADPAC) in an interactive package. Throughflow analysis and design capability was developed in ADPAC through the addition of blade force and blockage terms to the governing equations. A GUI was developed to simplify user input and automate the many tasks required to perform turbomachinery analysis and design. The coupling of the various programs was done in such a way that alternative solvers or grid generators could be easily incorporated into the TADS framework. Results of aerodynamic calculations using the TADS system are presented for a multistage compressor, a multistage turbine, two highly loaded fans, and several single stage compressor and turbine example cases.

  14. CFD-based surrogate modeling of liquid rocket engine components via design space refinement and sensitivity assessment

    NASA Astrophysics Data System (ADS)

    Mack, Yolanda

    Computational fluid dynamics (CFD) can be used to improve the design and optimization of rocket engine components that traditionally rely on empirical calculations and limited experimentation. CFD based-design optimization can be made computationally affordable through the use of surrogate modeling which can then facilitate additional parameter sensitivity assessments. The present study investigates surrogate-based adaptive design space refinement (DSR) using estimates of surrogate uncertainty to probe the CFD analyses and to perform sensitivity assessments for complex fluid physics associated with liquid rocket engine components. Three studies were conducted. First, a surrogate-based preliminary design optimization was conducted to improve the efficiency of a compact radial turbine for an expander cycle rocket engine while maintaining low weight. Design space refinement was used to identify function constraints and to obtain a high accuracy surrogate model in the region of interest. A merit function formulation for multi-objective design point selection reduced the number of design points by an order of magnitude while maintaining good surrogate accuracy among the best trade-off points. Second, bluff body-induced flow was investigated to identify the physics and surrogate modeling issues related to the flow's mixing dynamics. Multiple surrogates and DSR were instrumental in identifying designs for which the CFD model was deficient and to help to pinpoint the nature of the deficiency. Next, a three-dimensional computational model was developed to explore the wall heat transfer of a GO2/GH2 shear coaxial single element injector. The interactions between turbulent recirculating flow structures, chemical kinetics, and heat transfer are highlighted. Finally, a simplified computational model of multi-element injector flows was constructed to explore the sensitivity of wall heating and improve combustion efficiency to injector element spacing. Design space refinement

  15. Variability in the Propagation Phase of CFD-Based Noise Prediction: Summary of Results From Category 8 of the BANC-III Workshop

    NASA Technical Reports Server (NTRS)

    Lopes, Leonard; Redonnet, Stephane; Imamura, Taro; Ikeda, Tomoaki; Zawodny, Nikolas; Cunha, Guilherme

    2015-01-01

    The usage of Computational Fluid Dynamics (CFD) in noise prediction typically has been a two part process: accurately predicting the flow conditions in the near-field and then propagating the noise from the near-field to the observer. Due to the increase in computing power and the cost benefit when weighed against wind tunnel testing, the usage of CFD to estimate the local flow field of complex geometrical structures has become more routine. Recently, the Benchmark problems in Airframe Noise Computation (BANC) workshops have provided a community focus on accurately simulating the local flow field near the body with various CFD approaches. However, to date, little effort has been given into assessing the impact of the propagation phase of noise prediction. This paper includes results from the BANC-III workshop which explores variability in the propagation phase of CFD-based noise prediction. This includes two test cases: an analytical solution of a quadrupole source near a sphere and a computational solution around a nose landing gear. Agreement between three codes was very good for the analytic test case, but CFD-based noise predictions indicate that the propagation phase can introduce 3dB or more of variability in noise predictions.

  16. Mechanistic facility safety and source term analysis

    SciTech Connect

    PLYS, M.G.

    1999-06-09

    A PC-based computer program was created for facility safety and source term analysis at Hanford The program has been successfully applied to mechanistic prediction of source terms from chemical reactions in underground storage tanks, hydrogen combustion in double contained receiver tanks, and proccss evaluation including the potential for runaway reactions in spent nuclear fuel processing. Model features include user-defined facility room, flow path geometry, and heat conductors, user-defined non-ideal vapor and aerosol species, pressure- and density-driven gas flows, aerosol transport and deposition, and structure to accommodate facility-specific source terms. Example applications are presented here.

  17. Assessing uncertainty in mechanistic models

    Treesearch

    Edwin J. Green; David W. MacFarlane; Harry T. Valentine

    2000-01-01

    Concern over potential global change has led to increased interest in the use of mechanistic models for predicting forest growth. The rationale for this interest is that empirical models may be of limited usefulness if environmental conditions change. Intuitively, we expect that mechanistic models, grounded as far as possible in an understanding of the biology of tree...

  18. From mechanistic to functional behaviorism.

    PubMed

    Moxley, R A

    1992-11-01

    A shift from mechanistic behaviorism to functional behaviorism is presented against the background of two historical traditions, one with an emphasis on form, the other with an emphasis on function. Skinner's work, which made more contributions to a functional behaviorism than to a mechanistic behaviorism, exemplifies this shift. The two traditions and an account of Skinner's development of functional relations are presented in order to show Skinner's contributions to aligning modern behavior analysis with the functional tradition.

  19. Electron transfer with self-assembled copper ions at Au-deposited biomimetic films: mechanistic ‘anomalies’ disclosed by temperature- and pressure-assisted fast-scan voltammetry

    NASA Astrophysics Data System (ADS)

    Khoshtariya, Dimitri E.; Dolidze, Tinatin D.; Tretyakova, Tatyana; van Eldik, Rudi

    2015-06-01

    It has been suggested that electron transfer (ET) processes occurring in complex environments capable of glass transitions, specifically in biomolecules, under certain conditions may experience the medium’s nonlinear response and nonergodic kinetic patterns. The interiors of self-assembled organic films (SAMs) deposited on solid conducting platforms (electrodes) are known to undergo glassy dynamics as well, hence they may also exhibit the abovementioned ‘irregularities’. We took advantage of Cu2+ ions as redox-active probes trapped in the Au-deposited  -COOH-terminated SAMs, either L-cysteine, or 3-mercaptopropionic acid diluted by the inert 2-mercaptoethanol, to systematically study the impact of glassy dynamics on ET using the fast-scan voltammetry technique and its temperature and high-pressure extensions. We found that respective kinetic data can be rationalized within the extended Marcus theory, taking into account the frictionally controlled (adiabatic) mechanism for short-range ET, and complications due to the medium’s nonlinear response and broken ergodicity. This combination shows up in essential deviations from the conventional energy gap (overpotential) dependence and in essentially nonlinear temperature (Arrhenius) and high-pressure patterns, respectively. Biomimetic aspects for these systems are also discussed in the context of recently published results for interfacial ET involving self-assembled blue copper protein (azurin) placed in contact with a glassy environment.

  20. Food for Thought ... Mechanistic Validation

    PubMed Central

    Hartung, Thomas; Hoffmann, Sebastian; Stephens, Martin

    2013-01-01

    Summary Validation of new approaches in regulatory toxicology is commonly defined as the independent assessment of the reproducibility and relevance (the scientific basis and predictive capacity) of a test for a particular purpose. In large ring trials, the emphasis to date has been mainly on reproducibility and predictive capacity (comparison to the traditional test) with less attention given to the scientific or mechanistic basis. Assessing predictive capacity is difficult for novel approaches (which are based on mechanism), such as pathways of toxicity or the complex networks within the organism (systems toxicology). This is highly relevant for implementing Toxicology for the 21st Century, either by high-throughput testing in the ToxCast/ Tox21 project or omics-based testing in the Human Toxome Project. This article explores the mostly neglected assessment of a test's scientific basis, which moves mechanism and causality to the foreground when validating/qualifying tests. Such mechanistic validation faces the problem of establishing causality in complex systems. However, pragmatic adaptations of the Bradford Hill criteria, as well as bioinformatic tools, are emerging. As critical infrastructures of the organism are perturbed by a toxic mechanism we argue that by focusing on the target of toxicity and its vulnerability, in addition to the way it is perturbed, we can anchor the identification of the mechanism and its verification. PMID:23665802

  1. HTGR Mechanistic Source Terms White Paper

    SciTech Connect

    Wayne Moe

    2010-07-01

    The primary purposes of this white paper are: (1) to describe the proposed approach for developing event specific mechanistic source terms for HTGR design and licensing, (2) to describe the technology development programs required to validate the design methods used to predict these mechanistic source terms and (3) to obtain agreement from the NRC that, subject to appropriate validation through the technology development program, the approach for developing event specific mechanistic source terms is acceptable

  2. Rational and Mechanistic Perspectives on Reinforcement Learning

    ERIC Educational Resources Information Center

    Chater, Nick

    2009-01-01

    This special issue describes important recent developments in applying reinforcement learning models to capture neural and cognitive function. But reinforcement learning, as a theoretical framework, can apply at two very different levels of description: "mechanistic" and "rational." Reinforcement learning is often viewed in mechanistic terms--as…

  3. Transitioning from AOP to IATA - Exploiting mechanistic ...

    EPA Pesticide Factsheets

    Slide presentation at satellite meeting of the QSAR2016 Meeting on How to Transition from AOP to IATA-Exploiting mechanistic insight for practical decision making. . Slide presentation at satellite meeting of the QSAR2016 Meeting on How to Transition from AOP to IATA-Exploiting mechanistic insight for practical decision making. .

  4. A generalized mechanistic codon model.

    PubMed

    Zaheri, Maryam; Dib, Linda; Salamin, Nicolas

    2014-09-01

    Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide substitution matrices, the equilibrium frequency of codons, and the selection rate parameter. The entities of the nucleotide substitution matrices and selection rate are considered as parameters of the model, which are optimized by maximum likelihood. Our fully mechanistic model allows the instantaneous substitution matrix between codons to be fully estimated with only 19 parameters instead of 3,721, by using the biological interdependence existing between positions within codons. We illustrate the properties of our models using computer simulations and assessed its relevance by comparing the AICc measures of our model and other models of codon evolution on simulations and a large range of empirical data sets. We show that our model fits most biological data better compared with the current codon models. Furthermore, the parameters in our model can be interpreted in a similar way as the exchangeability rates found in empirical codon models. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Mechanistic insights into nicotine withdrawal

    PubMed Central

    Paolini, Michael; De Biasi, Mariella

    2012-01-01

    Smoking is responsible for over 400,000 premature deaths in the United States every year, making it the leading cause of preventable death. In addition, smoking-related illness leads to billions of dollars in healthcare expenditures and lost productivity annually. The public is increasingly aware that successfully abstaining from smoking at any age can add years to one’s life and reduce many of the harmful effects of smoking. Although the majority of smokers desire to quit, only a small fraction of attempts to quit are actually successful. The symptoms associated with nicotine withdrawal are a primary deterrent to cessation and they need to be quelled to avoid early relapse. This review will focus on the neuroadaptations caused by chronic nicotine exposure and discuss how those changes lead to a withdrawal syndrome upon smoking cessation. Besides examining how nicotine usurps the endogenous reward system, we will discuss how the habenula is part of a circuit that plays a critical role in the aversive effects of high nicotine doses and nicotine withdrawal. We will also provide an updated summary of the role of various nicotinic receptor subtypes in the mechanisms of withdrawal. This growing knowledge provides mechanistic insights into current and future smoking cessation therapies. PMID:21782803

  6. Negative mechanistic reasoning in medical intervention assessment.

    PubMed

    Jerkert, Jesper

    2015-12-01

    Traditionally, mechanistic reasoning has been assigned a negligible role in standard EBM (evidence-based medicine) literature, although some recent authors have argued for an upgrade. Even so, the mechanistic reasoning that has received attention has almost exclusively been positive--both in an epistemic sense of claiming that there is a mechanistic chain and in a health-related sense of there being claimed benefits for the patient. Negative mechanistic reasoning has been neglected, both in the epistemic and in the health-related sense. I distinguish three main types of negative mechanistic reasoning and subsume them under a new definition of mechanistic reasoning in the context of assessing medical interventions. This definition is wider than a previous suggestion in the literature. Each negative type corresponds to a range of evidential strengths, and it is argued that there are differences with respect to typical evidential strengths. The variety of negative mechanistic reasoning should be acknowledged in EBM, and it presents a serious challenge to proponents of so-called medical hierarchies of evidence.

  7. Development of a Guinea Pig Lung Deposition Model

    DTIC Science & Technology

    2016-01-01

    6 3.4. MECHANISTIC MODEL OF PARTICLE DEPOSITION IN THE LUNG ................................. 7 4.0 SOFTWARE IMPLEMENTATION...4 Figure 2. Particle deposition in the lung of the guinea pig via endotracheal breathing...10 Figure 3. Deposition fraction of various size particles at different lung depths. ..................................... 11 Figure 4

  8. Mechanistic models in computational social science

    NASA Astrophysics Data System (ADS)

    Holme, Petter; Liljeros, Fredrik

    2015-09-01

    Quantitative social science is not only about regression analysis or, in general, data inference. Computer simulations of social mechanisms have an over 60 years long history. They have been used for many different purposes—to test scenarios, to test the consistency of descriptive theories (proof-of-concept models), to explore emergent phenomena, for forecasting, etc. In this essay, we sketch these historical developments, the role of mechanistic models in the social sciences and the influences from the natural and formal sciences. We argue that mechanistic computational models form a natural common ground for social and natural sciences, and look forward to possible future information flow across the social-natural divide.

  9. Mechanistic Indicators of Childhood Asthma (MICA) Study

    EPA Science Inventory

    The Mechanistic Indicators of Childhood Asthma (MICA) Study has been designed to incorporate state-of-the-art technologies to examine the physiological and environmental factors that interact to increase the risk of asthmatic responses. MICA is primarily a clinically-bases obser...

  10. Reductive photocarboxylation of phenanthrene: A mechanistic investigation

    SciTech Connect

    Nikolaitchik, A.V.; Rodgers, M.A.J.; Neckers, D.C.

    1996-02-09

    Mechanistic aspects of photochemicl reactions between phenathrene and carbon dioxide while in the presence of N,N-dimethylaniline was studied. Five products were produced as characterized by NMR and GC-MS. The authors related changes in product yields to changes in reaction conditions. 31 refs., 6 figs., 3 tabs.

  11. Testing mechanistic models of growth in insects.

    PubMed

    Maino, James L; Kearney, Michael R

    2015-11-22

    Insects are typified by their small size, large numbers, impressive reproductive output and rapid growth. However, insect growth is not simply rapid; rather, insects follow a qualitatively distinct trajectory to many other animals. Here we present a mechanistic growth model for insects and show that increasing specific assimilation during the growth phase can explain the near-exponential growth trajectory of insects. The presented model is tested against growth data on 50 insects, and compared against other mechanistic growth models. Unlike the other mechanistic models, our growth model predicts energy reserves per biomass to increase with age, which implies a higher production efficiency and energy density of biomass in later instars. These predictions are tested against data compiled from the literature whereby it is confirmed that insects increase their production efficiency (by 24 percentage points) and energy density (by 4 J mg(-1)) between hatching and the attainment of full size. The model suggests that insects achieve greater production efficiencies and enhanced growth rates by increasing specific assimilation and increasing energy reserves per biomass, which are less costly to maintain than structural biomass. Our findings illustrate how the explanatory and predictive power of mechanistic growth models comes from their grounding in underlying biological processes.

  12. Mechanistic Indicators of Childhood Asthma (MICA) Study

    EPA Science Inventory

    The Mechanistic Indicators of Childhood Asthma (MICA) Study has been designed to incorporate state-of-the-art technologies to examine the physiological and environmental factors that interact to increase the risk of asthmatic responses. MICA is primarily a clinically-bases obser...

  13. Applying mechanistic models in bioprocess development.

    PubMed

    Lencastre Fernandes, Rita; Bodla, Vijaya Krishna; Carlquist, Magnus; Heins, Anna-Lena; Eliasson Lantz, Anna; Sin, Gürkan; Gernaey, Krist V

    2013-01-01

    The available knowledge on the mechanisms of a bioprocess system is central to process analytical technology. In this respect, mechanistic modeling has gained renewed attention, since a mechanistic model can provide an excellent summary of available process knowledge. Such a model therefore incorporates process-relevant input (critical process variables)-output (product concentration and product quality attributes) relations. The model therefore has great value in planning experiments, or in determining which critical process variables need to be monitored and controlled tightly. Mechanistic models should be combined with proper model analysis tools, such as uncertainty and sensitivity analysis. When assuming distributed inputs, the resulting uncertainty in the model outputs can be decomposed using sensitivity analysis to determine which input parameters are responsible for the major part of the output uncertainty. Such information can be used as guidance for experimental work; i.e., only parameters with a significant influence on model outputs need to be determined experimentally. The use of mechanistic models and model analysis tools is demonstrated in this chapter. As a practical case study, experimental data from Saccharomyces cerevisiae fermentations are used. The data are described with the well-known model of Sonnleitner and Käppeli (Biotechnol Bioeng 28:927-937, 1986) and the model is analyzed further. The methods used are generic, and can be transferred easily to other, more complex case studies as well.

  14. Exploring Organic Mechanistic Puzzles with Molecular Modeling

    ERIC Educational Resources Information Center

    Horowitz, Gail; Schwartz, Gary

    2004-01-01

    The molecular modeling was used to reinforce more general skills such as deducing and drawing reaction mechanisms, analyzing reaction kinetics and thermodynamics and drawing reaction coordinate energy diagrams. This modeling was done through the design of mechanistic puzzles, involving reactions not familiar to the students.

  15. Exploring Organic Mechanistic Puzzles with Molecular Modeling

    ERIC Educational Resources Information Center

    Horowitz, Gail; Schwartz, Gary

    2004-01-01

    The molecular modeling was used to reinforce more general skills such as deducing and drawing reaction mechanisms, analyzing reaction kinetics and thermodynamics and drawing reaction coordinate energy diagrams. This modeling was done through the design of mechanistic puzzles, involving reactions not familiar to the students.

  16. Testing mechanistic models of growth in insects

    PubMed Central

    Maino, James L.; Kearney, Michael R.

    2015-01-01

    Insects are typified by their small size, large numbers, impressive reproductive output and rapid growth. However, insect growth is not simply rapid; rather, insects follow a qualitatively distinct trajectory to many other animals. Here we present a mechanistic growth model for insects and show that increasing specific assimilation during the growth phase can explain the near-exponential growth trajectory of insects. The presented model is tested against growth data on 50 insects, and compared against other mechanistic growth models. Unlike the other mechanistic models, our growth model predicts energy reserves per biomass to increase with age, which implies a higher production efficiency and energy density of biomass in later instars. These predictions are tested against data compiled from the literature whereby it is confirmed that insects increase their production efficiency (by 24 percentage points) and energy density (by 4 J mg−1) between hatching and the attainment of full size. The model suggests that insects achieve greater production efficiencies and enhanced growth rates by increasing specific assimilation and increasing energy reserves per biomass, which are less costly to maintain than structural biomass. Our findings illustrate how the explanatory and predictive power of mechanistic growth models comes from their grounding in underlying biological processes. PMID:26609084

  17. Mechanistic fracture criteria for the failure of human cortical bone

    SciTech Connect

    Nalla, Ravi K.; Kinney, John H.; Ritchie, Robert O.

    2002-12-13

    A mechanistic understanding of fracture in human bone is critical to predicting fracture risk associated with age and disease. Despite extensive work, a mechanistic framework for describing how the underlying microstructure affects the failure mode in bone is lacking.

  18. Toward mechanistic classification of enzyme functions.

    PubMed

    Almonacid, Daniel E; Babbitt, Patricia C

    2011-06-01

    Classification of enzyme function should be quantitative, computationally accessible, and informed by sequences and structures to enable use of genomic information for functional inference and other applications. Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often converge to similar mechanisms too, suggesting that reaction mechanisms could be used to develop finer-grained functional descriptions than provided by the Enzyme Commission (EC) system currently in use. Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic similarities. Together, these provide a foundation for new classifications of enzyme function.

  19. New mechanistic interpretations for nitrone reactivity.

    PubMed

    Merino, Pedro; Tejero, Tomás; Delso, Ignacio; Matute, Rosa

    2017-03-22

    The reactivity of nitrones in cycloadditions and related reactions is revisited by introducing a topological perspective. In particular, the study of electron localization function (ELF) along a reaction pathway allows evaluating bond reorganization showing that in several cases the bonds are formed in a sequential way, the second one being formed once the first one is already formed. Both classical 1,3-dipolar cycloadditions and Mannich-type reactions revealed unexpected features often underestimated in classical mechanistic studies.

  20. Mechanistic materials modeling for nuclear fuel performance

    DOE PAGES

    Tonks, Michael R.; Andersson, David; Phillpot, Simon R.; ...

    2017-03-15

    Fuel performance codes are critical tools for the design, certification, and safety analysis of nuclear reactors. However, their ability to predict fuel behavior under abnormal conditions is severely limited by their considerable reliance on empirical materials models correlated to burn-up (a measure of the number of fission events that have occurred, but not a unique measure of the history of the material). In this paper, we propose a different paradigm for fuel performance codes to employ mechanistic materials models that are based on the current state of the evolving microstructure rather than burn-up. In this approach, a series of statemore » variables are stored at material points and define the current state of the microstructure. The evolution of these state variables is defined by mechanistic models that are functions of fuel conditions and other state variables. The material properties of the fuel and cladding are determined from microstructure/property relationships that are functions of the state variables and the current fuel conditions. Multiscale modeling and simulation is being used in conjunction with experimental data to inform the development of these models. Finally, this mechanistic, microstructure-based approach has the potential to provide a more predictive fuel performance capability, but will require a team of researchers to complete the required development and to validate the approach.« less

  1. CFD based draft tube hydraulic design optimization

    NASA Astrophysics Data System (ADS)

    McNabb, J.; Devals, C.; Kyriacou, S. A.; Murry, N.; Mullins, B. F.

    2014-03-01

    The draft tube design of a hydraulic turbine, particularly in low to medium head applications, plays an important role in determining the efficiency and power characteristics of the overall machine, since an important proportion of the available energy, being in kinetic form leaving the runner, needs to be recovered by the draft tube into static head. For large units, these efficiency and power characteristics can equate to large sums of money when considering the anticipated selling price of the energy produced over the machine's life-cycle. This same draft tube design is also a key factor in determining the overall civil costs of the powerhouse, primarily in excavation and concreting, which can amount to similar orders of magnitude as the price of the energy produced. Therefore, there is a need to find the optimum compromise between these two conflicting requirements. In this paper, an elaborate approach is described for dealing with this optimization problem. First, the draft tube's detailed geometry is defined as a function of a comprehensive set of design parameters (about 20 of which a subset is allowed to vary during the optimization process) and are then used in a non-uniform rational B-spline based geometric modeller to fully define the wetted surfaces geometry. Since the performance of the draft tube is largely governed by 3D viscous effects, such as boundary layer separation from the walls and swirling flow characteristics, which in turn governs the portion of the available kinetic energy which will be converted into pressure, a full 3D meshing and Navier-Stokes analysis is performed for each design. What makes this even more challenging is the fact that the inlet velocity distribution to the draft tube is governed by the runner at each of the various operating conditions that are of interest for the exploitation of the powerhouse. In order to determine these inlet conditions, a combined steady-state runner and an initial draft tube analysis, using a stage interface between them, must first be performed for each operating condition. Due to the computationally intensive nature of the evaluation process, the efficiency of the optimization algorithm becomes important. Therefore, a state-of-the-art hierarchical-metamodel-assisted evolutionary algorithm is used.

  2. A mechanistic analysis of the Birch Reduction.

    PubMed

    Zimmerman, Howard E

    2012-02-21

    The Birch Reduction is one of the main reactions of organic chemistry. The reaction involves the reaction of dissolving metals in ammonia with aromatic compounds to produce 1,4-cyclohexadienes. Discovered by Arthur Birch in 1944, the reaction occupies 300 pages in Organic Reactions to describe its synthetic versatility. Thus, it is remarkable that the reaction mechanism has been so very controversial and only relatively recently has been firmly established. Perhaps this is not that surprising, since the reaction also has many unusual and esoteric mechanistic facets. Here, I provide a description of how I have applied ever-evolving levels of quantum mechanics and a novel experimental test to understand details of the mechanism and the origins of the selectivities observed in the Birch reduction. The reaction involves an initial radical anion resulting from introduction of an electron from the blue liquid ammonia solution of free electrons formed by the dissolution of Li or related metals. This radical anion is protonated by an alcohol and then further reduced to a carbanion. Finally, the carbanion is protonated using a second proton to afford a nonconjugated cyclohexadiene. The regiochemistry depends on substituents present. With 18 resonance structures in the case of anisole radical anion, prediction of the initial protonation site would seem difficult. Nevertheless, computational methods from Hückel theory through modern density functional calculations do correctly predict the site of protonation. An esoteric test established this mechanism experimentally. The nature of the carbanion also is of mechanistic interest, and the preponderance of the resonance structure shown was revealed from Hückel calculations involving variable bond orders. For the trianion from benzoic acid, parallel questions about structure are apparent, and have been answered. Some mechanistic questions are answered experimentally and some by modern computations. Recently, our mechanistic

  3. Mechanistic considerations in small fish carcinogenicity testing.

    PubMed

    Law, J M

    2001-01-01

    Historically, small fish species have proven useful both as environmental sentinels and as versatile test animals in toxicity and carcinogenicity bioassays. They can be bred in large numbers, have low maintenance and bioassay costs, and have a low background incidence of tumors. However, more mechanistic information is needed to help validate the information garnered from these models and to keep pace with other more fully developed animal models. This paper focuses on mechanistic considerations when using small fish models for carcinogenicity testing. Several small aquarium fish species have proven useful. The Japanese medaka is perhaps the best characterized small fish model for carcinogenicity testing; however, the zebrafish is emerging as an important model because it is well characterized genetically. Both route and methodology of exposure may affect the outcome of the study. Most studies have been conducted by introducing the test compound into the ambient water, but dietary exposures and embryo microinjection have also been used. Other considerations in study design include use of an initiating carcinogen, such as diethlynitrosamine, and differences in xenobiotic metabolism, such as the fact that fish CYP2B is refractory to phenobarbital induction. The small size of these models has perhaps limited some types of mechanistic studies, such as formation and repair of DNA adducts in response to carcinogen exposure. However, improved analytical methods are allowing greater resolution and should be applied to small fish species. Slide-based methods such as immunohistochemistry are an important adjunct to routine histopathology and should be included in study design. However, there is a need for development of more species-specific antibodies for fish research. There is also a need for more fish-specific data on cytokines, serum biochemistry, and oncogenes to strengthen the use of these important test models.

  4. Mechanistic studies of carbon monoxide reduction

    SciTech Connect

    Geoffroy, G.L.

    1990-06-12

    The progress made during the current grant period (1 January 1988--1 April 1990) in three different areas of research is summarized. The research areas are: (1) oxidatively-induced double carbonylation reactions to form {alpha}-ketoacyl complexes and studies of the reactivity of the resulting compounds, (2) mechanistic studies of the carbonylation of nitroaromatics to form isocyanates, carbamates, and ureas, and (3) studies of the formation and reactivity of unusual metallacycles and alkylidene ligands supported on binuclear iron carbonyl fragments. 18 refs., 5 figs., 1 tab.

  5. Composite Nanomechanics: A Mechanistic Properties Prediction

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Handler, Louis M.; Manderscheid, Jane M.

    2007-01-01

    A unique mechanistic theory is described to predict the properties of nanocomposites. The theory is based on composite micromechanics with progressive substructuring down to a nanoscale slice of a nanofiber where all the governing equations are formulated. These equations have been programmed in a computer code. That computer code is used to predict 25 properties of a mononanofiber laminate. The results are presented graphically and discussed with respect to their practical significance. Most of the results show smooth distributions. Results for matrix-dependent properties show bimodal through-the-thickness distribution with discontinuous changes from mode to mode.

  6. Composite Nanomechanics: A Mechanistic Properties Prediction

    NASA Technical Reports Server (NTRS)

    Chamis, Christos C.; Handler, Louis M.; Manderscheid, Jane M.

    2007-01-01

    A unique mechanistic theory is described to predict the properties of nanocomposites. The theory is based on composite micromechanics with progressive substructuring down to a nanoscale slice of a nanofiber where all the governing equations are formulated. These equations hav e been programmed in a computer code. That computer code is used to predict 25 properties of a mononanofiber laminate. The results are pr esented graphically and discussed with respect to their practical sig nificance. Most of the results show smooth distributions. Results for matrix-dependent properties show bimodal through-the-thickness distr ibution with discontinuous changes from mode to mode.

  7. Tear gas: an epidemiological and mechanistic reassessment

    PubMed Central

    Rothenberg, Craig; Achanta, Satyanarayana; Svendsen, Erik R.

    2016-01-01

    Deployments of tear gas and pepper spray have rapidly increased worldwide. Large amounts of tear gas have been used in densely populated cities, including Cairo, Istanbul, Rio de Janeiro, Manama (Bahrain), and Hong Kong. In the United States, tear gas was used extensively during recent riots in Ferguson, Missouri. Whereas tear gas deployment systems have rapidly improved—with aerial drone systems tested and requested by law enforcement—epidemiological and mechanistic research have lagged behind and have received little attention. Case studies and recent epidemiological studies revealed that tear gas agents can cause lung, cutaneous, and ocular injuries, with individuals affected by chronic morbidities at high risk for complications. Mechanistic studies identified the ion channels TRPV1 and TRPA1 as targets of capsaicin in pepper spray, and of the tear gas agents chloroacetophenone, CS, and CR. TRPV1 and TRPA1 localize to pain‐sensing peripheral sensory neurons and have been linked to acute and chronic pain, cough, asthma, lung injury, dermatitis, itch, and neurodegeneration. In animal models, transient receptor potential inhibitors show promising effects as potential countermeasures against tear gas injuries. On the basis of the available data, a reassessment of the health risks of tear gas exposures in the civilian population is advised, and development of new countermeasures is proposed. PMID:27391380

  8. Tear gas: an epidemiological and mechanistic reassessment.

    PubMed

    Rothenberg, Craig; Achanta, Satyanarayana; Svendsen, Erik R; Jordt, Sven-Eric

    2016-08-01

    Deployments of tear gas and pepper spray have rapidly increased worldwide. Large amounts of tear gas have been used in densely populated cities, including Cairo, Istanbul, Rio de Janeiro, Manama (Bahrain), and Hong Kong. In the United States, tear gas was used extensively during recent riots in Ferguson, Missouri. Whereas tear gas deployment systems have rapidly improved-with aerial drone systems tested and requested by law enforcement-epidemiological and mechanistic research have lagged behind and have received little attention. Case studies and recent epidemiological studies revealed that tear gas agents can cause lung, cutaneous, and ocular injuries, with individuals affected by chronic morbidities at high risk for complications. Mechanistic studies identified the ion channels TRPV1 and TRPA1 as targets of capsaicin in pepper spray, and of the tear gas agents chloroacetophenone, CS, and CR. TRPV1 and TRPA1 localize to pain-sensing peripheral sensory neurons and have been linked to acute and chronic pain, cough, asthma, lung injury, dermatitis, itch, and neurodegeneration. In animal models, transient receptor potential inhibitors show promising effects as potential countermeasures against tear gas injuries. On the basis of the available data, a reassessment of the health risks of tear gas exposures in the civilian population is advised, and development of new countermeasures is proposed.

  9. Appropriateness of mechanistic and non-mechanistic models for the application of ultrafiltration to mixed waste

    SciTech Connect

    Foust, Henry; Ghosehajra, Malay

    2007-07-01

    This study asks two questions: (1) How appropriate is the use of a basic filtration equation to the application of ultrafiltration of mixed waste, and (2) How appropriate are non-parametric models for permeate rates (volumes)? To answer these questions, mechanistic and non-mechanistic approaches are developed for permeate rates and volumes associated with an ultrafiltration/mixed waste system in dia-filtration mode. The mechanistic approach is based on a filtration equation which states that t/V vs. V is a linear relationship. The coefficients associated with this linear regression are composed of physical/chemical parameters of the system and based the mass balance equation associated with the membrane and associated developing cake layer. For several sets of data, a high correlation is shown that supports the assertion that t/V vs. V is a linear relationship. It is also shown that non-mechanistic approaches, i.e., the use of regression models to are not appropriate. One models considered is Q(p) = a*ln(Cb)+b. Regression models are inappropriate because the scale-up from a bench scale (pilot scale) study to full-scale for permeate rates (volumes) is not simply the ratio of the two membrane surface areas. (authors)

  10. Validating CFD Predictions of Pharmaceutical Aerosol Deposition with In Vivo Data.

    PubMed

    Tian, Geng; Hindle, Michael; Lee, Sau; Longest, P Worth

    2015-10-01

    CFD provides a powerful approach to evaluate the deposition of pharmaceutical aerosols; however, previous studies have not compared CFD results of deposition throughout the lungs with in vivo data. The in vivo datasets selected for comparison with CFD predictions included fast and slow clearance of monodisperse aerosols as well as 2D gamma scintigraphy measurements for a dry powder inhaler (DPI) and softmist inhaler (SMI). The CFD model included the inhaler, a characteristic model of the mouth-throat (MT) and upper tracheobronchial (TB) airways, stochastic individual pathways (SIPs) representing the remaining TB region, and recent CFD-based correlations to predict pharmaceutical aerosol deposition in the alveolar airways. For the monodisperse aerosol, CFD predictions of total lung deposition agreed with in vivo data providing a percent relative error of 6% averaged across aerosol sizes of 1-7 μm. With the DPI and SMI, deposition was evaluated in the MT, central airways (bifurcations B1-B7), and intermediate plus peripheral airways (B8 through alveoli). Across these regions, CFD predictions produced an average relative error <10% for each inhaler. CFD simulations with the SIP modeling approach were shown to accurately predict regional deposition throughout the lungs for multiple aerosol types and different in vivo assessment methods.

  11. Validating CFD Predictions of Pharmaceutical Aerosol Deposition with In Vivo Data

    PubMed Central

    Tian, Geng; Hindle, Michael; Lee, Sau; Longest, P. Worth

    2015-01-01

    Purpose CFD provides a powerful approach to evaluate the deposition of pharmaceutical aerosols; however, previous studies have not compared CFD results of deposition throughout the lungs with in vivo data. Methods The in vivo datasets selected for comparison with CFD predictions included fast and slow clearance of monodisperse aerosols as well as 2D gamma scintigraphy measurements for a dry powder inhaler (DPI) and softmist inhaler (SMI). The CFD model included the inhaler, a characteristic model of the mouth-throat (MT) and upper tracheobronchial (TB) airways, stochastic individual pathways (SIPs) representing the remaining TB region, and recent CFD-based correlations to predict pharmaceutical aerosol deposition in the alveolar airways. Results For the monodisperse aerosol, CFD predictions of total lung deposition agreed with in vivo data providing a percent relative error of 6% averaged across aerosol sizes of 1-7μm. With the DPI and SMI, deposition was evaluated in the MT, central airways (bifurcations B1-B7), and intermediate plus peripheral airways (B8 through alveoli). Across these regions, CFD predictions produced an average relative error <10% for each inhaler. Conclusions CFD simulations with the SIP modeling approach were shown to accurately predict regional deposition throughout the lungs for multiple aerosol types and different in vivo assessment methods. PMID:25944585

  12. Reaction Coordinates and Mechanistic Hypothesis Tests.

    PubMed

    Peters, Baron

    2016-05-27

    Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.

  13. Obesity, Diabetes and Cancer: A Mechanistic Perspective

    PubMed Central

    Cifarelli, V; Hursting, SD

    2016-01-01

    Nearly 35% of adults and 20% of children in the United States are obese, defined as having a body mass index (BMI) ≥ 30 kg/m2. Obesity is an established risk factor for many cancers, and obesity-associated metabolic perturbations often manifest in Type 2 diabetes mellitus and/or the metabolic syndrome. As part of the growth-promoting, proinflammatory microenvironment of the obese and/or diabetic state, crosstalk between macrophages, adipocytes, and epithelial cells occurs via metabolically-regulated hormones, cytokines, and other mediators to enhance cancer risk and/or progression. This review synthesizes the evidence on key biological mechanisms underlying the associations between obesity, diabetes and cancer, with particular emphasis on enhancements in growth factor signaling, inflammation, and vascular integrity processes. These interrelated pathways represent mechanistic targets for disrupting the obesity-diabetes-cancer link, and several diabetes drugs, such as metformin and rosiglitazone, are being intensely studied for repurposing as cancer chemopreventive agents.

  14. Mechanistic issues in asparagine synthetase catalysis.

    PubMed

    Richards, N G; Schuster, S M

    1998-01-01

    The enzymatic synthesis of asparagine is an ATP-dependent process that utilizes the nitrogen atom derived from either glutamine or ammonia. Despite a long history of kinetic and mechanistic investigation, there is no universally accepted catalytic mechanism for this seemingly straightforward carboxyl group activating enzyme, especially as regards those steps immediately preceding amide bond formation. This chapter considers four issues dealing with the mechanism: (a) the structural organization of the active site(s) partaking in glutamine utilization and aspartate activation; (b) the relationship of asparagine synthetase to other amidotransferases; (c) the way in which ATP is used to activate the beta-carboxyl group; and (d) the detailed mechanism by which nitrogen is transferred.

  15. Reaction Coordinates and Mechanistic Hypothesis Tests

    NASA Astrophysics Data System (ADS)

    Peters, Baron

    2016-05-01

    Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.

  16. Mechanistic investigations of the ethylene tetramerisation reaction.

    PubMed

    Overett, Matthew J; Blann, Kevin; Bollmann, Annette; Dixon, John T; Haasbroek, Daleen; Killian, Esna; Maumela, Hulisani; McGuinness, David S; Morgan, David H

    2005-08-03

    The unprecedented selective tetramerisation of ethylene to 1-octene was recently reported. In the present study various mechanistic aspects of this novel transformation were investigated. The unusually high 1-octene selectivity in chromium-catalyzed ethylene tetramerisation reactions is caused by the unique extended metallacyclic mechanism in operation. Both 1-octene and higher 1-alkenes are formed by further ethylene insertion into a metallacycloheptane intermediate, whereas 1-hexene is formed by elimination from this species as in other reported trimerisation reactions. This is supported by deuterium labeling studies, analysis of the molar distribution of 1-alkene products, and identification of secondary co-oligomerization reaction products. In addition, the formation of two C6 cyclic products, methylenecyclopentane and methylcyclopentane, is discussed, and a bimetallic disproportionation mechanism to account for the available data is proposed.

  17. Mechanistic interplay between ceramide and insulin resistance

    PubMed Central

    Reali, Federico; Morine, Melissa J.; Kahramanoğulları, Ozan; Raichur, Suryaprakash; Schneider, Hans-Christoph; Crowther, Daniel; Priami, Corrado

    2017-01-01

    Recent research adds to a growing body of literature on the essential role of ceramides in glucose homeostasis and insulin signaling, while the mechanistic interplay between various components of ceramide metabolism remains to be quantified. We present an extended model of C16:0 ceramide production through both the de novo synthesis and the salvage pathways. We verify our model with a combination of published models and independent experimental data. In silico experiments of the behavior of ceramide and related bioactive lipids in accordance with the observed transcriptomic changes in obese/diabetic murine macrophages at 5 and 16 weeks support the observation of insulin resistance only at the later phase. Our analysis suggests the pivotal role of ceramide synthase, serine palmitoyltransferase and dihydroceramide desaturase involved in the de novo synthesis and the salvage pathways in influencing insulin resistance versus its regulation. PMID:28112248

  18. Using helium-oxygen to improve regional deposition of inhaled particles: mechanical principles.

    PubMed

    Katz, I; Pichelin, M; Montesantos, S; Majoral, C; Martin, A; Conway, J; Fleming, J; Venegas, J; Greenblatt, E; Caillibotte, G

    2014-04-01

    Helium-oxygen has been used for decades as a respiratory therapy conjointly with aerosols. It has also been shown under some conditions to be a means to provide more peripheral, deeper, particle deposition for inhalation therapies. Furthermore, we can also consider deposition along parallel paths that are quite different, especially in a heterogeneous pathological lung. It is in this context that it is hypothesized that helium-oxygen can improve regional deposition, leading to more homogeneous deposition by increasing deposition in ventilation-deficient lung regions. Analytical models of inertial impaction, sedimentation, and diffusion are examined to illustrate the importance of gas property values on deposition distribution through both fluid mechanics- and particle mechanics-based mechanisms. Also considered are in vitro results from a bench model for a heterogeneously obstructed lung. In vivo results from three-dimensional (3D) imaging techniques provide visual examples of changes in particle deposition patterns in asthmatics that are further analyzed using computational fluid dynamics (CFD). Based on analytical modeling, it is shown that deeper particle deposition is expected when breathing helium-oxygen, as compared with breathing air. A bench model has shown that more homogeneous ventilation distribution is possible breathing helium-oxygen in the presence of heterogeneous obstructions representative of central airway obstructions. 3D imaging of asthmatics has confirmed that aerosol delivery with a helium-oxygen carrier gas results in deeper and more homogeneous deposition distributions. CFD results are consistent with the in vivo imaging and suggest that the mechanics of gas particle interaction are the source of the differences seen in deposition patterns. However, intersubject variability in response to breathing helium-oxygen is expected, and an example of a nonresponder is shown where regional deposition is not significantly changed.

  19. A systematic approach for identifying and presenting mechanistic evidence in human health assessments

    PubMed Central

    Kushman, Mary E.; Kraft, Andrew D.; Guyton, Kathryn Z.; Chiu, Weihsueh A.; Makris, Susan L.; Rusyn, Ivan

    2013-01-01

    Clear documentation of literature search and presentation methodologies can improve transparency in chemical hazard assessments. We sought to improve clarity for the scientific support for cancer mechanisms of action using a systematic approach to literature retrieval, selection, and presentation of studies. The general question was “What are the mechanisms by which a chemical may cause carcinogenicity in the target tissue?” Di(2-ethylhexyl)phthalate was used as a case study chemical with a complex database of >3,000 publications. Relevant mechanistic events were identified from published reviews. The PubMed search strategy included relevant synonyms and wildcards for DEHP and its metabolites, mechanistic events, and species of interest. Tiered exclusion/inclusion criteria for study pertinence were defined, and applied to the retrieved literature. Manual curation was conducted for mechanistic events with large literature databases. Literature trees documented identification and selection of the literature evidence. The selected studies were summarized in evidence tables accompanied by succinct narratives. Primary publications were deposited into the Health and Environmental Research Online (http://hero.epa.gov/) database and identified by pertinence criteria and key terms to permit organized retrieval. This approach contributes to human health assessment by effectively managing a large volume of literature, improving transparency, and facilitating subsequent synthesis of information across studies. PMID:23959061

  20. Intriguing mechanistic labyrinths in gold(i) catalysis

    PubMed Central

    Obradors, Carla

    2014-01-01

    Many mechanistically intriguing reactions have been developed in the last decade using gold(i) as catalyst. Here we review the main mechanistic proposals in gold-catalysed activation of alkynes and allenes, in which this metal plays a central role by stabilising a variety of complex cationic intermediates. PMID:24176910

  1. Mechanistically based mapping of human cardiac fibrillation

    PubMed Central

    Zaman, Junaid A. B.

    2016-01-01

    Abstract The mechanisms underpinning human cardiac fibrillation remain elusive. In his 1913 paper ‘On dynamic equilibrium in the heart’, Mines proposed that an activation wave front could propagate repeatedly in a circle, initiated by a stimulus in the vulnerable period. While the dynamics of activation and recovery are central to cardiac fibrillation, these physiological data are rarely used in clinical mapping. Fibrillation is a rapid irregular rhythm with spatiotemporal disorder resulting from two fundamental mechanisms – sources in preferred cardiac regions or spatially diffuse self‐sustaining activity, i.e. with no preferred source. On close inspection, however, this debate may also reflect mapping technique. Fibrillation is initiated from triggers by regional dispersion in repolarization, slow conduction and wavebreak, then sustained by non‐uniform interactions of these mechanisms. Notably, optical mapping of action potentials in atrial fibrillation (AF) show spiral wave sources (rotors) in nearly all studies including humans, while most traditional electrogram analyses of AF do not. Techniques may diverge in fibrillation because electrograms summate non‐coherent waves within an undefined field whereas optical maps define waves with a visually defined field. Also fibrillation operates at the limits of activation and recovery, which are well represented by action potentials while fibrillatory electrograms poorly represent repolarization. We conclude by suggesting areas for study that may be used, until such time as optical mapping is clinically feasible, to improve mechanistic understanding and therapy of human cardiac fibrillation. PMID:26607671

  2. Mechanistic simulation of line-edge roughness

    NASA Astrophysics Data System (ADS)

    Biafore, John J.; Smith, Mark D.; Robertson, Stewart A.; Graves, Trey

    2007-03-01

    Physically-based photoresist models, such as those in PROLITH, have been very successful in describing photolithography from a continuum standpoint. These models allow engineers to accurately predict the final resist CD on the wafer and to analyze process robustness. However, as the critical dimension continues to shrink, yield-limiting phenomena are observed that are related to the molecular nature and reaction kinetics of photoresist materials. An example of these phenomena is line-edge roughness (LER). In this paper, the origin of LER is hypothesized to be caused by fluctuations occurring in the initial position of the reactants, fluctuations during the exposure process (shot noise) and fluctuations occurring during thermally-induced reaction-diffusion (post-exposure bake). We have developed a lattice-based mechanistic simulator to better understand the stochastic nature of reactant initial position, the exposure step, the importance of the discrete nature of the reactants, the coupling to the deprotection kinetics and the deep complexity evident in the diffusion-limited acid-quencher reaction.

  3. Semiconductor photocatalysis--mechanistic and synthetic aspects.

    PubMed

    Kisch, Horst

    2013-01-14

    Preceding work on photoelectrochemistry at semiconductor single-crystal electrodes has formed the basis for the tremendous growth in the three last decades in the field of photocatalysis at semiconductor powders. The reason for this is the unique ability of inorganic semiconductor surfaces to photocatalyze concerted reduction and oxidation reactions of a large variety of electron-donor and -acceptor substrates. Whereas great attention was paid to water splitting and the exhaustive aerobic degradation of pollutants, only a small amount of research also explored synthetic aspects. After introducing the basic mechanistic principles, standard experiments for the preparation and characterization of visible light active photocatalysts as well as the investigation of reaction mechanisms are discussed. Novel atom-economic C-C and C-N coupling reactions illustrate the relevance of semiconductor photocatalysis for organic synthesis, and demonstrate that the multidisciplinary field combines classical photochemistry with electrochemistry, solid-state chemistry, and heterogeneous catalysis. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Mechanistic Reactive Burn Modeling of Solid Explosives

    SciTech Connect

    Y.Horie; Y.Hamate; D.Greening

    2003-04-01

    This report describes a computational framework for reactive burn modeling of solid explosives and the development of a test case where physical mechanisms represent RDX or RDX-based materials. The report is a sequel to LA-13794-MS, ''A Unifying Framework for Hot Spots and the Ignition of Energetic Materials,'' where we proposed a new approach to the building of a general purpose model that captures the essential features of the three primary origins of hot-spot formation: void collapse, shear banding, friction. The purpose of the present report is to describe the continuing task of coupling the unifying hot-spot model to hydrodynamic calculations to develop a mechanistic reactive burn model. The key components of the coupling include energy localization, the growth of hot spots, overall hot-spot behavior, and a phase-averaged mixture equation of state (EOS) in a Mie-Grueneisen form. The nucleation and growth of locally heated regions is modeled by a phenomenological treatment as well as a statistical model based on an exponential size distribution. The Mie-Grueneisen form of the EOS is one of many possible choices and is not a critical selection for implementing the model. In this report, model calculations are limited to proof-of-concept illustrations for shock loading. Results include (1) shock ignition and growth-to-detonation, (2) double shock ignition, and (3) quenching and reignition. A comparative study of Pop-plots is discussed based on the statistical model.

  5. Polymyxin B hemoperfusion: a mechanistic perspective.

    PubMed

    Ronco, Claudio; Klein, David J

    2014-06-09

    Direct hemoperfusion therapy with polymyxin B immobilized fiber cartridge (PMX-DHP) is an established strategy in the treatment of septic shock in Japan and parts of Western Europe. PMX-DHP is currently the subject of a pivotal North American randomized controlled trial (EUPHRATES) in patients with septic shock and confirmed endotoxemia, as measured by the endotoxin activity assay. The major mechanism of action of this therapy is the removal of circulating endotoxin. High affinity binding of circulating endotoxin by the PMX-DHP column may decrease circulating endotoxin levels by up to 90% after two standard treatments. Basic research has shown reductions in circulating cytokine levels and in renal tubular apoptosis. Clinical research has shown that PMX-DHP therapy results in hemodynamic improvements, improvements in oxygenation, renal function, and reductions in mortality. Further research is needed to further define additional patient populations with endotoxemia that may benefit from PMX-DHP therapy as well as to further elucidate dosing, timing, and additional information on mechanisms of action. This review will present the mechanistic rationale for this targeted strategy of endotoxin removal using PMX-DHP in endotoxemic septic patients, highlighting both the specific effects of the therapy and the evidence accumulated so far of clinical improvement following this therapy in terms of recovery of organ function.

  6. Polymyxin B hemoperfusion: a mechanistic perspective

    PubMed Central

    2014-01-01

    Direct hemoperfusion therapy with polymyxin B immobilized fiber cartridge (PMX-DHP) is an established strategy in the treatment of septic shock in Japan and parts of Western Europe. PMX-DHP is currently the subject of a pivotal North American randomized controlled trial (EUPHRATES) in patients with septic shock and confirmed endotoxemia, as measured by the endotoxin activity assay. The major mechanism of action of this therapy is the removal of circulating endotoxin. High affinity binding of circulating endotoxin by the PMX-DHP column may decrease circulating endotoxin levels by up to 90% after two standard treatments. Basic research has shown reductions in circulating cytokine levels and in renal tubular apoptosis. Clinical research has shown that PMX-DHP therapy results in hemodynamic improvements, improvements in oxygenation, renal function, and reductions in mortality. Further research is needed to further define additional patient populations with endotoxemia that may benefit from PMX-DHP therapy as well as to further elucidate dosing, timing, and additional information on mechanisms of action. This review will present the mechanistic rationale for this targeted strategy of endotoxin removal using PMX-DHP in endotoxemic septic patients, highlighting both the specific effects of the therapy and the evidence accumulated so far of clinical improvement following this therapy in terms of recovery of organ function. PMID:25043934

  7. A mechanistic damage model for ligaments.

    PubMed

    Barrett, Jeff M; Callaghan, Jack P

    2017-08-16

    The accuracy of biomechanical models is predicated on the realism by which they represent their biomechanical tissues. Unfortunately, most models use phenomenological ligament models that neglect the behaviour in the failure region. Therefore, the purpose of this investigation was to test whether a mechanistic model of ligamentous tissue portrays behaviour representative of actual ligament failure tests. The model tracks the time-evolution of a population of collagen fibres in a theoretical ligament. Each collagen fibre is treated as an independent linear cables with constant stiffness. Model equations were derived by assuming these fibres act as a continuum and applying a conservation law akin to Huxley's muscle model. A breaking function models the rate of collagen fibre breakage at a given displacement, and was chosen to be a linear function for this preliminary analysis. The model was fitted to experimental average curves for the cervical anterior longitudinal ligament. In addition, the model was cyclically loaded to test whether the tissue model behaves similarly. The model agreed very well with experiment with an RMS error of 14.23 N and an R(2) of 0.995. Cyclic loading exhibited a reduction in force similar to experimental data. The proposed model showcases behaviour reminiscent of actual ligaments being strained to failure and undergoing cyclic load. Future work could incorporate viscous effects, or validate the model further by testing it in various loading conditions. Characterizing the breaking function more accurately would also lead to better results. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Alkylation of phenol: a mechanistic view.

    PubMed

    Ma, Qisheng; Chakraborty, Deb; Faglioni, Francesco; Muller, Rick P; Goddard, William A; Harris, Thomas; Campbell, Curt; Tang, Yongchun

    2006-02-16

    The current work utilizes the ab initio density functional theory (DFT) to develop a molecular level of the mechanistic understanding on the phenol alkylation in the presence of a cation-exchange resin catalyst, Amberlyst-15. The catalyst is modeled with the benzene sulfonic acid, and the effect of this acid on olefins such as isopropene (i-Pr) and tributene (t-Bu) in a phenol solution mimics the experimental condition. A neutral-pathway mechanism is established to account for early-stage high concentration of the phenolic ether observed in experiments. The mechanism involves an exothermic reaction between olefin and the benzene sulfonic acid to form ester followed by three reaction pathways leading to direct O-alkylation, o-C-alkylation, and p-C-alkylation. Our calculations conclude that O-alkylation to form the phenolic ether is the most energetically favorable in the neutral condition. An ionic rearrangement mechanism describes intramolecular migrations of the alkyl group from the phenolic ether to form C-alkylphenols, while the positively charged protonation significantly lowers transition barriers for these migrations. The ionic rearrangement mechanism accounts for high yields of o-C-alkylphenol and p-C-alkylphenol. Competition between the H atom and the alkyl R group at the substitutive site of the protonated ortho configuration is found to be the determining factor to the ortho/para ratio of C-alkylation products.

  9. Somatodendritic dopamine release: recent mechanistic insights

    PubMed Central

    Rice, Margaret E.; Patel, Jyoti C.

    2015-01-01

    Dopamine (DA) is a key transmitter in motor, reward and cogitative pathways, with DA dysfunction implicated in disorders including Parkinson's disease and addiction. Located in midbrain, DA neurons of the substantia nigra pars compacta project via the medial forebrain bundle to the dorsal striatum (caudate putamen), and DA neurons in the adjacent ventral tegmental area project to the ventral striatum (nucleus accumbens) and prefrontal cortex. In addition to classical vesicular release from axons, midbrain DA neurons exhibit DA release from their cell bodies and dendrites. Somatodendritic DA release leads to activation of D2 DA autoreceptors on DA neurons that inhibit their firing via G-protein-coupled inwardly rectifying K+ channels. This helps determine patterns of DA signalling at distant axonal release sites. Somatodendritically released DA also acts via volume transmission to extrasynaptic receptors that modulate local transmitter release and neuronal activity in the midbrain. Thus, somatodendritic release is a pivotal intrinsic feature of DA neurons that must be well defined in order to fully understand the physiology and pathophysiology of DA pathways. Here, we review recent mechanistic aspects of somatodendritic DA release, with particular emphasis on the Ca2+ dependence of release and the potential role of exocytotic proteins. PMID:26009764

  10. Mechanistic Indicators of Childhood Asthma (MICA): piloting ...

    EPA Pesticide Factsheets

    Background: Modem methods in molecular biology and advanced computational tools show promise in elucidating complex interactions that occur between genes and environmental factors in diseases such as asthma; however appropriately designed studies are critical for these methods to reach their full potential. Objective: We used a case-control study to investigate whether genomic data (blood gene expression), viewed together with a spectrum of exposure effects and susceptibility markers (blood, urine and nail), can provide a mechanistic explanation for the increased susceptibility of asthmatics to ambient air pollutants. Methods: We studied 205 non-asthmatic and asthmatic children, (9-12 years of age) who participated in a clinical study in Detroit, Michigan. The study combines a traditional epidemiological design with an integrative approach to investigate the environmental exposure of children to indoor-outdoor air. The study includes measurements of internal dose (metals, allergen specific IgE, PAH and VOC metabolites) and clinical measures of health outcome (immunological, cardiovascular and respiratory). Results: Expected immunological indications of asthma have been obtained. In addition, initial results from our analyses point to the complex nature of childhood health and risk factors linked to metabolic syndrome (obesity, blood pressure and dyslipidemia). For example, 31% and 34% of the asthmatic MICA subjects were either overweight (BMI > 25) o

  11. Ligand interactions with galactose oxidase: mechanistic insights.

    PubMed Central

    Whittaker, M M; Whittaker, J W

    1993-01-01

    Interactions between galactose oxidase and small molecules have been explored using a combination of optical absorption, circular dichroism, and electron paramagnetic resonance (EPR) spectroscopies to detect complex formation and characterize the products. Anions bind directly to the cupric center in both active and inactive galactose oxidase, converting to complexes with optical and EPR spectra that are distinctly different from those of the starting aquo enzyme. Azide binding is coupled to stoichiometric proton uptake by the enzyme, reflecting the generation of a strong base (pKa > 9) in the active site anion adduct. At low temperature, the aquo enzyme converts to a form that exhibits the characteristic optical and EPR spectra of an anion complex, apparently reflecting deprotonation of the coordinated water. Anion binding results in a loss of the optical transition arising from coordinated tyrosine, implying displacement of the axial tyrosine ligand on forming the adduct. Nitric oxide binds to galactose oxidase, forming a specific complex exhibiting an unusual EPR spectrum with all g values below 2. The absence of Cu splitting in this spectrum and the observation that the cupric EPR signal from the active site metal ion is not significantly decreased in the complex suggest a nonmetal interaction site for NO in galactose oxidase. These results have been interpreted in terms of a mechanistic scheme where substrate binding displaces a tyrosinate ligand from the active site cupric ion, generating a base that may serve to deprotonate the coordinated hydroxyl group of the substrate, activating it for oxidation. The protein-NO interactions may probe a nonmetal O2 binding site in this enzyme. PMID:8386015

  12. Application of Mechanistic Toxicology Data to Ecological Risk Assessments

    EPA Science Inventory

    The ongoing evolution of knowledge and tools in the areas of molecular biology, bioinformatics, and systems biology holds significant promise for reducing uncertainties associated with ecological risk assessment. As our understanding of the mechanistic basis of responses of organ...

  13. Application of Mechanistic Toxicology Data to Ecological Risk Assessments

    EPA Science Inventory

    The ongoing evolution of knowledge and tools in the areas of molecular biology, bioinformatics, and systems biology holds significant promise for reducing uncertainties associated with ecological risk assessment. As our understanding of the mechanistic basis of responses of organ...

  14. Security Deposits

    DTIC Science & Technology

    1987-04-01

    Tenant requirements: Provide a forwarding address. Failure by tenant to pay delinquent rent within twenty days after delivery of written demand makes...dispute boards, track down delinquent soldiers, and to actually collect the money back from the soldier. Finance cannot simply withhold pay - it can do...United States, and rents and deposits are notoriously high. Third, Fort Ord happened to be the site of a much publicized suicide by a teenage boy in

  15. Recommended Tritium Oxide Deposition Velocity For Use In Savannah River Site Safety Analyses

    SciTech Connect

    Lee, P. L.; Murphy, C. E.; Viner, B. J.; Hunter, C. H.

    2012-07-31

    This report documents the results of examining the deposition velocity of water to forests, the residence time of HTO in forests, and the relation between deposition velocity and residence time with specific consideration given to the topography and experimental work performed at SRS. A simple mechanistic model is used to obtain plausible deposition velocity and residence time values where experimental data are not available and recommendations are made for practical application in a safety analysis model.

  16. Explanation and inference: mechanistic and functional explanations guide property generalization.

    PubMed

    Lombrozo, Tania; Gwynne, Nicholas Z

    2014-01-01

    The ability to generalize from the known to the unknown is central to learning and inference. Two experiments explore the relationship between how a property is explained and how that property is generalized to novel species and artifacts. The experiments contrast the consequences of explaining a property mechanistically, by appeal to parts and processes, with the consequences of explaining the property functionally, by appeal to functions and goals. The findings suggest that properties that are explained functionally are more likely to be generalized on the basis of shared functions, with a weaker relationship between mechanistic explanations and generalization on the basis of shared parts and processes. The influence of explanation type on generalization holds even though all participants are provided with the same mechanistic and functional information, and whether an explanation type is freely generated (Experiment 1), experimentally provided (Experiment 2), or experimentally induced (Experiment 2). The experiments also demonstrate that explanations and generalizations of a particular type (mechanistic or functional) can be experimentally induced by providing sample explanations of that type, with a comparable effect when the sample explanations come from the same domain or from a different domains. These results suggest that explanations serve as a guide to generalization, and contribute to a growing body of work supporting the value of distinguishing mechanistic and functional explanations.

  17. Predicting interactions from mechanistic information: Can omic data validate theories?

    SciTech Connect

    Borgert, Christopher J.

    2007-09-01

    To address the most pressing and relevant issues for improving mixture risk assessment, researchers must first recognize that risk assessment is driven by both regulatory requirements and scientific research, and that regulatory concerns may expand beyond the purely scientific interests of researchers. Concepts of 'mode of action' and 'mechanism of action' are used in particular ways within the regulatory arena, depending on the specific assessment goals. The data requirements for delineating a mode of action and predicting interactive toxicity in mixtures are not well defined from a scientific standpoint due largely to inherent difficulties in testing certain underlying assumptions. Understanding the regulatory perspective on mechanistic concepts will be important for designing experiments that can be interpreted clearly and applied in risk assessments without undue reliance on extrapolation and assumption. In like fashion, regulators and risk assessors can be better equipped to apply mechanistic data if the concepts underlying mechanistic research and the limitations that must be placed on interpretation of mechanistic data are understood. This will be critically important for applying new technologies to risk assessment, such as functional genomics, proteomics, and metabolomics. It will be essential not only for risk assessors to become conversant with the language and concepts of mechanistic research, including new omic technologies, but also, for researchers to become more intimately familiar with the challenges and needs of risk assessment.

  18. Explanation and inference: mechanistic and functional explanations guide property generalization

    PubMed Central

    Lombrozo, Tania; Gwynne, Nicholas Z.

    2014-01-01

    The ability to generalize from the known to the unknown is central to learning and inference. Two experiments explore the relationship between how a property is explained and how that property is generalized to novel species and artifacts. The experiments contrast the consequences of explaining a property mechanistically, by appeal to parts and processes, with the consequences of explaining the property functionally, by appeal to functions and goals. The findings suggest that properties that are explained functionally are more likely to be generalized on the basis of shared functions, with a weaker relationship between mechanistic explanations and generalization on the basis of shared parts and processes. The influence of explanation type on generalization holds even though all participants are provided with the same mechanistic and functional information, and whether an explanation type is freely generated (Experiment 1), experimentally provided (Experiment 2), or experimentally induced (Experiment 2). The experiments also demonstrate that explanations and generalizations of a particular type (mechanistic or functional) can be experimentally induced by providing sample explanations of that type, with a comparable effect when the sample explanations come from the same domain or from a different domains. These results suggest that explanations serve as a guide to generalization, and contribute to a growing body of work supporting the value of distinguishing mechanistic and functional explanations. PMID:25309384

  19. From formamide to purine: an energetically viable mechanistic reaction pathway.

    PubMed

    Wang, Jing; Gu, Jiande; Nguyen, Minh Tho; Springsteen, Greg; Leszczynski, Jerzy

    2013-02-28

    A step-by-step mechanistic pathway following the transformation of formamide to purine through a five-membered ring intermediate has been explored by density functional theory computations. The highlight of the mechanistic route detailed here is that the proposed pathway represents the simplest reaction pathway. All necessary reactants are generated from a single starting compound, formamide, through energetically viable reactions. Several important reaction steps are involved in this mechanistic route: formylation-dehydration, Leuckart reduction, five- and six-membered ring-closure, and deamination. On the basis of the study of noncatalytic pathways, catalytic water has been found to provide energetically viable step-by-step mechanistic pathways. Among these reaction steps, five-member ring-closure is the rate-determining step. The energy barrier (ca. 42 kcal/mol) of this rate-control step is somewhat lower than the rate-determining step (ca. 44 kcal/mol) for a pyrimidine-based pathway reported previously. The mechanistic pathway reported herein is less energetically demanding than for previously proposed routes to adenine.

  20. Mechanistic micro-structural theory of soft tissues growth and remodeling: tissues with unidirectional fibers.

    PubMed

    Lanir, Yoram

    2015-04-01

    A new mechanistic theory was developed for soft tissues growth and remodeling (G&R). The theory considers tissues with unidirectional fibers. It is based on the loading-dependent local turnover events of each constituent and on the resulting evolution of the tissue micro-structure, the tissue dimensions and its mechanical properties. The theory incorporates the specific mechanical properties and turnover kinetics of each constituent, thereby establishing a general framework which can serve for future integration of additional mechanisms involved in G&R. The feasibility of the theory was examined by considering a specific realization of tissues with one fibrous constituent (collagen fibers), assuming a specific loading-dependent first-order fiber's turnover kinetics and the fiber's deposition characteristics. The tissue was subjected to a continuous constant rate growth. Model parameters were adopted from available data. The resulting predictions show qualitative agreement with a number of well-known features of tissues including the fibers' non-uniform recruitment density distribution, the associated tissue convex nonlinear stress-stretch relationship, and the development of tissue pre-stretch and pre-stress states. These results show that mechanistic micro-structural modeling of soft tissue G&R based on first principles can successfully capture the evolution of observed tissues' structure and size, and of their associated mechanical properties.

  1. Why did Jacques Monod make the choice of mechanistic determinism?

    PubMed

    Loison, Laurent

    2015-06-01

    The development of molecular biology placed in the foreground a mechanistic and deterministic conception of the functioning of macromolecules. In this article, I show that this conception was neither obvious, nor necessary. Taking Jacques Monod as a case study, I detail the way he gradually came loose from a statistical understanding of determinism to finally support a mechanistic understanding. The reasons of the choice made by Monod at the beginning of the 1950s can be understood only in the light of the general theoretical schema supported by the concept of mechanistic determinism. This schema articulates three fundamental notions for Monod, namely that of the rigidity of the sequence of the genetic program, that of the intrinsic stability of macromolecules (DNA and proteins), and that of the specificity of molecular interactions.

  2. Managing mechanistic and organic structure in health care organizations.

    PubMed

    Olden, Peter C

    2012-01-01

    Managers at all levels in a health care organization must organize work to achieve the organization's mission and goals. This requires managers to decide the organization structure, which involves dividing the work among jobs and departments and then coordinating them all toward the common purpose. Organization structure, which is reflected in an organization chart, may range on a continuum from very mechanistic to very organic. Managers must decide how mechanistic versus how organic to make the entire organization and each of its departments. To do this, managers should carefully consider 5 factors for the organization and for each individual department: external environment, goals, work production, size, and culture. Some factors may push toward more mechanistic structure, whereas others may push in the opposite direction toward more organic structure. Practical advice can help managers at all levels design appropriate structure for their departments and organization.

  3. Radical behaviorism and scientific frameworks. From mechanistic to relational accounts.

    PubMed

    Chiesa, M

    1992-11-01

    A substantial portion of B. F. Skinner's scholarship was devoted to developing methods and terms for a scientific study of behavior. Three concepts central to scientific accounts--cause, explanation, and theory--are examined to illustrate the distinction between mechanistic and relational frameworks and radical behaviorism's relationship to those frameworks. Informed by a scientific tradition that explicitly rejects mechanistic interpretations, radical behaviorism provides a distinctive stance in contemporary psychology. The present analysis suggests that radical behaviorism makes closer contact with the "new world view" advocated by physicists and philosophers of science than does much of contemporary psychology.

  4. A mechanistic approach to tracing anthropometric charts: the extended mechanistic growth function method.

    PubMed

    Spada, Elena; Gilli, Giulio; Coscia, Alessandra; Milani, Silvano

    2015-01-01

    The Extended Mechanistic Growth Function (EMGF) method (Clementi et al. [1999]: Am J Med Genet 87:317-323) is a possible alternative to the Cole and Green LMS method ([1992] Stat Med 11:1305-1319) to construct cross-sectional anthropometric charts. It differs from the technique used by Kuczmarski et al. ([2002]: Vital Health Stat 11:1-190) to trace the CDC growth charts in that all centiles are simultaneously fitted with a single function. The aim of this study is to show how an EMGF model can be designed. To illustrate the structure and properties of the EMGF method, the data of the Italian Neonatal Study (Bertino et al. [2010]: J Pediatr Gastroenterol Nutr 51:353-361) were analyzed. The dataset included the birth weight of 45,272 single liveborn babies with gestational ages ranging from 23 to 42 weeks. The EMGF method consists of three steps. In the preliminary step, selected age-dependent raw centiles of the anthropometric trait are computed. In the smoothing step, all centiles are simultaneously fitted with a growth function extended with the inclusion of a few extra parameters. In the transformation step, estimates of the age-dependent L (skewness), M (median), and S (coefficient of variation) parameters are derived. A four-parameter generalized logistic function, extended with five parameters to model between-sex differences, distance between centiles and their slope, was found to fit the raw centiles of birth weight distribution with a residual standard deviation of 51.3 g. The EMGF method represents a bridge to link cross-sectional and longitudinal studies and allows us to identify milestones of the median growth in a population in the same way used for individual profiles. © 2014 Wiley Periodicals, Inc.

  5. DEVELOPMENT AND VALIDATION OF A MECHANISTIC GROUND SPRAYER MODEL

    EPA Science Inventory

    In the last ten years the Spray Drift Task Force (SDTF), U.S. Environmental Protection Agency (EPA), USDA Agricultural Research Service, and USDA Forest Service cooperated in the refinement and evaluation of a mechanistically-based aerial spray model (contained within AGDISP and ...

  6. Mechanistically Consistent Reduced Models of Synthetic Gene Networks

    PubMed Central

    Mier-y-Terán-Romero, Luis; Silber, Mary; Hatzimanikatis, Vassily

    2013-01-01

    Designing genetic networks with desired functionalities requires an accurate mathematical framework that accounts for the essential mechanistic details of the system. Here, we formulate a time-delay model of protein translation and mRNA degradation by systematically reducing a detailed mechanistic model that explicitly accounts for the ribosomal dynamics and the cleaving of mRNA by endonucleases. We exploit various technical and conceptual advantages that our time-delay model offers over the mechanistic model to probe the behavior of a self-repressing gene over wide regions of parameter space. We show that a heuristic time-delay model of protein synthesis of a commonly used form yields a notably different prediction for the parameter region where sustained oscillations occur. This suggests that such heuristics can lead to erroneous results. The functional forms that arise from our systematic reduction can be used for every system that involves transcription and translation and they could replace the commonly used heuristic time-delay models for these processes. The results from our analysis have important implications for the design of synthetic gene networks and stress that such design must be guided by a combination of heuristic models and mechanistic models that include all relevant details of the process. PMID:23663853

  7. A simple mechanistic model to interpret the effects of narcotics.

    PubMed

    Baas, J; Spurgeon, D; Broerse, M

    2015-01-01

    In this research we will show the advantages of using a time-independent dose metric in a mechanistic model to evaluate toxic effects for different narcotic compounds on different species. We will show how different already existing QSARs can be combined within a mechanistic framework to 1) make predictions of lethal thresholds; 2) show some limitations in the use of existing QSARs; 3) show how a mechanistic framework solves some conceptual problems in current approaches and 4) show how such a framework can be used to be of aid in an experimental setup in predicting the outcome of a survival experiment. The approach we chose is based on the simplest mechanistic model available, a scaled one-compartment model to describe uptake and elimination and hazard model to link the exposure to effects on survival. Within this theoretical framework a prediction for an internal threshold for effects on survival of 3 mmol/kg bw can be made, which should be similar for different species and independent of the partitioning characteristics of the toxicant. To demonstrate this, a threshold for 51 different species was derived, which indeed appeared to lie in a relatively small range, typically between 1 and 10 mmol/kg bw.

  8. A Mechanistic Model for Predicting Lung Inflammogenicity of Oxide Nanoparticles.

    PubMed

    Burello, Enrico

    2017-10-01

    This study presents a mechanistic model for identifying oxide nanoparticles that induce a high level of neutrophils in the bronchoalveolar lavage fluid, an important marker for lung inflammogenicity. The model is based on 4 nanoparticles' physicochemical properties, ie, the reactivity, surface charge, wettability, and dissolution. First, I calculate these properties and show that theoretical values reproduce acceptably the experimental measurements. Then, I combine these properties with mechanistic knowledge to build a classification model for the prediction of acute invivo lung inflammogenicity, measured as the total number of polymorphonuclear neutrophils. The model uses reactivity and dissolution properties of nanoparticles as toxicological initiating events, whereas surface charge and wettability are characteristics involved in the interactions between the nanoparticles and the lung surfactant, eventually leading to increased cellular uptake and bioaccumulation. The model is validated on a set of 43 oxide nanoparticles tested invivo to confirm that acute lung inflammation can be described using this mechanistic framework. In addition, I also develop a linear regression model for insoluble nanoparticles to quantitatively predict the polymorphonuclear neutrophil count as a function of reactivity and surface charge. The proposed models are based on mechanistic knowledge and can support the development of adverse outcome pathways, risk assessment frameworks and safe design strategies at early stages of material's R&D. © The Author 2017. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. Does Mechanistic Thinking Improve Student Success in Organic Chemistry?

    ERIC Educational Resources Information Center

    Grove, Nathaniel P.; Cooper, Melanie M.; Cox, Elizabeth L.

    2012-01-01

    The use of the curved-arrow notation to depict electron flow during mechanistic processes is one of the most important representational conventions in the organic chemistry curriculum. Our previous research documented a disturbing trend: when asked to predict the products of a series of reactions, many students do not spontaneously engage in…

  10. DEVELOPMENT AND VALIDATION OF A MECHANISTIC GROUND SPRAYER MODEL

    EPA Science Inventory

    In the last ten years the Spray Drift Task Force (SDTF), U.S. Environmental Protection Agency (EPA), USDA Agricultural Research Service, and USDA Forest Service cooperated in the refinement and evaluation of a mechanistically-based aerial spray model (contained within AGDISP and ...

  11. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems

    PubMed Central

    Transtrum, Mark K.; Qiu, Peng

    2016-01-01

    The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior. PMID:27187545

  12. Rearrangements of Allylic Sulfinates to Sulfones: A Mechanistic Study

    ERIC Educational Resources Information Center

    Ball, David B.; Mollard, Paul; Voigtritter, Karl R.; Ball, Jenelle L.

    2010-01-01

    Most current organic chemistry textbooks are organized by functional groups and those of us who teach organic chemistry use functional-group organization in our courses but ask students to learn organic chemistry from a mechanistic approach. To enrich and extend the chemical understanding and knowledge of pericyclic-type reactions for chemistry…

  13. MECHANISTIC AND SOURCE UNDERSTANDING OF PCDD/F FORMATION

    EPA Science Inventory

    The paper discusses mechanistic and source understanding of polychlorinated dibenzo-p-dioxin and dibenzofuran (PCDD/F) formation. (NOTE: Considerable research effort has been expended over the last 15-plus years to understand how combustion sources result in formation of PCDDs/F...

  14. A mechanistic assessment of nutrient flushing at the catchment scale

    Treesearch

    Willem J. van Verseveld; Jeffrey J. McDonnell; Kate Lajtha

    2008-01-01

    This paper mechanistically assesses the flushing mechanism of DOC, DON, and DIN at the hillslope and catchment scales during two storm events, in a small catchment (WS10), H.J. Andrews Experimental Forest in the western Cascade Mountains of Oregon. Using a combination of natural tracer and hydrometric data, and end-member mixing analysis, we were able to describe the...

  15. Mechanistic investigation on the formation of indolizines from 2-enynylpyridines.

    PubMed

    Lahoz, Inma R; Sicre, Cristina; Navarro-Vázquez, Armando; Silva López, Carlos; Cid, María-Magdalena

    2009-11-05

    2,3,7-Trisubstituted indolizines were obtained from E- or Z-2-enynyl-4-substituted pyridines. The mechanistic pathway involves a base-catalyzed double-bond isomerization, if the E-isomer is the starting material, followed by a concerted pseudocoarctate cyclization.

  16. Does Mechanistic Thinking Improve Student Success in Organic Chemistry?

    ERIC Educational Resources Information Center

    Grove, Nathaniel P.; Cooper, Melanie M.; Cox, Elizabeth L.

    2012-01-01

    The use of the curved-arrow notation to depict electron flow during mechanistic processes is one of the most important representational conventions in the organic chemistry curriculum. Our previous research documented a disturbing trend: when asked to predict the products of a series of reactions, many students do not spontaneously engage in…

  17. Rearrangements of Allylic Sulfinates to Sulfones: A Mechanistic Study

    ERIC Educational Resources Information Center

    Ball, David B.; Mollard, Paul; Voigtritter, Karl R.; Ball, Jenelle L.

    2010-01-01

    Most current organic chemistry textbooks are organized by functional groups and those of us who teach organic chemistry use functional-group organization in our courses but ask students to learn organic chemistry from a mechanistic approach. To enrich and extend the chemical understanding and knowledge of pericyclic-type reactions for chemistry…

  18. MECHANISTIC AND SOURCE UNDERSTANDING OF PCDD/F FORMATION

    EPA Science Inventory

    The paper discusses mechanistic and source understanding of polychlorinated dibenzo-p-dioxin and dibenzofuran (PCDD/F) formation. (NOTE: Considerable research effort has been expended over the last 15-plus years to understand how combustion sources result in formation of PCDDs/F...

  19. Ferritin Diversity: Mechanistic Studies, Disease Implications, and Materials Chemistry

    NASA Astrophysics Data System (ADS)

    Hilton, Robert J.

    2011-07-01

    The study of ferritin includes a rich history of discoveries and scientific progress. Initially, the composition of ferritin was determined. Soon, it was shown that ferritin is a spherical, hollow protein. Eventually, over several decades of research, the structure and some function of this interesting protein was elucidated. However, the ferritin field was not completely satisfied. Today, for example, researchers are interested in refining the details of ferritin function, in discovering the role of ferritin in a variety of diseases, and in using ferritin for materials chemistry applications. The work presented in this dissertation highlights the progress that we have made in each of these three areas: (1) Mechanistic studies: The buffer used during horse spleen ferritin iron loading significantly influences the mineralization process and the quantity of iron deposited in ferritin. The ferrihydrite core of ferritin is crystalline and ordered when iron is loaded into ferritin in the presence of imidazole buffer. On the other hand, when iron is loaded into ferritin in the presence of MOPS buffer, the ferrihydrite core is less crystalline and less ordered, and a smaller amount of total iron is loaded in ferritin. We also show that iron can be released from the ferritin core in a non-reductive manner. The rate of Fe3+ release from horse spleen ferritin was measured using the Fe3+-specific chelator desferoxamine. We show that iron release occurs by three kinetic events. (2) Disease studies: In order to better understand iron disruption during disease states, we performed in vitro assays that mimicked chronic kidney disease. We tested the hypothesis that elevated levels of serum phosphate interrupted normal iron binding by transferrin and ferritin. Results show that phosphate competes for iron, forming an iron(III)-phosphate complex that is inaccessible to either transferrin or ferritin. Ferritin samples separated from the iron(III)-phosphate complex shows that as the

  20. A framework for recognizing mechanistic reasoning in student scientific inquiry

    NASA Astrophysics Data System (ADS)

    Russ, Rosemary S.

    A central ambition of science education reform is to help students develop abilities for scientific inquiry. Education research is thus rightly focused on defining what constitutes "inquiry" and developing tools for assessing it. There has been progress with respect to particular aspects of inquiry, namely student abilities for controlled experimentation and scientific argumentation. However, we suggest that in addition to these frameworks for assessing the structure of inquiry we need frameworks for analyzing the substance of that inquiry. In this work we draw attention to and evaluate the substance of student mechanistic reasoning. Both within the history and philosophy of science and within science education research, scientific inquiry is characterized in part as understanding the causal mechanisms that underlie natural phenomena. The challenge for science education, however, is that there has not been the same progress with respect to making explicit what constitutes mechanistic reasoning as there has been in making explicit other aspects of inquiry. This dissertation attempts to address this challenge. We adapt an account of mechanism in professional research science to develop a framework for reliably recognizing mechanistic reasoning in student discourse. The coding scheme articulates seven specific aspects of mechanistic reasoning and can be used to systematically analyze narrative data for patterns in student thinking. It provides a tool for detecting quality reasoning that may be overlooked by more traditional assessments. We apply the mechanism coding scheme to video and written data from a range of student inquiries, from large group discussions among first grade students to the individual problem solving of graduate students. While the primary result of this work is the coding scheme itself and the finding that it provides a reliable means of analyzing transcript data for evidence of mechanistic thinking, the rich descriptions we develop in each case

  1. Answering evolutionary questions: a guide for mechanistic biologists

    PubMed Central

    Masel, Joanna; Promislow, Daniel

    2016-01-01

    Summary The questions and methods of molecular biology and evolutionary biology are clearly distinct, yet a unified approach can lead to deep insights. Unfortunately, attempts to unify these approaches are fraught with pitfalls. In this informal series of questions and answers, we offer the mechanistically oriented biologist a set of steps to come up with evolutionarily reasonable and meaningful hypotheses. We emphasize the critical power and importance of carefully constructed null hypotheses, and we illustrate our ideas with examples representing a range of topics, from the biology of aging, to protein structure, to speciation, and more. We also stress the importance of mathematics as the lingua franca for biologists of all stripes, and encourage mechanistic biologists to seek out quantitative collaborators to build explicit mathematical models, making their assumptions explicit, and their logic clear and testable. Biologists in all realms of inquiry stand to gain from strong bridges between our disciplines. PMID:27151396

  2. Mechanistic Fermentation Models for Process Design, Monitoring, and Control.

    PubMed

    Mears, Lisa; Stocks, Stuart M; Albaek, Mads O; Sin, Gürkan; Gernaey, Krist V

    2017-08-21

    Mechanistic models require a significant investment of time and resources, but their application to multiple stages of fermentation process development and operation can make this investment highly valuable. This Opinion article discusses how an established fermentation model may be adapted for application to different stages of fermentation process development: planning, process design, monitoring, and control. Although a longer development time is required for such modeling methods in comparison to purely data-based model techniques, the wide range of applications makes them a highly valuable tool for fermentation research and development. In addition, in a research environment, where collaboration is important, developing mechanistic models provides a platform for knowledge sharing and consolidation of existing process understanding. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Mechanistic pathway modeling for industrial biotechnology: challenging but worthwhile.

    PubMed

    Wiechert, Wolfgang; Noack, Stephan

    2011-10-01

    Mechanistic (also called kinetic) models quantitatively describe dynamic and steady states of biochemical pathways. They are based on network structure (stoichiometry), regulatory information (enzyme inhibitors and activators) and the corresponding reaction kinetics. Although this approach to understand and predict the behavior of biochemical networks has now been in use for almost half a century, its experimental foundation has dramatically changed in the data-rich age of systems biology. Large mechanistic models, ranging up to the genome scale, are now being built and lots of data are available to validate and test them. From the broad scope of possible modeling applications, this survey focuses on the recent developments and central problems of metabolic network modeling in the field of bioprocess development for industrial biotechnology.

  4. Mechanistic model for catalytic recombination during aerobraking maneuvers

    NASA Technical Reports Server (NTRS)

    Willey, Ronald J.

    1989-01-01

    Several mechanistic models are developed to predict recombination coefficients for use in heat shield design for reusable surface insulation (RSI) on aerobraking vehicles such as space shuttles. The models are applied over a temperature range of 300 to 1800 K and a stagnation pressure range of 0 to 3,000 Pa. A four parameter model in temperature was found to work best; however, several models (including those with atom concentrations at the surface) were also investigated. Mechanistic models developed with atom concentration terms may be applicable when sufficient data becomes available. The requirement is shown for recombination experiments in the 300 to 1000 K and 1500 to 1850 K temperature range, with deliberate concentration variations.

  5. Millifluidics for Chemical Synthesis and Time-resolved Mechanistic Studies

    PubMed Central

    Krishna, Katla Sai; Biswas, Sanchita; Navin, Chelliah V.; Yamane, Dawit G.; Miller, Jeffrey T.; Kumar, Challa S.S.R.

    2013-01-01

    Procedures utilizing millifluidic devices for chemical synthesis and time-resolved mechanistic studies are described by taking three examples. In the first, synthesis of ultra-small copper nanoclusters is described. The second example provides their utility for investigating time resolved kinetics of chemical reactions by analyzing gold nanoparticle formation using in situ X-ray absorption spectroscopy. The final example demonstrates continuous flow catalysis of reactions inside millifluidic channel coated with nanostructured catalyst. PMID:24327099

  6. New mechanistic studies on the proline-catalyzed aldol reaction

    PubMed Central

    List, Benjamin; Hoang, Linh; Martin, Harry J.

    2004-01-01

    The mechanism of the proline-catalyzed aldol reaction has stimulated considerable debate, and despite limited experimental data, at least five different mechanisms have been proposed. Complementary to recent theoretical studies we have initiated an experimental program with the goal of clarifying some of the basic mechanistic questions concerning the proline-catalyzed aldol reaction. Here we summarize our discoveries in this area and provide further evidence for the involvement of enamine intermediates. PMID:15073330

  7. Mechanistic insights into cyclooxygenase irreversible inactivation by aspirin.

    PubMed

    Tosco, Paolo; Lazzarato, Loretta

    2009-06-01

    A mechanistic hypothesis for the acetylation of cyclooxygenase (COX) by aspirin is proposed on the basis of a QM/MM study. This mechanism is consistent with previous experimental findings by other investigators. Ser 530 appears to be acetylated under intramolecular general base catalysis provided by the carboxylate moiety of aspirin, while Tyr 385 plays a crucial role in orienting and polarizing the acetyl group.

  8. Home range analysis using a mechanistic home range model

    SciTech Connect

    Moorcroft, P.R. . Dept. of Ecology and Evolutionary Biology); Lewis, M.A. . Dept. of Mathematics) Crabtree, R.L. . Dept. of Fish and Wildlife Resources)

    1999-07-01

    The traditional models used to characterize animal home ranges have no mechanistic basis underlying their descriptions of space use, and as a result, the analysis of animal home ranges has primarily been a descriptive endeavor. In this paper, the authors characterize coyote (Canis latrans) home range patterns using partial differential equations for expected space use that are formally derived from underlying descriptions of individual movement behavior. To the authors' knowledge, this is the first time that mechanistic models have been used to characterize animal home ranges. The results provide empirical support for a model formulation of movement response to scent marks, and suggest that having relocation data for individuals in adjacent groups is necessary to capture the spatial arrangement of home range boundaries. The authors then show how the model fits can be used to obtain predictions for individual movement and scent marking behavior and to predict changes in home range patterns. More generally, the findings illustrate how mechanistic models permit the development of a predictive theory for the relationship between movement behavior and animal spatial distribution.

  9. Structural and mechanistic aspects of Amt/Rh proteins.

    PubMed

    Javelle, Arnaud; Lupo, Domenico; Li, Xiao-Dan; Merrick, Mike; Chami, Mohamed; Ripoche, Pierre; Winkler, Fritz K

    2007-06-01

    Amt/Rh proteins, which mediate movement of ammonium across cell membranes, are spread throughout the three kingdoms of life. Most functional studies on various members of the family have been performed using cellular assays in heterologous expression systems, which are, however, not very well suited for detailed mechanistic studies. Although now generally considered to be ammonia conducting channels, based on a number of experimental studies and structural insights, the possibility remains that some plant Amts facilitate net ammonium ion transport. The Escherichia coli channel AmtB has become the model system of choice for analysis of the mechanism of ammonia conductance, increasingly also through molecular dynamics simulations. Further progress in a more detailed mechanistic understanding of these proteins requires a reliable in vitro assay using purified protein, allowing quantitative kinetic measurements under a variety of experimental conditions for different Amt/Rh proteins, including mutants. Here, we critically review the existing functional data in the context of the most interesting and unresolved mechanistic questions and we present our results, obtained using an in vitro assay set up with the purified E. coli channel AmtB.

  10. Chemical diversity approach for evaluating mechanistic relatedness among toxicological phenomena.

    PubMed

    Pollack, N; Cunningham, A R; Klopman, G; Rosenkranz, H S

    1999-12-01

    The CASE/MULTICASE structure-activity relationship (SAR) system was used to assess a new procedure to investigate the mechanistic relatedness of various toxicological endpoints. The method consisted of predicting the activity of 10,000 randomly selected chemicals using validated and characterized SAR models from a variety of biological and toxicological endpoints. The prevalence of chemicals predicted to possess the ability to induce two or more toxicological effects simultaneously should provide a measure of the mechanistic relatedness of these phenomena. Eight toxicological endpoints were predicted and the results were compared to predictions based on an eye irritation SAR model. Allergic contact dermatitis demonstrated a 29.6% greater than expected overlap between expected and observed results (p < 0.001). Similar results were seen for respiratory hypersensitivity (33.1%), sensory irritation (28.9%), cell toxicity (25.9%), and Ah receptor binding (19.8%). A lesser degree of overlap was seen between eye irritation and Salmonella mutagenicity (11.5%) and the inhibition of gap junction intercellular communication (6.7%). Moreover, a negative overlap, suggesting possibly an antagonistic phenomena, was observed between eye irritation and alpha 2 mu-induced nephropathy. These results indicate that this method can provide a useful tool to investigate mechanistic relatedness between diverse toxicological endpoints.

  11. From the exposome to mechanistic understanding of chemical ...

    EPA Pesticide Factsheets

    BACKGROUND: Current definitions of the exposome expand beyond the initial idea to consider the totality of exposure and aim to relate to biological effects. While the exposome has been established for human health, its principles can be extended to include broader ecological issues. The assessment of exposure is tightly interlinked with hazard assessment. OBJECTIVES: We explore if mechanistic understanding of the causal links between exposure and adverse effects on human health and the environment can be improved by integrating the exposome approach with the adverse outcome pathway (AOP) concept - a framework to structure and organize the sequence of toxicological events from an initial molecular interaction of a chemical to an adverse outcome.METHODS: This review was informed by a Workshop organized by the Integrated Project EXPOSOME at the UFZ Helmholtz Centre for Environmental Research in Leipzig, Germany. DISCUSSION: The exposome encompasses all chemicals, including exogenous chemicals and endogenous compounds that are produced in response to external factors. By complementing the exposome research with the AOP concept, we can achieve a better mechanistic understanding, weigh the importance of various components of the exposome, and determine primary risk drivers. The ability to interpret multiple exposures and mixture effects at the mechanistic level requires a more holistic approach facilitated by the exposome concept.CONCLUSION: Incorporating the AOP conc

  12. Deposition head for laser

    DOEpatents

    Lewis, Gary K.; Less, Richard M.

    1999-01-01

    A deposition head for use as a part of apparatus for forming articles from materials in particulate form in which the materials are melted by a laser beam and deposited at points along a tool path to form an article of the desired shape and dimensions. The deposition head delivers the laser beam and powder to a deposition zone, which is formed at the tip of the deposition head. A controller comprised of a digital computer directs movement of the deposition zone along the tool path and provides control signals to adjust apparatus functions, such as the speed at which the deposition head moves along the tool path.

  13. Novel interconnect deposition technology

    NASA Astrophysics Data System (ADS)

    Speckman, D. M.; Wendt, J. P.

    1991-12-01

    A new series of experiments was initiated to improve current interconnect deposition technology for integrated circuits. Preliminary aluminum deposition experiments were carried out using trimethylamine(alane) as the precursor, and some mildly reflective, uniform aluminum films were successfully deposited on glass slides, suggesting that chemical vapor deposition (CVD) will be a practicable deposition technique for advanced integrated circuit interconnect films. CVD studies of aluminum and zirconium- and hafnium-diboride thin films are continuing.

  14. Deposit model for volcanogenic uranium deposits

    USGS Publications Warehouse

    Breit, George N.; Hall, Susan M.

    2011-01-01

    The International Atomic Energy Agency's tabulation of volcanogenic uranium deposits lists 100 deposits in 20 countries, with major deposits in Russia, Mongolia, and China. Collectively these deposits are estimated to contain uranium resources of approximately 500,000 tons of uranium, which amounts to 6 percent of the known global resources. Prior to the 1990s, these deposits were considered to be small (less than 10,000 tons of uranium) with relatively low to moderate grades (0.05 to 0.2 weight percent of uranium). Recent availability of information on volcanogenic uranium deposits in Asia highlighted the large resource potential of this deposit type. For example, the Streltsovskoye district in eastern Russia produced more than 100,000 tons of uranium as of 2005; with equivalent resources remaining. Known volcanogenic uranium deposits within the United States are located in Idaho, Nevada, Oregon, and Utah. These deposits produced an estimated total of 800 tons of uranium during mining from the 1950s through the 1970s and have known resources of 30,000 tons of uranium. The most recent estimate of speculative resources proposed an endowment of 200,000 tons of uranium.

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

    PubMed

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

    2017-04-02

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

  16. Advanced Reach Tool (ART): development of the mechanistic model.

    PubMed

    Fransman, Wouter; Van Tongeren, Martie; Cherrie, John W; Tischer, Martin; Schneider, Thomas; Schinkel, Jody; Kromhout, Hans; Warren, Nick; Goede, Henk; Tielemans, Erik

    2011-11-01

    This paper describes the development of the mechanistic model within a collaborative project, referred to as the Advanced REACH Tool (ART) project, to develop a tool to model inhalation exposure for workers sharing similar operational conditions across different industries and locations in Europe. The ART mechanistic model is based on a conceptual framework that adopts a source receptor approach, which describes the transport of a contaminant from the source to the receptor and defines seven independent principal modifying factors: substance emission potential, activity emission potential, localized controls, segregation, personal enclosure, surface contamination, and dispersion. ART currently differentiates between three different exposure types: vapours, mists, and dust (fumes, fibres, and gases are presently excluded). Various sources were used to assign numerical values to the multipliers to each modifying factor. The evidence used to underpin this assessment procedure was based on chemical and physical laws. In addition, empirical data obtained from literature were used. Where this was not possible, expert elicitation was applied for the assessment procedure. Multipliers for all modifying factors were peer reviewed by leading experts from industry, research institutes, and public authorities across the globe. In addition, several workshops with experts were organized to discuss the proposed exposure multipliers. The mechanistic model is a central part of the ART tool and with advancing knowledge on exposure, determinants will require updates and refinements on a continuous basis, such as the effect of worker behaviour on personal exposure, 'best practice' values that describe the maximum achievable effectiveness of control measures, the intrinsic emission potential of various solid objects (e.g. metal, glass, plastics, etc.), and extending the applicability domain to certain types of exposures (e.g. gas, fume, and fibre exposure).

  17. [Mechanistic examination of organometallic electron transfer reactions: Annual report, 1989

    SciTech Connect

    Not Available

    1989-12-31

    Our mechanistic examination of electron transfer reactions between organometallic complexes has required data from our stopped-flow infrared spectrophotometer that was constructed in the first year. Our research on organometallic electron transfer reaction mechanisms was recognized by an invitation to the Symposium on Organometallic Reaction Mechanisms at the National ACS meeting in Miami. We have obtained a reasonable understanding of the electron transfer reactions between metal cations and anions and between metal carbonyl anions and metal carbonyl dimers. In addition we have begun to obtain data on the outer sphere electron transfer between metal carbonyl anions and coordination complexes and on reactions involving cluster anions.

  18. Mechanistic systems modeling to guide drug discovery and development

    PubMed Central

    Schmidt, Brian J.; Papin, Jason A.; Musante, Cynthia J.

    2013-01-01

    A crucial question that must be addressed in the drug development process is whether the proposed therapeutic target will yield the desired effect in the clinical population. Pharmaceutical and biotechnology companies place a large investment on research and development, long before confirmatory data are available from human trials. Basic science has greatly expanded the computable knowledge of disease processes, both through the generation of large omics data sets and a compendium of studies assessing cellular and systemic responses to physiologic and pathophysiologic stimuli. Given inherent uncertainties in drug development, mechanistic systems models can better inform target selection and the decision process for advancing compounds through preclinical and clinical research. PMID:22999913

  19. Opioid receptors: Structural and mechanistic insights into pharmacology and signaling

    PubMed Central

    Shang, Yi; Filizola, Marta

    2015-01-01

    Opioid receptors are important drug targets for pain management, addiction, and mood disorders. Although substantial research on these important subtypes of G protein-coupled receptors has been conducted over the past two decades to discover ligands with higher specificity and diminished side effects, currently used opioid therapeutics remain suboptimal. Luckily, recent advances in structural biology of opioid receptors provide unprecedented insights into opioid receptor pharmacology and signaling. We review here a few recent studies that have used the crystal structures of opioid receptors as a basis for revealing mechanistic details of signal transduction mediated by these receptors, and for the purpose of drug discovery. PMID:25981301

  20. Opioid receptors: Structural and mechanistic insights into pharmacology and signaling.

    PubMed

    Shang, Yi; Filizola, Marta

    2015-09-15

    Opioid receptors are important drug targets for pain management, addiction, and mood disorders. Although substantial research on these important subtypes of G protein-coupled receptors has been conducted over the past two decades to discover ligands with higher specificity and diminished side effects, currently used opioid therapeutics remain suboptimal. Luckily, recent advances in structural biology of opioid receptors provide unprecedented insights into opioid receptor pharmacology and signaling. We review here a few recent studies that have used the crystal structures of opioid receptors as a basis for revealing mechanistic details of signal transduction mediated by these receptors, and for the purpose of drug discovery.

  1. A mechanistic, stochastic, population model of egg production.

    PubMed

    Johnston, S A; Gous, R M

    2007-04-01

    1. A mechanistic, stochastic egg production model is presented. Mean age at first egg may be predicted from the lighting programme applied during rearing, using the Bristol-Reading model (Lewis et al., 2002). 2. Rate of ovulation is determined by an amended version of the mathematical model of the ovulatory cycle, originally proposed by Etches and Schoch (1984). 3. Oviposition times are estimated from ovulation times. 4. Yolk, albumen and shell weights are calculated using allometric functions. 5. The model predicts egg production of a theoretical flock of laying hens for a full laying year, including random occurrences of double-yolked and soft-shelled eggs and internal ovulations.

  2. Mechanistic equations for membrane transport of multicomponent solutions.

    PubMed

    Suchanek, G

    2006-03-01

    In the present article, mechanistic equations for membrane transport of N + 1-component solutions have been derived. The major specific investigation result is the introduction - for ternary solutions - of two diffusion coefficients omega(d1) and omega(d2) for solutes, as well as two cross coefficients omega(d12) and omega(d21) for these solutes. The latter parameters may be treated as coefficients of interdiffusion. The expansion of the description of substance transport to include the N + 1-component solutions does not formulate any additional physical phenomena other than those which are formulated by the transport equations for three-component solutions.

  3. Mechanistic modeling of CHF in forced-convection subcooled boiling

    SciTech Connect

    Podowski, M.Z.; Alajbegovic, A.; Kurul, N.; Drew, D.A.; Lahey, R.T. Jr.

    1997-05-01

    Because of the complexity of phenomena governing boiling heat transfer, the approach to solve practical problems has traditionally been based on experimental correlations rather than mechanistic models. The recent progress in computational fluid dynamics (CFD), combined with improved experimental techniques in two-phase flow and heat transfer, makes the use of rigorous physically-based models a realistic alternative to the current simplistic phenomenological approach. The objective of this paper is to present a new CFD model for critical heat flux (CHF) in low quality (in particular, in subcooled boiling) forced-convection flows in heated channels.

  4. Nonlinear Krylov acceleration for CFD-based aeroelasticity

    NASA Astrophysics Data System (ADS)

    Feng, Z.; Soulaı¨Mani, A.; Saad, Y.

    2009-01-01

    A nonlinear computational aeroelasticity model based on the Euler equations of compressible flows and the linear elastodynamic equations for structures is developed. The Euler equations are solved on dynamic meshes using the ALE kinematic description. Thus, the mesh constitutes another field governed by pseudo-elastodynamic equations. The three fields are discretized using proper finite element formulations which satisfy the geometric conservation law. A matcher module is incorporated for the purpose of pairing the grids on the fluid-structure interface and for transferring the loads and displacements between the fluid and structure solvers. Two solution strategies (Gauss-Seidel and Schur-complement) for solving the non-linear aeroelastic system are discussed. By using second-order time discretization scheme, we are able to utilize large time steps in the computations. The numerical results on the AGARD 445.6 aeroelastic wing compare well with the experimental results and show that the Schur-complement coupling algorithm is more robust than the Gauss-Seidel algorithm for relatively large oscillation amplitudes.

  5. CFD-Based Design Optimization Tool Developed for Subsonic Inlet

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The traditional approach to the design of engine inlets for commercial transport aircraft is a tedious process that ends with a less-than-optimum design. With the advent of high-speed computers and the availability of more accurate and reliable computational fluid dynamics (CFD) solvers, numerical optimization processes can effectively be used to design an aerodynamic inlet lip that enhances engine performance. The designers' experience at Boeing Corporation showed that for a peak Mach number on the inlet surface beyond some upper limit, the performance of the engine degrades excessively. Thus, our objective was to optimize efficiency (minimize the peak Mach number) at maximum cruise without compromising performance at other operating conditions. Using a CFD code NPARC, the NASA Lewis Research Center, in collaboration with Boeing, developed an integrated procedure at Lewis to find the optimum shape of a subsonic inlet lip and a numerical optimization code, ADS. We used a GRAPE-based three-dimensional grid generator to help automate the optimization procedure. The inlet lip shape at the crown and the keel was described as a superellipse, and the superellipse exponents and radii ratios were considered as design variables. Three operating conditions: cruise, takeoff, and rolling takeoff, were considered in this study. Three-dimensional Euler computations were carried out to obtain the flow field. At the initial design, the peak Mach numbers for maximum cruise, takeoff, and rolling takeoff conditions were 0.88, 1.772, and 1.61, respectively. The acceptable upper limits on the takeoff and rolling takeoff Mach numbers were 1.55 and 1.45. Since the initial design provided by Boeing was found to be optimum with respect to the maximum cruise condition, the sum of the peak Mach numbers at takeoff and rolling takeoff were minimized in the current study while the maximum cruise Mach number was constrained to be close to that at the existing design. With this objective, the optimum design satisfied the upper limits at takeoff and rolling takeoff while retaining the desirable cruise performance. Further studies are being conducted to include static and cross-wind operating conditions in the design optimization procedure. This work was carried out in collaboration with Dr. E.S. Reddy of NYMA, Inc.

  6. CFD-Based Design Optimization for Single Element Rocket Injector

    NASA Technical Reports Server (NTRS)

    Vaidyanathan, Rajkumar; Tucker, Kevin; Papila, Nilay; Shyy, Wei

    2003-01-01

    To develop future Reusable Launch Vehicle concepts, we have conducted design optimization for a single element rocket injector, with overall goals of improving reliability and performance while reducing cost. Computational solutions based on the Navier-Stokes equations, finite rate chemistry, and the k-E turbulence closure are generated with design of experiment techniques, and the response surface method is employed as the optimization tool. The design considerations are guided by four design objectives motivated by the consideration in both performance and life, namely, the maximum temperature on the oxidizer post tip, the maximum temperature on the injector face, the adiabatic wall temperature, and the length of the combustion zone. Four design variables are selected, namely, H2 flow angle, H2 and O2 flow areas with fixed flow rates, and O2 post tip thickness. In addition to establishing optimum designs by varying emphasis on the individual objectives, better insight into the interplay between design variables and their impact on the design objectives is gained. The investigation indicates that improvement in performance or life comes at the cost of the other. Best compromise is obtained when improvements in both performance and life are given equal importance.

  7. CFD Based Computations of Flexible Helicopter Blades for Stability Analysis

    NASA Technical Reports Server (NTRS)

    Guruswamy, Guru P.

    2011-01-01

    As a collaborative effort among government aerospace research laboratories an advanced version of a widely used computational fluid dynamics code, OVERFLOW, was recently released. This latest version includes additions to model flexible rotating multiple blades. In this paper, the OVERFLOW code is applied to improve the accuracy of airload computations from the linear lifting line theory that uses displacements from beam model. Data transfers required at every revolution are managed through a Unix based script that runs jobs on large super-cluster computers. Results are demonstrated for the 4-bladed UH-60A helicopter. Deviations of computed data from flight data are evaluated. Fourier analysis post-processing that is suitable for aeroelastic stability computations are performed.

  8. CFD-based Modeling of Inflight Mercury Capture

    SciTech Connect

    Madsen, J.I.; O'Brien, T.J.

    2007-01-01

    A numerical model of sorbent injection and in-flight mercury capture is presented. There are few existing models of mercury capture, and these typically make gross assumptions of plug gas flow, no velocity slip between particle and gas phase, and uniform sorbent dispersion. All of these assumptions are overcome with the current model, which combines the physics of mass transfer at the microscopic sorbent scale with macroscopic flow conditions provided via Computational Fluid Dynamics (CFD) simulations. The implication is a cost-efficient tool for design of injection systems that maximize capture efficiency. The modeling framework will be presented along with results based on simulation of sites from the DOE/NETL sorbent injection field test program.

  9. Modeling skin sensitization potential of mechanistically hard-to-be-classified aniline and phenol compounds with quantum mechanistic properties.

    PubMed

    Ouyang, Qin; Wang, Lirong; Mu, Ying; Xie, Xiang-Qun

    2014-12-24

    Advanced structure-activity relationship (SAR) modeling can be used as an alternative tool for identification of skin sensitizers and in improvement of the medical diagnosis and more effective practical measures to reduce the causative chemical exposures. It can also circumvent ethical concern of using animals in toxicological tests, and reduce time and cost. Compounds with aniline or phenol moieties represent two large classes of frequently skin sensitizing chemicals but exhibiting very variable, and difficult to predict, potency. The mechanisms of action are not well-understood. A group of mechanistically hard-to-be-classified aniline and phenol chemicals were collected. An in silico model was established by statistical analysis of quantum descriptors for the determination of the relationship between their chemical structures and skin sensitization potential. The sensitization mechanisms were investigated based on the features of the established model. Then the model was utilized to analyze a subset of FDA approved drugs containing aniline and/or phenol groups for prediction of their skin sensitization potential. A linear discriminant model using the energy of the highest occupied molecular orbital (ϵHOMO) as the descriptor yielded high prediction accuracy. The contribution of ϵHOMO as a major determinant may suggest that autoxidation or free radical binding could be involved. The model was further applied to predict allergic potential of a subset of FDA approved drugs containing aniline and/or phenol moiety. The predictions imply that similar mechanisms (autoxidation or free radical binding) may also play a role in the skin sensitization caused by these drugs. An accurate and simple quantum mechanistic model has been developed to predict the skin sensitization potential of mechanistically hard-to-be-classified aniline and phenol chemicals. The model could be useful for the skin sensitization potential predictions of a subset of FDA approved drugs.

  10. Modeling of batch sorber system: kinetic, mechanistic, and thermodynamic modeling

    NASA Astrophysics Data System (ADS)

    Mishra, Vishal

    2016-09-01

    The present investigation has dealt with the biosorption of copper and zinc ions on the surface of egg-shell particles in the liquid phase. Various rate models were evaluated to elucidate the kinetics of copper and zinc biosorptions, and the results indicated that the pseudo-second-order model was more appropriate than the pseudo-first-order model. The curve of the initial sorption rate versus the initial concentration of copper and zinc ions also complemented the results of the pseudo-second-order model. Models used for the mechanistic modeling were the intra-particle model of pore diffusion and Bangham's model of film diffusion. The results of the mechanistic modeling together with the values of pore and film diffusivities indicated that the preferential mode of the biosorption of copper and zinc ions on the surface of egg-shell particles in the liquid phase was film diffusion. The results of the intra-particle model showed that the biosorption of the copper and zinc ions was not dominated by the pore diffusion, which was due to macro-pores with open-void spaces present on the surface of egg-shell particles. The thermodynamic modeling reproduced the fact that the sorption of copper and zinc was spontaneous, exothermic with the increased order of the randomness at the solid-liquid interface.

  11. The coefficient of restitution of pressurized balls: a mechanistic model

    NASA Astrophysics Data System (ADS)

    Georgallas, Alex; Landry, Gaëtan

    2016-01-01

    Pressurized, inflated balls used in professional sports are regulated so that their behaviour upon impact can be anticipated and allow the game to have its distinctive character. However, the dynamics governing the impacts of such balls, even on stationary hard surfaces, can be extremely complex. The energy transformations, which arise from the compression of the gas within the ball and from the shear forces associated with the deformation of the wall, are examined in this paper. We develop a simple mechanistic model of the dependence of the coefficient of restitution, e, upon both the gauge pressure, P_G, of the gas and the shear modulus, G, of the wall. The model is validated using the results from a simple series of experiments using three different sports balls. The fits to the data are extremely good for P_G > 25 kPa and consistent values are obtained for the value of G for the wall material. As far as the authors can tell, this simple, mechanistic model of the pressure dependence of the coefficient of restitution is the first in the literature. *%K Coefficient of Restitution, Dynamics, Inflated Balls, Pressure, Impact Model

  12. Trichloroethylene: Mechanistic, Epidemiologic and Other Supporting Evidence of Carcinogenic Hazard

    PubMed Central

    Rusyn, Ivan; Chiu, Weihsueh A.; Lash, Lawrence H.; Kromhout, Hans; Hansen, Johnni; Guyton, Kathryn Z.

    2013-01-01

    The chlorinated solvent trichloroethylene (TCE) is a ubiquitous environmental pollutant. The carcinogenic hazard of TCE was the subject of a 2012 evaluation by a Working Group of the International Agency for Research on Cancer (IARC). Information on exposures, relevant data from epidemiologic studies, bioassays in experimental animals, and toxicity and mechanism of action studies was used to conclude that TCE is carcinogenic to humans (Group 1). This article summarizes the key evidence forming the scientific bases for the IARC classification. Exposure to TCE from environmental sources (including from hazardous waste sites and contaminated water) is common throughout the world. While workplace use of TCE has been declining, occupational exposures remain of concern, especially in developing countries. Strongest human evidence is from studies of occupational TCE exposure and kidney cancer. Positive, although less consistent, associations were reported for liver cancer and non-Hodgkin's lymphoma. TCE is carcinogenic at multiple sites in multiple species and strains of experimental animals. The mechanistic evidence includes extensive data on the toxicokinetics and genotoxicity of TCE and its metabolites. Together, available evidence provided a cohesive database supporting the human cancer hazard of TCE, particularly in the kidney. For other target sites of carcinogenicity, mechanistic and other data were found to be more limited. Important sources of susceptibility to TCE toxicity and carcinogenicity were also reviewed by the Working Group. In all, consideration of the multiple evidence streams presented herein informed the IARC conclusions regarding the carcinogenicity of TCE. PMID:23973663

  13. New web-based applications for mechanistic case diagramming.

    PubMed

    Dee, Fred R; Haugen, Thomas H; Kreiter, Clarence D

    2014-01-01

    The goal of mechanistic case diagraming (MCD) is to provide students with more in-depth understanding of cause and effect relationships and basic mechanistic pathways in medicine. This will enable them to better explain how observed clinical findings develop from preceding pathogenic and pathophysiological events. The pedagogic function of MCD is in relating risk factors, disease entities and morphology, signs and symptoms, and test and procedure findings in a specific case scenario with etiologic pathogenic and pathophysiological sequences within a flow diagram. In this paper, we describe the addition of automation and predetermined lists to further develop the original concept of MCD as described by Engelberg in 1992 and Guerrero in 2001. We demonstrate that with these modifications, MCD is effective and efficient in small group case-based teaching for second-year medical students (ratings of ~3.4 on a 4.0 scale). There was also a significant correlation with other measures of competency, with a 'true' score correlation of 0.54. A traditional calculation of reliability showed promising results (α =0.47) within a low stakes, ungraded environment. Further, we have demonstrated MCD's potential for use in independent learning and TBL. Future studies are needed to evaluate MCD's potential for use in medium stakes assessment or self-paced independent learning and assessment. MCD may be especially relevant in returning students to the application of basic medical science mechanisms in the clinical years.

  14. From Data Patterns to Mechanistic Models in Acute Critical Illness

    PubMed Central

    Aerts, Jean-Marie; Haddad, Wassim M.; An, Gary; Vodovotz, Yoram

    2014-01-01

    The complexity of the physiologic and inflammatory response in acute critical illness has stymied the accurate diagnosis and development of therapies. The Society for Complex Acute Illness was formed a decade ago with the goal of leveraging multiple complex systems approaches in order to address this unmet need. Two main paths of development have characterized the Society’s approach: i) data pattern analysis, either defining the diagnostic/prognostic utility of complexity metrics of physiological signals or multivariate analyses of molecular and genetic data, and ii) mechanistic mathematical and computational modeling, all being performed with an explicit translational goal. Here, we summarize the progress to date on each of these approaches, along with pitfalls inherent in the use of each approach alone. We suggest that the next decade holds the potential to merge these approaches, connecting patient diagnosis to treatment via mechanism-based dynamical system modeling and feedback control, and allowing extrapolation from physiologic signals to biomarkers to novel drug candidates. As a predicate example, we focus on the role of data-driven and mechanistic models in neuroscience, and the impact that merging these modeling approaches can have on general anesthesia. PMID:24768566

  15. Surgery for malignant gliomas: mechanistic reasoning and slippery statistics.

    PubMed

    Mitchell, Patrick; Ellison, David W; Mendelow, A David

    2005-07-01

    Current surgical treatment of malignant gliomas largely depends on mechanistic reasoning and data collected in non-randomised studies. Technological advance has enabled more accurate resection of tumours and preservation of eloquent brain areas but ethical considerations have restricted randomised trials on the efficacy of surgery to one small trial that found a 3 month survival advantage for patients over age 65 years who received surgery and interim analysis of a larger trial. There is an argument for surgery as a palliative measure in patients with symptoms caused by mechanisms that are surgically remediable. Whether there is any survival advantage from surgery in patients other than those with immediately life-threatening, surgically remediable complications, such as raised intracranial pressure, is unclear. The available data show that if such an advantage does exist, it is modest at best. Adjuvant treatments given surgically are being studied. Chemotherapy wafers are the most prominent of the adjuvant treatments but the evidence available is insufficient to recommend their use in routine practice. In this review we examine the prevailing mechanistic model and observational data; we assess how these are applied and the priorities they indicate for future research.

  16. Splicing in immune cells-mechanistic insights and emerging topics.

    PubMed

    Schaub, Annalisa; Glasmacher, Elke

    2017-04-01

    Differential splicing of mRNAs not only enables regulation of gene expression levels, but also ensures a high degree of gene-product diversity. The extent to which splicing of mRNAs is utilized as a mechanism in immune cells has become evident within the last few years. Still, only a few of these mechanisms have been well studied. In this review, we discuss some of the best-understood mechanisms, for instance the differential splicing of CD45 in T cells, as well as immunoglobulin genes in B cells. Beyond that we provide general mechanistic insights on how, when and where this process takes place and discuss the current knowledge regarding these topics in immune cells. We also highlight some of the reported links to immune-related diseases, genome-wide sequencing studies that revealed thousands of differentially spliced transcripts, as well as splicing studies on immune cells that remain mechanistically not fully understood. We thereby display potential emerging topics for future studies centered on splicing mechanisms in immune cells. © The Author 2017. Published by Oxford University Press on behalf of The Japanese Society for Immunology.

  17. Photosynthetic water oxidation vs. mitochondrial oxygen reduction: distinct mechanistic parallels.

    PubMed

    Silverstein, Todd P

    2011-08-01

    The photosynthetic oxygen evolving complex (PSII-OEC) and the mitochondrial cytochrome c oxidase (CcO) not only catalyze anti-parallel reactions (the OEC oxidizes water to dioxygen, whereas CcO reduces dioxygen to water), they also share a number of uncanny molecular and mechanistic similarities. Both feature a redox-active polymetallic cluster that includes a key tyrosine, and both utilize a two-phase mechanism. In one phase the polymetallic cluster undergoes four sequential one-electron transfers: In the PSII-OEC, four successive photooxidations of the photosystem II reaction center P680 (to P680(+)) allows acceptance of 4 × 1e- from the Mn(4)Ca cluster; in CcO, four reduced cytochrome c Fe(2+) cations donate 4 × 1e- to the bimetallic center. In the second phase for each enzyme, the polymetallic cluster undergoes a single four-electron transfer with the O(2)/2 H(2)O redox couple. Intriguing mechanistic similarities between these two complex redox enzymes first delineated over a decade ago by Hoganson/Proshlyakov/Babcock et al. are updated and expanded in this article.

  18. Noncanonical IFN Signaling: Mechanistic Linkage of Genetic and Epigenetic Events

    PubMed Central

    Ahmed, Chulbul M.

    2016-01-01

    The canonical model of cytokine signaling via the JAK/STAT pathway dominates our view of signal transduction but provides no insight into the significance of the simultaneous presence of activated JAKs and STATs in the nucleus of cells treated with cytokines. Such a mechanistic shortcoming challenges the usefulness of the model in its present form. Focusing on the interferon (IFN) cytokines, we have developed a noncanonical model of IFN signaling that naturally connects activated JAKs and STATs at or near response elements of genes that are activated by the IFNs. Specifically, cells treated with IFNγ showed association of activated STAT1α and JAK2 at the GAS element of genes activated by IFNγ. For IFNα treated cells, the association involved activated STAT1α and TYK2 JAK kinase at the ISRE promoter. The power of the noncanonical model is that it provides mechanistic insight into specific gene activation at the level of the associated epigenetics, akin to that of steroid/steroid receptor signaling. PMID:28077919

  19. Trichloroethylene: Mechanistic, epidemiologic and other supporting evidence of carcinogenic hazard.

    PubMed

    Rusyn, Ivan; Chiu, Weihsueh A; Lash, Lawrence H; Kromhout, Hans; Hansen, Johnni; Guyton, Kathryn Z

    2014-01-01

    The chlorinated solvent trichloroethylene (TCE) is a ubiquitous environmental pollutant. The carcinogenic hazard of TCE was the subject of a 2012 evaluation by a Working Group of the International Agency for Research on Cancer (IARC). Information on exposures, relevant data from epidemiologic studies, bioassays in experimental animals, and toxicity and mechanism of action studies was used to conclude that TCE is carcinogenic to humans (Group 1). This article summarizes the key evidence forming the scientific bases for the IARC classification. Exposure to TCE from environmental sources (including hazardous waste sites and contaminated water) is common throughout the world. While workplace use of TCE has been declining, occupational exposures remain of concern, especially in developing countries. The strongest human evidence is from studies of occupational TCE exposure and kidney cancer. Positive, although less consistent, associations were reported for liver cancer and non-Hodgkin lymphoma. TCE is carcinogenic at multiple sites in multiple species and strains of experimental animals. The mechanistic evidence includes extensive data on the toxicokinetics and genotoxicity of TCE and its metabolites. Together, available evidence provided a cohesive database supporting the human cancer hazard of TCE, particularly in the kidney. For other target sites of carcinogenicity, mechanistic and other data were found to be more limited. Important sources of susceptibility to TCE toxicity and carcinogenicity were also reviewed by the Working Group. In all, consideration of the multiple evidence streams presented herein informed the IARC conclusions regarding the carcinogenicity of TCE.

  20. Emerging mechanistic targets in lung injury induced by combustion-generated particles.

    PubMed

    Fariss, Marc W; Gilmour, M Ian; Reilly, Christopher A; Liedtke, Wolfgang; Ghio, Andrew J

    2013-04-01

    The mechanism for biological effect following exposure to combustion-generated particles is incompletely defined. The identification of pathways regulating the acute toxicological effects of these particles provides specific targets for therapeutic manipulation in an attempt to impact disease following exposures. Transient receptor potential (TRP) cation channels were identified as "particle sensors" in that their activation was coupled with the initiation of protective responses limiting airway deposition and inflammatory responses, which promote degradation and clearance of the particles. TRPA1, V1, V4, and M8 have a capacity to mediate adverse effects after exposure to combustion-generated particulate matter (PM); relative contributions of each depend upon particle composition, dose, and deposition. Exposure of human bronchial epithelial cells to an organic extract of diesel exhaust particle was followed by TRPV4 mediating Ca(++) influx, increased RAS expression, mitogen-activated protein kinase signaling, and matrix metalloproteinase-1 activation. These novel pathways of biological effect can be targeted by compounds that specifically inhibit critical signaling reactions. In addition to TRPs and calcium biochemistry, humic-like substances (HLS) and cell/tissue iron equilibrium were identified as potential mechanistic targets in lung injury after particle exposure. In respiratory epithelial cells, iron sequestration by HLS in wood smoke particle (WSP) was associated with oxidant generation, cell signaling, transcription factor activation, and release of inflammatory mediators. Similar to WSP, cytotoxic insoluble nanosized spherical particles composed of HLS were isolated from cigarette smoke condensate. Therapies that promote bioelimination of HLS and prevent the disruption of iron homeostasis could function to reduce the harmful effects of combustion-generated PM exposure.

  1. Emerging Mechanistic Targets in Lung Injury Induced by Combustion-Generated Particles

    PubMed Central

    Fariss, Marc W.; Gilmour, M. Ian; Reilly, Christopher A.; Liedtke, Wolfgang; Ghio, Andrew J.

    2013-01-01

    The mechanism for biological effect following exposure to combustion-generated particles is incompletely defined. The identification of pathways regulating the acute toxicological effects of these particles provides specific targets for therapeutic manipulation in an attempt to impact disease following exposures. Transient receptor potential (TRP) cation channels were identified as “particle sensors” in that their activation was coupled with the initiation of protective responses limiting airway deposition and inflammatory responses, which promote degradation and clearance of the particles. TRPA1, V1, V4, and M8 have a capacity to mediate adverse effects after exposure to combustion-generated particulate matter (PM); relative contributions of each depend upon particle composition, dose, and deposition. Exposure of human bronchial epithelial cells to an organic extract of diesel exhaust particle was followed by TRPV4 mediating Ca++ influx, increased RAS expression, mitogen-activated protein kinase signaling, and matrix metalloproteinase-1 activation. These novel pathways of biological effect can be targeted by compounds that specifically inhibit critical signaling reactions. In addition to TRPs and calcium biochemistry, humic-like substances (HLS) and cell/tissue iron equilibrium were identified as potential mechanistic targets in lung injury after particle exposure. In respiratory epithelial cells, iron sequestration by HLS in wood smoke particle (WSP) was associated with oxidant generation, cell signaling, transcription factor activation, and release of inflammatory mediators. Similar to WSP, cytotoxic insoluble nanosized spherical particles composed of HLS were isolated from cigarette smoke condensate. Therapies that promote bioelimination of HLS and prevent the disruption of iron homeostasis could function to reduce the harmful effects of combustion-generated PM exposure. PMID:23322347

  2. Myocardial steatosis as a possible mechanistic link between diastolic dysfunction and coronary microvascular dysfunction in women.

    PubMed

    Wei, Janet; Nelson, Michael D; Szczepaniak, Edward W; Smith, Laura; Mehta, Puja K; Thomson, Louise E J; Berman, Daniel S; Li, Debiao; Bairey Merz, C Noel; Szczepaniak, Lidia S

    2016-01-01

    Women with coronary microvascular dysfunction (CMD) and no obstructive coronary artery disease (CAD) have increased rates of heart failure with preserved ejection fraction (HFpEF). The mechanisms of HFpEF are not well understood. Ectopic fat deposition in the myocardium, termed myocardial steatosis, is frequently associated with diastolic dysfunction in other metabolic diseases. We investigated the prevalence of myocardial steatosis and diastolic dysfunction in women with CMD and subclinical HFpEF. In 13 women, including eight reference controls and five women with CMD and evidence of subclinical HFpEF (left ventricular end-diastolic pressure >12 mmHg), we measured myocardial triglyceride content (TG) and diastolic function, by proton magnetic resonance spectroscopy and magnetic resonance tissue tagging, respectively. When compared with reference controls, women with CMD had higher myocardial TG content (0.83 ± 0.12% vs. 0.43 ± 0.06%; P = 0.025) and lower diastolic circumferential strain rate (168 ± 12 vs. 217 ± 15%/s; P = 0.012), with myocardial TG content correlating inversely with diastolic circumferential strain rate (r = -0.779; P = 0.002). This study provides proof-of-concept that myocardial steatosis may play an important mechanistic role in the development of diastolic dysfunction in women with CMD and no obstructive CAD. Detailed longitudinal studies are warranted to explore specific treatment strategies targeting myocardial steatosis and its effect on diastolic function.

  3. Myocardial steatosis as a possible mechanistic link between diastolic dysfunction and coronary microvascular dysfunction in women

    PubMed Central

    Nelson, Michael D.; Szczepaniak, Edward W.; Smith, Laura; Mehta, Puja K.; Thomson, Louise E. J.; Berman, Daniel S.; Li, Debiao; Bairey Merz, C. Noel; Szczepaniak, Lidia S.

    2015-01-01

    Women with coronary microvascular dysfunction (CMD) and no obstructive coronary artery disease (CAD) have increased rates of heart failure with preserved ejection fraction (HFpEF). The mechanisms of HFpEF are not well understood. Ectopic fat deposition in the myocardium, termed myocardial steatosis, is frequently associated with diastolic dysfunction in other metabolic diseases. We investigated the prevalence of myocardial steatosis and diastolic dysfunction in women with CMD and subclinical HFpEF. In 13 women, including eight reference controls and five women with CMD and evidence of subclinical HFpEF (left ventricular end-diastolic pressure >12 mmHg), we measured myocardial triglyceride content (TG) and diastolic function, by proton magnetic resonance spectroscopy and magnetic resonance tissue tagging, respectively. When compared with reference controls, women with CMD had higher myocardial TG content (0.83 ± 0.12% vs. 0.43 ± 0.06%; P = 0.025) and lower diastolic circumferential strain rate (168 ± 12 vs. 217 ± 15%/s; P = 0.012), with myocardial TG content correlating inversely with diastolic circumferential strain rate (r = −0.779; P = 0.002). This study provides proof-of-concept that myocardial steatosis may play an important mechanistic role in the development of diastolic dysfunction in women with CMD and no obstructive CAD. Detailed longitudinal studies are warranted to explore specific treatment strategies targeting myocardial steatosis and its effect on diastolic function. PMID:26519031

  4. Mechanistic Insights on the Photosensitized Chemistry of a Fatty Acid at the Air/Water Interface

    PubMed Central

    2016-01-01

    Interfaces are ubiquitous in the environment and many atmospheric key processes, such as gas deposition, aerosol, and cloud formation are, at one stage or another, strongly impacted by physical and chemical processes occurring at interfaces. Here, the photoinduced chemistry of an air/water interface coated with nonanoic acid—a fatty acid surfactant we use as a proxy for chemically complex natural aqueous surface microlayers—was investigated as a source of volatile and semivolatile reactive organic species. The carboxylic acid coating significantly increased the propensity of photosensitizers, chosen to mimic those observed in real environmental waters, to partition to the interface and enhance reactivity there. Photochemical formation of functionalized and unsaturated compounds was systematically observed upon irradiation of these coated surfaces. The role of a coated interface appears to be critical in providing a concentrated medium allowing radical–radical reactions to occur in parallel with molecular oxygen additions. Mechanistic insights are provided from extensive analysis of products observed in both gas and aqueous phases by online switchable reagent ion-time of flight-mass spectrometry and by off-line ultraperformance liquid chromatography coupled to a Q Exactive high resolution mass spectrometer through heated electrospray ionization, respectively. PMID:27611489

  5. Development of animal models underlining mechanistic connections between prostate inflammation and cancer.

    PubMed

    Mimeault, Murielle; Batra, Surinder K

    2013-02-10

    The characterization of animal models has indicated that the genetic, dietary and environmental factors and hormonal imbalance may influence the risk to develop prostate inflammatory lesions and prostate cancer (PC) confirming human epidemiologic data. It is now established that the prostate inflammatory response typically results in major changes in the local microenvironment of epithelial cells of the prostate gland, including an intense stromal remodeling, activation of fibroblasts, infiltration of immune cells such as mast cells, macrophages and B and T lymphocytes and collagen deposition. The immune cells recruited at prostate inflammatory lesions and myofibroblasts may contribute to the release of numerous pro-inflammatory cytokines and chemokines that in turn can promote the oxidative stress, genomic instability and proliferation of epithelial cells. The accumulation of additional genetic and/or epigenetic alterations in prostatic stem/progenitor cells may subsequently culminate to their malignant transformation and PC initiation and progression and more particularly with advancing age. The potential mechanistic relationships between the molecular events associated with the persistent inflammatory response and prostate carcinogenesis have important implications for optimizing the current therapies against different prostatic disorders and PCs.

  6. Cascadia Tsunami Deposit Database

    USGS Publications Warehouse

    Peters, Robert; Jaffe, Bruce; Gelfenbaum, Guy; Peterson, Curt

    2003-01-01

    The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have been compiled from 52 studies, documenting 59 sites from northern California to Vancouver Island, British Columbia that contain known or potential tsunami deposits. Bibliographical references are provided for all sites included in the database. Cascadia tsunami deposits are usually seen as anomalous sand layers in coastal marsh or lake sediments. The studies cited in the database use numerous criteria based on sedimentary characteristics to distinguish tsunami deposits from sand layers deposited by other processes, such as river flooding and storm surges. Several studies cited in the database contain evidence for more than one tsunami at a site. Data categories include age, thickness, layering, grainsize, and other sedimentological characteristics of Cascadia tsunami deposits. The database documents the variability observed in tsunami deposits found along the Cascadia margin.

  7. Quantifying fat, oil, and grease deposit formation kinetics.

    PubMed

    Iasmin, Mahbuba; Dean, Lisa O; Ducoste, Joel J

    2016-01-01

    Fat, oil, and grease (FOG) deposits formed in sanitary sewers are calcium-based saponified solids that are responsible for a significant number of nationwide sanitary sewer overflows (SSOs) across United States. In the current study, the kinetics of lab-based saponified solids were determined to understand the kinetics of FOG deposit formation in sewers for two types of fat (Canola and Beef Tallow) and two types of calcium sources (calcium chloride and calcium sulfate) under three pH (7 ± 0.5, 10 ± 0.5, and ≈14) and two temperature conditions (22 ± 0.5 and 45 ± 0.5 °C). The results of this study displayed quick reactions of a fraction of fats with calcium ions to form calcium based saponified solids. Results further showed that increased palmitic fatty acid content in source fats, the magnitude of the pH, and temperature significantly affect the FOG deposit formation and saponification rates. The experimental data of the kinetics were compared with two empirical models: a) Cotte saponification model and b) Foubert crystallization model and a mass-action based mechanistic model that included alkali driven hydrolysis of triglycerides. Results showed that the mass action based mechanistic model was able to predict changes in the rate of formation of saponified solids under the different experimental conditions compared to both empirical models. The mass-action based saponification model also revealed that the hydrolysis of Beef Tallow was slower compared to liquid Canola fat resulting in smaller quantities of saponified solids. This mechanistic saponification model, with its ability to track the saponified solids chemical precursors, may provide an initial framework to predict the spatial formation of FOG deposits in municipal sewers using system wide sewer collection modeling software. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Conservative or reactive? Mechanistic chemical perspectives on organic matter stability

    NASA Astrophysics Data System (ADS)

    Koch, Boris

    2016-04-01

    Carbon fixation by terrestrial and marine primary production has a fundamental seasonal effect on the atmospheric carbon content and it profoundly contributes to long-term carbon storage in form of organic matter (OM) in soils, water, and sediments. The efficacy of this sequestration process strongly depends on the degree of OM persistence. Therefore, one of the key issues in dissolved and particulate OM research is to assess the stability of reservoirs and to quantify their contribution to global carbon fluxes. Incubation experiments are helpful to assess OM stability during the first, early diagenetic turnover induced by sunlight or microbes. However, net carbon fluxes within the global carbon cycle also act on much longer time scales, which are not amenable in experiments. It is therefore critical to improve our mechanistic understanding to be able to assess potential future changes in the organic matter cycle. This session contribution highlights some achievements and open questions in the field. An improved mechanistic understanding of OM turnover particularly depends on the molecular characterization of biogeochemical processes and their kinetics: (i) in soils and sediments, aggregation/disaggregation of OM is primarily controlled by its molecular composition. Hence, the chemical composition determines the transfer of organic carbon from the large particulate to the small dissolved organic matter reservoir - an important substrate for microbial metabolism. (ii) In estuaries, dissolved organic carbon gradients usually suggest conservative behavior, whereas molecular-level studies reveal a substantial chemical modification of terrestrial DOM along the land-ocean interface. (iii) In the ocean, previous studies have shown that the recalcitrance of OM depends on bulk concentration and energy yield. However, ultrahigh resolution mass spectrometry in combination with radiocarbon analyses also emphasized that stability is tightly connected to molecular composition

  9. Mechanistic Perspectives on Organic Photoredox Catalysis for Aromatic Substitutions.

    PubMed

    Majek, Michal; Jacobi von Wangelin, Axel

    2016-10-18

    Photoredox catalysis has emerged as a powerful tool for the utilization of visible light to drive chemical reactions between organic molecules that exhibit two rather ubiquitous properties: colorlessness and redox-activity. The photocatalyst, however, requires significant absorption in the visible spectrum and reversible redox activity. This very general framework has led to the development of several new modes of reactivity based on electron and energy transfer steps between photoexcited catalyst states and various organic molecules. In the past years, major effort has been devoted to photoredox-catalytic aromatic substitutions involving an initial reductive activation of various aryl electrophiles by the photocatalyst, which opens a new entry into selective arene functionalizations within organic synthesis endeavors. This, however, has led to a unilateral emphasis of synthetic developments including catalyst modifications, substrate scope studies, and combinations with other chemical processes. This Account summarizes recent reports of new protocols for the synthesis of aromatic esters, thioethers, boronates, sulfonates, heterobiaryls, deuteroarenes, and other functionalized arenes under mild photoredox conditions with organic dyes. On the other hand, mechanistic studies were largely neglected. This Account emphasizes the most relevant experiments and techniques, which can greatly assist in the exploration of the mechanistic foundation of aromatic photoredox substitutions and the design of new chemical reactivities. The nature and physicochemical properties of the employed organic dyes, the control of its acid-base chemistry, the choice of the irradiation sources, and the concentrations of substrates and dyes are demonstrated to decisively affect the activity of organic photocatalysts, the chemo- and regioselectivities of reactions, and the operating mechanisms. Several methods of distinction between photocatalytic and radical chain processes are being discussed

  10. A new mechanistic framework to predict OCS fluxes in soils

    NASA Astrophysics Data System (ADS)

    Sauze, Joana; Ogee, Jérôme; Launois, Thomas; Kesselmeier, Jürgen; Van Diest, Heidi; Wingate, Lisa

    2015-04-01

    A better description of the amplitude of photosynthetic and respiratory gross CO2 fluxes at large scales is needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulfide (COS) is the most abundant sulphur gas in the atmosphere and has been proposed as a new tracer of gross photosynthesis, as the uptake of COS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. However, soils also exchange COS with the atmosphere and there is growing evidence that this flux must also be accounted for in atmospheric budgets. In this context a new mechanistic description of soil-atmosphere COS exchange is clearly needed. Soils can take up COS from the atmosphere as the soil biota also contain CA, and COS emissions from soils have also been reported in agricultural fields or anoxic soils. Previous studies have also shown that soil COS fluxes present an optimum soil water content and soil temperature. Here we propose a new mechanistic framework to predict the fluxes of COS between the soils and the atmosphere. We describe the COS soil budget by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of COS by CA is total and irreversible. To describe COS diffusion through the soil matrix, we use different formulations of soil air-filled pore space and temperature, depending on the turbulence level above the soil surface. Using this model we are able to explain the observed presence of an optimum temperature for soil COS uptake and show how this optimum can shift to cooler temperatures in the presence of soil COS emissions. Our model can also explain the observed optimum with soil moisture content previously described in the literature (e.g. Van Diest & Kesselmeier, 2008) as a result of diffusional constraints on COS hydrolysis. These diffusional constraints are also responsible for the response of COS uptake to soil

  11. Perspectives on the Application of Mechanistic Information in Chemical Hazard and Dose-Response Assessments

    EPA Science Inventory

    This overview summarizes several EPA Assessment publications reviewing approaches for applying mechanistic information in human health risk assessment and exploring opportunities for progress in this area.

  12. Perspectives on the Application of Mechanistic Information in Chemical Hazard and Dose-Response Assessments

    EPA Science Inventory

    This overview summarizes several EPA Assessment publications reviewing approaches for applying mechanistic information in human health risk assessment and exploring opportunities for progress in this area.

  13. Dry deposition velocities

    SciTech Connect

    Sehmel, G.A.

    1984-03-01

    Dry deposition velocities are very difficult to predict accurately. In this article, reported values of dry deposition velocities are summarized. This summary includes values from the literature on field measurements of gas and particle dry deposition velocities, and the uncertainties inherent in extrapolating field results to predict dry deposition velocities are discussed. A new method is described for predicting dry deposition velocity using a least-squares correlation of surface mass transfer resistances evaluated in wind tunnel experiments. 14 references, 4 figures, 1 table.

  14. Biomimetic thin film deposition

    NASA Astrophysics Data System (ADS)

    Rieke, P. C.; Campbell, A. A.; Tarasevich, B. J.; Fryxell, G. E.; Bentjen, S. B.

    1991-04-01

    Surfaces derivatized with organic functional groups were used to promote the deposition of thin films of inorganic minerals. These derivatized surfaces were designed to mimic the nucleation proteins that control mineral deposition during formation of bone, shell, and other hard tissues in living organisms. By the use of derivatized substrates control was obtained over the phase of mineral deposited, the orientation of the crystal lattice and the location of deposition. These features are of considerable importance in many technically important thin films, coatings, and composite materials. Methods of derivatizing surfaces are considered and examples of controlled mineral deposition are presented.

  15. Micelle confined mechanistic pathway for 4-nitrophenol reduction.

    PubMed

    Roy, Anindita; Debnath, Biplab; Sahoo, Ramkrishna; Aditya, Teresa; Pal, Tarasankar

    2017-05-01

    The model 4-nitrophenol reduction has been carried out by different groups in presence of metallic or even non-metallic catalyst elaborating different mechanistic aspects. In the present investigation, we have thoroughly studied the hydrogenation of 4-nitrophenol in a completely metal free homogeneous condition. The introduction of a non-fluorescent probe unequivocally generates a fluorescent molecule that indirectly justifies the anion radical stabilization in the micelle. The reduction mechanism under metal-free condition was proposed and the concept of stabilization of anion radical transition state of 4-nitrophenol at the positively charged Stern layer of anionic micelle was established. The plausible reduction mechanism has also enlightened the graphene-like conducting property of Stern layer of the homogeneous micellar system. Furthermore, the confinement effect for catalysis has also been authenticated by supporting experimental evidences. The borrowed concept of catalysis in confinement drives the catalytic study to a new era of catalysis.

  16. Mechanistic characterization of chloride interferences in electrothermal atomization systems

    USGS Publications Warehouse

    Shekiro, J.M.; Skogerboe, R.K.; Taylor, H.E.

    1988-01-01

    A computer-controlled spectrometer with a photodiode array detector has been used for wavelength and temperature resolved characterization of the vapor produced by an electrothermal atomizer. The system has been used to study the chloride matrix interference on the atomic absorption spectrometric determination of manganese and copper. The suppression of manganese and copper atom populations by matrix chlorides such as those of calcium and magnesium is due to the gas-phase formation of an analyte chloride species followed by the diffusion of significant fractions of these species from the atom cell prior to completion of the atomization process. The analyte chloride species cannot be formed when matrix chlorides with metal-chloride bond dissociation energies above those of the analyte chlorides are the principal entitles present. The results indicate that multiple wavelength spectrometry used to obtain temperature-resolved spectra is a viable tool in the mechanistic characterization of interference effects observed with electrothermal atomization systems. ?? 1988 American Chemical Society.

  17. Mechanistic model for void distribution in flashing flow

    SciTech Connect

    Riznic, J.; Ishii, M.; Afgan, N.

    1987-01-01

    A problem of discharging of an initially subcooled liquid from a high pressure condition into a low pressure environment is quite important in several industrial systems such as nuclear reactors and chemical reactors. A new model for the flashing process is proposed here based on the wall nucleation theory, bubble growth model and drift-flux bubble transport model. In order to calculate the bubble number density, the bubble number transport equation with a distributed source from the wall nucleation sites is used. The model predictions in terms of the void fraction are compared to Moby Dick and BNL experimental data. It shows that satisfactory agreements could be obtained from the present model without any floating parameter to be adjusted with data. This result indicates that, at least for the experimental conditions considered here, the mechanistic prediction of the flashing phenomenon is possible based on the present wall nucleation based model. 43 refs., 4 figs.

  18. Enhancer function: mechanistic and genome-wide insights come together.

    PubMed

    Plank, Jennifer L; Dean, Ann

    2014-07-03

    Enhancers establish spatial or temporal patterns of gene expression that are critical for development, yet our understanding of how these DNA cis-regulatory elements function from a distance to increase transcription of their target genes and shape the cellular transcriptome has been gleaned primarily from studies of individual genes or gene families. High-throughput sequencing studies place enhancer-gene interactions within the 3D context of chromosome folding, inviting a new look at enhancer function and stimulating provocative new questions. Here, we integrate these whole-genome studies with recent mechanistic studies to illuminate how enhancers physically interact with target genes, how enhancer activity is regulated during development, and the role of noncoding RNAs transcribed from enhancers in their function.

  19. Halogenation of aromatic compounds: thermodynamic, mechanistic and ecological aspects.

    PubMed

    Dolfing, J

    1998-10-15

    Biological halogenation of aromatic compounds implies the generation of reducing equivalents in the form of e.g. NADH. Thermodynamic calculations show that coupling the halogenation step to a step in which the reducing equivalents are oxidized with a potent oxidant such as O2 or N2O makes the halogenation reaction thermodynamically feasible without the input of additional energy in the form of e.g. NADH. In a current model on the halogenation of tryptophan to 7-chloro-L-tryptophan NADH and O2 are proposed as co-substrates in a reaction in which the aromatic compound is oxidized via an epoxide as intermediate. The thermodynamic calculations thus indicate that such a route hinges on mechanistic insights but has no thermodynamic necessity. Furthermore the calculations suggest that halogenation of tryptophan and other aromatic compounds should be possible with N2O, and possibly even with nitrate replacing O2 as the oxidant.

  20. Obesity, energy balance, and cancer: a mechanistic perspective.

    PubMed

    Hursting, Stephen D

    2014-01-01

    Nearly 36 % of adults and 20 % of children in the USA are obese, defined as a body mass index (BMI) ≥30 kg/m(2). Obesity, which is accompanied by metabolic dysregulation often manifesting in the metabolic syndrome, is an established risk factor for many cancers. Within the growth-promoting, proinflammatory environment of the obese state, cross talk between macrophages, adipocytes, and epithelial cells occurs via obesity-associated hormones, cytokines, and other mediators that may enhance cancer risk and/or progression. This chapter synthesizes the evidence on key biological mechanisms underlying the obesity-cancer link, with particular emphasis on obesity-associated enhancements in growth factor signaling, inflammation, and vascular integrity processes, as well as obesity-dependent microenvironmental perturbations, including the epithelial-to-mesenchymal transition. These interrelated pathways represent possible mechanistic targets for disrupting the obesity-cancer link.

  1. Mechanistic modeling confronts the complexity of molecular cell biology.

    PubMed

    Phair, Robert D

    2014-11-05

    Mechanistic modeling has the potential to transform how cell biologists contend with the inescapable complexity of modern biology. I am a physiologist-electrical engineer-systems biologist who has been working at the level of cell biology for the past 24 years. This perspective aims 1) to convey why we build models, 2) to enumerate the major approaches to modeling and their philosophical differences, 3) to address some recurrent concerns raised by experimentalists, and then 4) to imagine a future in which teams of experimentalists and modelers build-and subject to exhaustive experimental tests-models covering the entire spectrum from molecular cell biology to human pathophysiology. There is, in my view, no technical obstacle to this future, but it will require some plasticity in the biological research mind-set.

  2. A mechanistic interpretation of the resonant wave-particle interaction

    NASA Astrophysics Data System (ADS)

    Chim, Chi Yung; O'Neil, Thomas M.

    2016-05-01

    This paper provides a simple mechanistic interpretation of the resonant wave-particle interaction of Landau. For the simple case of a Langmuir wave in a Vlasov plasma, the non-resonant electrons satisfy an oscillator equation that is driven resonantly by the bare electric field from the resonant electrons, and in the case of wave damping, this complex driver field is of a phase to reduce the oscillation amplitude. The wave-particle resonant interaction also occurs in waves governed by 2D E × B drift dynamics, such as a diocotron wave. In this case, the bare electric field from the resonant electrons causes E × B drift motion back in the core plasma, reducing the amplitude of the wave.

  3. From patterns to emerging processes in mechanistic urban ecology.

    PubMed

    Shochat, Eyal; Warren, Paige S; Faeth, Stanley H; McIntyre, Nancy E; Hope, Diane

    2006-04-01

    Rapid urbanization has become an area of crucial concern in conservation owing to the radical changes in habitat structure and loss of species engendered by urban and suburban development. Here, we draw on recent mechanistic ecological studies to argue that, in addition to altered habitat structure, three major processes contribute to the patterns of reduced species diversity and elevated abundance of many species in urban environments. These activities, in turn, lead to changes in animal behavior, morphology and genetics, as well as in selection pressures on animals and plants. Thus, the key to understanding urban patterns is to balance studying processes at the individual level with an integrated examination of environmental forces at the ecosystem scale.

  4. A mechanistic interpretation of the resonant wave-particle interaction

    SciTech Connect

    Chim, Chi Yung; O'Neil, Thomas M.

    2016-05-15

    This paper provides a simple mechanistic interpretation of the resonant wave-particle interaction of Landau. For the simple case of a Langmuir wave in a Vlasov plasma, the non-resonant electrons satisfy an oscillator equation that is driven resonantly by the bare electric field from the resonant electrons, and in the case of wave damping, this complex driver field is of a phase to reduce the oscillation amplitude. The wave-particle resonant interaction also occurs in waves governed by 2D E × B drift dynamics, such as a diocotron wave. In this case, the bare electric field from the resonant electrons causes E × B drift motion back in the core plasma, reducing the amplitude of the wave.

  5. Atrial Fibrillation and Hypertension: Mechanistic, Epidemiologic, and Treatment Parallels.

    PubMed

    Ogunsua, Adedotun A; Shaikh, Amir Y; Ahmed, Mohamed; McManus, David D

    2015-01-01

    Atrial fibrillation (AF) is an increasingly prevalent condition and the most common sustained arrhythmia encountered in ambulatory and hospital practice. Several clinical risk factors for AF include age, sex, valvular heart disease, obesity, sleep apnea, heart failure, and hypertension (HTN). Of all the risk factors, HTN is the most commonly encountered condition in patients with incident AF. Hypertension is associated with a 1.8-fold increase in the risk of developing new-onset AF and a 1.5-fold increase in the risk of progression to permanent AF. Hypertension predisposes to cardiac structural changes that influence the development of AF such as atrial remodeling. The renin angiotensin aldosterone system has been demonstrated to be a common mechanistic link in the pathogenesis of HTN and AF. Importantly, HTN is one of the few modifiable AF risk factors, and guideline-directed management of HTN may reduce the incidence of AF.

  6. Mechanistic Investigations into the Application of Sulfoxides in Carbohydrate Synthesis

    PubMed Central

    Brabham, Robin

    2016-01-01

    Abstract The utility of sulfoxides in a diverse range of transformations in the field of carbohydrate chemistry has seen rapid growth since the first introduction of a sulfoxide as a glycosyl donor in 1989. Sulfoxides have since developed into more than just anomeric leaving groups, and today have multiple roles in glycosylation reactions. These include as activators for thioglycosides, hemiacetals, and glycals, and as precursors to glycosyl triflates, which are essential for stereoselective β‐mannoside synthesis, and bicyclic sulfonium ions that facilitate the stereoselective synthesis of α‐glycosides. In this review we highlight the mechanistic investigations undertaken in this area, often outlining strategies employed to differentiate between multiple proposed reaction pathways, and how the conclusions of these investigations have and continue to inform upon the development of more efficient transformations in sulfoxide‐based carbohydrate synthesis. PMID:26744250

  7. Mechanistic Role of Thioredoxin 2 in Heart Failure.

    PubMed

    Chen, Chaofei; Chen, Haixuan; Zhou, Huanjiao Jenny; Ji, Weidong; Min, Wang

    2017-01-01

    Thioredoxin 2 (Trx2) is a pivotal mitochondrial protein that regulates redox signaling. The mitochondrial Trx2 is expressed ubiquitously, but it is found at the highest levels in metabolically active tissues like the heart. Global gene knockout of Trx2 results in embryonic lethality, likely due to the increased cellular oxidative stress. Moreover, mice with cardiac-specific Trx2 deletion develop spontaneous dilated cardiomyopathy (DCM), correlating with increased apoptosis stress kinase-1 (ASK1) signaling and increased cardiomyocyte apoptosis. Cardiomyocyte apoptosis is a common mechanism in the pathogenesis of heart failure. Our results show that Trx2 is essential for maintaining cardiac function. In this chapter, we summarize the key mechanistic role of Trx2 in preserving cardiac function by suppressing mitochondrial reactive oxygen species (ROS) generation and by inhibiting ASK1-dependent apoptosis in heart failure. Trx2 and ASK1 represent promising targets to develop therapeutic strategies for the treatment of DCM and heart failure.

  8. Calorie restriction and cancer prevention: a mechanistic perspective

    PubMed Central

    2013-01-01

    Calorie restriction (CR) is one of the most potent broadly acting dietary interventions for inducing weight loss and for inhibiting cancer in experimental models. Translation of the mechanistic lessons learned from research on CR to cancer prevention strategies in human beings is important given the high prevalence of excess energy intake, obesity, and metabolic syndrome in many parts of the world and the established links between obesity-associated metabolic perturbations and increased risk or progression of many types of cancer. This review synthesizes findings on the biological mechanisms underlying many of the anticancer effects of CR, with emphasis on the impact of CR on growth factor signaling pathways, inflammation, cellular and systemic energy homeostasis pathways, vascular perturbations, and the tumor microenvironment. These CR-responsive pathways and processes represent targets for translating CR research into effective cancer prevention strategies in human beings. PMID:24280167

  9. Antidepressants and gabapentinoids in neuropathic pain: Mechanistic insights.

    PubMed

    Kremer, Mélanie; Salvat, Eric; Muller, André; Yalcin, Ipek; Barrot, Michel

    2016-12-03

    Neuropathic pain arises as a consequence of a lesion or disease affecting the somatosensory system. It is generally chronic and challenging to treat. The recommended pharmacotherapy for neuropathic pain includes the use of some antidepressants, such as tricyclic antidepressants (TCAs) (amitriptyline…) or serotonin and noradrenaline re-uptake inhibitors (duloxetine…), and/or anticonvulsants such as the gabapentinoids gabapentin or pregabalin. Antidepressant drugs are not acute analgesics but require a chronic treatment to relieve neuropathic pain, which suggests the recruitment of secondary downstream mechanisms as well as long-term molecular and neuronal plasticity. Noradrenaline is a major actor for the action of antidepressant drugs in a neuropathic pain context. Mechanistic hypotheses have implied the recruitment of noradrenergic descending pathways as well as the peripheral recruitment of noradrenaline from sympathetic fibers sprouting into dorsal root ganglia; and importance of both α2 and β2 adrenoceptors have been reported. These monoamine re-uptake inhibitors may also indirectly act as anti-proinflammatory cytokine drugs; and their therapeutic action requires the opioid system, particularly the mu (MOP) and/or delta (DOP) opioid receptors. Gabapentinoids, which target the voltage-dependent calcium channels α2δ-1 subunit, inhibit calcium currents, thus decreasing the excitatory transmitter release and spinal sensitization. Gabapentinoids also activate the descending noradrenergic pain inhibitory system coupled to spinal α2 adrenoceptors. Gabapentinoid treatment may also indirectly impact on neuroimmune actors, like proinflammatory cytokines. These drugs are effective against neuropathic pain both with acute administration at high dose and with repeated administration. This review focuses on mechanistic knowledge concerning chronic antidepressant treatment and gabapentinoid treatment in a neuropathic pain context. Copyright © 2016 IBRO. Published by

  10. Assembly Line Polyketide Synthases: Mechanistic Insights and Unsolved Problems

    PubMed Central

    2015-01-01

    Two hallmarks of assembly line polyketide synthases have motivated an interest in these unusual multienzyme systems, their stereospecificity and their capacity for directional biosynthesis. In this review, we summarize the state of knowledge regarding the mechanistic origins of these two remarkable features, using the 6-deoxyerythronolide B synthase as a prototype. Of the 10 stereocenters in 6-deoxyerythronolide B, the stereochemistry of nine carbon atoms is directly set by ketoreductase domains, which catalyze epimerization and/or diastereospecific reduction reactions. The 10th stereocenter is established by the sequential action of three enzymatic domains. Thus, the problem has been reduced to a challenge in mainstream enzymology, where fundamental gaps remain in our understanding of the structural basis for this exquisite stereochemical control by relatively well-defined active sites. In contrast, testable mechanistic hypotheses for the phenomenon of vectorial biosynthesis are only just beginning to emerge. Starting from an elegant theoretical framework for understanding coupled vectorial processes in biology [Jencks, W. P. (1980) Adv. Enzymol. Relat. Areas Mol. Biol. 51, 75–106], we present a simple model that can explain assembly line polyketide biosynthesis as a coupled vectorial process. Our model, which highlights the important role of domain–domain interactions, not only is consistent with recent observations but also is amenable to further experimental verification and refinement. Ultimately, a definitive view of the coordinated motions within and between polyketide synthase modules will require a combination of structural, kinetic, spectroscopic, and computational tools and could be one of the most exciting frontiers in 21st Century enzymology. PMID:24779441

  11. Informing phenomenological structural bone remodelling with a mechanistic poroelastic model.

    PubMed

    Villette, Claire C; Phillips, Andrew T M

    2016-02-01

    Studies suggest that fluid motion in the extracellular space may be involved in the cellular mechanosensitivity at play in the bone tissue adaptation process. Previously, the authors developed a mesoscale predictive structural model of the femur using truss elements to represent trabecular bone, relying on a phenomenological strain-based bone adaptation algorithm. In order to introduce a response to bending and shear, the authors considered the use of beam elements, requiring a new formulation of the bone adaptation drivers. The primary goal of the study presented here was to isolate phenomenological drivers based on the results of a mechanistic approach to be used with a beam element representation of trabecular bone in mesoscale structural modelling. A single-beam model and a microscale poroelastic model of a single trabecula were developed. A mechanistic iterative adaptation algorithm was implemented based on fluid motion velocity through the bone matrix pores to predict the remodelled geometries of the poroelastic trabecula under 42 different loading scenarios. Regression analyses were used to correlate the changes in poroelastic trabecula thickness and orientation to the initial strain outputs of the beam model. Linear (R(2) > 0.998) and third-order polynomial (R(2) > 0.98) relationships were found between change in cross section and axial strain at the central axis, and between beam reorientation and ratio of bending strain to axial strain, respectively. Implementing these relationships into the phenomenological predictive algorithm for the mesoscale structural femur has the potential to produce a model combining biofidelic structure and mechanical behaviour with computational efficiency.

  12. Assembly line polyketide synthases: mechanistic insights and unsolved problems.

    PubMed

    Khosla, Chaitan; Herschlag, Daniel; Cane, David E; Walsh, Christopher T

    2014-05-13

    Two hallmarks of assembly line polyketide synthases have motivated an interest in these unusual multienzyme systems, their stereospecificity and their capacity for directional biosynthesis. In this review, we summarize the state of knowledge regarding the mechanistic origins of these two remarkable features, using the 6-deoxyerythronolide B synthase as a prototype. Of the 10 stereocenters in 6-deoxyerythronolide B, the stereochemistry of nine carbon atoms is directly set by ketoreductase domains, which catalyze epimerization and/or diastereospecific reduction reactions. The 10th stereocenter is established by the sequential action of three enzymatic domains. Thus, the problem has been reduced to a challenge in mainstream enzymology, where fundamental gaps remain in our understanding of the structural basis for this exquisite stereochemical control by relatively well-defined active sites. In contrast, testable mechanistic hypotheses for the phenomenon of vectorial biosynthesis are only just beginning to emerge. Starting from an elegant theoretical framework for understanding coupled vectorial processes in biology [Jencks, W. P. (1980) Adv. Enzymol. Relat. Areas Mol. Biol. 51, 75-106], we present a simple model that can explain assembly line polyketide biosynthesis as a coupled vectorial process. Our model, which highlights the important role of domain-domain interactions, not only is consistent with recent observations but also is amenable to further experimental verification and refinement. Ultimately, a definitive view of the coordinated motions within and between polyketide synthase modules will require a combination of structural, kinetic, spectroscopic, and computational tools and could be one of the most exciting frontiers in 21st Century enzymology.

  13. Mechanistic models of biofilm growth in porous media

    NASA Astrophysics Data System (ADS)

    Jaiswal, Priyank; Al-Hadrami, Fathiya; Atekwana, Estella A.; Atekwana, Eliot A.

    2014-07-01

    Nondestructive acoustics methods can be used to monitor in situ biofilm growth in porous media. In practice, however, acoustic methods remain underutilized due to the lack of models that can translate acoustic data into rock properties in the context of biofilm. In this paper we present mechanistic models of biofilm growth in porous media. The models are used to quantitatively interpret arrival times and amplitudes recorded in the 29 day long Davis et al. (2010) physical scale biostimulation experiment in terms of biofilm morphologies and saturation. The model pivots on addressing the sediment elastic behavior using the lower Hashin-Shtrikman bounds for grain mixing and Gassmann substitution for fluid saturation. The time-lapse P wave velocity (VP; a function of arrival times) is explained by a combination of two rock models (morphologies); "load bearing" which assumes the biofilm as an additional mineral in the rock matrix and "pore filling" which assumes the biofilm as an additional fluid phase in the pores. The time-lapse attenuation (QP-1; a function of amplitudes), on the other hand, can be explained adequately in two ways; first, through squirt flow where energy is lost from relative motion between rock matrix and pore fluid, and second, through an empirical function of porosity (φ), permeability (κ), and grain size. The squirt flow model-fitting results in higher internal φ (7% versus 5%) and more oblate pores (0.33 versus 0.67 aspect ratio) for the load-bearing morphology versus the pore-filling morphology. The empirical model-fitting results in up to 10% increase in κ at the initial stages of the load-bearing morphology. The two morphologies which exhibit distinct mechanical and hydraulic behavior could be a function of pore throat size. The biofilm mechanistic models developed in this study can be used for the interpretation of seismic data critical for the evaluation of biobarriers in bioremediation, microbial enhanced oil recovery, and CO2

  14. Mechanistic Analysis of the Saccharomyces cerevisiae Kinesin Kar3*S

    PubMed Central

    Mackey, Andrew T.; Sproul, Lisa R.; Sontag, Christopher A.; Satterwhite, Lisa L.; Correia, John J.; Gilbert, Susan P.

    2005-01-01

    Kar3 is a minus-end-directed microtubule motor that is implicated in meiotic and mitotic spindle function in Saccharomyces cerevisiae. To date, the only truncated protein of Kar3 that has been reported to promote unidirectional movement in vitro is GSTKar3. This motor contains an NH2-terminal glutathione S-transferase (GST) tag followed by the Kar3 sequence that is predicted to form an extended α-helical coiled-coil. The α-helical domain leads into the neck linker and COOH-terminal motor domain. Kar3 does not homodimerize with itself but forms a heterodimer with either Cik1 or Vik1, both of which are non-motor polypeptides. We evaluated the microtubule-GSTKar3 complex in comparison to the microtubule-Kar3 motor domain complex to determine the distinctive mechanistic features required for GSTKar3 motility. Our results indicate that ATP binding was significantly faster for GSTKar3 than that observed previously for the Kar3 motor domain. In addition, microtubule-activated ADP release resulted in an intermediate that bound ADP weakly in contrast to the Kar3 motor domain, suggesting that after ADP release, the microtubule-GSTKar3 motor binds ATP in preference to ADP. The kinetics also showed that GST-Kar3 readily detached from the microtubule rather than remaining bound for multiple ATP turnovers. These results indicate that the extended α-helical domain NH2-terminal to the catalytic core provides the structural transitions in response to the ATPase cycle that are critical for motility and that dimerization is not specifically required. This study provides the foundation to define the mechanistic contributions of Cik1 and Vik1 for Kar3 force generation and function in vivo. PMID:15385545

  15. Parameter and uncertainty estimation for mechanistic, spatially explicit epidemiological models

    NASA Astrophysics Data System (ADS)

    Finger, Flavio; Schaefli, Bettina; Bertuzzo, Enrico; Mari, Lorenzo; Rinaldo, Andrea

    2014-05-01

    Epidemiological models can be a crucially important tool for decision-making during disease outbreaks. The range of possible applications spans from real-time forecasting and allocation of health-care resources to testing alternative intervention mechanisms such as vaccines, antibiotics or the improvement of sanitary conditions. Our spatially explicit, mechanistic models for cholera epidemics have been successfully applied to several epidemics including, the one that struck Haiti in late 2010 and is still ongoing. Calibration and parameter estimation of such models represents a major challenge because of properties unusual in traditional geoscientific domains such as hydrology. Firstly, the epidemiological data available might be subject to high uncertainties due to error-prone diagnosis as well as manual (and possibly incomplete) data collection. Secondly, long-term time-series of epidemiological data are often unavailable. Finally, the spatially explicit character of the models requires the comparison of several time-series of model outputs with their real-world counterparts, which calls for an appropriate weighting scheme. It follows that the usual assumption of a homoscedastic Gaussian error distribution, used in combination with classical calibration techniques based on Markov chain Monte Carlo algorithms, is likely to be violated, whereas the construction of an appropriate formal likelihood function seems close to impossible. Alternative calibration methods, which allow for accurate estimation of total model uncertainty, particularly regarding the envisaged use of the models for decision-making, are thus needed. Here we present the most recent developments regarding methods for parameter and uncertainty estimation to be used with our mechanistic, spatially explicit models for cholera epidemics, based on informal measures of goodness of fit.

  16. Toxic neuropathies: Mechanistic insights based on a chemical perspective.

    PubMed

    LoPachin, Richard M; Gavin, Terrence

    2015-06-02

    2,5-Hexanedione (HD) and acrylamide (ACR) are considered to be prototypical among chemical toxicants that cause central-peripheral axonopathies characterized by distal axon swelling and degeneration. Because the demise of distal regions was assumed to be causally related to the onset of neurotoxicity, substantial effort was devoted to deciphering the respective mechanisms. Continued research, however, revealed that expression of the presumed hallmark morphological features was dependent upon the daily rate of toxicant exposure. Indeed, many studies reported that the corresponding axonopathic changes were late developing effects that occurred independent of behavioral and/or functional neurotoxicity. This suggested that the toxic axonopathy classification might be based on epiphenomena related to dose-rate. Therefore, the goal of this mini-review is to discuss how quantitative morphometric analyses and the establishment of dose-dependent relationships helped distinguish primary, mechanistically relevant toxicant effects from non-specific consequences. Perhaps more importantly, we will discuss how knowledge of neurotoxicant chemical nature can guide molecular-level research toward a better, more rational understanding of mechanism. Our discussion will focus on HD, the neurotoxic γ-diketone metabolite of the industrial solvents n-hexane and methyl-n-butyl ketone. Early investigations suggested that HD caused giant neurofilamentous axonal swellings and eventual degeneration in CNS and PNS. However, as our review will point out, this interpretation underwent several iterations as the understanding of γ-diketone chemistry improved and more quantitative experimental approaches were implemented. The chemical concepts and design strategies discussed in this mini-review are broadly applicable to the mechanistic studies of other chemicals (e.g., n-propyl bromine, methyl methacrylate) that cause toxic neuropathies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  17. Toxic Neuropathies: Mechanistic Insights Based On A Chemical Perspective

    PubMed Central

    LoPachin, Richard M.; Gavin, Terrence

    2014-01-01

    2,5-Hexanedione (HD) and acrylamide (ACR) are considered to be prototypical among chemical toxicants that cause central-peripheral axonopathies characterized by distal axon swelling and degeneration. Because the demise of distal regions was assumed to be causally related to the onset of neurotoxicity, substantial effort was devoted to deciphering the respective mechanisms. Continued research, however, revealed that expression of the presumed hallmark morphological features was dependent upon the daily rate of toxicant exposure. Indeed, many studies reported that the corresponding axonopathic changes were late developing effects that occurred independent of behavioral and/or functional neurotoxicity. This suggested that the toxic axonopathy classification might be based on epiphenomena related to dose-rate. Therefore, the goal of this mini-review is to discuss how quantitative morphometric analyses and the establishment of dose-dependent relationships helped distinguish primary, mechanistically relevant toxicant effects from non-specific consequences. Perhaps more importantly, we will discuss how knowledge of neurotoxicant chemical nature can guide molecular-level research toward a better, more rational understanding of mechanism. Our discussion will focus on HD, the neurotoxic γ-diketone metabolite of the industrial solvents n-hexane and methyl-n-butyl ketone. Early investigations suggested that HD caused giant neurofilamentous axonal swellings and eventual degeneration in CNS and PNS. However, as our review will point out, this interpretation underwent several iterations as the understanding of γ-diketone chemistry improved and more quantitative experimental approaches were implemented. The chemical concepts and design strategies discussed in this mini-review are broadly applicable to the mechanistic studies of other chemicals (e.g., n-propyl bromine, methyl methacrylate) that cause toxic neuropathies. PMID:25218479

  18. A Mechanistic Approach for the Prediction of Critical Power in BWR Fuel Bundles

    NASA Astrophysics Data System (ADS)

    Chandraker, Dinesh Kumar; Vijayan, Pallipattu Krishnan; Sinha, Ratan Kumar; Aritomi, Masanori

    The critical power corresponding to the Critical Heat Flux (CHF) or dryout condition is an important design parameter for the evaluation of safety margins in a nuclear fuel bundle. The empirical approaches for the prediction of CHF in a rod bundle are highly geometric specific and proprietary in nature. The critical power experiments are very expensive and technically challenging owing to the stringent simulation requirements for the rod bundle tests involving radial and axial power profiles. In view of this, the mechanistic approach has gained momentum in the thermal hydraulic community. The Liquid Film Dryout (LFD) in an annular flow is the mechanism of CHF under BWR conditions and the dryout modeling has been found to predict the CHF quite accurately for a tubular geometry. The successful extension of the mechanistic model of dryout to the rod bundle application is vital for the evaluation of critical power in the rod bundle. The present work proposes the uniform film flow approach around the rod by analyzing individual film of the subchannel bounded by rods with different heat fluxes resulting in different film flow rates around a rod and subsequently distributing the varying film flow rates of a rod to arrive at the uniform film flow rate as it has been found that the liquid film has a strong tendency to be uniform around the rod. The FIDOM-Rod code developed for the dryout prediction in BWR assemblies provides detailed solution of the multiple liquid films in a subchannel. The approach of uniform film flow rate around the rod simplifies the liquid film cross flow modeling and was found to provide dryout prediction with a good accuracy when compared with the experimental data of 16, 19 and 37 rod bundles under BWR conditions. The critical power has been predicted for a newly designed 54 rod bundle of the Advanced Heavy Water Reactor (AHWR). The selected constitutive models for the droplet entrainment and deposition rates validated for the dryout in tube were

  19. Airfoil deposition model

    NASA Technical Reports Server (NTRS)

    Kohl, F. J.

    1982-01-01

    The methodology to predict deposit evolution (deposition rate and subsequent flow of liquid deposits) as a function of fuel and air impurity content and relevant aerodynamic parameters for turbine airfoils is developed in this research. The spectrum of deposition conditions encountered in gas turbine operations includes the mechanisms of vapor deposition, small particle deposition with thermophoresis, and larger particle deposition with inertial effects. The focus is on using a simplified version of the comprehensive multicomponent vapor diffusion formalism to make deposition predictions for: (1) simple geometry collectors; and (2) gas turbine blade shapes, including both developing laminar and turbulent boundary layers. For the gas turbine blade the insights developed in previous programs are being combined with heat and mass transfer coefficient calculations using the STAN 5 boundary layer code to predict vapor deposition rates and corresponding liquid layer thicknesses on turbine blades. A computer program is being written which utilizes the local values of the calculated deposition rate and skin friction to calculate the increment in liquid condensate layer growth along a collector surface.

  20. Ionized cluster beam deposition

    NASA Technical Reports Server (NTRS)

    Kirkpatrick, A. R.

    1983-01-01

    Ionized Cluster Beam (ICB) deposition, a new technique originated by Takagi of Kyoto University in Japan, offers a number of unique capabilities for thin film metallization as well as for deposition of active semiconductor materials. ICB allows average energy per deposited atom to be controlled and involves impact kinetics which result in high diffusion energies of atoms on the growth surface. To a greater degree than in other techniques, ICB involves quantitative process parameters which can be utilized to strongly control the characteristics of films being deposited. In the ICB deposition process, material to be deposited is vaporized into a vacuum chamber from a confinement crucible at high temperature. Crucible nozzle configuration and operating temperature are such that emerging vapor undergoes supercondensation following adiabatic expansion through the nozzle.

  1. Predictive Analysis of Mechanistic Triggers and Mitigation Strategies for Pathological Scarring in Skin Wounds

    DTIC Science & Technology

    2017-01-12

    of January 12, 2017. This information is current as Scarring in Skin Wounds and Mitigation Strategies for Pathological Predictive Analysis of...Predictive Analysis of Mechanistic Triggers and Mitigation Strategies for Pathological Scarring in Skin Wounds Sridevi Nagaraja,* Lin Chen,† Jian Zhou...problem of increasing prevalence, with poorly understood mechanistic triggers and limited therapeutic options. In this study , we employed an

  2. ElectroSpark Deposition

    DTIC Science & Technology

    2007-01-25

    ElectroSpark Deposition Hard Chrome Alternatives Team Joint Cadmium Alternatives Team Canadian Hard Chrome Alternatives Team Joint Group on Pollution...00-2007 to 00-00-2007 4. TITLE AND SUBTITLE ElectroSpark Deposition 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...Processes, Inc. ElectroSpark Deposition (ESD) Results of Materials Testing and Technology Insertion January 25, 2007 Advanced Surfaces And Processes, Inc. 3

  3. Riparian seed dispersal: transport and depositional processes

    NASA Astrophysics Data System (ADS)

    Cunnings, A.; Johnson, E. A.; Martin, Y. E.

    2012-04-01

    Riparian tree population dynamics are linked to the physical processes controlled by the hydrogeomorphic setting. In particular, fluvial seed dispersal is influenced by a combination of factors including the hydrology, fluvial geomorphology, and seed dispersal traits. This study examines the influence of stream flow patterns on the transportation and deposition of buoyant seeds by applying a one dimensional transport model. Conceptually, the model separates the stream into two components: the main channel and transient storage /deposition zones. The hydrologic processes are governed by an advection-dispersion equation and numerically solved using the Crank-Nicolson method. Additional terms in the equation allow for model variation in the flow regime (lateral inflow and outflow) and the incorporation of a transient storage/deposition component where seeds may be detained. The model parameters are based on a bedrock-gravel bed river with pool-riffle morphology where we conducted field experimentation in Coastal Northern California. The riparian zone of the study reach is inhabited by White Alder (Alnus rhombifolia) which disperses buoyant seeds in late winter/early spring coinciding with the latter part of the wet, Mediterranean climate. Artificial seeds with similar characteristic traits of buoyancy, density and Bond Number to White Alder seeds were used to quantify transport times and identify storage areas. The model output captures a greater number of seeds during a receding hydrograph due to the increase in transient storage. Typically, this is found in shallow stream margins where the flow is divergent such as areas with back-eddies. In the field, this is associated with the ends of gravel bars or riffles where flow expansion causes secondary flows. The results demonstrate the importance of transient storage for seed transport and depositional processes and emphasize the need for improved measurement techniques, in lieu of empirical coefficients, to advance the

  4. Predicting subsurface uranium transport: Mechanistic modeling constrained by experimental data

    NASA Astrophysics Data System (ADS)

    Ottman, Michael; Schenkeveld, Walter D. C.; Kraemer, Stephan

    2017-04-01

    Depleted uranium (DU) munitions and their widespread use throughout conflict zones around the world pose a persistent health threat to the inhabitants of those areas long after the conclusion of active combat. However, little emphasis has been put on developing a comprehensive, quantitative tool for use in remediation and hazard avoidance planning in a wide range of environments. In this context, we report experimental data on U interaction with soils and sediments. Here, we strive to improve existing risk assessment modeling paradigms by incorporating a variety of experimental data into a mechanistic U transport model for subsurface environments. 20 different soils and sediments from a variety of environments were chosen to represent a range of geochemical parameters that are relevant to U transport. The parameters included pH, organic matter content, CaCO3, Fe content and speciation, and clay content. pH ranged from 3 to 10, organic matter content from 6 to 120 g kg-1, CaCO3 from 0 to 700 g kg-1, amorphous Fe content from 0.3 to 6 g kg-1 and clay content from 4 to 580 g kg-1. Sorption experiments were then performed, and linear isotherms were constructed. Sorption experiment results show that among separate sets of sediments and soils, there is an inverse correlation between both soil pH and CaCO¬3 concentration relative to U sorptive affinity. The geological materials with the highest and lowest sorptive affinities for U differed in CaCO3 and organic matter concentrations, as well as clay content and pH. In a further step, we are testing if transport behavior in saturated porous media can be predicted based on adsorption isotherms and generic geochemical parameters, and comparing these modeling predictions with the results from column experiments. The comparison of these two data sets will examine if U transport can be effectively predicted from reactive transport modeling that incorporates the generic geochemical parameters. This work will serve to show

  5. Simulations of Enhancer Evolution Provide Mechanistic Insights into Gene Regulation

    PubMed Central

    Duque, Thyago; Samee, Md. Abul Hassan; Kazemian, Majid; Pham, Hannah N.; Brodsky, Michael H.; Sinha, Saurabh

    2014-01-01

    There is growing interest in models of regulatory sequence evolution. However, existing models specifically designed for regulatory sequences consider the independent evolution of individual transcription factor (TF)–binding sites, ignoring that the function and evolution of a binding site depends on its context, typically the cis-regulatory module (CRM) in which the site is located. Moreover, existing models do not account for the gene-specific roles of TF-binding sites, primarily because their roles often are not well understood. We introduce two models of regulatory sequence evolution that address some of the shortcomings of existing models and implement simulation frameworks based on them. One model simulates the evolution of an individual binding site in the context of a CRM, while the other evolves an entire CRM. Both models use a state-of-the art sequence-to-expression model to predict the effects of mutations on the regulatory output of the CRM and determine the strength of selection. We use the new framework to simulate the evolution of TF-binding sites in 37 well-studied CRMs belonging to the anterior–posterior patterning system in Drosophila embryos. We show that these simulations provide accurate fits to evolutionary data from 12 Drosophila genomes, which includes statistics of binding site conservation on relatively short evolutionary scales and site loss across larger divergence times. The new framework allows us, for the first time, to test hypotheses regarding the underlying cis-regulatory code by directly comparing the evolutionary implications of the hypothesis with the observed evolutionary dynamics of binding sites. Using this capability, we find that explicitly modeling self-cooperative DNA binding by the TF Caudal (CAD) provides significantly better fits than an otherwise identical evolutionary simulation that lacks this mechanistic aspect. This hypothesis is further supported by a statistical analysis of the distribution of intersite

  6. A new mechanistic framework to predict OCS fluxes from soils

    NASA Astrophysics Data System (ADS)

    Ogée, Jérôme; Sauze, Joana; Kesselmeier, Jürgen; Genty, Bernard; Van Diest, Heidi; Launois, Thomas; Wingate, Lisa

    2016-04-01

    Estimates of photosynthetic and respiratory fluxes at large scales are needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulfide (OCS) is the most abundant sulfur gas in the atmosphere and has been proposed as a new tracer of photosynthetic gross primary productivity (GPP), as the uptake of OCS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. However soils also exchange OCS with the atmosphere, which complicates the retrieval of GPP from atmospheric budgets. Indeed soils can take up large amounts of OCS from the atmosphere as soil microorganisms also contain CA, and OCS emissions from soils have been reported in agricultural fields or anoxic soils. To date no mechanistic framework exists to describe this exchange of OCS between soils and the atmosphere, but empirical results, once upscaled to the global scale, indicate that OCS consumption by soils dominates OCS emission and its contribution to the atmospheric budget is large, at about one third of the OCS uptake by vegetation, also with a large uncertainty. Here, we propose a new mechanistic model of the exchange of OCS between soils and the atmosphere that builds on our knowledge of soil CA activity from CO2 oxygen isotopes. In this model the OCS soil budget is described by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of OCS by CA is total and irreversible. Using this model we are able to explain the observed presence of an optimum temperature for soil OCS uptake and show how this optimum can shift to cooler temperatures in the presence of soil OCS emission. Our model can also explain the observed optimum with soil moisture content previously described in the literature as a result of diffusional constraints on OCS hydrolysis. These diffusional constraints are also responsible for the response of OCS uptake to soil weight and

  7. Modeling Bird Migration under Climate Change: A Mechanistic Approach

    NASA Technical Reports Server (NTRS)

    Smith, James A.

    2009-01-01

    How will migrating birds respond to changes in the environment under climate change? What are the implications for migratory success under the various accelerated climate change scenarios as forecast by the Intergovernmental Panel on Climate Change? How will reductions or increased variability in the number or quality of wetland stop-over sites affect migratory bird species? The answers to these questions have important ramifications for conservation biology and wildlife management. Here, we describe the use of continental scale simulation modeling to explore how spatio-temporal changes along migratory flyways affect en-route migration success. We use an individually based, biophysical, mechanistic, bird migration model to simulate the movement of shorebirds in North America as a tool to study how such factors as drought and wetland loss may impact migratory success and modify migration patterns. Our model is driven by remote sensing and climate data and incorporates important landscape variables. The energy budget components of the model include resting, foraging, and flight, but presently predation is ignored. Results/Conclusions We illustrate our model by studying the spring migration of sandpipers through the Great Plains to their Arctic breeding grounds. Why many species of shorebirds have shown significant declines remains a puzzle. Shorebirds are sensitive to stop-over quality and spacing because of their need for frequent refueling stops and their opportunistic feeding patterns. We predict bird "hydrographs that is, stop-over frequency with latitude, that are in agreement with the literature. Mean stop-over durations predicted from our model for nominal cases also are consistent with the limited, but available data. For the shorebird species simulated, our model predicts that shorebirds exhibit significant plasticity and are able to shift their migration patterns in response to changing drought conditions. However, the question remains as to whether this

  8. A new mechanistic framework to predict OCS fluxes from soils

    NASA Astrophysics Data System (ADS)

    Ogée, J.; Sauze, J.; Kesselmeier, J.; Genty, B.; Van Diest, H.; Launois, T.; Wingate, L.

    2015-09-01

    Estimates of photosynthetic and respiratory fluxes at large scales is needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulphide (OCS) is the most abundant sulphur gas in the atmosphere and has been proposed as a new tracer of photosynthesis (GPP), as the uptake of OCS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. But soils also exchange OCS with the atmosphere which complicates the retrieval of GPP from atmospheric budgets. Indeed soils can take up large amounts of OCS from the atmosphere as soil microorganisms also contain CA, and OCS emissions from soils have been reported in agricultural fields or anoxic soils. To date no mechanistic framework exists to describe this exchange of OCS between soils and the atmosphere but empirical results, once upscaled to the global scale, indicate that OCS consumption by soils dominates over production and its contribution to the atmospheric budget is large, at about one third of the OCS uptake by vegetation, with also a large uncertainty. Here, we propose a new mechanistic model of the exchange of OCS between soils and the atmosphere that builds on our knowledge of soil CA activity from CO2 oxygen isotopes. In this model the OCS soil budget is described by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of OCS by CA is total and irreversible. Using this model we are able to explain the observed presence of an optimum temperature for soil OCS uptake and show how this optimum can shift to cooler temperatures in the presence of soil OCS emissions. Our model can also explain the observed optimum with soil moisture content previously described in the literature as a result of diffusional constraints on OCS hydrolysis. These diffusional constraints are also responsible for the response of OCS uptake to soil weight and depth observed previously. In

  9. A new mechanistic framework to predict OCS fluxes from soils

    NASA Astrophysics Data System (ADS)

    Ogee, J.; Sauze, J.; Kesselmeier, J.; Genty, B.; Whelan, M.; Launois, T.; Wingate, L.

    2015-12-01

    A better description of the amplitude of photosynthetic and respiratory gross CO2 fluxes at large scales is needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulphide (OCS) has been proposed as a new tracer of gross photosynthesis (GPP), as the uptake of OCS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. But soils also exchange OCS with the atmosphere which complicates the retrieval of GPP from atmospheric budgets. Indeed soils can take up large amounts of OCS from the atmosphere as soil microorganisms also contain CA, and OCS emissions from soils have been reported in agricultural or anoxic soils. To date no mechanistic framework exists to describe this exchange of OCS between soils and the atmosphere but empirical results, once up-scaled to the global scale, indicate that OCS consumption by soils dominates over production and its contribution to the atmospheric budget is large, at about one third of the OCS uptake by vegetation, with also a large uncertainty. Here, we propose a new mechanistic model of the exchange of OCS between soils and the atmosphere that builds on our knowledge of soil CA activity from CO2 oxygen isotopes. In this model the OCS soil budget is described by a first-order reaction-diffusion-production equation, assuming that the hydrolysis of OCS by CA is total and irreversible. Using this model we are able to explain the observed presence of an optimum temperature for soil OCS uptake and show how this optimum can shift to cooler temperatures in the presence of soil OCS emissions. Our model can also explain the observed optimum with soil moisture content previously described in the literature as a result of diffusional constraints on OCS hydrolysis. In order to simulate the exact OCS uptake rates and patterns observed on several soils collected from a range of biomes, different CA activities

  10. Development of a mechanistic model for forced convection subcooled boiling

    NASA Astrophysics Data System (ADS)

    Shaver, Dillon R.

    The focus of this work is on the formulation, implementation, and testing of a mechanistic model of subcooled boiling. Subcooled boiling is the process of vapor generation on a heated wall when the bulk liquid temperature is still below saturation. This is part of a larger effort by the US DoE's CASL project to apply advanced computational tools to the simulation of light water reactors. To support this effort, the formulation of the dispersed field model is described and a complete model of interfacial forces is formulated. The model has been implemented in the NPHASE-CMFD computer code with a K-epsilon model of turbulence. The interfacial force models are built on extensive work by other authors, and include novel formulations of the turbulent dispersion and lift forces. The complete model of interfacial forces is compared to experiments for adiabatic bubbly flows, including both steady-state and unsteady conditions. The same model is then applied to a transient gas/liquid flow in a complex geometry of fuel channels in a sodium fast reactor. Building on the foundation of the interfacial force model, a mechanistic model of forced-convection subcooled boiling is proposed. This model uses the heat flux partitioning concept and accounts for condensation of bubbles attached to the wall. This allows the model to capture the enhanced heat transfer associated with boiling before the point of net generation of vapor, a phenomenon consistent with existing experimental observations. The model is compared to four different experiments encompassing flows of light water, heavy water, and R12 at different pressures, in cylindrical channels, an internally heated annulus, and a rectangular channel. The experimental data includes axial and radial profiles of both liquid temperature and vapor volume fraction, and the agreement can be considered quite good. The complete model is then applied to simulations of subcooled boiling in nuclear reactor subchannels consistent with the

  11. Kinetic and Mechanistic Investigations of Atom Abstraction Reactions

    NASA Astrophysics Data System (ADS)

    Stevens, Philip Stanford

    1990-01-01

    reaction does not contribute significantly to the observed ozone depletion over Antarctica. These deviations bring the predictive power of the trends into question. The valuable mechanistic insight gained from trend comparisons is shown to outweigh the loss of predictive power, as these trends provide a benchmark for the mechanistic understanding of atom abstraction reactions.

  12. Modeling Bird Migration under Climate Change: A Mechanistic Approach

    NASA Technical Reports Server (NTRS)

    Smith, James A.

    2009-01-01

    How will migrating birds respond to changes in the environment under climate change? What are the implications for migratory success under the various accelerated climate change scenarios as forecast by the Intergovernmental Panel on Climate Change? How will reductions or increased variability in the number or quality of wetland stop-over sites affect migratory bird species? The answers to these questions have important ramifications for conservation biology and wildlife management. Here, we describe the use of continental scale simulation modeling to explore how spatio-temporal changes along migratory flyways affect en-route migration success. We use an individually based, biophysical, mechanistic, bird migration model to simulate the movement of shorebirds in North America as a tool to study how such factors as drought and wetland loss may impact migratory success and modify migration patterns. Our model is driven by remote sensing and climate data and incorporates important landscape variables. The energy budget components of the model include resting, foraging, and flight, but presently predation is ignored. Results/Conclusions We illustrate our model by studying the spring migration of sandpipers through the Great Plains to their Arctic breeding grounds. Why many species of shorebirds have shown significant declines remains a puzzle. Shorebirds are sensitive to stop-over quality and spacing because of their need for frequent refueling stops and their opportunistic feeding patterns. We predict bird "hydrographs that is, stop-over frequency with latitude, that are in agreement with the literature. Mean stop-over durations predicted from our model for nominal cases also are consistent with the limited, but available data. For the shorebird species simulated, our model predicts that shorebirds exhibit significant plasticity and are able to shift their migration patterns in response to changing drought conditions. However, the question remains as to whether this

  13. Mechanistic insights into cognate substrate discrimination during proofreading in translation.

    PubMed

    Hussain, Tanweer; Kamarthapu, Venu; Kruparani, Shobha P; Deshmukh, Mandar V; Sankaranarayanan, Rajan

    2010-12-21

    Editing/proofreading by aminoacyl-tRNA synthetases is an important quality control step in the accurate translation of the genetic code that removes noncognate amino acids attached to tRNA. Defects in the process of editing result in disease conditions including neurodegeneration. While proofreading, the cognate amino acids larger by a methyl group are generally thought to be sterically rejected by the editing modules as envisaged by the "Double-Sieve Model." Strikingly using solution based direct binding studies, NMR-heteronuclear single quantum coherence (HSQC) and isothermal titration calorimetry experiments, with an editing domain of threonyl-tRNA synthetase, we show that the cognate substrate can gain access and bind to the editing pocket. High-resolution crystal structural analyses reveal that functional positioning of substrates rather than steric exclusion is the key for the mechanism of discrimination. A strategically positioned "catalytic water" molecule is excluded to avoid hydrolysis of the cognate substrate using a "RNA mediated substrate-assisted catalysis mechanism" at the editing site. The mechanistic proof of the critical role of RNA in proofreading activity is a completely unique solution to the problem of cognate-noncognate selection mechanism.

  14. Mechanistic modeling of insecticide risks to breeding birds in ...

    EPA Pesticide Factsheets

    Insecticide usage in the United States is ubiquitous in urban, suburban, and rural environments. In evaluating data for an insecticide registration application and for registration review, scientists at the United States Environmental Protection Agency (USEPA) assess the fate of the insecticide and the risk the insecticide poses to the environment and non-target wildlife. At the present time, current USEPA risk assessments do not include population-level endpoints. In this paper, we present a new mechanistic model, which allows risk assessors to estimate the effects of insecticide exposure on the survival and seasonal productivity of birds known to use agricultural fields during their breeding season. The new model was created from two existing USEPA avian risk assessment models, the Terrestrial Investigation Model (TIM v.3.0) and the Markov Chain Nest Productivity model (MCnest). The integrated TIM/MCnest model has been applied to assess the relative risk of 12 insecticides used to control corn pests on a suite of 31 avian species known to use cornfields in midwestern agroecosystems. The 12 insecticides that were assessed in this study are all used to treat major pests of corn (corn root worm borer, cutworm, and armyworm). After running the integrated TIM/MCnest model, we found extensive differences in risk to birds among insecticides, with chlorpyrifos and malathion (organophosphates) generally posing the greatest risk, and bifenthrin and ë-cyhalothrin (

  15. Ultrasound enhanced ethanol production from Parthenium hysterophorus: A mechanistic investigation.

    PubMed

    Singh, Shuchi; Sarma, Shyamali; Agarwal, Mayank; Goyal, Arun; Moholkar, Vijayanand S

    2015-01-01

    This study presents mechanistic investigations in ultrasound-assisted bioethanol fermentation using Parthenium hysterophorus biomass. Ultrasound (35 kHz, 10% duty cycle) has been used for sonication. Experimental results were fitted to mathematical model; the kinetic and physiological parameters in the model were obtained using Genetic Algorithm (GA) based optimization. In control experiments (mechanical shaking), maximum ethanol titer of 10.93 g/L and cell mass concentration of 5.26 g/L was obtained after 18 h. In test experiments (mechanical shaking and intermittent sonication), ethanol titer of 12.14 g/L and cell mass concentration of 5.7 g/L was obtained in 10h. This indicated ∼ 2 × enhanced productivity of ethanol and cell mass with sonication. Trends in model parameters obtained after fitting of model to experimental data essentially revealed that beneficial influence of ultrasound on fermentation is a manifestation of enhanced trans-membrane transportation and dilution of toxic substances due to strong micro-convection induced by ultrasound. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Circadian rhythms and addiction: Mechanistic insights and future directions

    PubMed Central

    Logan, Ryan W.; Williams, Wilbur P.; McClung, Colleen A.

    2014-01-01

    Circadian rhythms are prominent in many physiological and behavioral functions. Circadian disruptions either by environmental or molecular perturbation can have profound health consequences, including the development and progression of addiction. Both animal and humans studies indicate extensive bidirectional relationships between the circadian system and drugs of abuse. Addicted individuals display disrupted rhythms, and chronic disruption or particular chronotypes, may increase the risk for substance abuse and relapse. Moreover, polymorphisms in circadian genes and an evening chronotype have been linked to mood and addiction disorders, and recent efforts suggest an association with the function of reward neurocircuitry. Animal studies are beginning to determine how altered circadian gene function results in drug induced neuroplasticity and behaviors. Many studies suggest a critical role for circadian rhythms in reward-related pathways in the brain and indicate that drugs of abuse directly affect the central circadian pacemaker. In this review, we highlight key findings demonstrating the importance of circadian rhythms in addiction, and how future studies will reveal important mechanistic insights into the involvement of circadian rhythms in drug addiction. PMID:24731209

  17. Mechanistic rationales for targeting interleukin-17A in spondyloarthritis.

    PubMed

    Raychaudhuri, Siba P; Raychaudhuri, Smriti K

    2017-03-08

    The term spondyloarthritis (SpA) is used to describe a group of inflammatory autoimmune diseases, including ankylosing spondylitis and psoriatic arthritis, with common genetic risk factors and clinical features. SpA is clinically distinct from rheumatoid arthritis and typically affects the spine, sacroiliac joints, entheses, and, less commonly, peripheral joints. Although the pathogenesis of SpA is not fully understood, recent findings have identified the interleukin (IL)-17 pathway as a key mediator of disease pathogenesis. Clinical evidence for the efficacy of IL-17A inhibition by biologic agents was initially shown in patients with chronic plaque psoriasis, another autoimmune disease mediated by the IL-17 pathway. Subsequently, similar positive efficacy for inhibition of IL-17A was seen in patients with ankylosing spondylitis and psoriatic arthritis. Inhibition of IL-17A may also improve cardiovascular and metabolic comorbidities often found in patients with SpA because studies have linked these disorders to the IL-17 pathway. In this review, we will examine key preclinical studies that demonstrated the mechanistic role of IL-17A in the development SpA and discuss how these observations were translated into clinical practice.

  18. Mechanistic aspects of photooxidation of polyhydroxylated molecules on metal oxides.

    SciTech Connect

    Shkrob, I. A.; Marin, T. M.; Sevilla, M. D.; Chemerisov, S.

    2011-03-24

    Polyhydroxylated molecules, including natural carbohydrates, are known to undergo photooxidation on wide-gap transition-metal oxides irradiated by ultraviolet light. In this study, we examine mechanistic aspects of this photoreaction on aqueous TiO{sub 2}, {alpha}-FeOOH, and {alpha}-Fe{sub 2}O{sub 3} particles using electron paramagnetic resonance (EPR) spectroscopy and site-selective deuteration. We demonstrate that the carbohydrates are oxidized at sites involved in the formation of oxo bridges between the chemisorbed carbohydrate molecule and metal ions at the oxide surface. This bridging inhibits the loss of water (which is the typical reaction of the analogous free radicals in bulk solvent) promoting instead a rearrangement that leads to elimination of the formyl radical. For natural carbohydrates, the latter reaction mainly involves carbon-1, whereas the main radical products of the oxidation are radical arising from H atom loss centered on carbon-1, -2, and -3 sites. Photoexcited TiO{sub 2} oxidizes all of the carbohydrates and polyols, whereas {alpha}-FeOOH oxidizes some of the carbohydrates, and {alpha}-Fe{sub 2}O{sub 3} is unreactive. These results serve as a stepping stone for understanding the photochemistry on mineral surfaces of more complex biomolecules such as nucleic acids.

  19. Mechanistic Investigation on ROS Resistance of Phosphorothioated DNA

    PubMed Central

    Wu, Tingting; Huang, Qiang; Wang, Xiao-Lei; Shi, Ting; Bai, Linquan; Liang, Jingdan; Wang, Zhijun; Deng, Zixin; Zhao, Yi-Lei

    2017-01-01

    Phosphorothioated DNA (PT-DNA) exhibits a mild anti-oxidant property both in vivo and in vitro. It was found that 8-OHdG and ROS levels were significantly lower in dnd+ (i.e. S+) E. coli., compared to a dnd− (i.e. S−) strain. Furthermore, different from traditional antioxidants, phosphorothioate compound presents an unexpectedly high capacity to quench hydroxyl radical. Oxidative product analysis by liquid chromatography-mass spectrometry and quantum mechanistic computation supported its unique anti-oxidant characteristic of the hydroxyl selectivity: phosphorothioate donates an electron to either hydroxyl radical or guanine radical derived from hydroxyl radical, leading to a PS• radical; a complex of PS• radical and OH− (i.e. the reductive product of hydroxyl radical) releases a highly reductive HS• radical, which scavenges more equivalents of oxidants in the way to high-covalent sulphur compounds such as sulphur, sulphite and sulphate. The PS-PO conversion (PS and PO denote phosphorus-sulphur and phosphorus-oxygen compounds, respectively) made a switch of extremely oxidative OH• to highly reductive HS• species, endowing PT-DNA with the observed high capacity in hydroxyl-radical neutralization. This plausible mechanism provides partial rationale as to why bacteria develop the resource-demanding PT modification on guanine-neighboring phosphates in genome. PMID:28216673

  20. Thermal hydrogen-atom transfer from methane: A mechanistic exercise

    NASA Astrophysics Data System (ADS)

    Schwarz, Helmut

    2015-06-01

    Hydrogen-atom transfer (HAT) constitutes a key process in a broad range of chemical transformations as it covers heterogeneous, homogeneous, and enzymatic reactions. While open-shell metal oxo species [MO]rad are no longer regarded as being involved in the heterogeneously catalyzed oxidative coupling of methane (2CH4 + → C2H6 + H2O), these reagents are rather versatile in bringing about (gas-phase) hydrogen-atom transfer, even from methane at ambient conditions. In this mini-review, various mechanistic scenarios will be presented, and it will be demonstrated how these are affected by the composition of the metal-oxide cluster ions. Examples will be discussed, how 'doping' the clusters permits the control of the charge and spin situation at the active site and, thus, the course of the reaction. Also, the interplay between supposedly inert support material and the active site - the so-called 'aristocratic atoms' - of the gas-phase catalyst will be addressed. Finally, gas-phase HAT from methane will be analyzed in the broader context of thermal activation of inert Csbnd H bonds by metal-oxo species.

  1. The mechanistic studies of acupuncture and moxibustion in Taiwan.

    PubMed

    Lin, Jaung-Geng; Chen, Yi-Hung

    2011-03-01

    Traditional Chinese acupuncture has a history of over 2500 years. It is effective in the treatment of many conditions with few side effects. The best known mechanism is via endogenous opiates and their receptors. In addition to opioids, researchers have focused on the role of central monoamimergic systems. Acupuncture therapy is used not only to relieve pain but also to treat various medical conditions in traditional Chinese medicine (TCM). Some experiments have revealed a relationship between acupuncture and the autonomic nervous system (ANS). Besides, electroacupuncture (EA) can modulate the imbalance between innate and acquired immune systems. This review is focusing on the mechanistic studies of acupuncture that my colleagues and I have performed in Taiwan in recent years. We found that EA analgesia was closely related to not only the serotonergic neurons but also the adrenergic neurons in the central nervous system. The electrophysiological recordings suggested the involvement of the cerebral cortex in acupuncture. Local somatothermal stimulation inhibited the motility of sphincter of Oddi and internal anal sphincter through nitrergic neural release of nitric oxide. Mild local heat stress upregulated hepatic gene expression of heat shock protein 70 and protected the liver from subsequent ischemia-reperfusion injury. These studies supplement the knowledge of the mechanism of acupuncture.

  2. Mechanistic aspects of photooxidation of polyhydroxylated molecules on metal oxides

    PubMed Central

    Shkrob, Ilya A.; Marin, Timothy M.; Chemerisov, Sergey D.; Sevilla, Michael D.

    2011-01-01

    Polyhydroxylated molecules, including natural carbohydrates, are known to undergo photooxidation on wide-gap transition metal oxides irradiated by ultraviolet light. In this study, we examine mechanistic aspects of this photoreaction on aqueous TiO2, α-FeOOH, and α-Fe2O3 particles using electron paramagnetic resonance (EPR) spectroscopy and site-selective deuteration. We demonstrate that the carbohydrates are oxidized at sites involved in the formation of oxo-bridges between the chemisorbed carbohydrate molecule and metal ions at the oxide surface. This bridging inhibits the loss of water (which is the typical reaction of the analogous free radicals in bulk solvent) promoting instead a rearrangement that leads to elimination of the formyl radical. For natural carbohydrates, the latter reaction mainly involves carbon-1, whereas the main radical products of the oxidation are radical arising from H atom loss centered on carbon-1, -2, and -3 sites. Photoexcited TiO2 oxidizes all of the carbohydrates and polyols, whereas α-FeOOH oxidizes some of the carbohydrates, and α-Fe2O3 is unreactive. These results serve as a stepping stone for understanding the photochemistry on mineral surfaces of more complex biomolecules such as nucleic acids. PMID:21532934

  3. Mechanistic Differences Leading to Infectious and Sterile Inflammation.

    PubMed

    Behnia, Faranak; Sheller, Samantha; Menon, Ramkumar

    2016-05-01

    Inflammation is a physiologic component of pregnancy and parturition. Overwhelming intrauterine inflammatory load promotes quiescent feto-maternal tissues into a contractile phenotype. Like inflammation, oxidative stress is an inevitable component of both pregnancy and parturition. Pathologic activation of host innate immune response to adverse pregnancy conditions can lead to premature activation of inflammatory and oxidative stress. Inflammation and oxidative stress markers seen with both sterile and infectious inflammation are often similar; therefore, it is difficult to understand causality of conditions like spontaneous preterm birth. This review demonstrates potential mechanistic pathways of activation of sterile and infectious inflammation. We demonstrate the activation of two unique pathways of inflammation by factors that are well-documented proxies for oxidative stress (cigarette smoke extract) and infection (lipopolysaccharide). Sterile inflammation seen after exposure to an oxidative stress inducer is due to cellular elemental damage resulting in p38 mitogen-activated protein kinase (MAPK) induced cellular senescence. Infectious inflammation is through activation of transcription factor NF-κB and independent of oxidative stress-associated damages and p38 MAPK-induced senescence. Understanding the differences in the inflammatory pathway activation by various risk factors is important to design better screening, diagnostic and intervention strategies to reduce the risks of adverse pregnancy outcomes.

  4. Mechanistic modeling of destratification in cryogenic storage tanks using ultrasonics.

    PubMed

    Jagannathan, T K; Mohanan, Srijith; Nagarajan, R

    2014-01-01

    Stratification is one of the main causes for vaporization of cryogens and increase of tank pressure during cryogenic storage. This leads subsequent problems such as cavitation in cryo-pumps, reduced length of storage time. Hence, it is vital to prevent stratification to improve the cost efficiency of storage systems. If stratified layers exist inside the tank, they have to be removed by suitable methods without venting the vapor. Sonication is one such method capable of keeping fluid layers mixed. In the present work, a mechanistic model for ultrasonic destratification is proposed and validated with destratification experiments done in water. Then, the same model is used to predict the destratification characteristics of cryogenic liquids such as liquid nitrogen (LN₂), liquid hydrogen (LH₂) and liquid ammonia (LNH₃). The destratification parameters are analysed for different frequencies of ultrasound and storage pressures by considering continuous and pulsed modes of ultrasonic operation. From the results, it is determined that use of high frequency ultrasound (low-power/continuous; high-power/pulsing) or low frequency ultrasound (continuous operation with moderate power) can both be effective in removing stratification.

  5. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse.

    PubMed

    Agarwal, Vinayak; Miles, Zachary D; Winter, Jaclyn M; Eustáquio, Alessandra S; El Gamal, Abrahim A; Moore, Bradley S

    2017-01-20

    Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.

  6. Fine particulate matter air pollution and atherosclerosis: Mechanistic insights.

    PubMed

    Bai, Yuntao; Sun, Qinghua

    2016-12-01

    Atherosclerosis is a progressive disease characterized by the accumulation of lipids and fibrous plaque in the arteries. Its etiology is very complicated and its risk factors primarily include genetic defects, smoking, hyperlipidemia, hypertension, lack of exercise, and infection. Recent studies suggest that fine particulate matter (PM2.5) air pollution may also contribute to the development of atherosclerosis. The present review integrates current experimental evidence with mechanistic pathways whereby PM2.5 exposure can promote the development of atherosclerosis. PM2.5-mediated enhancement of atherosclerosis is likely due to its pro-oxidant and pro-inflammatory effects, involving multiple organs, different cell types, and various molecular mediators. Studies about the effects of PM2.5inhalation on atherosclerosis may yield a better understanding of the link between air pollution and major cardiovascular diseases, and provide useful information for policy makers to determine acceptable levels of PM2.5 air quality. This article is part of a Special Issue entitled Air Pollution, edited by Wenjun Ding, Andrew J. Ghio and Weidong Wu. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Mechanistic modelling of the drying behaviour of single pharmaceutical granules.

    PubMed

    Mortier, Séverine Thérèse F C; De Beer, Thomas; Gernaey, Krist V; Vercruysse, Jurgen; Fonteyne, Margot; Remon, Jean Paul; Vervaet, Chris; Nopens, Ingmar

    2012-04-01

    The trend to move towards continuous production processes in pharmaceutical applications enhances the necessity to develop mechanistic models to understand and control these processes. This work focuses on the drying behaviour of a single wet granule before tabletting, using a six-segmented fluidised bed drying system, which is part of a fully continuous from-powder-to-tablet manufacturing line. The drying model is based on a model described by Mezhericher et al. and consists of two submodels. In the first drying phase (submodel 1), the surface water evaporates, while in the second drying phase (submodel 2), the water inside the granule evaporates. The second submodel contains an empirical power coefficient, β. A sensitivity analysis was performed to study the influence of parameters on the moisture content of single pharmaceutical granules, which clearly points towards the importance of β on the drying behaviour. Experimental data with the six-segmented fluidised bed dryer were collected to calibrate β. An exponential dependence on the drying air temperature was found. Independent experiments were done for the validation of the drying model.

  8. Mechanistic understanding of monosaccharide-air flow battery electrochemistry

    NASA Astrophysics Data System (ADS)

    Scott, Daniel M.; Tsang, Tsz Ho; Chetty, Leticia; Aloi, Sekotilani; Liaw, Bor Yann

    Recently, an inexpensive monosaccharide-air flow battery configuration has been demonstrated to utilize a strong base and a mediator redox dye to harness electrical power from the partial oxidation of glucose. Here the mechanistic understanding of glucose oxidation in this unique glucose-air power source is further explored by acid-base titration experiments, 13C NMR, and comparison of results from chemically different redox mediators (indigo carmine vs. methyl viologen) and sugars (fructose vs. glucose) via studies using electrochemical techniques. Titration results indicate that gluconic acid is the main product of the cell reaction, as supported by evidence in the 13C NMR spectra. Using indigo carmine as the mediator dye and fructose as the energy source, an abiotic cell configuration generates a power density of 1.66 mW cm -2, which is greater than that produced from glucose under similar conditions (ca. 1.28 mW cm -2). A faster transition from fructose into the ene-diol intermediate than from glucose likely contributed to this difference in power density.

  9. Mechanistic Enzymology of the Radical SAM Enzyme DesII.

    PubMed

    Ruszczycky, Mark W; Liu, Hung-Wen

    2015-04-01

    DesII is a member of the radical SAM family of enzymes that catalyzes radical-mediated transformations of TDP-4-amino-4,6-didexoy-D-glucose as well as other sugar nucleotide diphosphates. Like nearly all radical SAM enzymes, the reactions begin with the reductive homolysis of SAM to produce a 5'-deoxyadenosyl radical which is followed by regiospecific hydrogen atom abstraction from the substrate. What happens next, however, depends on the nature of the substrate radical so produced. In the case of the biosynthetically relevant substrate, a radical-mediated deamination ensues; however, when this amino group is replaced with a hydroxyl, one instead observes dehydrogenation. The factors that govern the fate of the initially generated substrate radical as well as the mechanistic details underlying these transformations have been a key focus of research into the chemistry of DesII. This review will discuss recent discoveries pertaining to the enzymology of DesII, how it may relate to understanding other radical-mediated lyases and dehydrogenases and the working hypotheses currently being investigated regarding the mechanism of DesII catalysis.

  10. Sleep, immunity, and circadian clocks: a mechanistic model.

    PubMed

    Bollinger, Thomas; Bollinger, Annalena; Oster, Henrik; Solbach, Werner

    2010-01-01

    The lack of sufficient amounts of sleep is a hallmark of modern living, and it is commonly perceived that in the long run this makes us sick. An increasing amount of scientific data indicate that sleep deprivation has detrimental effects on immune function. Conversely, immune responses feedback on sleep phase and architecture. Several studies have investigated the impact of short-term sleep deprivation on different immune parameters, whereas only a few studies have addressed the influence of sleep restriction on the immune system. In many cases, sleep deprivation and restriction impair immune responses by disrupting circadian rhythms at the level of immune cells, which might be a consequence of disrupted endocrine and physiological circadian rhythms. Little is known about the mechanisms underlying the circadian regulation of immunity, but recent studies have suggested that local as well as central circadian clocks drive the rhythms of immune function. In this review, we present a mechanistic model which proposes that sleep (through soluble factors and body temperature) primes immune cells on the one hand, and, on the other hand, provides a timing signal for hematopoietic circadian clocks. We hypothesize that chronic sleep disruption desynchronizes these clocks and, through this mechanism, deregulates immune responses. Copyright © 2010 S. Karger AG, Basel.

  11. Mechanistic insights into acyclovir-polyethylene glycol 20000 binary dispersions

    PubMed Central

    Venkateskumar, Krishnamoorthy; Parasuraman, Subramani; Gunasunderi, Raju; Sureshkumar, Krishnan; Nayak, M. Muralidhar; Shah, Syed Adnan Ali; Kassen, Khoo; Kai, Heng Wei

    2016-01-01

    Objective: The objective of this study is to provide a mechanistic insight into solubility enhancement and dissolution of acyclovir (ACY) by polyethylene glycol20000 (PEG20000). Materials and Methods: Solid dispersions with differing ratios of drug (ACY) and carrier (PEG20000) were prepared and evaluated by phase solubility, in vitro release studies, kinetic analysis, in situ perfusion, and in vitro permeation studies. Solid state characterization was also done by Powder X-Ray Diffraction (PXRD), Differential Scanning Calorimetry (DSC), Fourier Transform Infrared spectroscopy (FT-IR) analysis and surface morphology was assessed by Polarizing Microscopic Image (PMI) analysis, Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), and Nuclear Magnetic Resonance (NMR) analysis. Results: Thermodynamic parameters proved the solubilization effect of carrier. The aqueous solubility and dissolution of ACY were increased in all samples. Formation of solid solution, crystallinity reduction, and absence of interaction between drug and carrier was proved by XRD, DSC, and FTIR analysis. The particle size reduction and change in surface morphology were confirmed by SEM and AFM and analysis. The permeation coefficient and amount of drug diffused was higher in samples as compared to ACY. The stability was high in dispersions, and it was proved by NMR analysis. Conclusion: The mechanical insights into the enhancement of solubility and dissolution could be used as a platform to improve the aqueous solubility for other poor water soluble drugs. PMID:28123988

  12. A mechanistic stochastic framework for regulating bacterial cell division.

    PubMed

    Ghusinga, Khem Raj; Vargas-Garcia, Cesar A; Singh, Abhyudai

    2016-07-26

    How exponentially growing cells maintain size homeostasis is an important fundamental problem. Recent single-cell studies in prokaryotes have uncovered the adder principle, where cells add a fixed size (volume) from birth to division, irrespective of their size at birth. To mechanistically explain the adder principle, we consider a timekeeper protein that begins to get stochastically expressed after cell birth at a rate proportional to the volume. Cell-division time is formulated as the first-passage time for protein copy numbers to hit a fixed threshold. Consistent with data, the model predicts that the noise in division timing increases with size at birth. Intriguingly, our results show that the distribution of the volume added between successive cell-division events is independent of the newborn cell size. This was dramatically seen in experimental studies, where histograms of the added volume corresponding to different newborn sizes collapsed on top of each other. The model provides further insights consistent with experimental observations: the distribution of the added volume when scaled by its mean becomes invariant of the growth rate. In summary, our simple yet elegant model explains key experimental findings and suggests a mechanism for regulating both the mean and fluctuations in cell-division timing for controlling size.

  13. Analytical techniques for mechanistic characterization of EUV photoresists

    NASA Astrophysics Data System (ADS)

    Grzeskowiak, Steven; Narasimhan, Amrit; Murphy, Michael; Ackerman, Christian; Kaminsky, Jake; Brainard, Robert L.; Denbeaux, Greg

    2017-03-01

    Extreme ultraviolet (EUV, 13.5 nm) lithography is the prospective technology for high volume manufacturing by the microelectronics industry. Significant strides towards achieving adequate EUV source power and availability have been made recently, but a limited rate of improvement in photoresist performance still delays the implementation of EUV. Many fundamental questions remain to be answered about the exposure mechanisms of even the relatively well understood chemically amplified EUV photoresists. Moreover, several groups around the world are developing revolutionary metal-based resists whose EUV exposure mechanisms are even less understood. Here, we describe several evaluation techniques to help elucidate mechanistic details of EUV exposure mechanisms of chemically amplified and metal-based resists. EUV absorption coefficients are determined experimentally by measuring the transmission through a resist coated on a silicon nitride membrane. Photochemistry can be evaluated by monitoring small outgassing reaction products to provide insight into photoacid generator or metal-based resist reactivity. Spectroscopic techniques such as thin-film Fourier transform infrared (FTIR) spectroscopy can measure the chemical state of a photoresist system pre- and post-EUV exposure. Additionally, electrolysis can be used to study the interaction between photoresist components and low energy electrons. Collectively, these techniques improve our current understanding of photomechanisms for several EUV photoresist systems, which is needed to develop new, better performing materials needed for high volume manufacturing.

  14. Mechanistic modelling of toxicokinetic processes within Myriophyllum spicatum.

    PubMed

    Heine, S; Schmitt, W; Schäffer, A; Görlitz, G; Buresová, H; Arts, G; Preuss, T G

    2015-02-01

    Effects of chemicals are, in most cases, caused by internal concentrations within organisms which rely on uptake and elimination kinetics. These processes might be key components for assessing the effects of time-variable exposure of chemicals which regularly occur in aquatic systems. However, the knowledge of toxicokinetic patterns caused by time-variable exposure is limited, and gaining such information is complex. In this work, a previously developed mechanistic growth model of Myriophyllum spicatum is coupled with a newly developed toxicokinetic part, providing a model that is able to predict uptake and elimination of chemicals, as well as distribution processes between plant compartments (leaves, stems, roots) of M. spicatum. It is shown, that toxicokinetic patterns, at least for most of the investigated chemicals, can be calculated in agreement with experimental observations, by only calibrating two chemical- specific parameters, the cuticular permeability and a plant/water partition coefficient. Through the model-based determination of the cuticular permeabilities of Isoproturon, Iofensulfuron, Fluridone, Imazamox and Penoxsulam, their toxicokinetic pattern can be described with the model approach. For the use of the model for predicting toxicokinetics of other chemicals, where experimental data is not available, equations are presented that are based on the log (P oct/wat) of a chemical and estimate parameters that are necessary to run the model. In general, a method is presented to analyze time-variable exposure of chemicals more in detail without conducting time and labour intensive experiments. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. MECHANISTIC AND BIOLOGICAL ASPECTS OF HELICASE ACTION ON DAMAGED DNA

    PubMed Central

    Suhasini, Avvaru N.; Brosh, Robert M.

    2010-01-01

    Helicases catalytically unwind structured nucleic acids in a nucleoside-triphosphate-dependent and directionally specific manner, and are essential for virtually all aspects of nucleic acid metabolism. ATPase-driven helicases which translocate along nucleic acids play a role in damage recognition or unwinding of a DNA tract containing the lesion. Although classical biochemical experiments provided evidence that bulky covalent adducts inhibit DNA unwinding catalyzed by certain DNA helicases in a strand-specific manner (i.e. , block to DNA unwinding restricted to adduct residence in the strand the helicase translocates), recent studies suggest more complex arrangements that may depend on the helicase under study, its assembly in a protein complex, and the type of structural DNA perturbation. Moreover, base and sugar phosphate backbone modifications exert effects on DNA helicases that suggest specialized tracking mechanisms. As a component of the replication stress response, the single-stranded DNA binding protein Replication Protein A (RPA) may serve to enable eukaryotic DNA helicases to overcome certain base lesions. Helicases play important roles in DNA damage signaling which also involve their partnership with RPA. In this review, we will discuss our current understanding of mechanistic and biological aspects of helicase action on damaged DNA. PMID:20574162

  16. A mechanistic stochastic framework for regulating bacterial cell division

    PubMed Central

    Ghusinga, Khem Raj; Vargas-Garcia, Cesar A.; Singh, Abhyudai

    2016-01-01

    How exponentially growing cells maintain size homeostasis is an important fundamental problem. Recent single-cell studies in prokaryotes have uncovered the adder principle, where cells add a fixed size (volume) from birth to division, irrespective of their size at birth. To mechanistically explain the adder principle, we consider a timekeeper protein that begins to get stochastically expressed after cell birth at a rate proportional to the volume. Cell-division time is formulated as the first-passage time for protein copy numbers to hit a fixed threshold. Consistent with data, the model predicts that the noise in division timing increases with size at birth. Intriguingly, our results show that the distribution of the volume added between successive cell-division events is independent of the newborn cell size. This was dramatically seen in experimental studies, where histograms of the added volume corresponding to different newborn sizes collapsed on top of each other. The model provides further insights consistent with experimental observations: the distribution of the added volume when scaled by its mean becomes invariant of the growth rate. In summary, our simple yet elegant model explains key experimental findings and suggests a mechanism for regulating both the mean and fluctuations in cell-division timing for controlling size. PMID:27456660

  17. Refined pipe theory for mechanistic modeling of wood development.

    PubMed

    Deckmyn, Gaby; Evans, Sam P; Randle, Tim J

    2006-06-01

    We present a mechanistic model of wood tissue development in response to changes in competition, management and climate. The model is based on a refinement of the pipe theory, where the constant ratio between sapwood and leaf area (pipe theory) is replaced by a ratio between pipe conductivity and leaf area. Simulated pipe conductivity changes with age, stand density and climate in response to changes in allocation or pipe radius, or both. The central equation of the model, which calculates the ratio of carbon (C) allocated to leaves and pipes, can be parameterized to describe the contrasting stem conductivity behavior of different tree species: from constant stem conductivity (functional homeostasis hypothesis) to height-related reduction in stem conductivity with age (hydraulic limitation hypothesis). The model simulates the daily growth of pipes (vessels or tracheids), fibers and parenchyma as well as vessel size and simulates the wood density profile and the earlywood to latewood ratio from these data. Initial runs indicate the model yields realistic seasonal changes in pipe radius (decreasing pipe radius from spring to autumn) and wood density, as well as realistic differences associated with the competitive status of trees (denser wood in suppressed trees).

  18. Mechanistic studies of malonic acid-mediated in situ acylation.

    PubMed

    Chandra, Koushik; Naoum, Johnny N; Roy, Tapta Kanchan; Gilon, Chaim; Gerber, R Benny; Friedler, Assaf

    2015-09-01

    We have previously introduced an easy to perform, cost-effective and highly efficient acetylation technique for solid phase synthesis (SPPS). Malonic acid is used as a precursor and the reaction proceeds via a reactive ketene that acetylates the target amine. Here we present a detailed mechanistic study of the malonic acid-mediated acylation. The influence of reaction conditions, peptide sequence and reagents was systematically studied. Our results show that the methodology can be successfully applied to different types of peptides and nonpeptidic molecules irrespective of their structure, sequence, or conformation. Using alkyl, phenyl, and benzyl malonic acid, we synthesized various acyl peptides with almost quantitative yields. The ketenes obtained from the different malonic acid derived precursors were characterized by in situ (1) H-NMR. The reaction proceeded in short reaction times and resulted in excellent yields when using uronium-based coupling agents, DIPEA as a base, DMF/DMSO/NMP as solvents, Rink amide/Wang/Merrifield resins, temperature of 20°C, pH 8-12 and 5 min preactivation at inert atmosphere. The reaction was unaffected by Lewis acids, transition metal ions, surfactants, or salt. DFT studies support the kinetically favorable concerted mechanism for CO2 and ketene formation that leads to the thermodynamically stable acylated products. We conclude that the malonic acid-mediated acylation is a general method applicable to various target molecules.

  19. Warming will affect phytoplankton differently: evidence through a mechanistic approach.

    PubMed

    Huertas, I Emma; Rouco, Mónica; López-Rodas, Victoria; Costas, Eduardo

    2011-12-07

    Although the consequences of global warming in aquatic ecosystems are only beginning to be revealed, a key to forecasting the impact on aquatic communities is an understanding of individual species' vulnerability to increased temperature. Despite their microscopic size, phytoplankton support about half of the global primary production, drive essential biogeochemical cycles and represent the basis of the aquatic food web. At present, it is known that phytoplankton are important targets and, consequently, harbingers of climate change in aquatic systems. Therefore, investigating the capacity of phytoplankton to adapt to the predicted warming has become a relevant issue. However, considering the polyphyletic complexity of the phytoplankton community, different responses to increased temperature are expected. We experimentally tested the effects of warming on 12 species of phytoplankton isolated from a variety of environments by using a mechanistic approach able to assess evolutionary adaptation (the so-called ratchet technique). We found different degrees of tolerance to temperature rises and an interspecific capacity for genetic adaptation. The thermal resistance level reached by each species is discussed in relation to their respective original habitats. Our study additionally provides evidence on the most resistant phytoplankton groups in a future warming scenario.

  20. Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling

    PubMed Central

    Ye, Hao; Beamish, Richard J.; Glaser, Sarah M.; Grant, Sue C. H.; Hsieh, Chih-hao; Richards, Laura J.; Schnute, Jon T.; Sugihara, George

    2015-01-01

    It is well known that current equilibrium-based models fall short as predictive descriptions of natural ecosystems, and particularly of fisheries systems that exhibit nonlinear dynamics. For example, model parameters assumed to be fixed constants may actually vary in time, models may fit well to existing data but lack out-of-sample predictive skill, and key driving variables may be misidentified due to transient (mirage) correlations that are common in nonlinear systems. With these frailties, it is somewhat surprising that static equilibrium models continue to be widely used. Here, we examine empirical dynamic modeling (EDM) as an alternative to imposed model equations and that accommodates both nonequilibrium dynamics and nonlinearity. Using time series from nine stocks of sockeye salmon (Oncorhynchus nerka) from the Fraser River system in British Columbia, Canada, we perform, for the the first time to our knowledge, real-data comparison of contemporary fisheries models with equivalent EDM formulations that explicitly use spawning stock and environmental variables to forecast recruitment. We find that EDM models produce more accurate and precise forecasts, and unlike extensions of the classic Ricker spawner–recruit equation, they show significant improvements when environmental factors are included. Our analysis demonstrates the strategic utility of EDM for incorporating environmental influences into fisheries forecasts and, more generally, for providing insight into how environmental factors can operate in forecast models, thus paving the way for equation-free mechanistic forecasting to be applied in management contexts. PMID:25733874

  1. Recent Structural and Mechanistic Insights into Endplate Acetylcholine Receptors

    PubMed Central

    Sine, Steven M.; Gao, Fan; Lee, Won Yong; Mukhtasimova, Nuriya; Wang, Hai-Long; Engel, Andrew G.

    2012-01-01

    Voluntary movement mediated by skeletal muscle relies on endplate acetylcholine receptors (AChR) to detect nerve-released ACh and depolarize themuscle fiber. Recent structural and mechanistic studies of the endplate AChR have catalyzed a leap in our understanding of the molecular steps in this chemical-to-electrical transduction process. Studies of acetylcholine binding protein (AChBP) give insight into ACh recognition, the first step in activation of the AChR. An atomic structural model of the Torpedo AChR at a resolution of 0.4 nm, together with single-ion channel recording methods, allow tracing of the link between the agonist binding event and gating of the ion channel, as well as determination of how the channel moves when it opens to allow flow of cations. Structural models of the human AChR enable precise mapping of disease-causing mutations, while studies of the speed with which single AChR channels open and close cast light on pathogenic mechanisms. PMID:18567853

  2. A global scale mechanistic model of the photosynthetic capacity

    NASA Astrophysics Data System (ADS)

    Xu, C.; Ali, A. A.; Fisher, R.; Wullschleger, S. D.; Rogers, A.; McDowell, N. G.; Wilson, C. J.

    2015-12-01

    Although plant photosynthetic capacity as determined by the maximum carboxylation rate (i.e., Vc,max25) and the maximum electron transport rate (i.e., Jmax25) at a reference temperature (generally 25oC) is known to vary substantially in space and time in response to environmental conditions, it is typically parameterized in Earth system models (ESMs) with tabulated values associated to plant functional types. In this study, we developed a mechanistic model of leaf utilization of nitrogen for assimilation (LUNA V1.0) to predict the photosynthetic capacity at the global scale under different environmental conditions, based on the optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The LUNA model was able to reasonably well capture the observed patterns of photosynthetic capacity in view that it explained approximately 55% of the variation in observed Vc,max25 and 65% of the variation in observed Jmax25 across the globe. Our model simulations under current and future climate conditions indicated that Vc,max25 could be most affected in high-latitude regions under a warming climate and that ESMs using a fixed Vc,max25 or Jmax25 by plant functional types were likely to substantially overestimate future global photosynthesis.

  3. Mechanistic insight into sonochemical biodiesel synthesis using heterogeneous base catalyst.

    PubMed

    Choudhury, Hanif A; Chakma, Sankar; Moholkar, Vijayanand S

    2014-01-01

    The beneficial effect of ultrasound on transesterification reaction is well known. Heterogeneous (or solid) catalysts for biodiesel synthesis have merit that they do not contaminate the byproduct of glycerol. In this paper, we have attempted to identify the mechanistic features of ultrasound-enhanced biodiesel synthesis with the base-catalyst of CaO. A statistical design of experiments (Box-Behnken) was used to identify the influence of temperature, alcohol to oil molar ratio and catalyst loading on transesterification yield. The optimum values of these parameters for the highest yield were identified through Response Surface Method (with a quadratic model) and ANOVA. These values are: temperature=62 °C, molar ratio=10:1 and catalyst loading=6 wt.%. The activation energy was determined as 82.3 kJ/mol, which is higher than that for homogeneous catalyzed system (for both acidic and basic catalyst). The experimental results have been analyzed vis-à-vis simulations of cavitation bubble dynamics. Due to 3-phase heterogeneity of the system, the yield was dominated by intrinsic kinetics, and the optimum temperature for the highest yield was close to boiling point of methanol. At this temperature, the influence of cavitation bubbles (in terms of both sonochemical and sonophysical effect) is negligible, and ultrasonic micro-streaming provided necessary convection in the system. The influence of all parameters on the reaction system was found to be strongly inter-dependent.

  4. AIR POLLUTION, INFLAMMATION AND PRETERM BIRTH: A POTENTIAL MECHANISTIC LINK

    PubMed Central

    Vadillo-Ortega, Felipe; Osornio-Vargas, Alvaro; Buxton, Miatta A.; Sánchez, Brisa N.; Rojas-Bracho, Leonora; Viveros-Alcaráz, Martin; Castillo-Castrejón, Marisol; Beltrán-Montoya, Jorge; Brown, Daniel G.; O´Neill, Marie S.

    2014-01-01

    Preterm birth is a public health issue of global significance, which may result in mortality during the perinatal period or may lead to major health and financial consequences due to lifelong impacts. Even though several risk factors for preterm birth have been identified, prevention efforts have failed to halt the increasing rates of preterm birth. Epidemiological studies have identified air pollution as an emerging potential risk factor for preterm birth. However, many studies were limited by study design and inadequate exposure assessment. Due to the ubiquitous nature of ambient air pollution and the potential public health significance of any role in causing preterm birth, a novel focus investigating possible causal mechanisms influenced by air pollution is therefore a global health priority. We hypothesize that air pollution may act together with other biological factors to induce systemic inflammation and influence the duration of pregnancy. Evaluation and testing of this hypothesis is currently being conducted in a prospective cohort study in Mexico City and will provide an understanding of the pathways that mediate the effects of air pollution on preterm birth. The important public health implication is that crucial steps in this mechanistic pathway can potentially be acted on early in pregnancy to reduce the risk of preterm birth. PMID:24382337

  5. Spectroscopic and Mechanistic Investigations of Dehaloperoxidase B from Amphitrite ornata†

    PubMed Central

    D’Antonio, Jennifer; D’Antonio, Edward L.; Thompson, Matthew K.; Bowden, Edmond F.; Franzen, Stefan; Smirnova, Tatyana; Ghiladi, Reza A.

    2010-01-01

    Dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a bifunctional enzyme that possesses both hemoglobin and peroxidase activities. Of the two DHP isoenzymes identified to date, much of the recent focus has been on DHP A, whereas very little is known pertaining to the activity, substrate specificity, mechanism of function, or spectroscopic properties of DHP B. Herein, we report the recombinant expression and purification of DHP B, as well as the details of our investigations into its catalytic cycle using biochemical assays, stopped-flow UV-visible, resonance Raman and rapid-freeze-quench electron paramagnetic resonance spectroscopies, and spectroelectrochemistry. Our experimental design reveals mechanistic insights and kinetic descriptions of the dehaloperoxidase mechanism which have not been previously reported for isoenzyme A. Namely, we demonstrate a novel reaction pathway in which the products of the oxidative dehalogenation of trihalophenols (dihaloquinones) are themselves capable of inducing formation of oxyferrous DHP B, and an updated catalytic cycle for DHP is proposed. We further demonstrate that unlike the traditional monofunctional peroxidases, the oxyferrous state in DHP is a peroxidase competent starting species, which suggests that the ferric oxidation state may not be an obligatory starting point for the enzyme. The data presented herein provide a link between the peroxidase and oxygen transport activities which furthers our understanding of how this bifunctional enzyme is able to unite its two inherent functions in one system. PMID:20545299

  6. Mechanistic evaluation of virus clearance by depth filtration.

    PubMed

    Venkiteshwaran, Adith; Fogle, Jace; Patnaik, Purbasa; Kowle, Ron; Chen, Dayue

    2015-01-01

    Virus clearance by depth filtration has not been well-understood mechanistically due to lack of quantitative data on filter charge characteristics and absence of systematic studies. It is generally believed that both electrostatic interactions and sized based mechanical entrapment contribute to virus clearance by depth filtration. In order to establish whether the effectiveness of virus clearance correlates with the charge characteristics of a given depth filter, a counter-ion displacement technique was employed to determine the ionic capacity for several depth filters. Two depth filters (Millipore B1HC and X0HC) with significant differences in ionic capacities were selected and evaluated for their ability to eliminate viruses. The high ionic capacity X0HC filter showed complete porcine parvovirus (PPV) clearance (eliminating the spiked viruses to below the limit of detection) under low conductivity conditions (≤2.5 mS/cm), achieving a log10 reduction factor (LRF) of > 4.8. On the other hand, the low ionic capacity B1HC filter achieved only ∼2.1-3.0 LRF of PPV clearance under the same conditions. These results indicate that parvovirus clearance by these two depth filters are mainly achieved via electrostatic interactions between the filters and PPV. When much larger xenotropic murine leukemia virus (XMuLV) was used as the model virus, complete retrovirus clearance was obtained under all conditions evaluated for both depth filters, suggesting the involvement of mechanisms other than just electrostatic interactions in XMuLV clearance.

  7. Mechanistic solutions to the opening of the Gulf of Mexico

    USGS Publications Warehouse

    Schouten, Hans; Klitgord, Kim D.

    1994-01-01

    Two mechanistic models-which are unlike the traditional plate-tectonic landfill models used for most proposed Pangea reconstructions of the Yucatán block-relate the Mesozoic opening of the Gulf of Mexico directly to the movement of the North and South American plates: (1) a previous piggyback model in which Yucatán moves with South America out of the western gulf and (2) a new edge-driven model in which the motion of the Yucatán block is caused by forces applied to its margins by the movement of the North and South American plates. In the second model, Yucatán moves out of the northern Gulf of Mexico as a gear or roller bearing. On the basis of magnetic edge anomalies around the gulf, this edge-driven model predicts that from the Bathonian to Tithonian (~170 to ~50 Ma), Yucatán was rotated ~60° counterclockwise as a rigid block between North and South America with rift propagation and extension occurring simultaneously in the Gulf of Mexico and Yucatán Basin.

  8. Mechanistic perspectives on cancer chemoprevention/chemotherapeutic effects of thymoquinone.

    PubMed

    Kundu, Juthika; Chun, Kyung-Soo; Aruoma, Okezie I; Kundu, Joydeb Kumar

    2014-10-01

    The bioactive natural products (plant secondary metabolites) are widely known to possess therapeutic value for the prevention and treatment of various chronic diseases including cancer. Thymoquinone (2-methyl-5-isopropyl-1,4-benzoquinone; TQ), a monoterpene present in black cumin seeds, exhibits pleiotropic pharmacological activities including antioxidant, anti-inflammatory, antidiabetic and antitumor effects. TQ inhibits experimental carcinogenesis in a wide range of animal models and has been shown to arrest the growth of various cancer cells in culture as well as xenograft tumors in vivo. The mechanistic basis of anticancer effects of TQ includes the inhibition of carcinogen metabolizing enzyme activity and oxidative damage of cellular macromolecules, attenuation of inflammation, induction of cell cycle arrest and apoptosis in tumor cells, blockade of tumor angiogenesis, and suppression of migration, invasion and metastasis of cancer cells. TQ shows synergistic and/or potentiating anticancer effects when combined with clinically used chemotherapeutic agents. At the molecular level, TQ targets various components of intracellular signaling pathways, particularly a variety of upstream kinases and transcription factors, which are aberrantly activated during the course of tumorigenesis.

  9. Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling.

    PubMed

    Ye, Hao; Beamish, Richard J; Glaser, Sarah M; Grant, Sue C H; Hsieh, Chih-Hao; Richards, Laura J; Schnute, Jon T; Sugihara, George

    2015-03-31

    It is well known that current equilibrium-based models fall short as predictive descriptions of natural ecosystems, and particularly of fisheries systems that exhibit nonlinear dynamics. For example, model parameters assumed to be fixed constants may actually vary in time, models may fit well to existing data but lack out-of-sample predictive skill, and key driving variables may be misidentified due to transient (mirage) correlations that are common in nonlinear systems. With these frailties, it is somewhat surprising that static equilibrium models continue to be widely used. Here, we examine empirical dynamic modeling (EDM) as an alternative to imposed model equations and that accommodates both nonequilibrium dynamics and nonlinearity. Using time series from nine stocks of sockeye salmon (Oncorhynchus nerka) from the Fraser River system in British Columbia, Canada, we perform, for the the first time to our knowledge, real-data comparison of contemporary fisheries models with equivalent EDM formulations that explicitly use spawning stock and environmental variables to forecast recruitment. We find that EDM models produce more accurate and precise forecasts, and unlike extensions of the classic Ricker spawner-recruit equation, they show significant improvements when environmental factors are included. Our analysis demonstrates the strategic utility of EDM for incorporating environmental influences into fisheries forecasts and, more generally, for providing insight into how environmental factors can operate in forecast models, thus paving the way for equation-free mechanistic forecasting to be applied in management contexts.

  10. Circadian rhythms and addiction: mechanistic insights and future directions.

    PubMed

    Logan, Ryan W; Williams, Wilbur P; McClung, Colleen A

    2014-06-01

    Circadian rhythms are prominent in many physiological and behavioral functions. Circadian disruptions either by environmental or molecular perturbation can have profound health consequences, including the development and progression of addiction. Both animal and humans studies indicate extensive bidirectional relationships between the circadian system and drugs of abuse. Addicted individuals display disrupted rhythms, and chronic disruption or particular chronotypes may increase the risk for substance abuse and relapse. Moreover, polymorphisms in circadian genes and an evening chronotype have been linked to mood and addiction disorders, and recent efforts suggest an association with the function of reward neurocircuitry. Animal studies are beginning to determine how altered circadian gene function results in drug-induced neuroplasticity and behaviors. Many studies suggest a critical role for circadian rhythms in reward-related pathways in the brain and indicate that drugs of abuse directly affect the central circadian pacemaker. In this review, we highlight key findings demonstrating the importance of circadian rhythms in addiction and how future studies will reveal important mechanistic insights into the involvement of circadian rhythms in drug addiction.

  11. A brief review of exercise, bipolar disorder, and mechanistic pathways

    PubMed Central

    Thomson, Daniel; Turner, Alyna; Lauder, Sue; Gigler, Margaret E.; Berk, Lesley; Singh, Ajeet B.; Pasco, Julie A.; Berk, Michael; Sylvia, Louisa

    2015-01-01

    Despite evidence that exercise has been found to be effective in the treatment of depression, it is unclear whether these data can be extrapolated to bipolar disorder. Available evidence for bipolar disorder is scant, with no existing randomized controlled trials having tested the impact of exercise on depressive, manic or hypomanic symptomatology. Although exercise is often recommended in bipolar disorder, this is based on extrapolation from the unipolar literature, theory and clinical expertise and not empirical evidence. In addition, there are currently no available empirical data on program variables, with practical implications on frequency, intensity and type of exercise derived from unipolar depression studies. The aim of the current paper is to explore the relationship between exercise and bipolar disorder and potential mechanistic pathways. Given the high rate of medical co-morbidities experienced by people with bipolar disorder, it is possible that exercise is a potentially useful and important intervention with regard to general health benefits; however, further research is required to elucidate the impact of exercise on mood symptomology. PMID:25788889

  12. Mechanistic modeling of broth temperature in outdoor photobioreactors.

    PubMed

    Béchet, Quentin; Shilton, Andy; Fringer, Oliver B; Muñoz, Raul; Guieysse, Benoit

    2010-03-15

    This study presents the first mechanistic model describing broth temperature in column photobioreactors as a function of static (location, reactor geometry) and dynamic (light irradiance, air temperature, wind velocity) parameters. Based on a heat balance on the liquid phase the model predicted temperature in a pneumatically agitated column photobioreactor (1 m(2) illuminated area, 0.19 m internal diameter, 50 L gas-free cultivation broth) operated outdoor in Singapore to an accuracy of 2.4 °C at the 95% confidence interval over the entire data set used (104 measurements from 7 different batches). Solar radiation (0 to 200 W) and air convection (-30 to 50 W)were the main contributors to broth temperature change. The model predicted broth temperature above 40 °C will be reached during summer months in the same photobioreactor operated in California, a value well over the maximum temperature tolerated by most commercial algae species. Accordingly, 18,000 and 5500 GJ year(-1) ha(-1) of heat energy must be removed to maintain broth temperature at or below 25 and 35 °C, respectively, assuming a reactor density of one reactor per square meter. Clearly, the significant issue of temperature control must be addressed when evaluating the technical feasibility, costs, and sustainability of large-scale algae production.

  13. Simplified mechanistic models of gene regulation for analysis and design

    PubMed Central

    Hancock, Edward J.; Stan, Guy-Bart; Arpino, James A. J.; Papachristodoulou, Antonis

    2015-01-01

    Simplified mechanistic models of gene regulation are fundamental to systems biology and essential for synthetic biology. However, conventional simplified models typically have outputs that are not directly measurable and are based on assumptions that do not often hold under experimental conditions. To resolve these issues, we propose a ‘model reduction’ methodology and simplified kinetic models of total mRNA and total protein concentration, which link measurements, models and biochemical mechanisms. The proposed approach is based on assumptions that hold generally and include typical cases in systems and synthetic biology where conventional models do not hold. We use novel assumptions regarding the ‘speed of reactions’, which are required for the methodology to be consistent with experimental data. We also apply the methodology to propose simplified models of gene regulation in the presence of multiple protein binding sites, providing both biological insights and an illustration of the generality of the methodology. Lastly, we show that modelling total protein concentration allows us to address key questions on gene regulation, such as efficiency, burden, competition and modularity. PMID:26063825

  14. A mechanistic physicochemical model of carbon dioxide transport in blood.

    PubMed

    O'Neill, David P; Robbins, Peter A

    2017-02-01

    A number of mathematical models have been produced that, given the Pco2 and Po2 of blood, will calculate the total concentrations for CO2 and O2 in blood. However, all these models contain at least some empirical features, and thus do not represent all of the underlying physicochemical processes in an entirely mechanistic manner. The aim of this study was to develop a physicochemical model of CO2 carriage by the blood to determine whether our understanding of the physical chemistry of the major chemical components of blood together with their interactions is sufficiently strong to predict the physiological properties of CO2 carriage by whole blood. Standard values are used for the ionic composition of the blood, the plasma albumin concentration, and the hemoglobin concentration. All Km values required for the model are taken from the literature. The distribution of bicarbonate, chloride, and H(+) ions across the red blood cell membrane follows that of a Gibbs-Donnan equilibrium. The system of equations that results is solved numerically using constraints for mass balance and electroneutrality. The model reproduces the phenomena associated with CO2 carriage, including the magnitude of the Haldane effect, very well. The structural nature of the model allows various hypothetical scenarios to be explored. Here we examine the effects of 1) removing the ability of hemoglobin to form carbamino compounds; 2) allowing a degree of Cl(-) binding to deoxygenated hemoglobin; and 3) removing the chloride (Hamburger) shift. The insights gained could not have been obtained from empirical models.

  15. Polymerization kinetics of wheat gluten upon thermosetting. A mechanistic model.

    PubMed

    Domenek, Sandra; Morel, Marie-Hélène; Bonicel, Joëlle; Guilbert, Stéphane

    2002-10-09

    Size exclusion high-performance liquid chromatography analysis was carried out on wheat gluten-glycerol blends subjected to different heat treatments. The elution profiles were analyzed in order to follow the solubility loss of protein fractions with specific molecular size. Owing to the known biochemical changes involved during the heat denaturation of gluten, a mechanistic mathematical model was developed, which divided the protein denaturation into two distinct reaction steps: (i) reversible change in protein conformation and (ii) protein precipitation through disulfide bonding between initially SDS-soluble and SDS-insoluble reaction partners. Activation energies of gluten unfolding, refolding, and precipitation were calculated with the Arrhenius law to 53.9 kJ x mol(-1), 29.5 kJ x mol(-1), and 172 kJ x mol(-1), respectively. The rate of protein solubility loss decreased as the cross-linking reaction proceeded, which may be attributed to the formation of a three-dimensional network progressively hindering the reaction. The enhanced susceptibility to aggregation of large molecules was assigned to a risen reaction probability due to their higher number of cysteine residues and to the increased percentage of unfolded and thereby activated proteins as complete protein refolding seemed to be an anticooperative process.

  16. Early Mechanistic Events in Biotin Dissociation from Streptavidin

    SciTech Connect

    Hyre, D. E.

    2002-01-01

    The streptavidin-biotin system has provided a unique opportunity to investigate the molecular details of ligand dissociation pathways. An underlying mechanistic question is whether ligand dissociation proceeds with a relatively ordered process of bond breaking and ligand escape. Here we report a joint computational and crystallographic study of the earliest events in biotin dissociation. In molecular dynamics potential of mean force simulations, a water molecule from a defined access channel intercalated into the hydrogen bond between Asp 128 and biotin, bridging them and stabilizing an intermediate state. In forced biotin dissociation simulations, this event led to subsequent bond breaking steps and ligand escape. In equilibrium simulations, the water molecule was sometimes observed to move back to the access channel with re-formation of the biotin hydrogen bond. Analysis of streptavidin crystal structures revealed a close overlap of crystallographically defined and simulated waters in the water access channel. These results suggest that biotin dissociation is initiated by stochastic coupling of water entry with lengthening of a specific biotin hydrogen-bonding interaction.

  17. Mechanistic explanation, cognitive systems demarcation, and extended cognition.

    PubMed

    van Eck, Dingmar; Looren de Jong, Huib

    2016-10-01

    Approaches to the Internalism-Externalism controversy in the philosophy of mind often involve both (broadly) metaphysical and explanatory considerations. Whereas originally most emphasis seems to have been placed on metaphysical concerns, recently the explanation angle is getting more attention. Explanatory considerations promise to offer more neutral grounds for cognitive systems demarcation than (broadly) metaphysical ones. However, it has been argued that explanation-based approaches are incapable of determining the plausibility of internalist-based conceptions of cognition vis-à-vis externalist ones. On this perspective, improved metaphysics is the route along which to solve the Internalist-Externalist stalemate. In this paper we challenge this claim. Although we agree that explanation-orientated approaches have indeed so far failed to deliver solid means for cognitive system demarcation, we elaborate a more promising explanation-oriented framework to address this issue. We argue that the mutual manipulability account of constitutive relevance in mechanisms, extended with the criterion of 'fat-handedness', is capable of plausibly addressing the cognitive systems demarcation problem, and thus able to decide on the explanatory traction of Internalist vs. Externalist conceptions, on a case-by-case basis. Our analysis also highlights why some other recent mechanistic takes on the problem of cognitive systems demarcation have been unsuccessful. We illustrate our claims with a case on gestures and learning.

  18. Anti-fibro-hepatocarcinogenic Chinese herbal medicines: A mechanistic overview

    PubMed Central

    Boye, Alex; Yang, Yan; Asenso, James; Wei, Wei

    2016-01-01

    Chinese herbal medicine (CHM) is an integral component of complementary/alternative medicine and it is increasingly becoming the preferred therapeutic modality for the treatment of liver fibrosis and hepatocellular carcinoma (HCC) worldwide. Accordingly, the World Health Organization (WHO) has attested to the popularity and efficacy of indigenous herbal therapies including CHM as a first line of treatment for some diseases including liver disorders. However, the WHO and drug discovery experts have always recommended that use of indigenous herbal remedies must go hand-in-hand with the requisite mechanistic elucidation so as to constitute a system of verification of efficacy within the ethnobotanical context of use. Although many CHM experts have advanced knowledge on CHM, nonetheless, more enlightenment is needed, particularly mechanisms of action of CHMs on fibro-hepato-carcinogenesis. We, herein, provide in-depth mechanisms of the action of CHMs which have demonstrated anti-fibro-hepatocarcinogenic effects, in pre-clinical and clinical studies as published in PubMed and other major scientific databases. Specifically, the review brings out the important signaling pathways, and their downstream targets which are modulated at multi-level by various anti-fibro-hepatocarcinogenic CHMs. PMID:27366355

  19. Rapid Discrimination Among Putative Mechanistic Models of Biochemical Systems

    PubMed Central

    Lomnitz, Jason G.; Savageau, Michael A.

    2016-01-01

    An overarching goal in molecular biology is to gain an understanding of the mechanistic basis underlying biochemical systems. Success is critical if we are to predict effectively the outcome of drug treatments and the development of abnormal phenotypes. However, data from most experimental studies is typically noisy and sparse. This allows multiple potential mechanisms to account for experimental observations, and often devising experiments to test each is not feasible. Here, we introduce a novel strategy that discriminates among putative models based on their repertoire of qualitatively distinct phenotypes, without relying on knowledge of specific values for rate constants and binding constants. As an illustration, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors. Our results show that the conventional models, based on their well-characterized components, cannot account for the experimental observations. We examine a total of 40 alternative hypotheses and show that only 5 have the potential to reproduce the experimental data, and one can do so with biologically relevant parameter values. PMID:27578053

  20. Mechanistic modeling of aberrant energy metabolism in human disease

    PubMed Central

    Sangar, Vineet; Eddy, James A.; Simeonidis, Evangelos; Price, Nathan D.

    2012-01-01

    Dysfunction in energy metabolism—including in pathways localized to the mitochondria—has been implicated in the pathogenesis of a wide array of disorders, ranging from cancer to neurodegenerative diseases to type II diabetes. The inherent complexities of energy and mitochondrial metabolism present a significant obstacle in the effort to understand the role that these molecular processes play in the development of disease. To help unravel these complexities, systems biology methods have been applied to develop an array of computational metabolic models, ranging from mitochondria-specific processes to genome-scale cellular networks. These constraint-based (CB) models can efficiently simulate aspects of normal and aberrant metabolism in various genetic and environmental conditions. Development of these models leverages—and also provides a powerful means to integrate and interpret—information from a wide range of sources including genomics, proteomics, metabolomics, and enzyme kinetics. Here, we review a variety of mechanistic modeling studies that explore metabolic functions, deficiency disorders, and aberrant biochemical pathways in mitochondria and related regions in the cell. PMID:23112774

  1. Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase)

    SciTech Connect

    Chen, Julian C.-H.; Mustyakimov, Marat; Schoenborn, Benno P.; Langan, Paul; Blum, Marc-Michael

    2010-11-01

    The structure and mechanism of diisopropyl fluorophosphatase (DFPase) have been studied using a variety of methods, including isotopic labelling, X-ray crystallography and neutron crystallography. The neutron structure of DFPase, mechanistic studies and subsequent rational design efforts are described. Diisopropyl fluorophosphatase (DFPase) is a calcium-dependent phosphotriesterase that acts on a variety of highly toxic organophosphorus compounds that act as inhibitors of acetylcholinesterase. The mechanism of DFPase has been probed using a variety of methods, including isotopic labelling, which demonstrated the presence of a phosphoenzyme intermediate in the reaction mechanism. In order to further elucidate the mechanism of DFPase and to ascertain the protonation states of the residues and solvent molecules in the active site, the neutron structure of DFPase was solved at 2.2 Å resolution. The proposed nucleophile Asp229 is deprotonated, while the active-site solvent molecule W33 was identified as water and not hydroxide. These data support a mechanism involving direct nucleophilic attack by Asp229 on the substrate and rule out a mechanism involving metal-assisted water activation. These data also allowed for the re-engineering of DFPase through rational design to bind and productively orient the more toxic S{sub P} stereoisomers of the nerve agents sarin and cyclosarin, creating a modified enzyme with enhanced overall activity and significantly increased detoxification properties.

  2. A mechanistic model for permeability evolution in fractured sorbing media

    NASA Astrophysics Data System (ADS)

    Wang, Shugang; Elsworth, Derek; Liu, Jishan

    2012-06-01

    A mechanistic model is presented to represent the evolution of permeability in fractured sorbing media such as coal beds and organic-rich shales. This model accommodates key competing processes of poromechanical dilation and sorption-induced swelling. We show that the significant difference in stiffness between fracture and matrix transforms the composite system from globally unconstrained to locally constrained by the development of a virtual "stiff shell" that envelops the perimeter of a representative elementary volume containing a fracture. It is this transformation that results in swelling-induced permeability reduction at low (sorbing) gas pressures and self consistently allows competitive dilation of the fracture as gas pressures are increased. Importantly, net dilation is shown to require a mismatch in the Biot coefficients of fracture and matrix with the coefficient for the fracture exceeding that for the matrix—a condition that is logically met. Permeability evolution is cast in terms of series and parallel models with the series model better replicating observational data. The model may be cast in terms of nondimensional parameters representing sorptive and poromechanical effects and modulated by the sensitivity of the fracture network to dilation or compaction of the individual fractures. This latter parameter encapsulates the effects of fracture spacing and initial permeability and scale changes in permeability driven by either sorption or poromechanical effects. This model is applied to well-controlled observational data for different ranks of coals and different gases (He, CO2) and satisfactory agreement is obtained.

  3. Environmental perception and epigenetic memory: mechanistic insight through FLC

    PubMed Central

    Berry, Scott; Dean, Caroline

    2015-01-01

    Chromatin plays a central role in orchestrating gene regulation at the transcriptional level. However, our understanding of how chromatin states are altered in response to environmental and developmental cues, and then maintained epigenetically over many cell divisions, remains poor. The floral repressor gene FLOWERING LOCUS C (FLC) in Arabidopsis thaliana is a useful system to address these questions. FLC is transcriptionally repressed during exposure to cold temperatures, allowing studies of how environmental conditions alter expression states at the chromatin level. FLC repression is also epigenetically maintained during subsequent development in warm conditions, so that exposure to cold may be remembered. This memory depends on molecular complexes that are highly conserved among eukaryotes, making FLC not only interesting as a paradigm for understanding biological decision-making in plants, but also an important system for elucidating chromatin-based gene regulation more generally. In this review, we summarize our understanding of how cold temperature induces a switch in the FLC chromatin state, and how this state is epigenetically remembered. We also discuss how the epigenetic state of FLC is reprogrammed in the seed to ensure a requirement for cold exposure in the next generation. Significance Statement FLOWERING LOCUS C (FLC) regulation provides a paradigm for understanding how chromatin can be modulated to determine gene expression in a developmental context. This review describes our current mechanistic understanding of how FLC expression is genetically specified and epigenetically regulated throughout the plant life cycle, and how this determines plant life-history strategy. PMID:25929799

  4. Bioavailability and Pharmacokinetics of Genistein: Mechanistic Studies on its ADME

    PubMed Central

    Yang, Zhen; Kulkarni, Kaustubh; Zhu, Wei; Hu, Ming

    2014-01-01

    Genistein, one of the most active natural flavonoids, exerts various biological effects including chemoprevention, antioxidation, antiproliferation and anticancer. More than 30 clinical trials of genistein with various disease indications have been conducted to evaluate its clinical efficacy. Based on many animals and human pharmacokinetic studies, it is well known that the most challenge issue for developing genistein as a chemoprevention agent is the low oral bioavailability, which may be the major reason relating to its ambiguous therapeutic effects and large interindividual variations in clinical trials. In order to better correlate pharmacokinetic to pharmacodynamics results in animals and clinical studies, an in-depth understanding of pharmacokinetic behavior of genistein and its ADME properties are needed. Numerous in vitro/in vivo ADME studies had been conducted to reveal the main factors contributing to the low oral bioavailability of genistein. Therefore, this review focuses on summarizing the most recent progress on mechanistic studies of genistein ADME and provides a systemic view of these processes to explain genistein pharmacokinetic behaviors in vivo. The better understanding of genistein ADME property may lead to development of proper strategy to improve genistein oral bioavailability via mechanism-based approaches. PMID:22583407

  5. Mechanistic investigation of beta-galactosidase-activated MR contrast agents.

    PubMed

    Urbanczyk-Pearson, Lauren M; Femia, Frank J; Smith, Jeffrey; Parigi, Giacomo; Duimstra, Joseph A; Eckermann, Amanda L; Luchinat, Claudio; Meade, Thomas J

    2008-01-07

    We report a mechanistic investigation of an isomeric series of beta-galactosidase-activated magnetic resonance contrast agents. Our strategy focuses on the synthesis of macrocyclic caged-complexes that coordinatively saturate a chelated lanthanide. Enzyme cleavage of the complex results in an open coordination site available for water that creates a detectable MR contrast agent. The complexes consist of a DO3A Gd(III) chelator modified with a galactopyranose at the N-10 position of the macrocycle. We observed significant differences in relaxometric properties and coordination geometry that can be correlated to subtle variations of the linker between the macrocycle and the galactopyranose. After synthesis and purification of the R, S, and racemic mixtures of complexes 1 and 3 and measurement of the hydration number, water residence lifetime, and longitudinal relaxation rates, we propose mechanisms for water exclusion from the lanthanide in the precleavage state. While the stereochemistry of the linker does not influence the agents' properties, the mechanism of water exclusion for each isomer is significantly influenced by the position of modification. Data for one series with a methyl group substituted on the sugar-macrocycle linker at the alpha-position suggests a steric mechanism where the galactopyranose sugar blocks water from the Gd(III) center. In contrast, our observations for a second series with methyl substitution at the beta position of the sugar-macrocycle linker are consistent with a mechanism in which a bidentate anion occupies two available coordination sites of Gd(III) in the precleavage state.

  6. Air pollution, inflammation and preterm birth: a potential mechanistic link.

    PubMed

    Vadillo-Ortega, Felipe; Osornio-Vargas, Alvaro; Buxton, Miatta A; Sánchez, Brisa N; Rojas-Bracho, Leonora; Viveros-Alcaráz, Martin; Castillo-Castrejón, Marisol; Beltrán-Montoya, Jorge; Brown, Daniel G; O'Neill, Marie S

    2014-02-01

    Preterm birth is a public health issue of global significance, which may result in mortality during the perinatal period or may lead to major health and financial consequences due to lifelong impacts. Even though several risk factors for preterm birth have been identified, prevention efforts have failed to halt the increasing rates of preterm birth. Epidemiological studies have identified air pollution as an emerging potential risk factor for preterm birth. However, many studies were limited by study design and inadequate exposure assessment. Due to the ubiquitous nature of ambient air pollution and the potential public health significance of any role in causing preterm birth, a novel focus investigating possible causal mechanisms influenced by air pollution is therefore a global health priority. We hypothesize that air pollution may act together with other biological factors to induce systemic inflammation and influence the duration of pregnancy. Evaluation and testing of this hypothesis is currently being conducted in a prospective cohort study in Mexico City and will provide an understanding of the pathways that mediate the effects of air pollution on preterm birth. The important public health implication is that crucial steps in this mechanistic pathway can potentially be acted on early in pregnancy to reduce the risk of preterm birth.

  7. A global scale mechanistic model of the photosynthetic capacity

    NASA Astrophysics Data System (ADS)

    Ali, A. A.; Xu, C.; Rogers, A.; Fisher, R. A.; Wullschleger, S. D.; McDowell, N. G.; Massoud, E. C.; Vrugt, J. A.; Muss, J. D.; Fisher, J. B.; Reich, P. B.; Wilson, C. J.

    2015-08-01

    Although plant photosynthetic capacity as determined by the maximum carboxylation rate (i.e., Vc, max25) and the maximum electron transport rate (i.e., Jmax25) at a reference temperature (generally 25 °C) is known to vary substantially in space and time in response to environmental conditions, it is typically parameterized in Earth system models (ESMs) with tabulated values associated to plant functional types. In this study, we developed a mechanistic model of leaf utilization of nitrogen for assimilation (LUNA V1.0) to predict the photosynthetic capacity at the global scale under different environmental conditions, based on the optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The LUNA model was able to reasonably well capture the observed patterns of photosynthetic capacity in view that it explained approximately 55 % of the variation in observed Vc, max25 and 65 % of the variation in observed Jmax25 across the globe. Our model simulations under current and future climate conditions indicated that Vc, max25 could be most affected in high-latitude regions under a warming climate and that ESMs using a fixed Vc, max25 or Jmax25 by plant functional types were likely to substantially overestimate future global photosynthesis.

  8. Diffusion theory in biology: a relic of mechanistic materialism.

    PubMed

    Agutter, P S; Malone, P C; Wheatley, D N

    2000-01-01

    Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metalbolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science.

  9. Warming will affect phytoplankton differently: evidence through a mechanistic approach

    PubMed Central

    Huertas, I. Emma; Rouco, Mónica; López-Rodas, Victoria; Costas, Eduardo

    2011-01-01

    Although the consequences of global warming in aquatic ecosystems are only beginning to be revealed, a key to forecasting the impact on aquatic communities is an understanding of individual species' vulnerability to increased temperature. Despite their microscopic size, phytoplankton support about half of the global primary production, drive essential biogeochemical cycles and represent the basis of the aquatic food web. At present, it is known that phytoplankton are important targets and, consequently, harbingers of climate change in aquatic systems. Therefore, investigating the capacity of phytoplankton to adapt to the predicted warming has become a relevant issue. However, considering the polyphyletic complexity of the phytoplankton community, different responses to increased temperature are expected. We experimentally tested the effects of warming on 12 species of phytoplankton isolated from a variety of environments by using a mechanistic approach able to assess evolutionary adaptation (the so-called ratchet technique). We found different degrees of tolerance to temperature rises and an interspecific capacity for genetic adaptation. The thermal resistance level reached by each species is discussed in relation to their respective original habitats. Our study additionally provides evidence on the most resistant phytoplankton groups in a future warming scenario. PMID:21508031

  10. A Mechanistic Link between Olfaction and Autism Spectrum Disorder.

    PubMed

    Rozenkrantz, Liron; Zachor, Ditza; Heller, Iris; Plotkin, Anton; Weissbrod, Aharon; Snitz, Kobi; Secundo, Lavi; Sobel, Noam

    2015-07-20

    Internal action models (IAMs) are brain templates for sensory-motor coordination underlying diverse behaviors. An emerging theory suggests that impaired IAMs are a common theme in autism spectrum disorder (ASD). However, whether impaired IAMs occur across sensory systems and how they relate to the major phenotype of ASD, namely impaired social communication, remains unclear. Olfaction relies on an IAM known as the sniff response, where sniff magnitude is automatically modulated to account for odor valence. To test the failed IAM theory in olfaction, we precisely measured the non-verbal non-task-dependent sniff response concurrent with pleasant and unpleasant odors in 36 children--18 with ASD and 18 matched typically developing (TD) controls. We found that whereas TD children generated a typical adult-like sniff response within 305 ms of odor onset, ASD children had a profoundly altered sniff response, sniffing equally regardless of odor valance. This difference persisted despite equal reported odor perception and allowed for 81% correct ASD classification based on the sniff response alone (binomial, p < 0.001). Moreover, increasingly aberrant sniffing was associated with increasingly severe ASD (r = -0.75, p < 0.001), specifically with social (r = -0.72, p < 0.001), but not motor (r < -0.38, p > 0.18), impairment. These results uncover a novel ASD marker implying a mechanistic link between the underpinnings of olfaction and ASD and directly linking an impaired IAM with impaired social abilities.

  11. Physical activity and its mechanistic effects on prostate cancer.

    PubMed

    Wekesa, A; Harrison, M; Watson, R W

    2015-09-01

    Beneficial effects of physical activity have been illustrated in numerous aspects of health. With the increasing incidence of prostate cancer and changes in physical activity of men, understanding the link between the two has important implications for changing this cancer burden. Both positive and negative associations between physical activity and prostate cancer have been previously demonstrated in observational epidemiological studies. Elucidating the biological mechanisms would lead to a better understanding of how physical activity influences the progression of prostate cancer. This review was undertaken to: (1) identify evidence in literature that demonstrates the effects of physical activity on skeletal muscle secretomes, (2) indicate the plausible signaling pathways these proteins might activate, and (3) identify evidence in literature that demonstrates the roles of the signaling pathways in prostate cancer progression and regression. We also discuss proposed biological mechanisms and signaling pathways by which physical activity may prevent the development and progression of prostate cancer. We discuss proteins involved in the normal and aberrant growth and development of the prostate gland that may be affected by physical activity. We further identify future directions for research, including a better understanding of the biological mechanisms, the need to standardize physical activity and identify mechanistic end points of physical activity that can then be correlated with outcomes.

  12. A windows based mechanistic subsidence prediction model for longwall mining

    SciTech Connect

    Begley, R.; Beheler, P.; Khair, A.W.

    1996-12-31

    The previously developed Mechanistic Subsidence Prediction Model (MSPM) has been incorporated into the graphical interface environment of MS Windows. MSPM has the unique capability of predicting maximum subsidence, angle of draw and the subsidence profile of a longwall panel at various locations for both the transverse and longitudinal orientations. The resultant enhanced model can be operated by individuals with little knowledge of subsidence prediction theories or little computer programming experience. In addition, predictions of subsidence can be made in a matter of seconds without the need to develop input data files or use the keyboard in some cases. The predictions are based upon the following input parameters: panel width, mining height, overburden depth, rock quality designation, and percent hard rock in the immediate roof, main roof and the entire overburden. The recently developed enhanced model has the capability to compare predictions in a graphical format for one half of the predicted subsidence profile based upon changes in input parameters easily and instantly on the same screen. In addition another screen can be obtained from a pull down menu where the operator can compare predictions for the entire subsidence profiles. This paper presents the background of the subsidence prediction model and the methodology of the enhanced model development. The paper also presents comparisons of subsidence predictions for several different sets of input parameters in addition to comparisons of the subsidence predictions with actual field data.

  13. In Vitro Multitissue Interface Model Supports Rapid Vasculogenesis and Mechanistic Study of Vascularization across Tissue Compartments.

    PubMed

    Buno, Kevin P; Chen, Xuemei; Weibel, Justin A; Thiede, Stephanie N; Garimella, Suresh V; Yoder, Mervin C; Voytik-Harbin, Sherry L

    2016-08-31

    A significant challenge facing tissue engineers is the design and development of complex multitissue systems, including vascularized tissue-tissue interfaces. While conventional in vitro models focus on either vasculogenesis (de novo formation of blood vessels) or angiogenesis (vessels sprouting from existing vessels or endothelial monolayers), successful therapeutic vascularization strategies will likely rely on coordinated integration of both processes. To address this challenge, we developed a novel in vitro multitissue interface model in which human endothelial colony forming cell (ECFC)-encapsulated tissue spheres are embedded within a surrounding tissue microenvironment. This highly reproducible approach exploits biphilic surfaces (nanostructured surfaces with distinct superhydrophobic and hydrophilic regions) to (i) support tissue compartments with user-specified matrix composition and physical properties as well as cell type and density and (ii) introduce boundary conditions that prevent the cell-mediated tissue contraction routinely observed with conventional three-dimensional monodispersion cultures. This multitissue interface model was applied to test the hypothesis that independent control of cell-extracellular matrix (ECM) and cell-cell interactions would affect vascularization within the tissue sphere as well as across the tissue-tissue interface. We found that high-cell-density tissue spheres containing 5 × 10(6) ECFCs/mL exhibit rapid and robust vasculogenesis, forming highly interconnected, stable (as indicated by type IV collagen deposition) vessel networks within only 3 days. Addition of adipose-derived stromal cells (ASCs) in the surrounding tissue further enhanced vasculogenesis within the sphere as well as angiogenic vessel elongation across the tissue-tissue boundary, with both effects being dependent on the ASC density. Overall, results show that the ECFC density and ECFC-ASC crosstalk, in terms of paracrine and mechanophysical signaling

  14. Deposition, Chapter 3

    Treesearch

    K.C. Weathers; J.A. Lynch

    2011-01-01

    To determine the effects of air pollution on ecological systems using the critical load approach, accurate estimates of total nitrogen (N) deposition are essential. Empirical critical loads are set by relating observed ecosystem responses to N deposition (measured, experimentally manipulated, or modeled).

  15. Radionuclide deposition control

    DOEpatents

    Brehm, William F.; McGuire, Joseph C.

    1980-01-01

    The deposition of radionuclides manganese-54, cobalt-58 and cobalt-60 from liquid sodium coolant is controlled by providing surfaces of nickel or high nickel alloys to extract the radionuclides from the liquid sodium, and by providing surfaces of tungsten, molybdenum or tantalum to prevent or retard radionuclide deposition.

  16. Domestic phosphate deposits

    USGS Publications Warehouse

    McKelvey, V.E.; Cathcart, J.B.; Altschuler, Z.S.; Swanson, R.W.; Lutz, Katherine

    1953-01-01

    Most of the worlds phosphate deposits can be grouped into six types: 1) igneous apatite deposits; 2) marine phosphorites; 3) residual phosphorites; 4) river pebble deposits; 5) phosphatized rock; and 6) guano. The igneous apatites and marine phosphorites form deposits measurable in millions or billions of tons; the residual deposits are measurable in thousands or millions; and the other types generally only in thousands of tons. Igneous apatite deposits have been mined on a small scale in New York, New Jersey, and Virginia. Marine phosphorites have been mined in Montana, Idaho, Utah, Wyoming, Arkansas, Tennessee, North Carolina, South Carolina, Georgia, and Florida. Residual phosphorites have been mined in Tennessee, Pennsylvania, and Florida. River pebble has been produced in South Carolina and Florida; phosphatized rock in Tennessee and Florida; and guano in New Mexico and Texas. Present production is limited almost entirely to Florida, Tennessee, Montana, Idaho, and Wyoming. Incomplete but recently partly revised estimates indicate the presence of about 5 billion tons of phosphate deposits in the United States that is minable under present economic conditions. Deposits too lean in quality or thickness to compete with those in the western and southeastern fields probably contain tens of billions of tons.

  17. Solution deposition assembly

    SciTech Connect

    Roussillon, Yann; Scholz, Jeremy H; Shelton, Addison; Green, Geoff T; Utthachoo, Piyaphant

    2014-01-21

    Methods and devices are provided for improved deposition systems. In one embodiment of the present invention, a deposition system is provided for use with a solution and a substrate. The system comprises of a solution deposition apparatus; at least one heating chamber, at least one assembly for holding a solution over the substrate; and a substrate curling apparatus for curling at least one edge of the substrate to define a zone capable of containing a volume of the solution over the substrate. In another embodiment of the present invention, a deposition system for use with a substrate, the system comprising a solution deposition apparatus; at heating chamber; and at least assembly for holding solution over the substrate to allow for a depth of at least about 0.5 microns to 10 mm.

  18. Trouvelot Crater Deposit

    NASA Image and Video Library

    2002-12-04

    Like many of the craters in the Oxia Palus region of Mars, Trouvelot Crater, shown in this NASA Mars Odyssey image, hosts an eroded, light-toned, sedimentary deposit on its floor. Compared with the much larger example in Becquerel Crater to the NE, the Trouvelot deposit has been so eroded by the scouring action of dark, wind-blown sand that very little of it remains. Tiny outliers of bright material separated from the main mass attest to the once, more really extensive coverage by the deposit. A similar observation can be made for White Rock, the best known example of a bright, crater interior deposit. The origin of the sediments in these deposits remains enigmatic but they are likely the result of fallout from ash or dust carried by the thin martian atmosphere. http://photojournal.jpl.nasa.gov/catalog/PIA04017

  19. Stratiform chromite deposit model

    USGS Publications Warehouse

    Schulte, Ruth F.; Taylor, Ryan D.; Piatak, Nadine M.; Seal, Robert R., II

    2010-01-01

    Stratiform chromite deposits are of great economic importance, yet their origin and evolution remain highly debated. Layered igneous intrusions such as the Bushveld, Great Dyke, Kemi, and Stillwater Complexes, provide opportunities for studying magmatic differentiation processes and assimilation within the crust, as well as related ore-deposit formation. Chromite-rich seams within layered intrusions host the majority of the world's chromium reserves and may contain significant platinum-group-element (PGE) mineralization. This model of stratiform chromite deposits is part of an effort by the U.S. Geological Survey's Mineral Resources Program to update existing models and develop new descriptive mineral deposit models to supplement previously published models for use in mineral-resource and mineral-environmental assessments. The model focuses on features that may be common to all stratiform chromite deposits as a way to gain insight into the processes that gave rise to their emplacement and to the significant economic resources contained in them.

  20. Plasma deposition of tungsten

    SciTech Connect

    Greenberg, K.E.

    1986-12-01

    Tungsten films were plasma-deposited using an abnormal glow discharge through a mixture of tungsten hexafluoride, hydrogen, and argon. The films adhered well to silicon, silicon dioxide, gallium arsenide, and aluminum substrates placed directly on the discharge cathode. Typical deposition rates were on the order of 160 Angstroms/minute with as-deposited film resistivities of 40 to 70 microohm-cm. The tungsten was analyzed using a number of techniques including x-ray diffraction, scanning electron microscopy, and Auger spectroscopy. Low-resistivity (<10 microohm-cm) films that adhered well to silicon dioxide were obtained with a two-step process utilizing plasma deposition and conventional chemical vapor deposition.

  1. Identification of key characteristics of male reproductive toxicants as an approach for screening and sorting mechanistic evidence.

    EPA Science Inventory

    The application of systematic review practices in human health assessment includes integration of multi-disciplinary evidence from epidemiological, experimental, and mechanistic studies. Although mode of action analysis relies on the evaluation of mechanistic and toxicological ou...

  2. Tsunami Deposit Data Base

    NASA Astrophysics Data System (ADS)

    Keating, B. H.; Wanink, M.

    2007-05-01

    A digital database has been established describing tsunami deposits around the world (3 phases; 15 months). The projects involved the review and tabulation of data derived from books, catalogs, journals, preprints, citations and abstracts (currently 1000 references), into a database designed to provide a comprehensive review of the types of tsunami deposits, their geographic distribution and location, sedimentary characteristics, fossil content, age, preservation, run-up, wave height and inundation observations, etc. (34 parameters). The tsunami occurrences can be divided into many subjects, e.g., Volcanogenic (N=375), Seismites (N=49), Co-seismic (N=258), K/T Boundary Impact-triggered debris flows (N=97), Landslides (N=43), etc. Numerous publications compare tsunami deposits to storm deposits (N=38), or analyze the origin of megaboulders (N=22). Tsunami deposits occur throughout geologic time (Pre-Cambrian to present day), and because of plate tectonics, they occur along plate margins (primarily subduction zones) as well as interior to plates. In addition, they occur in epi-continental seas, fjords, etc. Few publications describe depositional processes. Deposits generated by tsunamis occur in multiple environments such as the marine, fresh water, and subaerial. Common characteristics of tsunami deposits include: 1) Deposition of thin sand sheets (can be normal, massive, inversely graded, chaotic or bimodal). 2) Erosional: basal uncomformity, mud balls, rip-up clasts, reworked fossils produced by scouring. 3) Lithology: Stacks of couplets reflecting marine incursions (often sands) into fresh water or subaerial environments (mud, soil, peat). 4) Fossil: Couplets reflects marine fossils, fresh water fossils or a mixed assemblage. 5) Geomorphology: The sand sheets taper landward and can rise in elevation. 6) Deformation: syn-depositional (soft sediments) and intraformational (stiff sediments).

  3. Mechanistic analysis of cavitation assisted transesterification on biodiesel characteristics.

    PubMed

    Sajjadi, Baharak; Abdul Aziz, A R; Ibrahim, Shaliza

    2015-01-01

    The influence of sonoluminescence transesterification on biodiesel physicochemical properties was investigated and the results were compared to those of traditional mechanical stirring. This study was conducted to identify the mechanistic features of ultrasonication by coupling statistical analysis of the experiments into the simulation of cavitation bubble. Different combinations of operational variables were employed for alkali-catalysis transesterification of palm oil. The experimental results showed that transesterification with ultrasound irradiation could change the biodiesel density by about 0.3kg/m(3); the viscosity by 0.12mm(2)/s; the pour point by about 1-2°C and the flash point by 5°C compared to the traditional method. Furthermore, 93.84% of yield with alcohol to oil molar ratio of 6:1 could be achieved through ultrasound assisted transesterification within only 20min. However, only 89.09% of reaction yield was obtained by traditional macro mixing/heating under the same condition. Based on the simulated oscillation velocity value, the cavitation phenomenon significantly contributed to generation of fine micro emulsion and was able to overcome mass transfer restriction. It was found that the sonoluminescence bubbles reached the temperature of 758-713K, pressure of 235.5-159.55bar, oscillation velocity of 3.5-6.5cm/s, and equilibrium radius of 17.9-13.7 times greater than its initial size under the ambient temperature of 50-64°C at the moment of collapse. This showed that the sonoluminescence bubbles were in the condition in which the decomposition phenomena were activated and the reaction rate was accelerated together with a change in the biodiesel properties. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. The attention schema theory: a mechanistic account of subjective awareness.

    PubMed

    Graziano, Michael S A; Webb, Taylor W

    2015-01-01

    We recently proposed the attention schema theory, a novel way to explain the brain basis of subjective awareness in a mechanistic and scientifically testable manner. The theory begins with attention, the process by which signals compete for the brain's limited computing resources. This internal signal competition is partly under a bottom-up influence and partly under top-down control. We propose that the top-down control of attention is improved when the brain has access to a simplified model of attention itself. The brain therefore constructs a schematic model of the process of attention, the 'attention schema,' in much the same way that it constructs a schematic model of the body, the 'body schema.' The content of this internal model leads a brain to conclude that it has a subjective experience. One advantage of this theory is that it explains how awareness and attention can sometimes become dissociated; the brain's internal models are never perfect, and sometimes a model becomes dissociated from the object being modeled. A second advantage of this theory is that it explains how we can be aware of both internal and external events. The brain can apply attention to many types of information including external sensory information and internal information about emotions and cognitive states. If awareness is a model of attention, then this model should pertain to the same domains of information to which attention pertains. A third advantage of this theory is that it provides testable predictions. If awareness is the internal model of attention, used to help control attention, then without awareness, attention should still be possible but should suffer deficits in control. In this article, we review the existing literature on the relationship between attention and awareness, and suggest that at least some of the predictions of the theory are borne out by the evidence.

  5. Mechanistic Understanding of Microbial Plugging for Improved Sweep Efficiency

    SciTech Connect

    Steven Bryant; Larry Britton

    2008-09-30

    Microbial plugging has been proposed as an effective low cost method of permeability reduction. Yet there is a dearth of information on the fundamental processes of microbial growth in porous media, and there are no suitable data to model the process of microbial plugging as it relates to sweep efficiency. To optimize the field implementation, better mechanistic and volumetric understanding of biofilm growth within a porous medium is needed. In particular, the engineering design hinges upon a quantitative relationship between amount of nutrient consumption, amount of growth, and degree of permeability reduction. In this project experiments were conducted to obtain new data to elucidate this relationship. Experiments in heterogeneous (layered) beadpacks showed that microbes could grow preferentially in the high permeability layer. Ultimately this caused flow to be equally divided between high and low permeability layers, precisely the behavior needed for MEOR. Remarkably, classical models of microbial nutrient uptake in batch experiments do not explain the nutrient consumption by the same microbes in flow experiments. We propose a simple extension of classical kinetics to account for the self-limiting consumption of nutrient observed in our experiments, and we outline a modeling approach based on architecture and behavior of biofilms. Such a model would account for the changing trend of nutrient consumption by bacteria with the increasing biomass and the onset of biofilm formation. However no existing model can explain the microbial preference for growth in high permeability regions, nor is there any obvious extension of the model for this observation. An attractive conjecture is that quorum sensing is involved in the heterogeneous bead packs.

  6. Mechanistic Study of Plasma Damage of Low k Dielectric Surfaces

    SciTech Connect

    Bao Junjing; Shi Hualiang; Huang Huai; Ho, P. S.; Liu Junjun; Goodner, M. D.; Moinpour, M.; Kloster, G. M.

    2007-10-31

    Plasma damage to low k dielectric materials was investigated from a mechanistic point of view. Low k dielectric films were treated by plasma Ar, O{sub 2}, N{sub 2}/H{sub 2}, N{sub 2} and H{sub 2} in a standard RIE chamber and the damage was characterized by Angle Resolved X-ray Photoelectron Spectroscopy (ARXPS), X-Ray Reflectivity (XRR), Fourier Transform Infrared Spectroscopy (FTIR) and Contact Angle measurements. Both carbon depletion and surface densification were observed on the top surface of damaged low k materials while the bulk remained largely unaffected. Plasma damage was found to be a complicated phenomenon involving both chemical and physical effects, depending on chemical reactivity and the energy and mass of the plasma species. A downstream hybrid plasma source with separate ions and atomic radicals was employed to study their respective roles in the plasma damage process. Ions were found to play a more important role in the plasma damage process. The dielectric constant of low k materials can increase up to 20% due to plasma damage and we attributed this to the removal of the methyl group making the low k surface hydrophilic. Annealing was generally effective in mitigating moisture uptake to restore the k value but the recovery was less complete for higher energy plasmas. Quantum chemistry calculation confirmed that physisorbed water in low k materials induces the largest increase of dipole moments in comparison with changes of surface bonding configurations, and is primarily responsible for the dielectric constant increase.

  7. Toward a mechanistic modeling of nitrogen limitation on vegetation dynamics

    SciTech Connect

    Xu, Chonggang; Fisher, Rosie; Wullschleger, Stan D; Wilson, Cathy; Cai, Michael; McDowell, Nathan

    2012-01-01

    Nitrogen is a dominant regulator of vegetation dynamics, net primary production, and terrestrial carbon cycles; however, most ecosystem models use a rather simplistic relationship between leaf nitrogen content and photosynthetic capacity. Such an approach does not consider how patterns of nitrogen allocation may change with differences in light intensity, growing-season temperature and CO{sub 2} concentration. To account for this known variability in nitrogen-photosynthesis relationships, we develop a mechanistic nitrogen allocation model based on a trade-off of nitrogen allocated between growth and storage, and an optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The developed model is able to predict the acclimation of photosynthetic capacity to changes in CO{sub 2} concentration, temperature, and radiation when evaluated against published data of V{sub c,max} (maximum carboxylation rate) and J{sub max} (maximum electron transport rate). A sensitivity analysis of the model for herbaceous plants, deciduous and evergreen trees implies that elevated CO{sub 2} concentrations lead to lower allocation of nitrogen to carboxylation but higher allocation to storage. Higher growing-season temperatures cause lower allocation of nitrogen to carboxylation, due to higher nitrogen requirements for light capture pigments and for storage. Lower levels of radiation have a much stronger effect on allocation of nitrogen to carboxylation for herbaceous plants than for trees, resulting from higher nitrogen requirements for light capture for herbaceous plants. As far as we know, this is the first model of complete nitrogen allocation that simultaneously considers nitrogen allocation to light capture, electron transport, carboxylation, respiration and storage, and the responses of each to altered environmental conditions. We expect this model could potentially improve our confidence in simulations of carbon-nitrogen interactions

  8. Human endotoxemia: a model for mechanistic insight and therapeutic targeting.

    PubMed

    Lowry, Stephen F

    2005-12-01

    The diversity of phenotypic manifestations, comorbidities, and therapeutic algorithms in patients with severe inflammation have confounded efforts to translate mechanistic insights from the bench top to the bedside. This dilemma has negatively impacted upon many therapeutic interventions that exhibited seemingly well-reasoned preclinical portfolios. Prudence urges the assessment of potent immunoregulatory therapies, wherever possible, in models that replicate the clinical phenotype absent overt manifestations of genetically or environmentally modified processes. The healthy human model of endotoxin administration (systemic or endobronchial) provides such an opportunity and has been used to great advantage for gaining insight into mechanisms of disease and for determination of therapeutic signal strength. When thoughtfully interpreted, the model may provide proof of principle as well as lessen the unpredictability of clinical responses. Although the broad characteristics of this model are well described in the literature, it is recognized that this model does not fully replicate the magnitude of initial inflammatory stress nor the latent spectrum of inflammation/sepsis-inducible organ system pathologies. Nevertheless, the similarities between the early, transient clinical phenotype, inducible physiochemical change, and biochemical pathway activation of this model to the early hyperdynamic phase of resuscitated injury and infection are striking. Rational testing of a therapeutic mechanism requires a quantifiable and reproducibly altered marker of the hypothetical mechanism. Given the modest nature of endotoxin induced insult, interventions that demonstrate target specific efficacy in conjunction with attenuated phenotype responses are more likely to exhibit efficacy within lower risk patient populations. By contrast, the model cannot predict clinical efficacy among higher risk patients nor in those who have endured extended periods of inflammatory stress.

  9. Acyclovir-Polyethylene Glycol 6000 Binary Dispersions: Mechanistic Insights.

    PubMed

    Venkateskumar, Krishnamoorthy; Parasuraman, Subramani; Gunasunderi, Raju; Sureshkumar, Krishnan; Nayak, M Muralidhar; Shah, Syed Adnan Ali; Khoo, Khassen; Kai, Heng Wei

    2016-12-21

    The dissolution and subsequent oral bioavailability of acyclovir (ACY) is limited by its poor aqueous solubility. An attempt has been made in this work to provide mechanistic insights into the solubility enhancement and dissolution of ACY by using the water-soluble carrier polyethylene glycol 6000 (PEG6000). Solid dispersions with varying ratios of the drug (ACY) and carrier (PEG6000) were prepared and evaluated by phase solubility, in vitro release studies, kinetic analysis, in situ perfusion, and in vitro permeation studies. Solid state characterization was done by powder X-ray diffraction (XRD), differential scanning calorimetry (DSC), and Fourier transform infrared (FTIR) analysis, and surface morphology was assessed by polarizing microscopic image analysis, scanning electron microscopy, atomic force microscopy, and nuclear magnetic resonance analysis. Thermodynamic parameters indicated the solubilization effect of the carrier. The aqueous solubility and dissolution of ACY was found to be higher in all samples. The findings of XRD, DSC, FTIR and NMR analysis confirmed the formation of solid solution, crystallinity reduction, and the absence of interaction between the drug and carrier. SEM and AFM analysis reports ratified the particle size reduction and change in the surface morphology in samples. The permeation coefficient and amount of ACY diffused were higher in samples in comparison to pure ACY. Stability was found to be higher in dispersions. The results suggest that the study findings provided clear mechanical insights into the solubility and dissolution enhancement of ACY in PEG6000, and such findings could lay the platform for resolving the poor aqueous solubility issues in formulation development.

  10. Vitamins C and E: Beneficial effects from a mechanistic perspective

    PubMed Central

    Traber, Maret G.; Stevens, Jan F.

    2011-01-01

    The mechanistic properties of two dietary antioxidants that are required by humans, vitamins C and E, are discussed relative to their biological effects. Vitamin C (ascorbic acid) is an essential cofactor for α-ketoglutarate-dependent dioxygenases. Examples are prolyl hydroxylases, which play a role in the biosynthesis of collagen and in down-regulation of hypoxia-inducible factor (HIF)-1, a transcription factor that regulates many genes responsible for tumor growth, energy metabolism, and neutrophil function and apoptosis. Vitamin C-dependent inhibition of the HIF pathway may provide alternative or additional approaches for controlling tumor progression, infections and inflammation. Vitamin E (α-tocopherol) functions as an essential lipid soluble antioxidant, scavenging hydroperoxyl radicals in lipid milieu. Human symptoms of vitamin E deficiency suggest that its antioxidant properties play a major role in protecting erythrocyte membranes and nervous tissues. As an antioxidant, vitamin C provides protection against oxidative stress-induced cellular damage by scavenging of reactive oxygen species, vitamin E-dependent neutralization of lipid hydroperoxyl radicals, and by protecting proteins from alkylation by electrophilic lipid peroxidation products. These bioactivities bear relevance to inflammatory disorders. Vitamin C plays also a role in the function of endothelial nitric oxide synthase (eNOS) by recycling the eNOS cofactor, tetrahydrobiopterin, which is relevant to arterial elasticity and blood pressure regulation. Evidence from plants supports a role for vitamin C in the formation of covalent adducts with electrophilic secondary metabolites. Mechanism-based effects of vitamin C and E supplementation on biomarkers and on clinical outcomes from randomized, placebo-controlled trials are emphasized in this review. PMID:21664268

  11. Mechanistic basis of infertility of mouse intersubspecific hybrids

    PubMed Central

    Bhattacharyya, Tanmoy; Gregorova, Sona; Mihola, Ondrej; Anger, Martin; Sebestova, Jaroslava; Denny, Paul; Simecek, Petr; Forejt, Jiri

    2013-01-01

    According to the Dobzhansky–Muller model, hybrid sterility is a consequence of the independent evolution of related taxa resulting in incompatible genomic interactions of their hybrids. The model implies that the incompatibilities evolve randomly, unless a particular gene or nongenic sequence diverges much faster than the rest of the genome. Here we propose that asynapsis of heterospecific chromosomes in meiotic prophase provides a recurrently evolving trigger for the meiotic arrest of interspecific F1 hybrids. We observed extensive asynapsis of chromosomes and disturbance of the sex body in >95% of pachynemas of Mus m. musculus × Mus m. domesticus sterile F1 males. Asynapsis was not preceded by a failure of double-strand break induction, and the rate of meiotic crossing over was not affected in synapsed chromosomes. DNA double-strand break repair was delayed or failed in unsynapsed autosomes, and misexpression of chromosome X and chromosome Y genes was detected in single pachynemas and by genome-wide expression profiling. Oocytes of F1 hybrid females showed the same kind of synaptic problems but with the incidence reduced to half. Most of the oocytes with pachytene asynapsis were eliminated before birth. We propose the heterospecific pairing of homologous chromosomes as a preexisting condition of asynapsis in interspecific hybrids. The asynapsis may represent a universal mechanistic basis of F1 hybrid sterility manifested by pachytene arrest. It is tempting to speculate that a fast-evolving subset of the noncoding genomic sequence important for chromosome pairing and synapsis may be the culprit. PMID:23329330

  12. Metabolic diseases and pro- and prebiotics: Mechanistic insights.

    PubMed

    Nakamura, Yukiko K; Omaye, Stanley T

    2012-06-19

    Metabolic diseases, such as obesity and type 2 diabetes, are world-wide health problems. The prevalence of metabolic diseases is associated with dynamic changes in dietary macronutrient intake during the past decades. Based on national statistics and from a public health viewpoint, traditional approaches, such as diet and physical activity, have been unsuccessful in decreasing the prevalence of metabolic diseases. Since the approaches strongly rely on individual's behavior and motivation, novel science-based strategies should be considered for prevention and therapy for the diseases. Metabolism and immune system are linked. Both overnutrition and infection result in inflammation through nutrient and pathogen sensing systems which recognize compounds with structural similarities. Dietary macronutrients (fats and sugars) can induce inflammation through activation of an innate immune receptor, Toll-like receptor 4 (TLR4). Long-term intake of diets high in fats and meats appear to induce chronic systemic low-grade inflammation, endotoxicity, and metabolic diseases. Recent investigations support the idea of the involvement of intestinal bacteria in host metabolism and preventative and therapeutic potentials of probiotic and prebiotic interventions for metabolic diseases. Specific intestinal bacteria seem to serve as lipopolysaccharide (LPS) sources through LPS and/or bacterial translocation into the circulation due to a vulnerable microbial barrier and increased intestinal permeability and to play a role in systemic inflammation and progression of metabolic diseases. This review focuses on mechanistic links between metabolic diseases (mainly obesity and type 2 diabetes), chronic systemic low-grade inflammation, intestinal environment, and nutrition and prospective views of probiotic and prebiotic interventions for the diseases.

  13. The ecological impacts of nighttime light pollution: a mechanistic appraisal.

    PubMed

    Gaston, Kevin J; Bennie, Jonathan; Davies, Thomas W; Hopkins, John

    2013-11-01

    The ecological impacts of nighttime light pollution have been a longstanding source of concern, accentuated by realized and projected growth in electrical lighting. As human communities and lighting technologies develop, artificial light increasingly modifies natural light regimes by encroaching on dark refuges in space, in time, and across wavelengths. A wide variety of ecological implications of artificial light have been identified. However, the primary research to date is largely focused on the disruptive influence of nighttime light on higher vertebrates, and while comprehensive reviews have been compiled along taxonomic lines and within specific research domains, the subject is in need of synthesis within a common mechanistic framework. Here we propose such a framework that focuses on the cross-factoring of the ways in which artificial lighting alters natural light regimes (spatially, temporally, and spectrally), and the ways in which light influences biological systems, particularly the distinction between light as a resource and light as an information source. We review the evidence for each of the combinations of this cross-factoring. As artificial lighting alters natural patterns of light in space, time and across wavelengths, natural patterns of resource use and information flows may be disrupted, with downstream effects to the structure and function of ecosystems. This review highlights: (i) the potential influence of nighttime lighting at all levels of biological organisation (from cell to ecosystem); (ii) the significant impact that even low levels of nighttime light pollution can have; and (iii) the existence of major research gaps, particularly in terms of the impacts of light at population and ecosystem levels, identification of intensity thresholds, and the spatial extent of impacts in the vicinity of artificial lights.

  14. Mechanistic studies of ubiquitin C-terminal hydrolase L1.

    PubMed

    Case, April; Stein, Ross L

    2006-02-21

    Ubiquitin C-terminal hydrolases (UCHs) cleave Ub-X bonds (Ub is ubiquitin and X an alcohol, an amine, or a protein) through a thioester intermediate that is produced by nucleophilic attack of the Cys residue of a Cys-SH/His-Im catalytic diad. We are studying the mechanism of UCH-L1, a UCH that is implicated in Parkinson's disease, and now wish to report our initial findings. (i) Pre-steady-state kinetic studies for UCH-L1-catalyzed hydrolysis of Ub-AMC (AMC, 7-amido-4-methylcoumarin) indicate that k(cat) is rate-limited by acyl-enzyme formation. Thus, K(m) = K(s), the dissociation constant for the Michaelis complex, and k(cat) = k(2), the rate constant for acyl-enzyme formation. (ii) For K(assoc) (=K(s)(-)(1)), DeltaC(p) = -0.8 kcal mol(-)(1) deg(-)(1) and is consistent with coupling between substrate association and a conformational change of the enzyme. For k(2), DeltaS(++) = 0 and suggests that in the E-S, substrate and active site residues are precisely aligned for reaction. (iii) Solvent isotope effects are (D)K(assoc) = 0.5 and (D)k(2) = 0.9, suggesting that the substrate binds to a form of free enzyme in which the active site Cys exists as the thiol. In the resultant Michaelis complex, the diad has tautomerized to ion pair Cys-S(-)/His-ImH(+). Subsequent attack of thiolate produces the acyl-enzyme species. In contrast, isotope effects for association of UCH-L1 with transition-state analogue ubiquitin aldehyde suggest that an alternative mechanistic pathway can sometimes be available to UCH-L1 involving general base-catalyzed attack of Cys-SH by His-Im.

  15. Conceptualising population health: from mechanistic thinking to complexity science.

    PubMed

    Jayasinghe, Saroj

    2011-01-20

    The mechanistic interpretation of reality can be traced to the influential work by René Descartes and Sir Isaac Newton. Their theories were able to accurately predict most physical phenomena relating to motion, optics and gravity. This paradigm had at least three principles and approaches: reductionism, linearity and hierarchy. These ideas appear to have influenced social scientists and the discourse on population health. In contrast, Complexity Science takes a more holistic view of systems. It views natural systems as being 'open', with fuzzy borders, constantly adapting to cope with pressures from the environment. These are called Complex Adaptive Systems (CAS). The sub-systems within it lack stable hierarchies, and the roles of agency keep changing. The interactions with the environment and among sub-systems are non-linear interactions and lead to self-organisation and emergent properties. Theoretical frameworks such as epi+demos+cracy and the ecosocial approach to health have implicitly used some of these concepts of interacting dynamic sub-systems. Using Complexity Science we can view population health outcomes as an emergent property of CAS, which has numerous dynamic non-linear interactions among its interconnected sub-systems or agents. In order to appreciate these sub-systems and determinants, one should acquire a basic knowledge of diverse disciplines and interact with experts from different disciplines. Strategies to improve health should be multi-pronged, and take into account the diversity of actors, determinants and contexts. The dynamic nature of the system requires that the interventions are constantly monitored to provide early feedback to a flexible system that takes quick corrections.

  16. Mechanistic kinetic models of enzymatic cellulose hydrolysis-A review.

    PubMed

    Jeoh, Tina; Cardona, Maria J; Karuna, Nardrapee; Mudinoor, Akshata R; Nill, Jennifer

    2017-07-01

    Bioconversion of lignocellulose forms the basis for renewable, advanced biofuels, and bioproducts. Mechanisms of hydrolysis of cellulose by cellulases have been actively studied for nearly 70 years with significant gains in understanding of the cellulolytic enzymes. Yet, a full mechanistic understanding of the hydrolysis reaction has been elusive. We present a review to highlight new insights gained since the most recent comprehensive review of cellulose hydrolysis kinetic models by Bansal et al. (2009) Biotechnol Adv 27:833-848. Recent models have taken a two-pronged approach to tackle the challenge of modeling the complex heterogeneous reaction-an enzyme-centric modeling approach centered on the molecularity of the cellulase-cellulose interactions to examine rate limiting elementary steps and a substrate-centric modeling approach aimed at capturing the limiting property of the insoluble cellulose substrate. Collectively, modeling results suggest that at the molecular-scale, how rapidly cellulases can bind productively (complexation) and release from cellulose (decomplexation) is limiting, while the overall hydrolysis rate is largely insensitive to the catalytic rate constant. The surface area of the insoluble substrate and the degrees of polymerization of the cellulose molecules in the reaction both limit initial hydrolysis rates only. Neither enzyme-centric models nor substrate-centric models can consistently capture hydrolysis time course at extended reaction times. Thus, questions of the true reaction limiting factors at extended reaction times and the role of complexation and decomplexation in rate limitation remain unresolved. Biotechnol. Bioeng. 2017;114: 1369-1385. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. Metabolic diseases and pro- and prebiotics: Mechanistic insights

    PubMed Central

    2012-01-01

    Metabolic diseases, such as obesity and type 2 diabetes, are world-wide health problems. The prevalence of metabolic diseases is associated with dynamic changes in dietary macronutrient intake during the past decades. Based on national statistics and from a public health viewpoint, traditional approaches, such as diet and physical activity, have been unsuccessful in decreasing the prevalence of metabolic diseases. Since the approaches strongly rely on individual’s behavior and motivation, novel science-based strategies should be considered for prevention and therapy for the diseases. Metabolism and immune system are linked. Both overnutrition and infection result in inflammation through nutrient and pathogen sensing systems which recognize compounds with structural similarities. Dietary macronutrients (fats and sugars) can induce inflammation through activation of an innate immune receptor, Toll-like receptor 4 (TLR4). Long-term intake of diets high in fats and meats appear to induce chronic systemic low-grade inflammation, endotoxicity, and metabolic diseases. Recent investigations support the idea of the involvement of intestinal bacteria in host metabolism and preventative and therapeutic potentials of probiotic and prebiotic interventions for metabolic diseases. Specific intestinal bacteria seem to serve as lipopolysaccharide (LPS) sources through LPS and/or bacterial translocation into the circulation due to a vulnerable microbial barrier and increased intestinal permeability and to play a role in systemic inflammation and progression of metabolic diseases. This review focuses on mechanistic links between metabolic diseases (mainly obesity and type 2 diabetes), chronic systemic low-grade inflammation, intestinal environment, and nutrition and prospective views of probiotic and prebiotic interventions for the diseases. PMID:22713169

  18. Mechanistic Aspects of Hydration of Guanine Radical Cations in DNA

    PubMed Central

    2015-01-01

    The mechanistic aspects of hydration of guanine radical cations, G•+ in double- and single-stranded oligonucleotides were investigated by direct time-resolved spectroscopic monitoring methods. The G•+ radical one-electron oxidation products were generated by SO4•– radical anions derived from the photolysis of S2O82– anions by 308 nm laser pulses. In neutral aqueous solutions (pH 7.0), after the complete decay of SO4•– radicals (∼5 μs after the actinic laser flash) the transient absorbance of neutral guanine radicals, G(-H)• with maximum at 312 nm, is dominant. The kinetics of decay of G(-H)• radicals depend strongly on the DNA secondary structure. In double-stranded DNA, the G(-H)• decay is biphasic with one component decaying with a lifetime of ∼2.2 ms and the other with a lifetime of ∼0.18 s. By contrast, in single-stranded DNA the G(-H)• radicals decay monophasically with a ∼ 0.28 s lifetime. The ms decay component in double-stranded DNA is correlated with the enhancement of 8-oxo-7,8-dihydroguanine (8-oxoG) yields which are ∼7 greater than in single-stranded DNA. In double-stranded DNA, it is proposed that the G(-H)• radicals retain radical cation character by sharing the N1-proton with the N3-site of C in the [G•+:C] base pair. This [G(-H)•:H+C ⇆ G•+:C] equilibrium allows for the hydration of G•+ followed by formation of 8-oxoG. By contrast, in single-stranded DNA, deprotonation of G•+ and the irreversible escape of the proton into the aqueous phase competes more effectively with the hydration mechanism, thus diminishing the yield of 8-oxoG, as observed experimentally. PMID:24689701

  19. Mechanistic Investigation of Toxaphene Induced Mouse Liver Tumors.

    PubMed

    Wang, Zemin; Neal, Barbara H; Lamb, James C; Klaunig, James E

    2015-10-01

    Chronic exposure to toxaphene resulted in an increase in liver tumors in B6C3F1 mice. This study was performed to investigate the mode of action of toxaphene induced mouse liver tumors. Following an initial 14 day dietary dose range-finding study in male mice, a mechanistic study (0, 3, 32, and 320 ppm toxaphene in diet for 7, 14, and 28 days of treatment) was performed to examine the potential mechanisms of toxaphene induced mouse liver tumors. Toxaphene induced a significant increase in expression of constitutive androstane receptor (CAR) target genes (Cyp2b10, Cyp3a11) at 32 and 320 ppm toxaphene. aryl hydrocarbon receptor (AhR) target genes (Cyp1a1 and Cyp1a2) were slightly increased in expression at the highest toxaphene dose (320 ppm). No increase in peroxisome proliferator-activated receptor alpha activity or related genes was seen following toxaphene treatment. Lipid peroxidation was seen following treatment with 320 ppm toxaphene. These changes correlated with increases in hepatic DNA synthesis. To confirm the role of CAR in this mode of action, CAR knockout mice (CAR(-/-)) treated with toxaphene confirmed that the induction of CAR responsive genes seen in wild-type mice was abolished following treatment with toxaphene for 14 days. These findings, taken together with previously reported studies, support the mode of action of toxaphene induced mouse liver tumors is through a nongenotoxic mechanism involving primarily a CAR-mediated processes that results in an increase in cell proliferation in the liver, promotes the clonal expansion of preneoplastic lesions leading to adenoma formation.

  20. Toward a Mechanistic Modeling of Nitrogen Limitation on Vegetation Dynamics

    PubMed Central

    Xu, Chonggang; Fisher, Rosie; Wullschleger, Stan D.; Wilson, Cathy J.; Cai, Michael; McDowell, Nate G.

    2012-01-01

    Nitrogen is a dominant regulator of vegetation dynamics, net primary production, and terrestrial carbon cycles; however, most ecosystem models use a rather simplistic relationship between leaf nitrogen content and photosynthetic capacity. Such an approach does not consider how patterns of nitrogen allocation may change with differences in light intensity, growing-season temperature and CO2 concentration. To account for this known variability in nitrogen-photosynthesis relationships, we develop a mechanistic nitrogen allocation model based on a trade-off of nitrogen allocated between growth and storage, and an optimization of nitrogen allocated among light capture, electron transport, carboxylation, and respiration. The developed model is able to predict the acclimation of photosynthetic capacity to changes in CO2 concentration, temperature, and radiation when evaluated against published data of Vc,max (maximum carboxylation rate) and Jmax (maximum electron transport rate). A sensitivity analysis of the model for herbaceous plants, deciduous and evergreen trees implies that elevated CO2 concentrations lead to lower allocation of nitrogen to carboxylation but higher allocation to storage. Higher growing-season temperatures cause lower allocation of nitrogen to carboxylation, due to higher nitrogen requirements for light capture pigments and for storage. Lower levels of radiation have a much stronger effect on allocation of nitrogen to carboxylation for herbaceous plants than for trees, resulting from higher nitrogen requirements for light capture for herbaceous plants. As far as we know, this is the first model of complete nitrogen allocation that simultaneously considers nitrogen allocation to light capture, electron transport, carboxylation, respiration and storage, and the responses of each to altered environmental conditions. We expect this model could potentially improve our confidence in simulations of carbon-nitrogen interactions and the vegetation feedbacks

  1. Two Mechanistic Pathways for Thienopyridine-Associated Thrombotic Thrombocytopenic Purpura

    PubMed Central

    Bennett, Charles L.; Kim, Benjamin; Zakarija, Anaadriana; Bandarenko, Nicholas; Pandey, Dilip K.; Buffie, Charlie G.; McKoy, June M.; Tevar, Amul D.; Cursio, John F.; Yarnold, Paul R.; Kwaan, Hau C.; De Masi, Davide; Sarode, Ravindra; Raife, Thomas J.; Kiss, Joseph E.; Raisch, Dennis W.; Davidson, Charles; Sadler, J. Evan; Ortel, Thomas L.; Zheng, X. Long; Kato, Seiji; Matsumoto, Masanori; Uemura, Masahito; Fujimura, Yoshihiro

    2011-01-01

    Objectives We sought to describe clinical and laboratory findings for a large cohort of patients with thienopyridine-associated thrombotic thrombocytopenic purpura (TTP). Background The thienopyridine derivatives, ticlopidine and clopidogrel, are the 2 most common drugs associated with TTP in databases maintained by the U.S. Food and Drug Administration (FDA). Methods Clinical reports of TTP associated with clopidogrel and ticlopidine were identified from medical records, published case reports, and FDA case reports (n = 128). Duration of thienopyridine exposure, clinical and laboratory findings, and survival were recorded. ADAMTS13 activity (n = 39) and inhibitor (n = 30) were measured for a subset of individuals. Results Compared with clopidogrel-associated TTP cases (n = 35), ticlopidine-associated TTP cases (n = 93) were more likely to have received more than 2 weeks of drug (90% vs. 26%), to be severely thrombocytopenic (84% vs. 60%), and to have normal renal function (72% vs. 45%) (p < 0.01 for each). Compared with TTP patients with ADAMTS13 activity >15% (n = 13), TTP patients with severely deficient ADAMTS13 activity (n = 26) were more likely to have received ticlopidine (92.3% vs. 46.2%, p < 0.003). Among patients who developed TTP >2 weeks after thienopyridine, therapeutic plasma exchange (TPE) increased likelihood of survival (84% vs. 38%, p < 0.05). Among patients who developed TTP within 2 weeks of starting thienopyridines, survival was 77% with TPE and 78% without. Conclusions Thrombotic thrombocytopenic purpura is a rare complication of thienopyridine treatment. This drug toxicity appears to occur by 2 different mechanistic pathways, characterized primarily by time of onset before versus after 2 weeks of thienopyridine administration. If TTP occurs after 2 weeks of ticlopidine or clopidogrel therapy, therapeutic plasma exchange must be promptly instituted to enhance likelihood of survival. PMID:17868804

  2. Labor inhibits placental mechanistic target of rapamycin complex 1 signaling.

    PubMed

    Lager, S; Aye, I L M H; Gaccioli, F; Ramirez, V I; Jansson, T; Powell, T L

    2014-12-01

    Labor induces a myriad of changes in placental gene expression. These changes may represent a physiological adaptation inhibiting placental cellular processes associated with a high demand for oxygen and energy (e.g., protein synthesis and active transport) thereby promoting oxygen and glucose transfer to the fetus. We hypothesized that mechanistic target of rapamycin complex 1 (mTORC1) signaling, a positive regulator of trophoblast protein synthesis and amino acid transport, is inhibited by labor. Placental tissue was collected from healthy, term pregnancies (n = 15 no-labor; n = 12 labor). Activation of Caspase-1, IRS1/Akt, STAT, mTOR, and inflammatory signaling pathways was determined by Western blot. NFĸB p65 and PPARγ DNA binding activity was measured in isolated nuclei. Labor increased Caspase-1 activation and mTOR complex 2 signaling, as measured by phosphorylation of Akt (S473). However, mTORC1 signaling was inhibited in response to labor as evidenced by decreased phosphorylation of mTOR (S2448) and 4EBP1 (T37/46 and T70). Labor also decreased NFĸB and PPARγ DNA binding activity, while having no effect on IRS1 or STAT signaling pathway. Several placental signaling pathways are affected by labor, which has implications for experimental design in studies of placental signaling. Inhibition of placental mTORC1 signaling in response to labor may serve to down-regulate protein synthesis and amino acid transport, processes that account for a large share of placental oxygen and glucose consumption. We speculate that this response preserves glucose and oxygen for transfer to the fetus during the stressful events of labor. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Labor Inhibits Placental Mechanistic Target of Rapamycin Complex 1 Signaling

    PubMed Central

    LAGER, Susanne; AYE, Irving L.M.H.; GACCIOLI, Francesca; RAMIREZ, Vanessa I.; JANSSON, Thomas; POWELL, Theresa L.

    2014-01-01

    Introduction Labor induces a myriad of changes in placental gene expression. These changes may represent a physiological adaptation inhibiting placental cellular processes associated with a high demand for oxygen and energy (e.g., protein synthesis and active transport) thereby promoting oxygen and glucose transfer to the fetus. We hypothesized that mechanistic target of rapamycin complex 1 (mTORC1) signaling, a positive regulator of trophoblast protein synthesis and amino acid transport, is inhibited by labor. Methods Placental tissue was collected from healthy, term pregnancies (n=15 no-labor; n=12 labor). Activation of Caspase-1, IRS1/Akt, STAT, mTOR, and inflammatory signaling pathways was determined by Western blot. NFκB p65 and PPARγ DNA binding activity was measured in isolated nuclei. Results Labor increased Caspase-1 activation and mTOR complex 2 signaling, as measured by phosphorylation of Akt (S473). However, mTORC1 signaling was inhibited in response to labor as evidenced by decreased phosphorylation of mTOR (S2448) and 4EBP1 (T37/46 and T70). Labor also decreased NFκB and PPARγ DNA binding activity, while having no effect on IRS1 or STAT signaling pathway. Discussion and conclusion Several placental signaling pathways are affected by labor, which has implications for experimental design in studies of placental signaling. Inhibition of placental mTORC1 signaling in response to labor may serve to down-regulate protein synthesis and amino acid transport, processes that account for a large share of placental oxygen and glucose consumption. We speculate that this response preserves glucose and oxygen for transfer to the fetus during the stressful events of labor. PMID:25454472

  4. The attention schema theory: a mechanistic account of subjective awareness

    PubMed Central

    Graziano, Michael S. A.; Webb, Taylor W.

    2015-01-01

    We recently proposed the attention schema theory, a novel way to explain the brain basis of subjective awareness in a mechanistic and scientifically testable manner. The theory begins with attention, the process by which signals compete for the brain’s limited computing resources. This internal signal competition is partly under a bottom–up influence and partly under top–down control. We propose that the top–down control of attention is improved when the brain has access to a simplified model of attention itself. The brain therefore constructs a schematic model of the process of attention, the ‘attention schema,’ in much the same way that it constructs a schematic model of the body, the ‘body schema.’ The content of this internal model leads a brain to conclude that it has a subjective experience. One advantage of this theory is that it explains how awareness and attention can sometimes become dissociated; the brain’s internal models are never perfect, and sometimes a model becomes dissociated from the object being modeled. A second advantage of this theory is that it explains how we can be aware of both internal and external events. The brain can apply attention to many types of information including external sensory information and internal information about emotions and cognitive states. If awareness is a model of attention, then this model should pertain to the same domains of information to which attention pertains. A third advantage of this theory is that it provides testable predictions. If awareness is the internal model of attention, used to help control attention, then without awareness, attention should still be possible but should suffer deficits in control. In this article, we review the existing literature on the relationship between attention and awareness, and suggest that at least some of the predictions of the theory are borne out by the evidence. PMID:25954242

  5. Mechanistic Insights into Homogeneous and Heterogeneous Asymmetric Iron Catalysis

    NASA Astrophysics Data System (ADS)

    Sonnenberg, Jessica

    Our group has been focused on replacing toxic and expensive precious metal catalysts with iron for the synthesis of enantiopure compounds for industrial applications. During an investigation into the mechanism of asymmetric transfer hydrogenation with our first generation iron-(P-N-N-P) catalysts we found substantial evidence for zero-valent iron nanoparticles coated in chiral ligand acting as the active site. Extensive experimental and computational experiments were undertaken which included NMR, DFT, reaction profile analysis, substoichiometric poisoning, electron microscope imaging, XPS and multiphasic analysis, all of which supported the fact that NPs were the active species in catalysis. Reversibility of this asymmetric reaction on the nanoparticle surface was then probed using oxidative kinetic resolution of racemic alcohols, yielding modest enantiopurity and high turnover frequencies (TOF) for a range of aromatic alcohols. Efficient dehydrogenation of ammonia-borane for hydrogen evolution and the formation of B-N oligomers was also shown using the NP system, yielding highly active systems, with a maximum TOF of 3.66 H2/s-1 . We have also begun to focus on the development of iron catalysts for asymmetric direct hydrogenation of ketones using hydrogen gas. New chiral iron-(P-N-P) catalysts were developed and shown to be quite active and selective for a wide range of substrates. Mechanistic investigations primarily using NMR and DFT indicated that a highly active trans-dihydride species was being formed during catalyst activation. Lastly, a new library of chiral P-N-P and P-NH-P ligands were developed, as well as their corresponding iron complexes, some of which show promise for the development of future generations of active asymmetric direct hydrogenation catalysts.

  6. Tightly Coupled Mechanistic Study of Materials in the Extreme Space Environment

    DTIC Science & Technology

    2016-10-11

    AFRL-AFOSR-VA-TR-2016-0338 Tightly Coupled Mechanistic Study of Materials in the Extreme Space Environment Adrianus Van Duin PENNSYLVANIA STATE...To)      01 Jul 2011 to 30 Jun 2016 4.  TITLE AND SUBTITLE Tightly Coupled Mechanistic Study of Materials in the Extreme Space Environment 5a...Public Release 13.  SUPPLEMENTARY NOTES 14.  ABSTRACT The Tightly Coupled Mechanistic Study of Materials in the Extreme Space Environment Group has worked

  7. EDITORIAL: Atomic layer deposition Atomic layer deposition

    NASA Astrophysics Data System (ADS)

    Godlewski, Marek

    2012-07-01

    The growth method of atomic layer deposition (ALD) was introduced in Finland by Suntola under the name of atomic layer epitaxy (ALE). The method was originally used for deposition of thin films of sulphides (ZnS, CaS, SrS) activated with manganese or rare-earth ions. Such films were grown for applications in thin-film electroluminescence (TFEL) displays. The ALE mode of growth was also tested in the case of molecular beam epitaxy. Films grown by ALD are commonly polycrystalline or even amorphous. Thus, the name ALE has been replaced by ALD. In the 80s ALD was developed mostly in Finland and neighboring Baltic countries. Deposition of a range of different materials was demonstrated at that time, including II-VI semiconductors (e.g. CdTe, CdS) and III-V (e.g. GaAs, GaN), with possible applications in e.g. photovoltaics. The number of publications on ALD was slowly increasing, approaching about 100 each year. A real boom in interest came with the development of deposition methods of thin films of high-k dielectrics. This research was motivated by a high leakage current in field-effect transistors with SiO2-based gate dielectrics. In 2007 Intel introduced a new generation of integrated circuits (ICs) with thin films of HfO2 used as gate isolating layers. In these and subsequent ICs, films of HfO2 are deposited by the ALD method. This is due to their unique properties. The introduction of ALD to the electronics industry led to a booming interest in the ALD growth method, with the number of publications increasing rapidly to well above 1000 each year. A number of new applications were proposed, as reflected in this special issue of Semiconductor Science and Technology. The included articles cover a wide range of possible applications—in microelectronics, transparent electronics, optoelectronics, photovoltaics and spintronics. Research papers and reviews on the basics of ALD growth are also included, reflecting a growing interest in precursor chemistry and growth

  8. Automatic Payroll Deposit System.

    ERIC Educational Resources Information Center

    Davidson, D. B.

    1979-01-01

    The Automatic Payroll Deposit System in Yakima, Washington's Public School District No. 7, directly transmits each employee's salary amount for each pay period to a bank or other financial institution. (Author/MLF)

  9. Chemical vapor deposition growth

    NASA Technical Reports Server (NTRS)

    Ruth, R. P.; Manasevit, H. M.; Kenty, J. L.; Moudy, L. A.; Simpson, W. I.; Yang, J. J.

    1976-01-01

    A chemical vapor deposition (CVD) reactor system with a vertical deposition chamber was used for the growth of Si films on glass, glass-ceramic, and polycrystalline ceramic substrates. Silicon vapor was produced by pyrolysis of SiH4 in a H2 or He carrier gas. Preliminary deposition experiments with two of the available glasses were not encouraging. Moderately encouraging results, however, were obtained with fired polycrystalline alumina substrates, which were used for Si deposition at temperatures above 1,000 C. The surfaces of both the substrates and the films were characterized by X-ray diffraction, reflection electron diffraction, scanning electron microscopy optical microscopy, and surface profilometric techniques. Several experiments were conducted to establish baseline performance data for the reactor system, including temperature distributions on the sample pedestal, effects of carrier gas flow rate on temperature and film thickness, and Si film growth rate as a function of temperature.

  10. World oil shale deposits

    SciTech Connect

    Hook, C.O.; Russell, P.L.

    1982-01-01

    The article estimates resources in-place and their oil equivalent. The major deposits are described in the U.S., Australia, USSR, Peoples Republic of China, Morocco, Israel, Jordan, Syria, Europe and South America. 2 refs.

  11. Colorful Polar Layered Deposits

    NASA Image and Video Library

    2016-03-23

    The North Polar layered deposits provide a record of recent climate changes on Mars as seen by NASA Mars Reconnaissance Orbiter spacecraft. Color variations between layers are due to differences in composition of the dust.

  12. Vapor Deposition Rig

    NASA Image and Video Library

    2015-01-27

    The Plasma Spray-Physical Vapor Deposition (PS-PVD) Rig at NASA Glenn Research Center. The rig helps develop coatings for next-generation aircraft turbine components and create more efficient engines.

  13. Electrospark deposition coatings

    NASA Astrophysics Data System (ADS)

    Sheely, W. F.

    1986-11-01

    Hard surfacing for wear resistant and low-friction coatings has been improved by means of advances in the computer controls in electronic circuitry of the electrospark deposition (ESD) process. coatings of nearly any electrically conductive metal alloy or cermet can be deposited on conductive materials. Thickness is usually two mils or less, but can be as high as 10 mils. ESD coatings can quadrupole cutting tool life.

  14. Electrospark deposition coatings

    SciTech Connect

    Sheely, W.F.

    1986-11-19

    Hard surfacing for wear resistant and low-friction coatings has been improved by means of advances in the computer controls in electronic circuitry of the electrospark deposition (ESD) process. coatings of nearly any electrically conductive metal alloy or cermet can be deposited on conductive materials. Thickness is usually two mils or less, but can be as high as 10 mils. ESD coatings can quadrupole cutting tool life. (DLC)

  15. Use of Gene Expression Changes in Blood to Elucidate Mechanistic Indicators of Childhood Asthma (MICA)

    EPA Science Inventory

    Risk assessment increasingly relies more heavily on mode of action, thus the identification of human bioindicators of disease becomes all the more important. Genomic methods represent a tool for both mode of action determination and bioindicator identification. The Mechanistic In...

  16. UTILITY OF MECHANISTIC MODELS FOR DIRECTING ADVANCED SEPARATIONS RESEARCH & DEVELOPMENT ACTIVITIES: Electrochemically Modulated Separation Example

    SciTech Connect

    Schwantes, Jon M.

    2009-06-01

    The objective for this work was to demonstrate the utility of mechanistic computer models designed to simulate actinide behavior for use in efficiently and effectively directing advanced laboratory R&D activities associated with developing advanced separations methods.

  17. ASSESSING POPULATION EXPOSURES TO MULTIPLE AIR POLLUTANTS USING A MECHANISTIC SOURCE-TO-DOSE MODELING FRAMEWORK

    EPA Science Inventory

    The Modeling Environment for Total Risks studies (MENTOR) system, combined with an extension of the SHEDS (Stochastic Human Exposure and Dose Simulation) methodology, provide a mechanistically consistent framework for conducting source-to-dose exposure assessments of multiple pol...

  18. ASSESSING POPULATION EXPOSURES TO MULTIPLE AIR POLLUTANTS USING A MECHANISTIC SOURCE-TO-DOSE MODELING FRAMEWORK

    EPA Science Inventory

    The Modeling Environment for Total Risks studies (MENTOR) system, combined with an extension of the SHEDS (Stochastic Human Exposure and Dose Simulation) methodology, provide a mechanistically consistent framework for conducting source-to-dose exposure assessments of multiple pol...

  19. Dose-response relationships and extrapolation in toxicology - Mechanistic and statistical considerations

    EPA Science Inventory

    Controversy on toxicological dose-response relationships and low-dose extrapolation of respective risks is often the consequence of misleading data presentation, lack of differentiation between types of response variables, and diverging mechanistic interpretation. In this chapter...

  20. Dose-response relationships and extrapolation in toxicology - Mechanistic and statistical considerations

    EPA Science Inventory

    Controversy on toxicological dose-response relationships and low-dose extrapolation of respective risks is often the consequence of misleading data presentation, lack of differentiation between types of response variables, and diverging mechanistic interpretation. In this chapter...

  1. Gemstone deposits of Serbia

    NASA Astrophysics Data System (ADS)

    Miladinović, Zoran; Simić, Vladimir; Jelenković, Rade; Ilić, Miloje

    2016-06-01

    Gemstone minerals in Serbia have never been regarded as an interesting and significant resource. Nevertheless, more than 150 deposits and occurrences have been recorded and some of them preliminarily explored in the last 50 years. The majority of deposits and occurrences are located within the Serbo-Macedonian metallogenic province and the most significant metallogenic units at the existing level of knowledge are the Fruska Gora ore district, Cer ore district, Sumadija metallogenic zone, Kopaonik metallogenic zone and Lece-Halkidiki metallogenic zone. The most important genetic type of deposits is hydrothermal, particularly in case of serpentinite/peridotite as host/parent rock. Placer deposits are also economically important. The dominant gemstones are silica minerals: chalcedony (Chrysoprase, carnelian, bluish chalcedony etc.), jasper (picture, landscape, red etc.), common opal (dendritic, green, milky white etc.), silica masses (undivided), and quartz (rock crystal, amethyst etc.). Beside silica minerals significant gemstones in Serbia include also beryl (aquamarine), garnet (almandine and pyrope), tourmaline, fluorite, rhodochrosite, carbonate-silica breccia, carbonate-silica onyx, silicified wood, howlite, serpentinite, marble onyx, and kyanite. This paper aims to present an overview of Serbian gemstone deposits and occurrences and their position based on a simplified gemstone metallogenic map of Serbia, as well as genetic-industrial classification of gemstone deposits and gemstone varieties.

  2. Clinical and Mechanistic Drivers of Acute Traumatic Coagulopathy

    PubMed Central

    Cohen, Mitchell Jay; Kutcher, Matt; Redick, Britt; Nelson, Mary; Call, Mariah; Knudson, M Margaret; Schreiber, Martin A; Bulger, Eileen M; Muskat, Peter; Alarcon, Louis H; Myers, John G; Rahbar, Mohammad H; Brasel, Karen J; Phelan, Herb A; del Junco, Deborah J; Fox, Erin E; Wade, Charles E; Holcomb, John B; Cotton, Bryan A; Matijevic, Nena

    2013-01-01

    Background Acute Traumatic Coagulopathy (ATC) occurs after severe injury and shock and is associated with increased bleeding, morbidity and mortality. The effects of ATC and hemostatic resuscitation on outcome are not well-explored. The PRospective Observational Multicenter Major Trauma Transfusion (PROMMTT) study provided a unique opportunity to characterize coagulation and the effects of resuscitation on ATC after severe trauma. Methods Blood samples were collected upon arrival on a subset of PROMMTT patients. Plasma clotting factor levels were prospectively assayed for coagulation factors. These data were analyzed with comprehensive PROMMTT clinical data. Results There were 1198 patients with laboratory results of whom 41.6% were coagulopathic. Using International Normalized Ratio (INR)≥1.3, 41.6% (448) of patients were coagulopathic while 20.5% (214) were coagulopathic using partial thromboplastin time (PTT)≥35. Coagulopathy was primarily associated with a combination of an ISS>15 and a BD<−6 (P<.05). Regression modeling for INR-based coagulopathy shows that pre-hospital crystalloid (odds ratio (OR)=1.05), Injury Severity Score (ISS, OR=1.03), Glasgow Coma Scale (OR=0.93), heart rate (OR=1.08), systolic blood pressure (OR=0.96), base deficit (BD, OR=0.92) and temperature (OR=0.84) were significant predictors of coagulopathy (all P<.03). A subset of 165 patients had blood samples collected and coagulation factor analysis performed. Elevated ISS and BD were associated with elevation of aPC and depletion of factors (all P<.05). Reductions in factors I, II, V, VIII and an increase in aPC drive ATC (all p<.04). Similar results were found for PTT-defined coagulopathy. Conclusions ATC is associated with depletion of factors I, II, V, VII, VIII, IX and X and is driven by the activation of the protein C system. These data provide additional mechanistic understanding of the drivers of coagulation abnormalities after injury. Further understanding of the drivers of

  3. Mechanistic, Mutational, and Structural Evaluation of a Taxus Phenylalanine Aminomutase

    SciTech Connect

    Feng, Lei; Wanninayake, Udayanga; Strom, Susan; Geiger, James; Walker, Kevin D.

    2014-10-02

    The structure of a phenylalanine aminomutase (TcPAM) from Taxus canadensis has been determined at 2.4 {angstrom} resolution. The active site of the TcPAM contains the signature 4-methylidene-1H-imidazol-5(4H)-one prosthesis, observed in all catalysts of the class I lyase-like family. This catalyst isomerizes (S)-{alpha}-phenylalanine to the (R)-{beta}-isomer by exchange of the NH{sub 2}/H pair. The stereochemistry of the TcPAM reaction product is opposite of the (S)-{beta}-tyrosine made by the mechanistically related tyrosine aminomutase (SgTAM) from Streptomyces globisporus. Since TcPAM and SgTAM share similar tertiary- and quaternary-structures and have several highly conserved aliphatic residues positioned analogously in their active sites for substrate recognition, the divergent product stereochemistries of these catalysts likely cannot be explained by differences in active site architecture. The active site of the TcPAM structure also is in complex with (E)-cinnamate; the latter functions as both a substrate and an intermediate. To account for the distinct (3R)-{beta}-amino acid stereochemistry catalyzed by TcPAM, the cinnamate skeleton must rotate the C{sub 1}-C{sub {alpha}} and C{sub ipso}-C{sub {beta}} bonds 180{sup o} in the active site prior to exchange and rebinding of the NH{sub 2}/H pair to the cinnamate, an event that is not required for the corresponding acrylate intermediate in the SgTAM reaction. Moreover, the aromatic ring of the intermediate makes only one direct hydrophobic interaction with Leu-104. A L104A mutant of TcPAM demonstrated an 1.5-fold increase in k{sub cat} and a decrease in K{sub M} values for sterically demanding 3'-methyl-{alpha}-phenylalanine and styryl-{alpha}-alanine substrates, compared to the kinetic parameters for TcPAM. These parameters did not change significantly for the mutant with 4'-methyl-{alpha}-phenylalanine compared to those for TcPAM.

  4. Mechanistic, mutational, and structural evaluation of a Taxus phenylalanine aminomutase.

    PubMed

    Feng, Lei; Wanninayake, Udayanga; Strom, Susan; Geiger, James; Walker, Kevin D

    2011-04-12

    The structure of a phenylalanine aminomutase (TcPAM) from Taxus canadensis has been determined at 2.4 Å resolution. The active site of the TcPAM contains the signature 4-methylidene-1H-imidazol-5(4H)-one prosthesis, observed in all catalysts of the class I lyase-like family. This catalyst isomerizes (S)-α-phenylalanine to the (R)-β-isomer by exchange of the NH2/H pair. The stereochemistry of the TcPAM reaction product is opposite of the (S)-β-tyrosine made by the mechanistically related tyrosine aminomutase (SgTAM) from Streptomyces globisporus. Since TcPAM and SgTAM share similar tertiary- and quaternary-structures and have several highly conserved aliphatic residues positioned analogously in their active sites for substrate recognition, the divergent product stereochemistries of these catalysts likely cannot be explained by differences in active site architecture. The active site of the TcPAM structure also is in complex with (E)-cinnamate; the latter functions as both a substrate and an intermediate. To account for the distinct (3R)-β-amino acid stereochemistry catalyzed by TcPAM, the cinnamate skeleton must rotate the C1-Cα and Cipso-Cβ bonds 180° in the active site prior to exchange and rebinding of the NH2/H pair to the cinnamate, an event that is not required for the corresponding acrylate intermediate in the SgTAM reaction. Moreover, the aromatic ring of the intermediate makes only one direct hydrophobic interaction with Leu-104. A L104A mutant of TcPAM demonstrated an ∼1.5-fold increase in kcat and a decrease in KM values for sterically demanding 3'-methyl-α-phenylalanine and styryl-α-alanine substrates, compared to the kinetic parameters for TcPAM. These parameters did not change significantly for the mutant with 4'-methyl-α-phenylalanine compared to those for TcPAM.

  5. Clinical and mechanistic drivers of acute traumatic coagulopathy.

    PubMed

    Cohen, Mitchell Jay; Kutcher, Matt; Redick, Britt; Nelson, Mary; Call, Mariah; Knudson, M Margaret; Schreiber, Martin A; Bulger, Eileen M; Muskat, Peter; Alarcon, Louis H; Myers, John G; Rahbar, Mohammad H; Brasel, Karen J; Phelan, Herb A; del Junco, Deborah J; Fox, Erin E; Wade, Charles E; Holcomb, John B; Cotton, Bryan A; Matijevic, Nena

    2013-07-01

    Acute traumatic coagulopathy (ATC) occurs after severe injury and shock and is associated with increased bleeding, morbidity, and mortality. The effects of ATC and hemostatic resuscitation on outcome are not well-explored. The PRospective Observational Multicenter Major Trauma Transfusion (PROMMTT) study provided a unique opportunity to characterize coagulation and the effects of resuscitation on ATC after severe trauma. Blood samples were collected upon arrival on a subset of PROMMTT patients. Plasma clotting factor levels were prospectively assayed for coagulation factors. These data were analyzed with comprehensive PROMMTT clinical data. There were 1,198 patients with laboratory results, of whom 41.6% were coagulopathic. Using international normalized ratio of 1.3 or greater, 41.6% of patients (448) were coagulopathic, while 20.5% (214) were coagulopathic using partial thromboplastin time of 35 or greater. Coagulopathy was primarily associated with a combination of an Injury Severity Score (ISS) of greater than 15 and a base deficit (BD) of less than -6 (p < 0.05). Regression modeling for international normalized ratio-based coagulopathy shows that prehospital crystalloid (odds ratio [OR], 1.05), ISS (OR, 1.03), Glasgow Coma Scale (GCS) score (OR, 0.93), heart rate (OR, 1.08), systolic blood pressure (OR, 0.96), BD (OR, 0.92), and temperature (OR, 0.84) were significant predictors of coagulopathy (all p < 0.03). A subset of 165 patients had blood samples collected and coagulation factor analysis performed. Elevated ISS and BD were associated with elevation of aPC and depletion of factors (all p < 0.05). Reductions in factors I, II, V, VIII and an increase in aPC drive ATC (all p < 0.04). Similar results were found for partial thromboplastin time-defined coagulopathy. ATC is associated with the depletion of factors I, II, V, VII, VIII, IX, and X and is driven by the activation of the protein C system. These data provide additional mechanistic understanding of the

  6. Toward a mechanistic modeling of nitrogen limitation for photosynthesis

    NASA Astrophysics Data System (ADS)

    Xu, C.; Fisher, R. A.; Travis, B. J.; Wilson, C. J.; McDowell, N. G.

    2011-12-01

    The nitrogen limitation is an important regulator for vegetation growth and global carbon cycle. Most current ecosystem process models simulate nitrogen effects on photosynthesis based on a prescribed relationship between leaf nitrogen and photosynthesis; however, there is a large amount of variability in this relationship with different light, temperature, nitrogen availability and CO2 conditions, which can affect the reliability of photosynthesis prediction under future climate conditions. To account for the variability in nitrogen-photosynthesis relationship under different environmental conditions, in this study, we developed a mechanistic model of nitrogen limitation for photosynthesis based on nitrogen trade-offs among light absorption, electron transport, carboxylization and carbon sink. Our model shows that strategies of nitrogen storage allocation as determined by tradeoff among growth and persistence is a key factor contributing to the variability in relationship between leaf nitrogen and photosynthesis. Nitrogen fertilization substantially increases the proportion of nitrogen in storage for coniferous trees but much less for deciduous trees, suggesting that coniferous trees allocate more nitrogen toward persistence compared to deciduous trees. The CO2 fertilization will cause lower nitrogen allocation for carboxylization but higher nitrogen allocation for storage, which leads to a weaker relationship between leaf nitrogen and maximum photosynthesis rate. Lower radiation will cause higher nitrogen allocation for light absorption and electron transport but less nitrogen allocation for carboxylyzation and storage, which also leads to weaker relationship between leaf nitrogen and maximum photosynthesis rate. At the same time, lower growing temperature will cause higher nitrogen allocation for carboxylyzation but lower allocation for light absorption, electron transport and storage, which leads to a stronger relationship between leaf nitrogen and maximum

  7. Mechanistic aspects of hydration of guanine radical cations in DNA.

    PubMed

    Rokhlenko, Yekaterina; Cadet, Jean; Geacintov, Nicholas E; Shafirovich, Vladimir

    2014-04-23

    The mechanistic aspects of hydration of guanine radical cations, G(•+) in double- and single-stranded oligonucleotides were investigated by direct time-resolved spectroscopic monitoring methods. The G(•+) radical one-electron oxidation products were generated by SO4(•-) radical anions derived from the photolysis of S2O8(2-) anions by 308 nm laser pulses. In neutral aqueous solutions (pH 7.0), after the complete decay of SO4(•-) radicals (∼5 μs after the actinic laser flash) the transient absorbance of neutral guanine radicals, G(-H)(•) with maximum at 312 nm, is dominant. The kinetics of decay of G(-H)(•) radicals depend strongly on the DNA secondary structure. In double-stranded DNA, the G(-H)(•) decay is biphasic with one component decaying with a lifetime of ∼2.2 ms and the other with a lifetime of ∼0.18 s. By contrast, in single-stranded DNA the G(-H)(•) radicals decay monophasically with a ∼ 0.28 s lifetime. The ms decay component in double-stranded DNA is correlated with the enhancement of 8-oxo-7,8-dihydroguanine (8-oxoG) yields which are ∼7 greater than in single-stranded DNA. In double-stranded DNA, it is proposed that the G(-H)(•) radicals retain radical cation character by sharing the N1-proton with the N3-site of C in the [G(•+):C] base pair. This [G(-H)(•):H(+)C ⇆ G(•+):C] equilibrium allows for the hydration of G(•+) followed by formation of 8-oxoG. By contrast, in single-stranded DNA, deprotonation of G(•+) and the irreversible escape of the proton into the aqueous phase competes more effectively with the hydration mechanism, thus diminishing the yield of 8-oxoG, as observed experimentally.

  8. Mechanistically Distinct Mouse Models for CRX-Associated Retinopathy

    PubMed Central

    Tran, Nicholas M.; Zhang, Alan; Zhang, Xiaodong; Huecker, Julie B.; Hennig, Anne K.; Chen, Shiming

    2014-01-01

    Cone-rod homeobox (CRX) protein is a “paired-like” homeodomain transcription factor that is essential for regulating rod and cone photoreceptor transcription. Mutations in human CRX are associated with the dominant retinopathies Retinitis Pigmentosa (RP), Cone-Rod Dystrophy (CoRD) and Leber Congenital Amaurosis (LCA), with variable severity. Heterozygous Crx Knock-Out (KO) mice (“+/−”) have normal vision as adults and fail to model the dominant human disease. To investigate how different mutant CRX proteins produce distinct disease pathologies, we generated two Crx Knock-IN (K-IN) mouse models: CrxE168d2 (“E168d2”) and CrxR90W (“R90W”). E168d2 mice carry a frameshift mutation in the CRX activation domain, Glu168del2, which is associated with severe dominant CoRD or LCA in humans. R90W mice carry a substitution mutation in the CRX homeodomain, Arg90Trp, which is associated with dominant mild late-onset CoRD and recessive LCA. As seen in human patients, heterozygous E168d2 (“E168d2/+”) but not R90W (“R90W/+”) mice show severely impaired retinal function, while mice homozygous for either mutation are blind and undergo rapid photoreceptor degeneration. E168d2/+ mice also display abnormal rod/cone morphology, greater impairment of CRX target gene expression than R90W/+ or +/− mice, and undergo progressive photoreceptor degeneration. Surprisingly, E168d2/+ mice express more mutant CRX protein than wild-type CRX. E168d2neo/+, a subline of E168d2 with reduced mutant allele expression, displays a much milder retinal phenotype, demonstrating the impact of Crx expression level on disease severity. Both CRX[E168d2] and CRX[R90W] proteins fail to activate transcription in vitro, but CRX[E168d2] interferes more strongly with the function of wild type (WT) CRX, supporting an antimorphic mechanism. E168d2 and R90W are mechanistically distinct mouse models for CRX-associated disease that will allow the elucidation of molecular mechanisms and testing of

  9. Mechanistic simulation of the vertical soil organic matter profile

    NASA Astrophysics Data System (ADS)

    Braakhekke, M.; Beer, C.; Reichstein, M.; Hoosbeek, M.; Kruijt, B.; Kabat, P.

    2013-12-01

    Soil organic matter (SOM) constitutes a large global pool of carbon that may play a considerable role for future climate. The vertical distribution of SOM in the profile may be important due to depth-dependence of physical, chemical, and biological conditions, and links to physical processes such as heat and moisture transport. The aim of this thesis is to develop a dynamic and mechanistic representation of the vertical SOM profile that can be applied for large scale simulations as a part of global ecosystem and earth system models. A model structure called SOMPROF was developed that dynamically simulates the SOM profile based on above and below ground litter input, decomposition, bioturbation, and liquid phase transport. Furthermore, three organic surface horizons are explicitly represented. Since the organic matter transport processes have been poorly quantified in the past and are difficult to observe directly, the model was calibrated with a Bayesian approach for two contrasting temperate forest sites in Europe. Different types of data were included in the parameter estimation, including: organic carbon stocks and concentrations, respiration rates, and excess lead-210 activity. The calibrations yielded good fits to the observations, and showed that the two sites differ considerably with respect to the relevance of the different processes. These differences agree well with expectations based on local conditions. However, the results also demonstrate the difficulties arising from convolution of the processes. Several parameters are poorly constrained and for one of the sites, several distinct regions in parameter space exist that yield acceptable fit. In a subsequent study it was found that radiocarbon observations can offer much additional constraint on several parameters, most importantly on the turnover rate of the slowest SOM fraction. Additionally, for one site, a prognostic simulation until 2100 was performed using the resulting a posteriori parameter

  10. Mechanistic modeling of turkey growth response to genotype and nutrition.

    PubMed

    Rivera-Torres, V; Ferket, P R; Sauvant, D

    2011-10-01

    Along with the fast genetic improvement, nutritional and environmental effects on poultry growth performance have made it necessary to develop growth models that have the flexibility to adapt to different genotypes and growing conditions. A mechanistic simulation model of energy and nutrient utilization in growing turkeys is presented herein. The model consists of simulating the average homeorhetic and homeostatic regulations associated with the utilization of circulating glucose, fatty acid, AA, and acetyl-CoA for protein and lipid retention in carcass, viscera, and feathers in a turkey population. Homeorhesis plays a major role in the control of protein and lipid turnover for the definition of genetic potential and feed intake, whereas homeostasis adjusts growth rate through protein and lipid turnover rates and, therefore, BW gain and feed intake to the growing conditions. Also, homeostasis enables the maintenance of a dynamic balance state during all the growing period through the control of circulating nutrient concentration. The model was developed and calibrated with experimental data that described energy utilization in male and female growing turkeys. Then, the ability of the model to adapt to genotypes and to predict the average response of a turkey population to dietary energy was evaluated. Model calibration showed simulations of energy and nutrient utilization that fitted well with the experimental data because ME was satisfyingly partitioned into heat production and energy retention as protein and lipid, and nutrient intake accurately partitioned BW gain into carcass, viscera, and feathers. The evaluation of the model was also satisfactory because BW gain and feed-to-gain ratio were globally in accordance with the observations in different male and female genotypes, in spite of an overestimation of the feed-to-gain ratio during the first weeks of age. Model evaluation showed that the BW gain and feed intake response of growing turkeys to dietary energy

  11. Mechanistic species distribution modelling as a link between physiology and conservation

    PubMed Central

    Evans, Tyler G.; Diamond, Sarah E.; Kelly, Morgan W.

    2015-01-01

    Climate change conservation planning relies heavily on correlative species distribution models that estimate future areas of occupancy based on environmental conditions encountered in present-day ranges. The approach benefits from rapid assessment of vulnerability over a large number of organisms, but can have poor predictive power when transposed to novel environments and reveals little in the way of causal mechanisms that define changes in species distribution or abundance. Having conservation planning rely largely on this single approach also increases the risk of policy failure. Mechanistic models that are parameterized with physiological information are expected to be more robust when extrapolating distributions to future environmental conditions and can identify physiological processes that set range boundaries. Implementation of mechanistic species distribution models requires knowledge of how environmental change influences physiological performance, and because this information is currently restricted to a comparatively small number of well-studied organisms, use of mechanistic modelling in the context of climate change conservation is limited. In this review, we propose that the need to develop mechanistic models that incorporate physiological data presents an opportunity for physiologists to contribute more directly to climate change conservation and advance the field of conservation physiology. We begin by describing the prevalence of species distribution modelling in climate change conservation, highlighting the benefits and drawbacks of both mechanistic and correlative approaches. Next, we emphasize the need to expand mechanistic models and discuss potential metrics of physiological performance suitable for integration into mechanistic models. We conclude by summarizing other factors, such as the need to consider demography, limiting broader application of mechanistic models in climate change conservation. Ideally, modellers, physiologists and

  12. Mechanistic species distribution modelling as a link between physiology and conservation.

    PubMed

    Evans, Tyler G; Diamond, Sarah E; Kelly, Morgan W

    2015-01-01

    Climate change conservation planning relies heavily on correlative species distribution models that estimate future areas of occupancy based on environmental conditions encountered in present-day ranges. The approach benefits from rapid assessment of vulnerability over a large number of organisms, but can have poor predictive power when transposed to novel environments and reveals little in the way of causal mechanisms that define changes in species distribution or abundance. Having conservation planning rely largely on this single approach also increases the risk of policy failure. Mechanistic models that are parameterized with physiological information are expected to be more robust when extrapolating distributions to future environmental conditions and can identify physiological processes that set range boundaries. Implementation of mechanistic species distribution models requires knowledge of how environmental change influences physiological performance, and because this information is currently restricted to a comparatively small number of well-studied organisms, use of mechanistic modelling in the context of climate change conservation is limited. In this review, we propose that the need to develop mechanistic models that incorporate physiological data presents an opportunity for physiologists to contribute more directly to climate change conservation and advance the field of conservation physiology. We begin by describing the prevalence of species distribution modelling in climate change conservation, highlighting the benefits and drawbacks of both mechanistic and correlative approaches. Next, we emphasize the need to expand mechanistic models and discuss potential metrics of physiological performance suitable for integration into mechanistic models. We conclude by summarizing other factors, such as the need to consider demography, limiting broader application of mechanistic models in climate change conservation. Ideally, modellers, physiologists and

  13. Unraveling molecular mechanistic differences in liver metabolism between lean and fat lines of Pekin duck (Anas platyrhynchos domestica): a proteomic study.

    PubMed

    Zheng, Aijuan; Chang, Wenhuan; Hou, Shuisheng; Zhang, Shu; Cai, Huiyi; Chen, Guilan; Lou, Ruiying; Liu, Guohua

    2014-02-26

    Duck is one of the major poultry meat sources for human consumption. To satisfy different eating habits, lean and fat strains of Pekin ducks have been developed. The objective of this study was to determine the molecular mechanistic differences in liver metabolism between two duck strains. The liver proteome of the Pekin duck lines was compared on days 1, 14, 28, and 42 posthatching using 2-DE based proteomics. There was a different abundance of 76 proteins in the livers of the two duck lines. Fat ducks strongly expressed proteins related to pathways of glycolysis, ATP synthesis, and protein catabolism, suggesting enhanced fat deposition rather than protein retention. In contrast, highly expressed proteins in lean ducks improved protein anabolism and reduced protein catabolism, resulting in an enhancement of lean meat deposition. Along with the decrease in fat deposition, the immune system of the lean duck strain may be enhanced by enhanced expression of proteins involved in stress response, immune defense, and antioxidant functions. These results indicate that selection pressure has shaped the two duck lines differently resulting in different liver metabolic capacities. These observed variations between the two strains at the molecular level are matched with physiological changes in growth performance and meat production. This information may have beneficial impacts in areas such as genetic modification through the manipulation of target proteins or genes in specific pathways to improve the efficiency of duck meat production. The objective of this study was to unravel molecular mechanistic differences in liver metabolism between lean and fat Pekin duck (Anas platyrhynchos domestica) strains. There was a different abundance of 76 proteins in the livers of the two duck lines. Enhanced protein expression in the fat ducks related to pathways of glycolysis, ATP synthesis and protein catabolism suggesting increased fat deposition rather than protein retention. In

  14. Becquerel Crater Deposit

    NASA Technical Reports Server (NTRS)

    2002-01-01

    (Released 28 May 2002) The finely layered deposit in Becquerel crater, seen in the center of this THEMIS image, is slowly being eroded away by the action of windblown sand. Dark sand from a source north of the bright deposit is collecting along its northern edge, forming impressive barchan style dunes. These vaguely boomerang-shaped dunes form with their two points extending in the downwind direction, demonstrating that the winds capable of moving sand grains come from the north. Grains that leave the dunes climb the eroding stair-stepped layers, collecting along the cliff faces before reaching the crest of the deposit. Once there, the sand grains are unimpeded and continue down the south side of the deposit without any significant accumulation until they fall off the steep cliffs of the southern margin. The boat-hull shaped mounds and ridges of bright material called yardangs form in response to the scouring action of the migrating sand. To the west, the deposit has thinned enough that the barchan dunes extend well into the deeply eroded north-south trending canyons. Sand that reaches the south side collects and reforms barchan dunes with the same orientation as those on the north side of the deposit. Note the abrupt transition between the bright material and the dark crater floor on the southern margin. Steep cliffs are present with no indication of rubble from the obvious erosion that produced them. The lack of debris at the base of the cliffs is evidence that the bright material is readily broken up into particles that can be transported away by the wind. The geological processes that are destroying the Becquerel crater deposit appear active today. But it is also possible that they are dormant, awaiting a particular set of climatic conditions that produces the right winds and perhaps even temperatures to allow the erosion to continue.

  15. Mechanistic model for the leaching of retorted rundle oil shale

    SciTech Connect

    Krol, A.A.; Bell, P.R.F.; Greenfield, P.F.

    1985-12-09

    The mechanisms involved in the leaching of inorganic components from oil shale mined at the Rundle deposit, Queensland, Australia, and retorted by the Lurgi-Ruhrgas process were examined. The phenomena of most significance were found to be solute dissolution, cation exchange, solution speciation and hydrodynamic and unsaturated flow effects. To check on the completeness of this characterization, a model was developed which describes the generation and transport of the major components (Ca, Mg, Na, K, Cl and SO/sub 4/) in the leachate as it infiltrates a column of dry retorted shale. Model predictions compare well with experimental results. It is concluded that the dominant mechanisms which control the rate of leaching have been recognized. 8 references, 11 figures.

  16. Oxide Deposition By PECVD

    NASA Astrophysics Data System (ADS)

    Ibbotson, Dale E.; Hsieh, Julian J.; Flamm, Daniel L.; Mucha, J. A.

    1989-03-01

    We have studied the chemical and physical properties of silicon oxide films plasma deposited from TEOS (tetraethoxysilane), to gain an understanding of the origins of (1) step coverage and (2) film stability. TEOS was diluted in helium/oxygen mixtures and deposited as a function of discharge frequency (150 kHz and 14 MHz) and 02 flow in a parallel plate reactor. The typical deposition conditions were 1 torr total pressure, 320°C substrate temperature, 1 -9% TEOS, 1 -80% 02, and -0.1 W/cm2 discharge power. Films deposited at high frequency with excess oxygen were generally oxygen-rich, chemically unstable and hygroscopic, while films deposited at low frequency were stable to moisture and slightly deficient in oxygen. However, coverage profiles of high frequency films showed an unusual degree of directionality, which could be used to advantage for the coating of high aspect ratio features. We suggest that a judicious combination of high and low frequency discharges may improve film properties while maintaining directional step coverage. Isotopic labeling experiments were performed using 1802 to gain insight into the origins of the oxygen that is contained in these PECVD films. Complete isotopic scrambling was not observed. Film composition data suggest that there is one tenacious Si-0 bond which remains with the silicon from the original TEOS molecule during the reaction to form Si02.

  17. Pulsed laser deposition: Prospects for commercial deposition of epitaxial films

    SciTech Connect

    Muenchausen, R.E.

    1999-03-01

    Pulsed laser deposition (PLD) is a physical vapor deposition (PVD) technique for the deposition of thin films. The vapor source is induced by the flash evaporation that occurs when a laser pulse of sufficient intensity (about 100 MW/cm{sup 2}) is absorbed by a target. In this paper the author briefly defines pulsed laser deposition, current applications, research directed at gaining a better understanding of the pulsed laser deposition process, and suggests some future directions to enable commercial applications.

  18. Mechanistically Driven Development of Iridium Catalysts for Asymmetric Allylic Substitution

    PubMed Central

    Hartwig, John F.; Stanley, Levi M.

    2010-01-01

    , with high branched-to-linear ratios and high enantioselectivities. Parallel mechanistic studies had revealed the metallacyclic structure of the active catalyst, and subsequent experiments with the purposefully formed metallacycle increased the reaction scope dramatically. Aromatic amines, azoles, ammonia, and amides and carbamates as ammonia equivalents all reacted with high selectivities and yields. Moreover, weakly basic enolates (such as silyl enol ethers) and enolate equivalents (such as enamines) also reacted, and other research groups have used this catalyst to conduct reactions of stabilized carbon nucleophiles in the absence of additional base. One hallmark of the reactions catalyzed by this iridium system is the invariably high enantioselectivity, which reflects a high stereoselectivity for formation of the allyl intermediate. Enantioselectivity typically exceeds 95%, regioselectivity for formation of branched over linear products is usually near 20:1, and yields generally exceed 75% and are often greater than 90%. Thus, the development of iridium catalysts for enantioselective allylic substitution shows how studies of reaction mechanism can lead to a particularly active and a remarkably general system for an enantioselective process. In this case, a readily accessible catalyst effects allylic substitution, with high enantioselectivity and regioselectivity complementary to that of the venerable palladium systems. PMID:20873839

  19. Anodic Cyclization Reactions and the Mechanistic Strategies That Enable Optimization.

    PubMed

    Feng, Ruozhu; Smith, Jake A; Moeller, Kevin D

    2017-09-19

    Oxidation reactions are powerful tools for synthesis because they allow us to reverse the polarity of electron-rich functional groups, generate highly reactive intermediates, and increase the functionality of molecules. For this reason, oxidation reactions have been and continue to be the subject of intense study. Central to these efforts is the development of mechanism-based strategies that allow us to think about the reactive intermediates that are frequently central to the success of the reactions and the mechanistic pathways that those intermediates trigger. For example, consider oxidative cyclization reactions that are triggered by the removal of an electron from an electron-rich olefin and lead to cyclic products that are functionalized for further elaboration. For these reactions to be successful, the radical cation intermediate must first be generated using conditions that limit its polymerization and then channeled down a productive desired pathway. Following the cyclization, a second oxidation step is necessary for product formation, after which the resulting cation must be quenched in a controlled fashion to avoid undesired elimination reactions. Problems can arise at any one or all of these steps, a fact that frequently complicates reaction optimization and can discourage the development of new transformations. Fortunately, anodic electrochemistry offers an outstanding opportunity to systematically probe the mechanism of oxidative cyclization reactions. The use of electrochemical methods allows for the generation of radical cations under neutral conditions in an environment that helps prevent polymerization of the intermediate. Once the intermediates have been generated, a series of "telltale indicators" can be used to diagnose which step in an oxidative cyclization is problematic for less successful transformation. A set of potential solutions to address each type of problem encountered has been developed. For example, problems with the initial

  20. Turbine Airfoil Deposition Models

    NASA Technical Reports Server (NTRS)

    Rosner, D. E.

    1984-01-01

    Gas turbine failures associated with sea-salt ingestion and sulfur-containing fuel impurities have directed attention to alkali sulfate deposition and the associated hot corrosion of gas turbine (GT) blades under some GT operating conditions. These salt deposits form thin, molten films which undermine the protective metal oxide coating normally found on GT blades. The prediction of molten salt deposition, flow and oxide dissolution, and their effects on the lifetime of turbine blades are examined. Goals include rationalizing and helping to predict corrosion patterns on operational GT rotor blades and stators, and ultimately providing some of the tools required to design laboratory simulators and future corrosion-resistant high-performance engines. Necessary background developments are reviewed first, and then recent results and tentative conclusions are presented along with a brief account of the present research plans.

  1. Venus - Landslide Deposits

    NASA Technical Reports Server (NTRS)

    1992-01-01

    The Magellan spacecraft has observed remnant landslide deposits apparently resulting from the collapse of volcanic structures. This image, centered at 45.2 degrees south latitude, 201.4 degrees east longitude, shows a collapse deposit 70 kilometers (43 miles) across. The bright, highly textured deposit near the center of the image probably consists of huge blocks of fractured volcanic rock, many as large as several hundred meters across. A remnant of the volcano itself, about 20 kilometers (12.4 miles) across, is seen at the center of the image. The distorted radar appearance of the volcano is a result of extremely steep slopes on the 'scars' from which the landslide material originated. A field of numerous small volcanic domes can be seen in the northern half of the image. The bright irregular lineaments trending to the north-northwest are ridges caused by regional tectonic deformation of the upper layers of the Venusian crust.

  2. Modelling airborne concentration and deposition rate of maize pollen

    NASA Astrophysics Data System (ADS)

    Jarosz, Nathalie; Loubet, Benjamin; Huber, Laurent

    2004-10-01

    The introduction of genetically modified (GM) crops has reinforced the need to quantify gene flow from crop to crop. This requires predictive tools which take into account meteorological conditions, canopy structure as well as pollen aerodynamic characteristics. A Lagrangian Stochastic (LS) model, called SMOP-2D (Stochastic Mechanistic model for Pollen dispersion and deposition in 2 Dimensions), is presented. It simulates wind dispersion of pollen by calculating individual pollen trajectories from their emission to their deposition. SMOP-2D was validated using two field experiments where airborne concentration and deposition rate of pollen were measured within and downwind from different sized maize (Zea mays) plots together with micrometeorological measurements. SMOP-2D correctly simulated the shapes of the concentration profiles but generally underestimated the deposition rates in the first 10 m downwind from the source. Potential explanations of this discrepancy are discussed. Incorrect parameterisation of turbulence in the transition from the crop to the surroundings is probably the most likely reason. This demonstrates that LS models for particle transfer need to be coupled with air-flow models under complex terrain conditions.

  3. Using a Mechanistic Reactive Transport Model to Represent Soil Organic Matter Dynamics and Climate Sensitivity

    NASA Astrophysics Data System (ADS)

    Guerry, N.; Riley, W. J.; Maggi, F.; Torn, M. S.; Kleber, M.

    2011-12-01

    The nature of long term Soil Organic Matter (SOM) dynamics is uncertain and the mechanisms involved are crudely represented in site, regional, and global models. Recent work challenging the paradigm that SOM is stabilized because of its sequential transformations to more intrinsically recalcitrant compounds motivated us to develop a mechanistic modeling framework that can be used to test hypotheses of SOM dynamics. We developed our C cycling model in TOUGHREACT, an established 3-dimensional reactive transport solver that accounts for multiple phases (aqueous, gaseous, sorbed), multiple species, advection and diffusion, and multiple microbial populations. Energy and mass exchange through the soil boundaries are accounted for via ground heat flux, rainfall, C sources (e.g., exudation, woody, leaf, root litter) and C losses (e.g., CO2 emissions and DOC deep percolation). SOM is categorized according to the various types of compounds commonly found in the above mentioned C sources and microbial byproducts, including poly- and monosaccharides, lignin, amino compounds, organic acids, nucleic acids, lipids, and phenols. Each of these compounds is accounted for by one or more representative species in the model. A reaction network was developed to describe the microbially-mediated processes and chemical interactions of these species, including depolymerization, microbial assimilation, respiration and deposition of byproducts, and incorporation of dead biomass into SOM stocks. Enzymatic reactions are characterized by Michaelis-Menten kinetics, with maximum reaction rates determined by the species' O/C ratio. Microbial activity is further regulated by soil moisture content, O2 availability, pH, and temperature. For the initial set of simulations, literature values were used to constrain microbial Monod parameters, Michaelis-Menten parameters, sorption parameters, physical protection, partitioning of microbial byproducts, and partitioning of litter inputs, although there is

  4. The sirtuin pathway in ageing and Alzheimer disease: mechanistic and therapeutic considerations.

    PubMed

    Bonda, David J; Lee, Hyoung-Gon; Camins, Antoni; Pallàs, Mercè; Casadesus, Gemma; Smith, Mark A; Zhu, Xiongwei

    2011-03-01

    Advances in gerontology have yielded crucial insights into the molecular and biochemical aspects of the ageing process. The sirtuin pathway, which is most notable for its association with the anti-ageing effects of calorie restriction, has received particular attention, and pharmacological or transgenic upregulation of the sirtuin pathway has shown promising results in laboratory models of ageing. Alzheimer's disease is a neurodegenerative disease that is imposing an increasing burden on society, and is the leading cause of senile dementia worldwide. The lack of therapies for Alzheimer's disease provides a strong incentive for the development of an effective treatment strategy and, interestingly, research has uncovered a mechanism of action of the sirtuin pathway that might have therapeutic potential for Alzheimer's disease. SIRT1, one of the seven mammalian proteins of the sirtuin family of NAD(+)-dependent deacetylases, has recently been shown to attenuate amyloidogenic processing of amyloid-β protein precursor (APP) in cell culture studies in vitro and in transgenic mouse models of Alzheimer's disease. Mechanistically, SIRT1 increases α-secretase production and activity through activation of the α-secretase gene ADAM10. Because α-secretase is the enzyme responsible for the non-amyloidogenic cleavage of APP, upregulation of α-secretase shifts APP processing to reduce the pathological accumulation of the presumptive toxic Aβ species that results from β-secretase and γ-secretase activity. Interestingly, the spatial patterns of Aβ deposition in the brain might correlate with increased aerobic glycolysis in those regions. Because aerobic glycolysis depletes cellular levels of NAD(+) (through a decreased NAD(+)/NADH ratio), it is possible that a corresponding downregulation of the NAD(+)-dependent sirtuin pathway contributes to the amyloidogenic processing of APP. WHERE NEXT?: The specific inhibition of Aβ generation by SIRT1 coupled with the potential link

  5. DEPOSITION AND EMISSION OF GASEOUS MERCURY TO AND FROM LAKE MICHIGAN DURING THE LAKE MICHIGAN MASS BALANCE STUDY (JULY, 1994 - OCTOBER, 1995)

    EPA Science Inventory

    This paper presents measurements of dissolved gaseous mercury (DGM) concentrations in Lake Michigan and the application of a mechanistic approach to estimate deposition and emission fluxes of gaseous mercury (Hg2+ and Hg0) to and from Lake Michigan. Measurements of DGM concentr...

  6. DEPOSITION AND EMISSION OF GASEOUS MERCURY TO AND FROM LAKE MICHIGAN DURING THE LAKE MICHIGAN MASS BALANCE STUDY (JULY, 1994 - OCTOBER, 1995)

    EPA Science Inventory

    This paper presents measurements of dissolved gaseous mercury (DGM) concentrations in Lake Michigan and the application of a mechanistic approach to estimate deposition and emission fluxes of gaseous mercury (Hg2+ and Hg0) to and from Lake Michigan. Measurements of DGM concentr...

  7. Laser assisted deposition

    NASA Technical Reports Server (NTRS)

    Dutta, S.

    1983-01-01

    Applications of laser-based processing techniques to solar cell metallization are discussed. Laser-assisted thermal or photolytic maskless deposition from organometallic vapors or solutions may provide a viable alternative to photovoltaic metallization systems currently in use. High power, defocused excimer lasers may be used in conjunction with masks as an alternative to direct laser writing to provide higher throughput. Repeated pulsing with excimer lasers may eliminate the need for secondary plating techniques for metal film buildup. A comparison between the thermal and photochemical deposition processes is made.

  8. Reactive polymer fused deposition manufacturing

    DOEpatents

    Kunc, Vlastimil; Rios, Orlando; Love, Lonnie J.; Duty, Chad E.; Johs, Alexander

    2017-05-16

    Methods and compositions for additive manufacturing that include reactive or thermosetting polymers, such as urethanes and epoxies. The polymers are melted, partially cross-linked prior to the depositing, deposited to form a component object, solidified, and fully cross-linked. These polymers form networks of chemical bonds that span the deposited layers. Application of a directional electromagnetic field can be applied to aromatic polymers after deposition to align the polymers for improved bonding between the deposited layers.

  9. "Total Deposition (TDEP) Maps"

    EPA Science Inventory

    The presentation provides an update on the use of a hybrid methodology that relies on measured values from national monitoring networks and modeled values from CMAQ to produce of maps of total deposition for use in critical loads and other ecological assessments. Additionally, c...

  10. Melas Chasma Deposits

    NASA Image and Video Library

    2003-01-09

    Erosion of the interior layered deposits of Melas Chasma, part of the huge Valles Marineris canyon system, has produced cliffs with examples of spur and gulley morphology and exposures of finely layered sediments, as seen in this NASA Mars Odyssey image.

  11. "Total Deposition (TDEP) Maps"

    EPA Science Inventory

    The presentation provides an update on the use of a hybrid methodology that relies on measured values from national monitoring networks and modeled values from CMAQ to produce of maps of total deposition for use in critical loads and other ecological assessments. Additionally, c...

  12. Chapter 5: Acid deposition

    Treesearch

    Cliff F. Hunt; Warren E. Heilman

    1999-01-01

    This publication provides information about the atmospheric conditions in and near the national forest in the Ozark-Ouachita Highlands: the Mark Twain in Missouri, the Ouachita in Arkansas and Oklahoma, and the Ozark and St. Francis in Arkansas. This report includes information about particulate matter, visibility, ozone concentrations, and acid deposition in the Ozark...

  13. Volcanogenic Massive Sulfide Deposit Density

    USGS Publications Warehouse

    Mosier, Dan L.; Singer, Donald A.; Berger, Vladimir I.

    2007-01-01

    A mineral-deposit density model for volcanogenic massive sulfide deposits was constructed from 38 well-explored control areas from around the world. Control areas contain at least one exposed volcanogenic massive sulfide deposit. The control areas used in this study contain 150 kuroko, 14 Urals, and 25 Cyprus massive sulfide subtypes of volcanogenic massive sulfide deposits. For each control area, extent of permissive rock, number of exposed volcanogenic massive sulfide deposits, map scale, deposit age, and deposit density were determined. The frequency distribution of deposit densities in these 38 control areas provides probabilistic estimates of the number of deposits for tracts that are permissive for volcanogenic massive sulfide deposits-90 percent of the control areas have densities of 100 or more deposits per 100,000 square kilometers, 50 percent of the control areas have densities of 700 or more deposits per 100,000 square kilometers, and 10 percent of the control areas have densities of 3,700 or more deposits per 100,000 square kilometers. Both map scale and the size of the control area are shown to be predictors of deposit density. Probabilistic estimates of the number of volcanogenic massive sulfide deposits can be made by conditioning the estimates on sizes of permissive area. The model constructed for this study provides a powerful tool for estimating the number of undiscovered volcanogenic massive sulfide deposits when conducting resource assessments. The value of these deposit densities is due to the consistency of these models with the grade and tonnage and the descriptive models. Mineral-deposit density models combined with grade and tonnage models allow reasonable estimates of the number, size, and grades of volcanogenic massive sulfide deposits to be made.

  14. 157 nm Pellicles (Thin Films) for Photolithography: Mechanistic Investigation of the VUV and UV-C Photolysis of Fluorocarbons

    SciTech Connect

    Lee, Kwangjoo; Jockusch, Steffen; Turro, Nicholas J.; French, Roger H.; Wheland, Robert C.; Lemon, M F.; Braun, Andre M.; Widerschpan, Tatjana; Dixon, David A.; Li, Jun; Ivan, Marius; Zimmerman, Paul

    2005-06-15

    The use of 157 nm as the next lower wavelength for photolithography for the production of semiconductors has created a need for transparent and radiation-durable polymers for use in soft pellicles, the polymer films which protect the chip from particle deposition. The most promising materials for pellicles are fluorinated polymers, but currently available fluorinated polymers undergo photodegradation and/or photodarkening upon long term exposure to 157 nm irradiation. To understand the mechanism of the photodegradation and photodarkening of fluorinated polymers, mechanistic studies on the photolysis of liquid model fluorocarbons, including perfluorobutylethyl ether and perfluoro-2 H-3-oxa-heptane, were performed employing UV, NMR, FTIR, GC, and GC/MS analyses. All hydrogen-containing compounds showed decreased photostability compared to the fully perfluorinated compounds. Irradiation in the presence of atmospheric oxygen showed reduced photostability compared to deoxygenated samples. Photolysis of the samples was performed at 157, 172, 185, and 254 nm and showed only minor wavelength dependence. Mechanisms for photodegradation of the fluorocarbons are proposed, which involve Rydberg excited states. Time-dependent density functional theory has been used to predict the excitation spectra of model compounds.

  15. Mechanistic platform knowledge of concomitant sugar uptake in Escherichia coli BL21(DE3) strains

    PubMed Central

    Wurm, David J.; Hausjell, Johanna; Ulonska, Sophia; Herwig, Christoph; Spadiut, Oliver

    2017-01-01

    When producing recombinant proteins, the use of Escherichia coli strain BL21(DE3) in combination with the T7-based pET-expression system is often the method of choice. In a recent study we introduced a mechanistic model describing the correlation of the specific glucose uptake rate (qs,glu) and the corresponding maximum specific lactose uptake rate (qs,lac,max) for a pET-based E. coli BL21(DE3) strain producing a single chain variable fragment (scFv). We showed the effect of qs,lac,max on productivity and product location underlining its importance for recombinant protein production. In the present study we investigated the mechanistic qs,glu/qs,lac,max correlation for four pET-based E. coli BL21(DE3) strains producing different recombinant products and thereby proved the mechanistic model to be platform knowledge for E. coli BL21(DE3). However, we found that the model parameters strongly depended on the recombinant product. Driven by this observation we tested different dynamic bioprocess strategies to allow a faster investigation of this mechanistic correlation. In fact, we succeeded and propose an experimental strategy comprising only one batch cultivation, one fed-batch cultivation as well as one dynamic experiment, to reliably determine the mechanistic model for qs,glu/qs,lac,max and get trustworthy model parameters for pET-based E. coli BL21(DE3) strains which are the basis for bioprocess development. PMID:28332595

  16. Putting the psychology back into psychological models: mechanistic versus rational approaches.

    PubMed

    Sakamoto, Yasuaki; Jones, Mattr; Love, Bradley C

    2008-09-01

    Two basic approaches to explaining the nature of the mind are the rational and the mechanistic approaches. Rational analyses attempt to characterize the environment and the behavioral outcomes that humans seek to optimize, whereas mechanistic models attempt to simulate human behavior using processes and representations analogous to those used by humans. We compared these approaches with regard to their accounts of how humans learn the variability of categories. The mechanistic model departs in subtle ways from rational principles. In particular, the mechanistic model incrementally updates its estimates of category means and variances through error-driven learning, based on discrepancies between new category members and the current representation of each category. The model yields a prediction, which we verify, regarding the effects of order manipulations that the rational approach does not anticipate. Although both rational and mechanistic models can successfully postdict known findings, we suggest that psychological advances are driven primarily by consideration of process and representation and that rational accounts trail these breakthroughs.

  17. Trouvelot Crater Deposit

    NASA Technical Reports Server (NTRS)

    2002-01-01

    [figure removed for brevity, see original site]

    Like many of the craters in the Oxia Palus region of Mars, Trouvelot Crater hosts an eroded, light-toned, sedimentary deposit on its floor. Compared with the much larger example in Becquerel Crater to the NE, the Trouvelot deposit has been so eroded by the scouring action of dark, wind-blown sand that very little of it remains. Tiny outliers of bright material separated from the main mass attest to the once, more really extensive coverage by the deposit. A similar observation can be made for White Rock, the best known example of a bright, crater interior deposit. The origin of the sediments in these deposits remains enigmatic but they are likely the result of fallout from ash or dust carried by the thin martian atmosphere.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  18. "Elementary, My Dear Deposit..."

    NASA Image and Video Library

    2017-06-28

    In this image, NASA's Mars Reconnaissance Orbiter (MRO) observes an impact crater with associated bright deposits that at first glance give the appearance of seasonal frost or ice accumulations. MRO has an onboard spectrometer called CRISM that can distinguish between ices and other minerals. Unfortunately, there is currently no coverage of this particular spot. However, it can be deduced through several lines of evidence that this is, in fact, not ice. Just like Earth, Mars experiences seasons that change as the planet orbits the Sun. Seasonal changes are most apparent at the higher latitudes. As these regions in each hemisphere enter their respective summer seasons, the Sun rises higher in the Martian sky causing frost and ice to sublimate, and illuminate more features across the landscape. As the high latitudes of each hemisphere move toward their respective winters, the days (called "sols") grow shorter and the sun hangs low on the horizon, giving rise to prolonged periods of cold, darkness, and frost accumulation. First, it should be noted that at the time this image was taken, the Southern hemisphere is at the end of the summer season, so any frost or ice deposits have long since sublimated away. Second, numerous HiRISE images of seasonal targets show that ice accumulates on pole-facing slopes. The deposits in question are situated on a slope that faces the equator, and would not accumulate deposits of frost. Thus, it can be concluded that these exposures are light-toned mineral deposits. https://photojournal.jpl.nasa.gov/catalog/PIA21766

  19. Computer-assisted mechanistic structure-activity studies: application to diverse classes of chemical carcinogens.

    PubMed Central

    Loew, G H; Poulsen, M; Kirkjian, E; Ferrell, J; Sudhindra, B S; Rebagliati, M

    1985-01-01

    In the first part of this paper we have indicated how the techniques and capabilities of theoretical chemistry, together with experimental results, can be used in a mechanistic approach to structure-activity studies of toxicity. In the second part, we have illustrated how this computer-assisted approach has been used to identify and calculate causally related molecular indicators of relative carcinogenic activity in five classes of chemical carcinogens: polycyclic aromatic hydrocarbons and their methyl derivatives, aromatic amines, chloroethanes, chloroalkenes and dialkyl nitrosamines. In each class of chemicals studied, candidate molecular indicators have been identified that could be useful in predictive screening of unknown compounds. In addition, further insights into some mechanistic aspects of chemical carcinogenesis have been obtained. Finally, experiments have been suggested to both verify the usefulness of the indicators and test their mechanistic implications. PMID:3905382

  20. Real-time forecasting of infectious disease dynamics with a stochastic semi-mechanistic model.

    PubMed

    Funk, Sebastian; Camacho, Anton; Kucharski, Adam J; Eggo, Rosalind M; Edmunds, W John

    2016-12-16

    Real-time forecasts of infectious diseases can help public health planning, especially during outbreaks. If forecasts are generated from mechanistic models, they can be further used to target resources or to compare the impact of possible interventions. However, paremeterising such models is often difficult in real time, when information on behavioural changes, interventions and routes of transmission are not readily available. Here, we present a semi-mechanistic model of infectious disease dynamics that was used in real time during the 2013-2016 West African Ebola epidemic, and show fits to a Ebola Forecasting Challenge conducted in late 2015 with simulated data mimicking the true epidemic. We assess the performance of the model in different situations and identify strengths and shortcomings of our approach. Models such as the one presented here which combine the power of mechanistic models with the flexibility to include uncertainty about the precise outbreak dynamics may be an important tool in combating future outbreaks.

  1. Applying math onto mechanisms: mechanistic knowledge is associated with the use of formal mathematical strategies.

    PubMed

    Liu, Allison S; Schunn, Christian D

    2017-01-01

    It is notoriously difficult for people to adaptively apply formal mathematical strategies learned in school to real-world contexts, even when they possess the required mathematical skills. The current study explores whether a problem context's mechanism can act as an "embodied analogy" onto which abstract mathematical concepts can be applied, leading to more frequent use of formal mathematical strategies. Participants were asked to program a robot to navigate a maze and to create a navigation strategy that would work for differently sized robots. We compared the strategy complexity of participants with high levels of mechanistic knowledge about the robot against participants with low levels of mechanistic knowledge about the robot. Mechanistic knowledge was significantly associated with the frequency and complexity of the mathematical strategies used by participants, suggesting that learning to recognize a problem context's mechanism may promote independent mathematical problem solving in applied contexts.

  2. Measurement, geospatial, and mechanistic models of public health hazard vulnerability and jurisdictional risk.

    PubMed

    Testa, Marcia A; Pettigrew, Mary L; Savoia, Elena

    2014-01-01

    County and state health departments are increasingly conducting hazard vulnerability and jurisdictional risk (HVJR) assessments for public health emergency preparedness and mitigation planning and evaluation to improve the public health disaster response; however, integration and adoption of these assessments into practice are still relatively rare. While the quantitative methods associated with complex analytic and measurement methods, causal inference, and decision theory are common in public health research, they have not been widely used in public health preparedness and mitigation planning. To address this gap, the Harvard School of Public Health PERLC's goal was to develop measurement, geospatial, and mechanistic models to aid public health practitioners in understanding the complexity of HVJR assessment and to determine the feasibility of using these methods for dynamic and predictive HVJR analyses. We used systematic reviews, causal inference theory, structural equation modeling (SEM), and multivariate statistical methods to develop the conceptual and mechanistic HVJR models. Geospatial mapping was used to inform the hypothetical mechanistic model by visually examining the variability and patterns associated with county-level demographic, social, economic, hazards, and resource data. A simulation algorithm was developed for testing the feasibility of using SEM estimation. The conceptual model identified the predictive latent variables used in public health HVJR tools (hazard, vulnerability, and resilience), the outcomes (human, physical, and economic losses), and the corresponding measurement subcomponents. This model was translated into a hypothetical mechanistic model to explore and evaluate causal and measurement pathways. To test the feasibility of SEM estimation, the mechanistic model path diagram was translated into linear equations and solved simultaneously using simulated data representing 192 counties. Measurement, geospatial, and mechanistic

  3. The regularity theory of mechanistic constitution and a methodology for constitutive inference.

    PubMed

    Harbecke, Jens

    2015-12-01

    This paper discusses a Boolean method for establishing constitutive regularity statements which, according to the regularity theory of mechanistic constitution, form the core of any mechanistic explanation in neuroscience. After presenting the regularity definition for the constitution relation, the paper develops a set of inference rules allowing one to establish constitutive hypotheses in light of certain kinds of empirical evidence. The general methodology consisting of these rules is characterized as having formed the basis of many successful explanatory projects in neuroscience. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Modeled Wet Nitrate Deposition

    EPA Pesticide Factsheets

    Modeled data on sulfate wet deposition was obtained from Dr. Jeff Grimm at Penn State Univ. Sulfate wet depostion causes acidification surface water bodies. See below regarding decriptions on how original data was produced. More information about these resources, including the variables used in this study, may be found here: https://edg.epa.gov/data/Public/ORD/NERL/ReVA/ReVA_Data.zip.

  5. Hydroxyapatite Deposition Disease

    DTIC Science & Technology

    2006-11-01

    calcific tendinitis or calcific periarthritis, is characterized by the deposition of calcium phosphate crystals (predominantly hydroxyapatite) in...site of HADD is the hip, where calcifications are usually found in the gluteus medius tendon or along the femur at various sites of tendinous ...posterolateral femoral diaphysis, as well as in various other tendinous attachments to the femur. Computed tomography is also helpful in the demonstration

  6. Intricately Rippled Sand Deposits

    NASA Technical Reports Server (NTRS)

    2006-01-01

    [figure removed for brevity, see original site] Click on the image for Intricately Rippled Sand Deposits (QTVR)

    NASA's Mars Exploration Rover Spirit welcomed the beginning of 2006 on Earth by taking this striking panorama of intricately rippled sand deposits in Gusev Crater on Mars. This is an approximate true-color rendering of the 'El Dorado' ripple field provided by Spirit over the New Year's holiday weekend. The view spans about 160 degrees in azimuth from left to right and consists of images acquired by Spirit's panoramic camera on Spirit's 708th and 710th Martian days, or sols, (Dec. 30, 2005 and Jan. 1, 2006). Spirit used the Pancam's 750-nanometer, 530-nanometer and 430-nanometer filters to capture the colors on Mars. Scientists have eliminated seams between individual frames in the sky portion of the mosaic to better simulate the vista a person standing on Mars would see. Spirit spent several days acquiring images, spectral data, and compositional and mineralogical information about these large sand deposits before continuing downhill toward 'Home Plate.'

  7. Electrophoretic deposition of biomaterials

    PubMed Central

    Boccaccini, A. R.; Keim, S.; Ma, R.; Li, Y.; Zhitomirsky, I.

    2010-01-01

    Electrophoretic deposition (EPD) is attracting increasing attention as an effective technique for the processing of biomaterials, specifically bioactive coatings and biomedical nanostructures. The well-known advantages of EPD for the production of a wide range of microstructures and nanostructures as well as unique and complex material combinations are being exploited, starting from well-dispersed suspensions of biomaterials in particulate form (microsized and nanoscale particles, nanotubes, nanoplatelets). EPD of biological entities such as enzymes, bacteria and cells is also being investigated. The review presents a comprehensive summary and discussion of relevant recent work on EPD describing the specific application of the technique in the processing of several biomaterials, focusing on (i) conventional bioactive (inorganic) coatings, e.g. hydroxyapatite or bioactive glass coatings on orthopaedic implants, and (ii) biomedical nanostructures, including biopolymer–ceramic nanocomposites, carbon nanotube coatings, tissue engineering scaffolds, deposition of proteins and other biological entities for sensors and advanced functional coatings. It is the intention to inform the reader on how EPD has become an important tool in advanced biomaterials processing, as a convenient alternative to conventional methods, and to present the potential of the technique to manipulate and control the deposition of a range of nanomaterials of interest in the biomedical and biotechnology fields. PMID:20504802

  8. Inkjet deposited circuit components

    NASA Astrophysics Data System (ADS)

    Bidoki, S. M.; Nouri, J.; Heidari, A. A.

    2010-05-01

    All-printed electronics as a means of achieving ultra-low-cost electronic circuits has attracted great interest in recent years. Inkjet printing is one of the most promising techniques by which the circuit components can be ultimately drawn (i.e. printed) onto the substrate in one step. Here, the inkjet printing technique was used to chemically deposit silver nanoparticles (10-200 nm) simply by ejection of silver nitrate and reducing solutions onto different substrates such as paper, PET plastic film and textile fabrics. The silver patterns were tested for their functionality to work as circuit components like conductor, resistor, capacitor and inductor. Different levels of conductivity were achieved simply by changing the printing sequence, inks ratio and concentration. The highest level of conductivity achieved by an office thermal inkjet printer (300 dpi) was 5.54 × 105 S m-1 on paper. Inkjet deposited capacitors could exhibit a capacitance of more than 1.5 nF (parallel plate 45 × 45 mm2) and induction coils displayed an inductance of around 400 µH (planar coil 10 cm in diameter). Comparison of electronic performance of inkjet deposited components to the performance of conventionally etched items makes the technique highly promising for fabricating different printed electronic devices.

  9. Uranium deposits of Brazil

    SciTech Connect

    1991-09-01

    Brazil is a country of vast natural resources, including numerous uranium deposits. In support of the country`s nuclear power program, Brazil has developed the most active uranium industry in South America. Brazil has one operating reactor (Angra 1, a 626-MWe PWR), and two under construction. The country`s economic challenges have slowed the progress of its nuclear program. At present, the Pocos de Caldas district is the only active uranium production. In 1990, the Cercado open-pit mine produced approximately 45 metric tons (MT) U{sub 3}O{sub 8} (100 thousand pounds). Brazil`s state-owned uranium production and processing company, Uranio do Brasil, announced it has decided to begin shifting its production from the high-cost and nearly depleted deposits at Pocos de Caldas, to lower-cost reserves at Lagoa Real. Production at Lagoa Real is schedules to begin by 1993. In addition to these two districts, Brazil has many other known uranium deposits, and as a whole, it is estimated that Brazil has over 275,000 MT U{sub 3}O{sub 8} (600 million pounds U{sub 3}O{sub 8}) in reserves.

  10. Sedimentary Deposits within Ius Chasma

    NASA Image and Video Library

    2015-07-15

    Sedimentary deposits are common within Valles Marineris. Most larger chasmata contain kilometer-thick light-toned layered deposits composed of sulfates. However, some of the chasmata, like Ius Chasma shown in this image from NASA Mars Reconnaissance Orbiter, lack these deposits or have much thinner deposits. The light-toned deposits in Ius Chasma are observed both along the floor and inner wallrock materials. Some of the light-toned deposits appear to post-date formation of the chasma floor, whereas other deposits appear to lie beneath wallrock materials, indicating they are older. By examining the stratigraphy using digital terrain models and 3D images, it should be possible to decipher the relative ages of the different geologic units. CRISM data may also provide insight into the mineralogy, which will tell scientists about the aqueous conditions that emplaced the light-toned deposits. http://photojournal.jpl.nasa.gov/catalog/PIA19855

  11. Silicon source for vacuum deposition

    NASA Technical Reports Server (NTRS)

    Racette, G. W.; Rutecki, D. J.

    1979-01-01

    Device using two independent silicon sources for ultra-high-vacuum deposition on large substrates can deposit P and N types of silicon simultaneously. Efficient water cooled copper shield supports and cools structure and isolates two filaments.

  12. Aerosol deposition on plant leaves

    Treesearch

    James B. Wedding; Roger W. Carlson; James J. Stukel; Fakhri A. Bazzaz

    1976-01-01

    An aerosol generator and wind tunnel system designed for use in aerosol deposition is described. Gross deposition on rough pubescent leaves was nearly 7 times greater than on smooth, waxy leaves. Results suggest that aerosol deposition, on a per unit area basis, for single horizontal streamlining leaves is similar to that for arrays of leaves under similar flow...

  13. Process and film characterization of chemical-bath-deposited ZnS thin films

    SciTech Connect

    Dona, J.M.; Herrero, J.

    1994-01-01

    Chemical-bath deposition of ZnS thin films from NH{sub 3}/NH{sub 2}-NH{sub 2}/SC(NH{sub 2}){sub 2}/ZnSO{sub 4} solutions has been studied. The effect of various process parameters on the growth and the film quality is presented. A first approach to a mechanistic interpretation of the chemical process is reported. The structural, optical, chemical, and electrical properties of the ZNS thin films deposited by this method have been studied. The electron diffraction (EDS) analysis shows that the films are microcrystalline with a cubic structure. EDS analysis has demonstrated that the films are highly stoichiometric. Scanning electron microscopy studies of the ZnS thin films deposited by this method show that the films are continuous and homogeneous. Electrical conductivity measurements have shown the highly resistivity nature of these films ({sigma} = 10{sup {minus}9} S/cm).

  14. Deposition of SOCs in forests

    SciTech Connect

    Horstmann, M.; McLachlan, M.S.

    1995-12-31

    The bulk deposition, wet-only deposition, dry-only deposition and ambient air concentrations of PCDD/Fs, PCBs and PAHs were measured in an 80 year old spruce forest, an 80 year old mixed deciduous (beech and oak) forest, and in an adjacent clearing over a period of 1--2 years. The deposition of the less volatile compounds that are primarily particle bound in the atmosphere was similar at both sites. These compounds were deposited primarily through wet deposition, as shown by the measurements in the clearing. In contrast, the deposition of the more volatile compounds was much higher at the forest sites than in the clearing. For instance, the annual deposition of Cl{sub 4}DF was 5 times higher in the spruce forest and 8 times higher in the deciduous forest. The excess deposition in the deciduous forest was almost completely due to the leaf fall in October--December, while about half of the excess deposition in the spruce forest was the result of needle fall. A further, as yet unexplained deposition mechanism accounted for the remainder of the flux in the spruce forest. Other studies have shown that more volatile SOCs are deposited to vegetation primarily through dry gaseous deposition. Hence, while forests have little influence on the deposition of less volatile compounds like the higher chlorinated PCDD/Fs and the 5--6 ring PAHs, dry deposition to leaves/needles and their subsequent falling to the forest floor make forest soils an extremely important sink for more volatile SOC.

  15. Creep of chemically vapor deposited SiC fibers

    NASA Technical Reports Server (NTRS)

    Dicarlo, J. A.

    1984-01-01

    The creep, thermal expansion, and elastic modulus properties for chemically vapor deposited SiC fibers were measured between 1000 and 1500 C. Creep strain was observed to increase logarithmically with time, monotonically with temperature, and linearly with tensile stress up to 600 MPa. The controlling activation energy was 480 + or - 20 kJ/mole. Thermal pretreatments near 1200 and 1450 C were found to significantly reduce fiber creep. These results coupled with creep recovery observations indicate that below 1400 C fiber creep is anelastic with neglible plastic component. This allowed a simple predictive method to be developed for describing fiber total deformation as a function of time, temperature, and stress. Mechanistic analysis of the property data suggests that fiber creep is the result of beta-SiC grain boundary sliding controlled by a small percent of free silicon in the grain boundaries.

  16. A mechanistic detachment rate model to predict soil erodibility due to fluvial and seepage forces

    USDA-ARS?s Scientific Manuscript database

    The erosion rate of cohesive soils is typically computed using an excess shear stress model based on the applied fluvial shear stress. However, no mechanistic approaches are available for incorporating additional forces such as localized groundwater seepage forces into the excess shear stress model...

  17. A Mechanistic Study of Arsenic (III) Rejection by Reverse Osmosis and Nanofiltration Membranes

    ERIC Educational Resources Information Center

    Suzuki, Tasuma

    2009-01-01

    Reverse osmosis/nanofiltration (RO/NF) membranes are capable to provide an effective barrier for a wide range of contaminants (including disinfection by-products precursors) in a single treatment step. However, solute rejection mechanisms by RO/NF membranes are not well understood. The lack of mechanistic information arises from experimental…

  18. Territoriality and home-range dynamics in meerkats, Suricata suricatta: a mechanistic modelling approach.

    PubMed

    Bateman, Andrew W; Lewis, Mark A; Gall, Gabriella; Manser, Marta B; Clutton-Brock, Tim H

    2015-01-01

    Multiple approaches exist to model patterns of space use across species, among them resource selection analysis, statistical home-range modelling and mechanistic movement modelling. Mechanistic home-range models combine the benefits of these approaches, describing emergent territorial patterns based on fine-scale individual- or group-movement rules and incorporating interactions with neighbours and the environment. These models have not, to date, been extended to dynamic contexts. Using mechanistic home-range models, we explore meerkat (Suricata suricatta) territorial patterns, considering scent marking, direct group interactions and habitat selection. We also extend the models to accommodate dynamic aspects of meerkat territoriality (territory development and territory shift). We fit models, representing multiple working hypotheses, to data from a long-term meerkat study in South Africa, and we compare models using Akaike's and Bayesian Information Criteria. Our results identify important features of meerkat territorial patterns. Notably, larger groups do not seem to control larger territories, and groups apparently prefer dune edges along a dry river bed. Our model extensions capture instances in which 1) a newly formed group interacts more strongly with its parent groups over time and 2) a group moves its territory core out of aversive habitat. This extends our mechanistic modelling framework in previously unexplored directions.

  19. Mechanistic home range models capture spatial patterns and dynamics of coyote territories in Yellowstone

    PubMed Central

    Moorcroft, Paul R; Lewis, Mark A; Crabtree, Robert L

    2006-01-01

    Patterns of space-use by individuals are fundamental to the ecology of animal populations influencing their social organization, mating systems, demography and the spatial distribution of prey and competitors. To date, the principal method used to analyse the underlying determinants of animal home range patterns has been resource selection analysis (RSA), a spatially implicit approach that examines the relative frequencies of animal relocations in relation to landscape attributes. In this analysis, we adopt an alternative approach, using a series of mechanistic home range models to analyse observed patterns of territorial space-use by coyote packs in the heterogeneous landscape of Yellowstone National Park. Unlike RSAs, mechanistic home range models are derived from underlying correlated random walk models of individual movement behaviour, and yield spatially explicit predictions for patterns of space-use by individuals. As we show here, mechanistic home range models can be used to determine the underlying determinants of animal home range patterns, incorporating both movement responses to underlying landscape heterogeneities and the effects of behavioural interactions between individuals. Our analysis indicates that the spatial arrangement of coyote territories in Yellowstone is determined by the spatial distribution of prey resources and an avoidance response to the presence of neighbouring packs. We then show how the fitted mechanistic home range model can be used to correctly predict observed shifts in the patterns of coyote space-use in response to perturbation. PMID:16769637

  20. Productivity of "Collisions Generate Heat" for Reconciling an Energy Model with Mechanistic Reasoning: A Case Study

    ERIC Educational Resources Information Center

    Scherr, Rachel E.; Robertson, Amy D.

    2015-01-01

    We observe teachers in professional development courses about energy constructing mechanistic accounts of energy transformations. We analyze a case in which teachers investigating adiabatic compression develop a model of the transformation of kinetic energy to thermal energy. Among their ideas is the idea that thermal energy is generated as a…

  1. Combining correlative and mechanistic habitat suitability models to improve ecological compensation.

    PubMed

    Meineri, Eric; Deville, Anne-Sophie; Grémillet, David; Gauthier-Clerc, Michel; Béchet, Arnaud

    2015-02-01

    Only a few studies have shown positive impacts of ecological compensation on species dynamics affected by human activities. We argue that this is due to inappropriate methods used to forecast required compensation in environmental impact assessments. These assessments are mostly descriptive and only valid at limited spatial and temporal scales. However, habitat suitability models developed to predict the impacts of environmental changes on potential species' distributions should provide rigorous science-based tools for compensation planning. Here we describe the two main classes of predictive models: correlative models and individual-based mechanistic models. We show how these models can be used alone or synoptically to improve compensation planning. While correlative models are easier to implement, they tend to ignore underlying ecological processes and lack accuracy. On the contrary, individual-based mechanistic models can integrate biological interactions, dispersal ability and adaptation. Moreover, among mechanistic models, those considering animal energy balance are particularly efficient at predicting the impact of foraging habitat loss. However, mechanistic models require more field data compared to correlative models. Hence we present two approaches which combine both methods for compensation planning, especially in relation to the spatial scale considered. We show how the availability of biological databases and software enabling fast and accurate population projections could be advantageously used to assess ecological compensation requirement efficiently in environmental impact assessments.

  2. DEVELOPING MECHANISTIC DATA FOR INCORPORATION INTO CANCER AND GENETIC RISK ASSESSMENTS: OLD PROBLEMS AND NEW APPROACHES

    EPA Science Inventory

    26th Lauriston S. Taylor Lecture
    DEVELOPING MECHANISTIC DATA FOR INCORPORATION INTO CANCER AND
    GENETIC RISK ASSESSMENTS: OLD PROBLEMS AND NEW APPROACHES
    R. Julian Preston, Environmental Carcinogenesis Division, U.S. Environmental Protection
    Agency, NHEERL, Research Tr...

  3. CHEMICAL MUTAGENESIS AND CARCINOGENESIS: INCORPORATION OF MECHANISTIC DATA INTO RISK ASSESSMENT

    EPA Science Inventory

    CHEMICAL MUTAGENESIS AND CARCINOGENESIS: INCORPORATION OF MECHANISTIC DATA INTO RISK ASSESSMENT

    The current understanding of cancer as a genetic disease, requiring a specific set of genomic alterations for a normal cell to form a metastatic tumor, has provided the oppor...

  4. A Mechanistic Study of Arsenic (III) Rejection by Reverse Osmosis and Nanofiltration Membranes

    ERIC Educational Resources Information Center

    Suzuki, Tasuma

    2009-01-01

    Reverse osmosis/nanofiltration (RO/NF) membranes are capable to provide an effective barrier for a wide range of contaminants (including disinfection by-products precursors) in a single treatment step. However, solute rejection mechanisms by RO/NF membranes are not well understood. The lack of mechanistic information arises from experimental…

  5. An Emphasis on Perception: Teaching Image Formation Using a Mechanistic Model of Vision.

    ERIC Educational Resources Information Center

    Allen, Sue; And Others

    An effective way to teach the concept of image is to give students a model of human vision which incorporates a simple mechanism of depth perception. In this study two almost identical versions of a curriculum in geometrical optics were created. One used a mechanistic, interpretive eye model, and in the other the eye was modeled as a passive,…

  6. Mechanistic assessment of hillslope transpiration controls of diel subsurface flow: a steady-state irrigation approach

    Treesearch

    H.R. Barnard; C.B. Graham; W.J. van Verseveld; J.R. Brooks; B.J. Bond; J.J. McDonnell

    2010-01-01

    Mechanistic assessment of how transpiration influences subsurface flow is necessary to advance understanding of catchment hydrology. We conducted a 24-day, steady-state irrigation experiment to quantify the relationships among soil moisture, transpiration and hillslope subsurface flow. Our objectives were to: (1) examine the time lag between maximum transpiration and...

  7. From Source to Sink: Mechanistic Reasoning Using the Electron-Pushing Formalism

    ERIC Educational Resources Information Center

    Bhattacharyya, Gautam

    2013-01-01

    Since the introduction of Morrison and Boyd's textbook in organic chemistry over 50 years ago, reaction mechanisms and mechanistic reasoning using the electron-pushing formalism (EPF) have become a mainstay of organic chemistry courses. In recent years there have even been several papers in this Journal and others detailing research on how…

  8. Development of a Mechanistically Based, Basin-Scale Stream Temperature Model: Applications to Cumulative Effects Modeling

    Treesearch

    Douglas Allen; William Dietrich; Peter Baker; Frank Ligon; Bruce Orr

    2007-01-01

    We describe a mechanistically-based stream model, BasinTemp, which assumes that direct shortwave radiation moderated by riparian and topographic shading, controls stream temperatures during the hottest part of the year. The model was developed to support a temperature TMDL for the South Fork Eel basin in Northern California and couples a GIS and a 1-D energy balance...

  9. New Simulation Methods to Facilitate Achieving a Mechanistic Understanding of Basic Pharmacology Principles in the Classroom

    ERIC Educational Resources Information Center

    Grover, Anita; Lam, Tai Ning; Hunt, C. Anthony

    2008-01-01

    We present a simulation tool to aid the study of basic pharmacology principles. By taking advantage of the properties of agent-based modeling, the tool facilitates taking a mechanistic approach to learning basic concepts, in contrast to the traditional empirical methods. Pharmacodynamics is a particular aspect of pharmacology that can benefit from…

  10. INCORPORATION OF MECHANISTIC INFORMATION IN THE ARSENIC PBPK MODEL DEVELOPMENT PROCESS

    EPA Science Inventory

    INCORPORATING MECHANISTIC INSIGHTS IN A PBPK MODEL FOR ARSENIC

    Elaina M. Kenyon, Michael F. Hughes, Marina V. Evans, David J. Thomas, U.S. EPA; Miroslav Styblo, University of North Carolina; Michael Easterling, Analytical Sciences, Inc.

    A physiologically based phar...

  11. Assessing Metal Levels in Children from the Mechanistic Indicators of Childhood Asthma(MICA) study

    EPA Science Inventory

    Toxic and essential metals levels can be used as health indicators. Here, we quantitatively compare and contrast toxic and essential metals levels in vacuum dust, urine, and fingernail samples of 109 children in Detroit, Michigan as part of The Mechanistic Indicators of Childhood...

  12. CHEMICAL MUTAGENESIS AND CARCINOGENESIS: INCORPORATION OF MECHANISTIC DATA INTO RISK ASSESSMENT

    EPA Science Inventory

    CHEMICAL MUTAGENESIS AND CARCINOGENESIS: INCORPORATION OF MECHANISTIC DATA INTO RISK ASSESSMENT

    The current understanding of cancer as a genetic disease, requiring a specific set of genomic alterations for a normal cell to form a metastatic tumor, has provided the oppor...

  13. USE OF MECHANISTIC DATA TO HELP DEFINE DOSE-RESPONSE CURVES

    EPA Science Inventory

    Use of Mechanistic Data to Help Define Dose-Response Curves

    The cancer risk assessment process described by the U.S. EPA necessitates a description of the dose-response curve for tumors in humans at low (environmental) exposures. This description can either be a default l...

  14. Assessing Metal Levels in Children from the Mechanistic Indicators of Childhood Asthma(MICA) study

    EPA Science Inventory

    Toxic and essential metals levels can be used as health indicators. Here, we quantitatively compare and contrast toxic and essential metals levels in vacuum dust, urine, and fingernail samples of 109 children in Detroit, Michigan as part of The Mechanistic Indicators of Childhood...

  15. Students' Interpretations of Mechanistic Language in Organic Chemistry before Learning Reactions

    ERIC Educational Resources Information Center

    Galloway, Kelli R.; Stoyanovich, Carlee; Flynn, Alison B.

    2017-01-01

    Research on mechanistic thinking in organic chemistry has shown that students attribute little meaning to the electron-pushing (i.e., curved arrow) formalism. At the University of Ottawa, a new curriculum has been developed in which students are taught the electron-pushing formalism prior to instruction on specific reactions--this formalism is…

  16. Incorporation of stochastic variability in mechanistic population pharmacokinetic models: handling the physiological constraints using normal transformations.

    PubMed

    Tsamandouras, Nikolaos; Wendling, Thierry; Rostami-Hodjegan, Amin; Galetin, Aleksandra; Aarons, Leon

    2015-08-01

    The utilisation of physiologically-based pharmacokinetic models for the analysis of population data is an approach with progressively increasing impact. However, as we move from empirical to complex mechanistic model structures, incorporation of stochastic variability in model parameters can be challenging due to the physiological constraints that may arise. Here, we investigated the most common types of constraints faced in mechanistic pharmacokinetic modelling and explored techniques for handling them during a population data analysis. An efficient way to impose stochastic variability on the parameters of interest without neglecting the underlying physiological constraints is through the assumption that they follow a distribution with support and properties matching the underlying physiology. It was found that two distributions that arise through transformations of the normal, the logit-normal generalisation and the logistic-normal, are excellent for such an application as not only they can satisfy the physiological constraints but also offer high flexibility during characterisation of the parameters' distribution. The statistical properties and practical advantages/disadvantages of these distributions for such an application were clearly displayed in the context of different modelling examples. Finally, a simulation study clearly illustrated the practical gains of the utilisation of the described techniques, as omission of population variability in physiological systems parameters leads to a biased/misplaced stochastic model with mechanistically incorrect variance structure. The current methodological work aims to facilitate the use of mechanistic/physiologically-based models for the analysis of population pharmacokinetic clinical data.

  17. New Simulation Methods to Facilitate Achieving a Mechanistic Understanding of Basic Pharmacology Principles in the Classroom

    ERIC Educational Resources Information Center

    Grover, Anita; Lam, Tai Ning; Hunt, C. Anthony

    2008-01-01

    We present a simulation tool to aid the study of basic pharmacology principles. By taking advantage of the properties of agent-based modeling, the tool facilitates taking a mechanistic approach to learning basic concepts, in contrast to the traditional empirical methods. Pharmacodynamics is a particular aspect of pharmacology that can benefit from…

  18. DEVELOPING MECHANISTIC DATA FOR INCORPORATION INTO CANCER AND GENETIC RISK ASSESSMENTS: OLD PROBLEMS AND NEW APPROACHES

    EPA Science Inventory

    26th Lauriston S. Taylor Lecture
    DEVELOPING MECHANISTIC DATA FOR INCORPORATION INTO CANCER AND
    GENETIC RISK ASSESSMENTS: OLD PROBLEMS AND NEW APPROACHES
    R. Julian Preston, Environmental Carcinogenesis Division, U.S. Environmental Protection
    Agency, NHEERL, Research Tr...

  19. A Cycloaromatization Protocol for Synthesis of Polysubstituted Phenol Derivatives: Method Development and Mechanistic Studies

    PubMed Central

    Spencer, William T.

    2012-01-01

    The scope of the cycloaromatization of propargylic ethers was explored using operationally simple air- and moisture-insensitive conditions. Highly substituted phenol derivatives were obtained in high yields. Mechanistic experiments indicate that the reaction occurs by an electrocyclization followed by 1,3-proton transfer. PMID:22891882

  20. From Source to Sink: Mechanistic Reasoning Using the Electron-Pushing Formalism

    ERIC Educational Resources Information Center

    Bhattacharyya, Gautam

    2013-01-01

    Since the introduction of Morrison and Boyd's textbook in organic chemistry over 50 years ago, reaction mechanisms and mechanistic reasoning using the electron-pushing formalism (EPF) have become a mainstay of organic chemistry courses. In recent years there have even been several papers in this Journal and others detailing research on how…

  1. INCORPORATION OF MECHANISTIC INFORMATION IN THE ARSENIC PBPK MODEL DEVELOPMENT PROCESS

    EPA Science Inventory

    INCORPORATING MECHANISTIC INSIGHTS IN A PBPK MODEL FOR ARSENIC

    Elaina M. Kenyon, Michael F. Hughes, Marina V. Evans, David J. Thomas, U.S. EPA; Miroslav Styblo, University of North Carolina; Michael Easterling, Analytical Sciences, Inc.

    A physiologically based phar...

  2. Predictive mechanistic bioenergetics to model habitat suitability of shellfish culture in coastal lakes

    NASA Astrophysics Data System (ADS)

    Rinaldi, A.; Montalto, V.; Manganaro, A.; Mazzola, A.; Mirto, S.; Sanfilippo, M.; Sarà, G.

    2014-05-01

    Quantitative tools based on mechanistic modelling of functional traits able to enhance the sustainability of aquaculture and most other human activities (i.e. reducing the likelihood of detrimental impacts optimising productions), are especially important factors in the decision to site aquaculture facilities in coastal lakes, ponds and lagoons and, in the case of detrimental impact, to adopt mitigation measures. We tested the ability of mechanistic functional trait based models to predict life history traits of cultivable shellfish in shallow coastal lakes. Dynamic Energy Budget (DEB) models were run to generate spatially explicit predictions of Mytilus galloprovincialis life history (LH) traits (e.g. body size and fecundity). Using fortnightly data of food supply and hourly data of body temperatures, and exploiting the power of mechanistic rules, we estimated the amount of faeces ejected by a fixed quantity of organisms cultivated in two shallow Southern Mediterranean (Sicily) lakes. These differed in terms of temperature and food density, implying large differences in life history traits of mussels in the two study areas. This information could help facilitate the selection of sites where environmental conditions are more suitable for aquaculture and contextually compatible with sustainability. The validation exercise obtained by comparing the predicted and observed data was nearly consistent. Therefore, a mechanistic functional traits-based model seems able to capture the link between habitat characteristics and functional traits of organisms, delineating the fundamental portion of an ecological niche, the possibility of predicting LH traits and potential ecological applications in the management of natural coastal resources.

  3. Mechanistic modeling of pesticide exposure: The missing keystone of honey bee toxicology.

    PubMed

    Sponsler, Douglas B; Johnson, Reed M

    2017-04-01

    The role of pesticides in recent honey bee losses is controversial, partly because field studies often fail to detect effects predicted by laboratory studies. This dissonance highlights a critical gap in the field of honey bee toxicology: there exists little mechanistic understanding of the patterns and processes of exposure that link honey bees to pesticides in their environment. The authors submit that 2 key processes underlie honey bee pesticide exposure: 1) the acquisition of pesticide by foraging bees, and 2) the in-hive distribution of pesticide returned by foragers. The acquisition of pesticide by foraging bees must be understood as the spatiotemporal intersection between environmental contamination and honey bee foraging activity. This implies that exposure is distributional, not discrete, and that a subset of foragers may acquire harmful doses of pesticide while the mean colony exposure would appear safe. The in-hive distribution of pesticide is a complex process driven principally by food transfer interactions between colony members, and this process differs importantly between pollen and nectar. High priority should be placed on applying the extensive literature on honey bee biology to the development of more rigorously mechanistic models of honey bee pesticide exposure. In combination with mechanistic effects modeling, mechanistic exposure modeling has the potential to integrate the field of honey bee toxicology, advancing both risk assessment and basic research. Environ Toxicol Chem 2017;36:871-881. © 2016 SETAC.

  4. A mechanistic treatment of the dominant soil nitrogen cycling processes: Model development, testing, and application

    USDA-ARS?s Scientific Manuscript database

    The development and initial application of a mechanistic model (TOUGHREACT-N) designed to characterize soil nitrogen (N) cycling and losses are described. The model couples advective and diffusive nutrient transport, multiple microbial biomass dynamics, and equilibrium and kinetic chemical reactions...

  5. Productivity of "Collisions Generate Heat" for Reconciling an Energy Model with Mechanistic Reasoning: A Case Study

    ERIC Educational Resources Information Center

    Scherr, Rachel E.; Robertson, Amy D.

    2015-01-01

    We observe teachers in professional development courses about energy constructing mechanistic accounts of energy transformations. We analyze a case in which teachers investigating adiabatic compression develop a model of the transformation of kinetic energy to thermal energy. Among their ideas is the idea that thermal energy is generated as a…

  6. Mechanistic home range models capture spatial patterns and dynamics of coyote territories in Yellowstone.

    PubMed

    Moorcroft, Paul R; Lewis, Mark A; Crabtree, Robert L

    2006-07-07

    Patterns of space-use by individuals are fundamental to the ecology of animal populations influencing their social organization, mating systems, demography and the spatial distribution of prey and competitors. To date, the principal method used to analyse the underlying determinants of animal home range patterns has been resource selection analysis (RSA), a spatially implicit approach that examines the relative frequencies of animal relocations in relation to landscape attributes. In this analysis, we adopt an alternative approach, using a series of mechanistic home range models to analyse observed patterns of territorial space-use by coyote packs in the heterogeneous landscape of Yellowstone National Park. Unlike RSAs, mechanistic home range models are derived from underlying correlated random walk models of individual movement behaviour, and yield spatially explicit predictions for patterns of space-use by individuals. As we show here, mechanistic home range models can be used to determine the underlying determinants of animal home range patterns, incorporating both movement responses to underlying landscape heterogeneities and the effects of behavioural interactions between individuals. Our analysis indicates that the spatial arrangement of coyote territories in Yellowstone is determined by the spatial distribution of prey resources and an avoidance response to the presence of neighbouring packs. We then show how the fitted mechanistic home range model can be used to correctly predict observed shifts in the patterns of coyote space-use in response to perturbation.

  7. Multi-chamber deposition system

    DOEpatents

    Jacobson, Richard L.; Jeffrey, Frank R.; Westerberg, Roger K.

    1989-06-27

    A system for the simultaneous deposition of different coatings onto a thin web within a large volume vacuum chamber is disclosed which chamber is provided with a plurality of deposition chambers in which the different layers are deposited onto the film as its moves from a supply roll to a finished take-up roll of coated web. The deposition chambers provided within the large vacuum chamber are provided with separate seals which minimize back diffusion of any dopant gas from adjacent deposition chambers.

  8. Multi-chamber deposition system

    DOEpatents

    Jacobson, Richard L.; Jeffrey, Frank R.; Westerberg, Roger K.

    1989-10-17

    A system for the simultaneous deposition of different coatings onto a thin web within a large volume vacuum chamber is disclosed which chamber is provided with a plurality of deposition chambers in which the different layers are deposited onto the film as its moves from a supply roll to a finished take-up roll of coated web. The deposition chambers provided within the large vacuum chamber are provided with separate seals which minimize back diffusion of any dopant gas from adjacent deposition chambers.

  9. Database of recent tsunami deposits

    USGS Publications Warehouse

    Peters, Robert; Jaffe, Bruce E.

    2010-01-01

    This report describes a database of sedimentary characteristics of tsunami deposits derived from published accounts of tsunami deposit investigations conducted shortly after the occurrence of a tsunami. The database contains 228 entries, each entry containing data from up to 71 categories. It includes data from 51 publications covering 15 tsunamis distributed between 16 countries. The database encompasses a wide range of depositional settings including tropical islands, beaches, coastal plains, river banks, agricultural fields, and urban environments. It includes data from both local tsunamis and teletsunamis. The data are valuable for interpreting prehistorical, historical, and modern tsunami deposits, and for the development of criteria to identify tsunami deposits in the geologic record.

  10. Coffee ring deposition in bands

    NASA Astrophysics Data System (ADS)

    Mandre, Shreyas; Wu, Ning; Aizenberg, Joanna; Mahadevan, Lakshminarayanan

    2010-11-01

    Microscopic particles suspended in a liquid are transported and deposited at a contact line, as the contact line recedes due to evaporation. A particle layer of uniform thickness is deposited if the particle concentration is above a threshold; below this threshold the deposit forms periodic bands oriented parallel to the contact line. We present a model for the formation of these bands based on evaporation leading to the breakup of the thin liquid film near the contact line. The threshold results from a competition between evaporation speed and deposition speed. Using this model, we predict the thickness and length of the bands, making the control of patterned deposition possible.

  11. Electrophoretic Deposition for Fabricating Microbatteries

    NASA Technical Reports Server (NTRS)

    West, William; Whitacre, Jay; Bugga, Ratnakumar

    2003-01-01

    An improved method of fabrication of cathodes of microbatteries is based on electrophoretic deposition. Heretofore, sputtering (for deposition) and the use of photoresist and liftoff (for patterning) have been the primary methods of fabricating components of microbatteries. The volume of active electrode material that can be deposited by sputtering is limited, and the discharge capacities of prior microbatteries have been limited accordingly. In addition, sputter deposition is slow. In contrast, electrophoretic deposition is much faster and has shown promise for increasing discharge capacities by a factor of 10, relative to those of microbatteries fabricated by prior methods.

  12. Fluidized Crater Ejecta Deposit

    NASA Technical Reports Server (NTRS)

    1998-01-01

    The Mars Orbiter Camera (MOC) onboard the Mars Global Surveyor (MGS) spacecraft continued to obtain high resolution images of the red planet into August 1998. At this time, each ground track (the portion of Mars available for MOC imaging on a given orbit) covers areas from about 40oN on the late afternoon side of the planet, up over the sunlit north polar cap, and down the early morning side of Mars to about 20oN latitude. Early morning and late afternoon views provide good shadowing to reveal subtle details on the martian surface. Views of Mars with such excellent lighting conditions will not be seen by MOC once MGS's Science Phasing Orbits end in mid-September 1998.

    The image shown here, MOC image 47903, was targeted on Friday afternoon (PDT), August 7, 1998. This picture of ejecta from a nameless 9.1 kilometer (5.7 mile)-diameter crater was designed to take full advantage of the present lighting conditions. When the image was taken (around 5:38 p.m. (PDT) on Saturday, August 8, 1998), the Sun had just risen and was only about 6o above the eastern horizon. With the Sun so low in the local sky, the contrast between sunlit and shadowed surfaces allowed new, subtle details to be revealed on the surface of the crater ejecta deposit.

    The crater shown here has ejecta of a type that was first identified in Mariner 9 and Viking Orbiter images as 'fluidized' ejecta. Ejecta is the material that is thrown out from the crater during the explosion that results when a meteor--piece of a comet or asteroid--collides with the planet. Fluidized ejecta is characterized by its lobate appearance, and sometimes by the presence of a ridge along the margin of the ejecta deposit. In the case of the crater shown here, there are two ridges that encircle the crater ejecta--this type of ejecta deposit is sometimes called a double-lobe rampart deposit. The MOC image shows that this particular crater also has 'normal' ejecta that occurs out on the plains, beyond the outermost ridge of

  13. Fluidized Crater Ejecta Deposit

    NASA Technical Reports Server (NTRS)

    1998-01-01

    The Mars Orbiter Camera (MOC) onboard the Mars Global Surveyor (MGS) spacecraft continued to obtain high resolution images of the red planet into August 1998. At this time, each ground track (the portion of Mars available for MOC imaging on a given orbit) covers areas from about 40oN on the late afternoon side of the planet, up over the sunlit north polar cap, and down the early morning side of Mars to about 20oN latitude. Early morning and late afternoon views provide good shadowing to reveal subtle details on the martian surface. Views of Mars with such excellent lighting conditions will not be seen by MOC once MGS's Science Phasing Orbits end in mid-September 1998.

    The image shown here, MOC image 47903, was targeted on Friday afternoon (PDT), August 7, 1998. This picture of ejecta from a nameless 9.1 kilometer (5.7 mile)-diameter crater was designed to take full advantage of the present lighting conditions. When the image was taken (around 5:38 p.m. (PDT) on Saturday, August 8, 1998), the Sun had just risen and was only about 6o above the eastern horizon. With the Sun so low in the local sky, the contrast between sunlit and shadowed surfaces allowed new, subtle details to be revealed on the surface of the crater ejecta deposit.

    The crater shown here has ejecta of a type that was first identified in Mariner 9 and Viking Orbiter images as 'fluidized' ejecta. Ejecta is the material that is thrown out from the crater during the explosion that results when a meteor--piece of a comet or asteroid--collides with the planet. Fluidized ejecta is characterized by its lobate appearance, and sometimes by the presence of a ridge along the margin of the ejecta deposit. In the case of the crater shown here, there are two ridges that encircle the crater ejecta--this type of ejecta deposit is sometimes called a double-lobe rampart deposit. The MOC image shows that this particular crater also has 'normal' ejecta that occurs out on the plains, beyond the outermost ridge of

  14. The Chilean nitrate deposits.

    USGS Publications Warehouse

    Ericksen, G.E.

    1983-01-01

    The nitrate deposits in the arid Atacama desert of northern Chile consist of saline-cemented surficial material, apparently formed in and near a playa lake that formerly covered the area. Many features of their distribution and chemical composition are unique. The author believes the principal sources of the saline constituents were the volcanic rocks of late Tertiary and Quaternary age in the Andes and that the nitrate is of organic origin. Possible sources of the nitrate, iodate, perchlorate and chromate are discussed. -J.J.Robertson

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

    PubMed

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

    2015-01-01

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

  16. Regulatory Technology Development Plan - Sodium Fast Reactor: Mechanistic Source Term – Trial Calculation

    SciTech Connect

    Grabaskas, David; Bucknor, Matthew; Jerden, James; Brunett, Acacia J.; Denman, Matthew; Clark, Andrew; Denning, Richard S.

    2016-10-01

    The potential release of radioactive material during a plant incident, referred to as the source term, is a vital design metric and will be a major focus of advanced reactor licensing. The U.S. Nuclear Regulatory Commission has stated an expectation for advanced reactor vendors to present a mechanistic assessment of the potential source term in their license applications. The mechanistic source term presents an opportunity for vendors to realistically assess the radiological consequences of an incident, and may allow reduced emergency planning zones and smaller plant sites. However, the development of a mechanistic source term for advanced reactors is not without challenges, as there are often numerous phenomena impacting the transportation and retention of radionuclides. This project sought to evaluate U.S. capabilities regarding the mechanistic assessment of radionuclide release from core damage incidents at metal fueled, pool-type sodium fast reactors (SFRs). The purpose of the analysis was to identify, and prioritize, any gaps regarding computational tools or data necessary for the modeling of radionuclide transport and retention phenomena. To accomplish this task, a parallel-path analysis approach was utilized. One path, led by Argonne and Sandia National Laboratories, sought to perform a mechanistic source term assessment using available codes, data, and models, with the goal to identify gaps in the current knowledge base. The second path, performed by an independent contractor, performed sensitivity analyses to determine the importance of particular radionuclides and transport phenomena in regards to offsite consequences. The results of the two pathways were combined to prioritize gaps in current capabilities.

  17. Are Mechanistic and Statistical QSAR Approaches Really Different? MLR Studies on 158 Cycloalkyl-Pyranones.

    PubMed

    Bhhatarai, Barun; Garg, Rajni; Gramatica, Paola

    2010-07-12

    Two parallel approaches for quantitative structure-activity relationships (QSAR) are predominant in literature, one guided by mechanistic methods (including read-across) and another by the use of statistical methods. To bridge the gap between these two approaches and to verify their main differences, a comparative study of mechanistically relevant and statistically relevant QSAR models, developed on a case study of 158 cycloalkyl-pyranones, biologically active on inhibition (Ki ) of HIV protease, was performed. Firstly, Multiple Linear Regression (MLR) based models were developed starting from a limited amount of molecular descriptors which were widely proven to have mechanistic interpretation. Then robust and predictive MLR models were developed on the same set using two different statistical approaches unbiased of input descriptors. Development of models based on Statistical I method was guided by stepwise addition of descriptors while Genetic Algorithm based selection of descriptors was used for the Statistical II. Internal validation, the standard error of the estimate, and Fisher's significance test were performed for both the statistical models. In addition, external validation was performed for Statistical II model, and Applicability Domain was verified as normally practiced in this approach. The relationships between the activity and the important descriptors selected in all the models were analyzed and compared. It is concluded that, despite the different type and number of input descriptors, and the applied descriptor selection tools or the algorithms used for developing the final model, the mechanistical and statistical approach are comparable to each other in terms of quality and also for mechanistic interpretability of modelling descriptors. Agreement can be observed between these two approaches and the better result could be a consensus prediction from both the models. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    PubMed Central

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

    2015-01-01

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

  19. Mechanistic-enriched models: integrating transcription factor networks and metabolic deregulation in cancer.

    PubMed

    Hernández-Lemus, Enrique; Siqueiros-García, J Mario

    2015-09-09

    In the present paper we will examine methodological frameworks to study complex genetic diseases (e.g. cancer) from the stand point of theoretical-computational biology combining both data-driven and hypothesis driven approaches. Our work focuses in the apparent counterpoint between two formal approaches to research in natural science: data- and hypothesis-driven inquiries. For a long time philosophers have recognized the mechanistic character of molecular biology explanations. On these grounds we suggest that hypothesis and data-driven approaches are not opposed to each other but that they may be integrated by the development of what we call enriched mechanistic models. We will elaborate around a case study from our laboratory that analyzed the relationship between transcriptional de-regulation of sets of genes that present both transcription factor and metabolic activity while at the same time have been associated with the presence of cancer. The way we do this is by analyzing structural, mechanistic and functional approaches to molecular level research in cancer biology. Emphasis will be given to data integration strategies to construct new explanations. Such analysis has led us to present a mechanistic-enriched model of the phenomenon. Such model pointed out to the way in which regulatory and thermodynamical behavior of gene regulation networks may be analyzed by means of gene expression data obtained from genome-wide analysis experiments in RNA from biopsy-captured tissue. The foundations of the model are given by the laws of thermodynamics and chemical physics and the approach is an enriched version of a mechanistic explanation. After analyzing the way we studied the coupling of metabolic and transcriptional deregulation in breast cancer, we have concluded that one plausible strategy to integrate data driven and hypothesis driven approaches is by means of resorting to fundamental and well established laws of physics and chemistry since these provide a solid

  20. A Mechanistic Understanding of North American Monsoon and Microphysical Properties of Ice Particles

    NASA Astrophysics Data System (ADS)

    Erfani, Ehsan

    A mechanistic understanding of the North American Monsoon (NAM) is suggested by incorporating local- and synoptic-scale processes. The local-scale mechanism describes the effect sea surface temperature (SST) in Gulf of California (GC) and how it contributes to the low-level moisture during the 2004 NAM. Before NAM onset, the strong low-level temperature inversion exists over the GC, but this inversion weakens with increasing GC SST and generally disappears once SSTs exceed 29.5°C, allowing the moist air, trapped in the MBL, to mix with free tropospheric air. This leads to a deep, moist layer that can be transported toward the NAM regions to produce thunderstorms. The synoptic scale mechanism is based on climatologies from 1983 to 2010 and explains that the warmest SSTs moving up the coast contributes to NAM convection and atmospheric heating, and consequently advancing the position of the anticyclone and the region of descent northward. In order to improve microphysical properties of ice clouds, this study develops self-consistent second order polynomial mass- and projected area-dimension (m-D and A-D) expressions that are valid over a much larger size range, compared to traditional power laws. Such expressions can easily be reduced to power laws for the size range of interest, in order to use in cloud and climate models. This was done by combining field measurements of individual ice particle m and D with airborne optical probe measurements of D, A and estimates of m. The resulting m-D and A-D expressions are functions of temperature and cloud type (synoptic vs. anvil), and are in good agreement with m-D power laws developed from recent field studies. These expressions also appear representative for heavily rimed dendrites occurring over the Sierra Nevada Mountains. By using the m-D field measurements of rimed and unrimed particles, and by developing theoretical methods, an approach was suggested for calculating rimed m and A, which has the benefit of accounting

  1. The importance of media roughness considerations for describing particle deposition in porous media

    NASA Astrophysics Data System (ADS)

    Jin, C.; Emelko, M.

    2016-12-01

    The morphology of media/collector surfaces (i.e., roughness) is one of the most important factors that has been recognized for decades; however, literature has been, for the most part, contradictory, non-mechanistic, and non-quantitative. A one-site kinetic model for attachment/detachment using a convection-diffusion model was used to evaluate particle deposition on collector surfaces in the packed beds. Rigorous controlled experiments addressing the impacts of surface roughness on particle deposition were conducted in parallel plate and packed bed systems; they demonstrated that a) surface roughness consistently influenced colloid deposition in a nonlinear, non-monotonic manner such that a critical roughness size associated with minimum particle deposition could be identified and b) collector surface roughness and background ionic strength concurrently influenced particle deposition. Excellent agreement between experimental data and numerical simulations was found when the most current knowledge representing hydrodynamic and interfacial forces associated with collector media roughness was represented. Although surface roughness also had a non-linear, non-monotonic impact on DLVO interaction energy at all separation distances, it was inadequate for describing and simulating particle deposition on surfaces with variable roughness. Notably, this work demonstrates that hydrodynamic effects can significantly alter particle deposition relative to expectations when only the DLVO force is considered. Moreover, the combined effects of hydrodynamics and interaction forces on particle deposition on rough, spherical media are not additive, but synergistic. Consideration of hydrodynamic contributions to particle deposition may help to explain discrepancies between model-based expectations and experimental outcomes and improve descriptions of particle deposition during physicochemical filtration in systems with non-smooth collector surfaces.

  2. Canyon Floor Deposits

    NASA Technical Reports Server (NTRS)

    2005-01-01

    [figure removed for brevity, see original site] Context image for PIA03598 Canyon Floor Deposits

    The layered and wind eroded deposits seen in this VIS image occur on the floor of Chandor Chasma.

    Image information: VIS instrument. Latitude 5.2S, Longitude 283.4E. 17 meter/pixel resolution.

    Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time.

    NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  3. Radioactive deposits in California

    USGS Publications Warehouse

    Walker, George W.; Lovering, Tom G.

    1954-01-01

    Reconnaissance examination by Government geologists of many areas, mine properties, and prospects in California during the period between 1948 and 1953 has confirmed the presence of radioactive materials in place at more than 40 localities. Abnormal radioactivity at these localities is due to concentrations of primary and secondary uranium minerals, to radon gas, radium (?), and to thorium minerals. Of the known occurrences only three were thought to contain uranium oxide (uranitite or pitchblende), 4 contained uranium-bearing columbate, tantalate, or titanate minerals, 12 contained secondary uranium minerals, such as autunite, carnotite, and torbernite, one contained radon gas, 7 contained thorium minerals, and, at the remaining 16 localities, the source of the anomalous radiation was not positively determined. The occurrences in which uranium oxide has been tentatively identified include the Rathgeb mine (Calaveras County), the Yerih group of claims (San Bernardino County), and the Rainbow claim (Madera County). Occurrences of secondary uranium minerals are largely confined to the arid desert regions of south-eastern California including deposits in San Bernardino, Kern, Inyo, and Imperial Counties. Uranium-bearing columbate, tantalate, or titanate minerals have been reported from pegmatite and granitic rock in southeastern and eastern California. Thorium minerals have been found in vein deposits in eastern San Bernardino County and from pegmatites and granitic rocks in various parts of southeastern California; placer concentrations of thorium minerals are known from nearly all areas in the State that are underlain, in part, by plutonic crystalline rocks. The primary uranium minerals occur principally as minute accessory crystals in pegmatite or granitic rock, or with base-metal sulfide minerals in veins. Thorium minerals also occur as accessory crystals in pegmatite or granitic rock, in placer deposits derived from such rock, and, at Mountain Pass, in veins

  4. 20 CFR 703.306 - Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...' COMPENSATION ACT AND RELATED STATUTES INSURANCE REGULATIONS Authorization of Self-Insurers § 703.306 Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits. A self-insurer or... deposited; conditions of deposit; acceptance of deposits. 703.306 Section 703.306 Employees' Benefits...

  5. 20 CFR 703.306 - Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...' COMPENSATION ACT AND RELATED STATUTES INSURANCE REGULATIONS Authorization of Self-Insurers § 703.306 Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits. A self-insurer or... deposited; conditions of deposit; acceptance of deposits. 703.306 Section 703.306 Employees' Benefits...

  6. 20 CFR 703.306 - Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...' COMPENSATION ACT AND RELATED STATUTES INSURANCE REGULATIONS Authorization of Self-Insurers § 703.306 Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits. A self-insurer or... deposited; conditions of deposit; acceptance of deposits. 703.306 Section 703.306 Employees' Benefits...

  7. 20 CFR 703.306 - Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...' COMPENSATION ACT AND RELATED STATUTES INSURANCE REGULATIONS Authorization of Self-Insurers § 703.306 Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits. A self-insurer or... deposited; conditions of deposit; acceptance of deposits. 703.306 Section 703.306 Employees' Benefits...

  8. 20 CFR 703.306 - Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... AND RELATED STATUTES INSURANCE REGULATIONS Authorization of Self-Insurers § 703.306 Kinds of negotiable securities that may be deposited; conditions of deposit; acceptance of deposits. A self-insurer or... deposited; conditions of deposit; acceptance of deposits. 703.306 Section 703.306 Employees'...

  9. Acid deposition in Asia: Emissions, deposition, and ecosystem effects

    NASA Astrophysics Data System (ADS)

    Duan, Lei; Yu, Qian; Zhang, Qiang; Wang, Zifa; Pan, Yuepeng; Larssen, Thorjørn; Tang, Jie; Mulder, Jan

    2016-12-01

    We review and synthesize the current state of knowledge regarding acid deposition and its environmental effects across Asia. The extent and magnitude of acid deposition in Asia became apparent only about one decade after this issue was well described in Europe and North America. In addition to the temperate zone, much of eastern and southern Asia is situated in the tropics and subtropics, climate zones hitherto little studied with respect to the effects of high loads of acid deposition. Surface waters across Asia are generally not sensitive to the effects of acid deposition, whereas soils in some regions are sensitive to acidification due to low mineral weathering. However, soil acidification was largely neutralized by such processes as base cation deposition, nitrate (NO3-) denitrification, and sulfate (SO42-) adsorption. Accompanying the decrease in S deposition in recent years, N deposition is of increasing concern in Asia. The acidifying effect of N deposition may be more important than S deposition in well drained tropical/subtropical soils due to high SO42- adsorption. The risk of regional soil acidification is a major threat in Eastern Asia, indicated by critical load exceedance in large areas.

  10. A Mechanistic study of Plasma Treatment Effects on Demineralized Dentin Surfaces for Improved Adhesive/Dentin Interface Bonding

    PubMed Central

    Dong, Xiaoqing; Chen, Meng; Wang, Yong; Yu, Qingsong

    2014-01-01

    Our previous work has shown that non-thermal plasma treatment of demineralized dentin significantly (p<0.05) improved adhesive/dentin bonding strength for dental composite restoration as compared with the untreated controls. This study is to achieve mechanistic understanding of the plasma treatment effects on dentin surface through investigating the plasma treated dentin surfaces and their interaction with adhesive monomer, 2-Hydroxyethyl methacrylate (HEMA). The plasma treated dentin surfaces from human third molars were evaluated by water contact angle measurements and scanning electron microscopy (SEM). It was found that plasma-treated dentin surface with subsequent HEMA immersion (Plasma/HEMA Treated) had much lower water contact angle compared with only plasma-treated (Plasma Treated) or only HEMA immersed (HEMA Treated) dentin surfaces. With prolong water droplet deposition time, water droplets spread out completely on the Plasma/HEMA Treated dentin surfaces. SEM images of Plasma/HEMA Treated dentin surfaces verified that dentin tubules were opened-up and filled with HEMA monomers. Extracted type I collagen fibrils, which was used as simulation of the exposed dentinal collagen fibrils after acid etching step, were plasma treated and analyzed with Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) spectra. FT-IR spectra of the Plasma/HEMA Treated collage fibrils showed broadened amide I peak at 1660 cm−1 and amide II at 1550 cm−1, which indicate secondary structure changes of the collagen fibrils. CD spectra indicated that 67.4% collagen helix structures were denatured after plasma treatment. These experimental results demonstrate that non-thermal argon plasma treatment was very effective in loosing collagen structure and enhancing adhesive monomer penetration, which are beneficial to thicker hybrid layer and longer resin tag formation, and consequently enhance adhesive/dentin interface bonding. PMID:25267936

  11. A Mechanistic study of Plasma Treatment Effects on Demineralized Dentin Surfaces for Improved Adhesive/Dentin Interface Bonding.

    PubMed

    Dong, Xiaoqing; Chen, Meng; Wang, Yong; Yu, Qingsong

    2014-07-01

    Our previous work has shown that non-thermal plasma treatment of demineralized dentin significantly (p<0.05) improved adhesive/dentin bonding strength for dental composite restoration as compared with the untreated controls. This study is to achieve mechanistic understanding of the plasma treatment effects on dentin surface through investigating the plasma treated dentin surfaces and their interaction with adhesive monomer, 2-Hydroxyethyl methacrylate (HEMA). The plasma treated dentin surfaces from human third molars were evaluated by water contact angle measurements and scanning electron microscopy (SEM). It was found that plasma-treated dentin surface with subsequent HEMA immersion (Plasma/HEMA Treated) had much lower water contact angle compared with only plasma-treated (Plasma Treated) or only HEMA immersed (HEMA Treated) dentin surfaces. With prolong water droplet deposition time, water droplets spread out completely on the Plasma/HEMA Treated dentin surfaces. SEM images of Plasma/HEMA Treated dentin surfaces verified that dentin tubules were opened-up and filled with HEMA monomers. Extracted type I collagen fibrils, which was used as simulation of the exposed dentinal collagen fibrils after acid etching step, were plasma treated and analyzed with Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) spectra. FT-IR spectra of the Plasma/HEMA Treated collage fibrils showed broadened amide I peak at 1660 cm(-1) and amide II at 1550 cm(-1), which indicate secondary structure changes of the collagen fibrils. CD spectra indicated that 67.4% collagen helix structures were denatured after plasma treatment. These experimental results demonstrate that non-thermal argon plasma treatment was very effective in loosing collagen structure and enhancing adhesive monomer penetration, which are beneficial to thicker hybrid layer and longer resin tag formation, and consequently enhance adhesive/dentin interface bonding.

  12. Experimental reproduction of tsunami deposit

    NASA Astrophysics Data System (ADS)

    Yoshii, T.; Matsuyama, M.; Tanaka, S.

    2015-12-01

    Understanding the process of sediment transport and deposition under a tsunami inundation is essential to provide the credible information about potential tsunamis from tsunami deposits. Detections of tsunami deposit has contributed to reveal centuries-old record of tsunami incursions. However, our knowledge is still not enough for evaluating the scale of past tsunamis using deposits. In this study, a laboratory experiment was conducted to investigate the relationship between the hydraulic condition and sedimentological features of tsunami deposit. The large wave flume in CRIEPI, one of the largest wave flume in the world, which has 205 m length, 3.4 m width and 6 m depth was used. The sandy beach with uniform slope (1/50) were made in the flume. Sand dune of 0.2 high was placed near the shoreline. The tsunami was made by the wave generator which has 2.2 m stroke. The wave at the shore line has 0.6 m depth and the horizontal velocity reached up to 3.5 m/s. The incursion of the wave and its return flow completely washed out the dune and resulted in the deposition especially near the dune. The thickness of deposit shows landward thinning and fining, which has been widely confirmed by field observations. In addition, sedimentary structures of the deposit was investigated using the method similar to that used in geological survey such as core sampling and relief peel sampling. The obtained samples were investigated using a X-ray computed tomography. The obtained CT-images shows that most part of deposition consists two or more subsections divided by horizontal lamination although the deposition near the dune has drastic and complex change thickness and grain size. The subsections shows upward-fining and upward-coarsening which are been reported as common sedimentary structures of tsunami deposit from field surveys. Considering the similarity of sedimentary structures in the deposit reconstructed in this experiment and actual tsunami deposits, this experiment succeeded

  13. Volcanology and mineral deposits

    USGS Publications Warehouse

    Lipman, P.W.

    1990-01-01

    In contrast, old volcanic regions, which host many of the world's major hydrothermal-vein, porphyry, and massive-sulfide ore deposits, have been studied mainly by economic geologists, regional stratigraphers, and structural geologists who have limited familiarity with the complexities of volcanic processes. Such "dead" volcanoes, ranging in age from a few million million years (tertiary) to a few billion years (Precambrian), are commonly incompletely and discontinuously preserved due to rapid erosion of originally high-standing volcanic edifices. They can be difficult to date reliably, especially in terms of the time scales of individual volcanic events, and are variably hydrothermally altered-impeding high-resolution petrologic and geochemical studies. Many volcanologists, geochemists, and geophysicists who work on active volcanoes accordingly have been reluctant to become involved in studies of such less tractable rocks. 

  14. Depositing Diamondlike Carbon Films

    NASA Technical Reports Server (NTRS)

    Mirtich, M. J.; Sovey, J. S.; Banks, B. A.

    1986-01-01

    New process demonstrated to make thin films (usually thousands of angstroms to few microns thick) that have properties of diamonds. Various plasma and ion-beam techniques employed to generate films. Films made by radio-frequency plasma decomposition of hydrocarbon gas or other alkanes, by low-energy carbon-ion-beam deposition, or by ion plating and dual ion technique using carbon target. Advantages of new process over others are films produced, though amorphous, are clear, extremely hard, chemically inert, of high resistivity, and have index of refraction of 3.2 properties similar to those of single-crystal diamonds. Films have possible uses in microelectronic applications, high-energy-laser and plastic windows, corrosion protection for metals, and other applications where desired properties of film shaped during the film-formation process.

  15. Chemical vapor deposition growth

    NASA Technical Reports Server (NTRS)

    Ruth, R. P.; Manasevit, H. M.; Kenty, J. L.; Moudy, L. A.; Simpson, W. I.; Yang, J. J.

    1976-01-01

    The chemical vapor deposition (CVD) method for the growth of Si sheet on inexpensive substrate materials is investigated. The objective is to develop CVD techniques for producing large areas of Si sheet on inexpensive substrate materials, with sheet properties suitable for fabricating solar cells meeting the technical goals of the Low Cost Silicon Solar Array Project. Specific areas covered include: (1) modification and test of existing CVD reactor system; (2) identification and/or development of suitable inexpensive substrate materials; (3) experimental investigation of CVD process parameters using various candidate substrate materials; (4) preparation of Si sheet samples for various special studies, including solar cell fabrication; (5) evaluation of the properties of the Si sheet material produced by the CVD process; and (6) fabrication and evaluation of experimental solar cell structures, using standard and near-standard processing techniques.

  16. Lunar western limb pyroclastic deposits

    NASA Technical Reports Server (NTRS)

    Coombs, Cassandra R.; Hawke, B. Ray

    1991-01-01

    It has become increasingly evident that the lunar pyroclastic volcanism played an important role in the formation and resurfacing of many areas of the Moon. On-going analysis of lunar Orbiter and Apollo photographs continues to locate and identify pyroclastic deposits and suggests that they just may be more ubiquitous than once thought. Located near mare/highland boundaries, many of these deposits formed contemporaneously with effusive mare volcanism. The mantling deposits formed as products of fire-fountaining. Probable source vents for these deposits include irregular depressions at the head of associated sinuous rilles and/or along irregular fractures in the floors of ancient craters. Here, researchers provide a brief synopsis of the nature of the dark mantling deposits and briefly discuss several newly identified deposits on the western limb.

  17. Endogenous murine Aβ increases amyloid deposition in APP23 but not in APPPS1 transgenic mice.

    PubMed

    Mahler, Jasmin; Morales-Corraliza, Jose; Stolz, Julia; Skodras, Angelos; Radde, Rebecca; Duma, Carmen C; Eisele, Yvonne S; Mazzella, Matthew J; Wong, Harrison; Klunk, William E; Nilsson, K Peter R; Staufenbiel, Matthias; Mathews, Paul M; Jucker, Mathias; Wegenast-Braun, Bettina M

    2015-07-01

    Endogenous murine amyloid-β peptide (Aβ) is expressed in most Aβ precursor protein (APP) transgenic mouse models of Alzheimer's disease but its contribution to β-amyloidosis remains unclear. We demonstrate ∼ 35% increased cerebral Aβ load in APP23 transgenic mice compared with age-matched APP23 mice on an App-null background. No such difference was found for the much faster Aβ-depositing APPPS1 transgenic mouse model between animals with or without the murine App gene. Nevertheless, both APP23 and APPPS1 mice codeposited murine Aβ, and immunoelectron microscopy revealed a tight association of murine Aβ with human Aβ fibrils. Deposition of murine Aβ was considerably less efficient compared with the deposition of human Aβ indicating a lower amyloidogenic potential of murine Aβ in vivo. The amyloid dyes Pittsburgh Compound-B and pentamer formyl thiophene acetic acid did not differentiate between amyloid deposits consisting of human Aβ and deposits of mixed human-murine Aβ. Our data demonstrate a differential effect of murine Aβ on human Aβ deposition in different APP transgenic mice. The mechanistically complex interaction of human and mouse Aβ may affect pathogenesis of the models and should be considered when models are used for translational preclinical studies.

  18. The deposit size frequency method for estimating undiscovered uranium deposits

    USGS Publications Warehouse

    McCammon, R.B.; Finch, W.I.

    1993-01-01

    The deposit size frequency (DSF) method has been developed as a generalization of the method that was used in the National Uranium Resource Evaluation (NURE) program to estimate the uranium endowment of the United States. The DSF method overcomes difficulties encountered during the NURE program when geologists were asked to provide subjective estimates of (1) the endowed fraction of an area judged favorable (factor F) for the occurrence of undiscovered uranium deposits and (2) the tons of endowed rock per unit area (factor T) within the endowed fraction of the favorable area. Because the magnitudes of factors F and T were unfamiliar to nearly all of the geologists, most geologists responded by estimating the number of undiscovered deposits likely to occur within the favorable area and the average size of these deposits. The DSF method combines factors F and T into a single factor (F??T) that represents the tons of endowed rock per unit area of the undiscovered deposits within the favorable area. Factor F??T, provided by the geologist, is the estimated number of undiscovered deposits per unit area in each of a number of specified deposit-size classes. The number of deposit-size classes and the size interval of each class are based on the data collected from the deposits in known (control) areas. The DSF method affords greater latitude in making subjective estimates than the NURE method and emphasizes more of the everyday experience of exploration geologists. Using the DSF method, new assessments have been made for the "young, organic-rich" surficial uranium deposits in Washington and idaho and for the solution-collapse breccia pipe uranium deposits in the Grand Canyon region in Arizona and adjacent Utah. ?? 1993 Oxford University Press.

  19. Momentum Deposition in Curvilinear Coordinates

    SciTech Connect

    Cleveland, Mathew Allen; Lowrie, Robert Byron; Rockefeller, Gabriel M.; Thompson, Kelly Glen; Wollaber, Allan Benton

    2015-08-03

    The momentum imparted into a material by thermal radiation deposition is an important physical process in astrophysics and inertial confinement fusion (ICF) simulations. In recent work we presented a new method of evaluating momentum deposition that relies on the combination of a time-averaged approximation and a numerical integration scheme. This approach robustly and efficiently evaluates the momentum deposition in spherical geometry. Future work will look to extend this approach to 2D cylindrical geometries.

  20. Particle Deposition onto Enclosure Surfaces

    DTIC Science & Technology

    2009-08-20

    8217, respectively. 27 Thatcher and Nazaroff47 studied the influence of different surface roughness on particle deposition under natural convection in...21 6.2 Airflow Characteristics Affecting Particle Deposition 22 6.2.1 Forced Convection 22 6.2.2 Natural Convection 24 6.3 Surface...particle size under natural convection conditions 24 6. Comparison of experimentally measured deposition velocity for surfaces of various

  1. Diverse Deposits in Melas Chasma

    NASA Image and Video Library

    2015-07-29

    This scene captured by NASA Mars Reconnaissance Orbiter includes chaotic deposits with a wide range of colors. The deposits are distinctive with both unique colors and small-scale textures such as fracture patterns. These are probably sedimentary rocks, transported and deposited in water or air. The original layers may have been jumbled in a landslide. Dark or reddish sand dunes cover some of the bedrock. http://photojournal.jpl.nasa.gov/catalog/PIA19860

  2. (Acidic deposition and the environment)

    SciTech Connect

    Garten, C.T.; Lindberg, S.E.; Van Miegroet, H.

    1990-10-24

    The travelers presented several papers at the Fourth International Conference on Acidic Deposition. These covered the following topics: atmospheric chemistry and deposition of airborne nitrogen compounds, soil solution chemistry in high-elevation spruce forests, and forest throughfall measurements for estimating total sulfur deposition to ecosystems. In addition, S. E. Lindberg was invited to organize and chair a conference session on Throughfall and Stemflow Experiments, and to present an invited lecture on Atmospheric Deposition and Canopy Interactions of Metals and Nitrogen in Forest Ecosystems: The Influence of Global Change'' at the 110th Anniversary Celebration of the Free University of Amsterdam.

  3. 78 FR 11604 - Deposit Insurance Regulations; Definition of Insured Deposit

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-19

    ... the resulting receivership effectively and fairly; and (4) enhancing international cooperation. The... from a right to payment in a liquidation. In light of these recent international developments, the FDIC... expanded international deposit insurance liability arising from dually payable deposits and associated...

  4. 76 FR 21265 - Interest on Deposits; Deposit Insurance Coverage

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-15

    ... CORPORATION 12 CFR Parts 329 and 330 RIN 3064-AD78 Interest on Deposits; Deposit Insurance Coverage AGENCY... comment. SUMMARY: Effective July 21, 2011, the statutory prohibition against the payment of interest on... a definition of ``interest'' that may assist the FDIC in interpreting a recent statutory amendment...

  5. Iridium thin films deposited via pulsed laser deposition

    NASA Astrophysics Data System (ADS)

    Chen, Chenglin

    High purity Ir thin films for future applications as transition-edge sensors were deposited on Si (100) via pulsed laser deposition. The iridium deposition rate was investigated and found to have a high value with the pulsed laser power higher than 4.2×10 9 W/cm 2 . At this laser intensity range, the PLD Ir films were deposited at substrate temperature ranging from 100 to 700°C. Ir thin films' characteristics were investigated at both room temperature and low temperature with the emphasis on study of the effect of the substrate temperature during deposition on the structure and morphology of the films. The PLD films exhibited a (110) preferentially oriented polycrystalline structure. Their average grain size increased from about 30 to 110 nm as the deposition temperature was raised from 100 to 600°C. With a 700°C substrate temperature the grain size jumped to 500 nm. Iridium silicide was found in the film deposited at 700°C substrate temperature. This indicated a critical deposition temperature between 600 and 700°C. A 50 mK platform was built for low temperature measurements. At low temperature, the Residual Resistance Ratio (RRR) of the Ir thin films had a typical value of 1.50. A typical transition curve of the film showed a transition temperature higher and wider than expected.

  6. Mechanistic modelling of cancer: some reflections from software engineering and philosophy of science.

    PubMed

    Cañete-Valdeón, José M; Wieringa, Roel; Smallbone, Kieran

    2012-12-01

    There is a growing interest in mathematical mechanistic modelling as a promising strategy for understanding tumour progression. This approach is accompanied by a methodological change of making research, in which models help to actively generate hypotheses instead of waiting for general principles to become apparent once sufficient data are accumulated. This paper applies recent research from philosophy of science to uncover three important problems of mechanistic modelling which may compromise its mainstream application, namely: the dilemma of formal and informal descriptions, the need to express degrees of confidence and the need of an argumentation framework. We report experience and research on similar problems from software engineering and provide evidence that the solutions adopted there can be transferred to the biological domain. We hope this paper can provoke new opportunities for further and profitable interdisciplinary research in the field.

  7. Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter

    NASA Astrophysics Data System (ADS)

    Grossmann, Nina; Vakkasoglu, Ahmet S.; Hulpke, Sabine; Abele, Rupert; Gaudet, Rachelle; Tampé, Robert

    2014-11-01

    The ATP-binding cassette (ABC) transporter associated with antigen processing (TAP) participates in immune surveillance by moving proteasomal products into the endoplasmic reticulum (ER) lumen for major histocompatibility complex class I loading and cell surface presentation to cytotoxic T cells. Here we delineate the mechanistic basis for antigen translocation. Notably, TAP works as a molecular diode, translocating peptide substrates against the gradient in a strict unidirectional way. We reveal the importance of the D-loop at the dimer interface of the two nucleotide-binding domains (NBDs) in coupling substrate translocation with ATP hydrolysis and defining transport vectoriality. Substitution of the conserved aspartate, which coordinates the ATP-binding site, decreases NBD dimerization affinity and turns the unidirectional primary active pump into a passive bidirectional nucleotide-gated facilitator. Thus, ATP hydrolysis is not required for translocation per se, but is essential for both active and unidirectional transport. Our data provide detailed mechanistic insight into how heterodimeric ABC exporters operate.

  8. Tautomeric stabilities of 4-fluorohistidine shed new light on mechanistic experiments with labeled ribonuclease A

    NASA Astrophysics Data System (ADS)

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2016-12-01

    Ribonuclease A is the oldest model for studying enzymatic mechanisms, yet questions remain about proton transfer within the active site. Seminal work by Jackson et al. (1994) labeled Ribonuclease A with 4-fluorohistidine, concluding that active-site histidines act as general acids and bases. Calculations of 4-fluorohistidine indicate that the π-tautomer is predominant in all simulated environments (by ∼17 kJ/mol), strongly suggesting that fluoro-labeled ribonuclease A functions with His119 in π-tautomer. The tautomeric form of His119 during proton transfer and tautomerism as a putative mechanistic step in wild-type RNase A remain open questions and should be considered in future mechanistic studies.

  9. A data-intensive approach to mechanistic elucidation applied to chiral anion catalysis

    PubMed Central

    Milo, Anat; Neel, Andrew J.; Toste, F. Dean; Sigman, Matthew S.

    2015-01-01

    Knowledge of chemical reaction mechanisms can facilitate catalyst optimization, but extracting that knowledge from a complex system is often challenging. Here we present a data-intensive method for deriving and then predictively applying a mechanistic model of an enantioselective organic reaction. As a validating case study, we selected an intramolecular dehydrogenative C-N coupling reaction, catalyzed by chiral phosphoric acid derivatives, in which catalyst-substrate association involves weak, non-covalent interactions. Little was previously understood regarding the structural origin of enantioselectivity in this system. Catalyst and substrate substituent effects were probed by systematic physical organic trend analysis. Plausible interactions between the substrate and catalyst that govern enantioselectivity were identified and supported experimentally, indicating that such an approach can afford an efficient means of leveraging mechanistic insight to optimize catalyst design. PMID:25678656

  10. FOAM3D: A numerical simulator for mechanistic prediciton of foam displacement in multidimensions

    SciTech Connect

    Kovscek, A.R.; Patzek, T.W.; Radke, C.J.

    1995-03-01

    Field application of foam is a technically viable enhanced oil recovery process (EOR) as demonstrated by recent steam-foam field studies. Traditional gas-displacement processes, such as steam drive, are improved substantially by controlling gas mobility and thereby improving volumetric displacement efficiency. For instance, Patzek and Koinis showed major oil-recovery response after about two years of foam injection in two different pilot studies at the Kern River field. They report increased production of 5.5 to 14% of the original oil in place over a five year period. Because reservoir-scale simulation is a vital component of the engineering and economic evaluation of any EOR project, efficient application of foam as a displacement fluid requires a predictive numerical model of foam displacement. A mechanistic model would also expedite scale-up of the process from the laboratory to the field scale. No general, mechanistic, field-scale model for foam displacement is currently in use.

  11. Mechanistic modelling of urania fuel evolution and fission product migration during irradiation and heating

    NASA Astrophysics Data System (ADS)

    Veshchunov, M. S.; Dubourg, R.; Ozrin, V. D.; Shestak, V. E.; Tarasov, V. I.

    2007-05-01

    The models of the mechanistic code MFPR (Module for Fission Product Release) developed by IBRAE in collaboration with IRSN are described briefly in the first part of the paper. The influence of microscopic defects in the UO2 crystal structure on fission-gas transport out of grains and release from fuel pellets is described. These defects include point defects such as vacancies, interstitials and fission atoms, and extended defects such as bubbles, pores and dislocations. The mechanistic description of chemically active elements behaviour (fission-induced) is based on complex association of diffusion-vaporisation mechanism involving multi-phase and multi-component thermo-chemical equilibrium at the grain boundary with accurate calculation of fuel oxidation. In the second part, results of the code applications are given to different situations: normal LWR reactor operation, high temperature annealing, loss of coolant accident (LOCA) and severe accidents conditions.

  12. Conceptual models for waste tank mechanistic analysis. Status report, January 1991

    SciTech Connect

    Allemann, R. T.; Antoniak, Z. I.; Eyler, L. L.; Liljegren, L. M.; Roberts, J. S.

    1992-02-01

    Pacific Northwest Laboratory (PNL) is conducting a study for Westinghouse Hanford Company (Westinghouse Hanford), a contractor for the US Department of Energy (DOE). The purpose of the work is to study possible mechanisms and fluid dynamics contributing to the periodic release of gases from double-shell waste storage tanks at the Hanford Site in Richland, Washington. This interim report emphasizing the modeling work follows two other interim reports, Mechanistic Analysis of Double-Shell Tank Gas Release Progress Report -- November 1990 and Collection and Analysis of Existing Data for Waste Tank Mechanistic Analysis Progress Report -- December 1990, that emphasized data correlation and mechanisms. The approach in this study has been to assemble and compile data that are pertinent to the mechanisms, analyze the data, evaluate physical properties and parameters, evaluate hypothetical mechanisms, and develop mathematical models of mechanisms.

  13. Mechanistic modelling of cancer: some reflections from software engineering and philosophy of science

    NASA Astrophysics Data System (ADS)

    Cañete-Valdeón, José M.; Wieringa, Roel; Smallbone, Kieran

    2012-12-01

    There is a growing interest in mathematical mechanistic modelling as a promising strategy for understanding tumour progression. This approach is accompanied by a methodological change of making research, in which models help to actively generate hypotheses instead of waiting for general principles to become apparent once sufficient data are accumulated. This paper applies recent research from philosophy of science to uncover three important problems of mechanistic modelling which may compromise its mainstream application, namely: the dilemma of formal and informal descriptions, the need to express degrees of confidence and the need of an argumentation framework. We report experience and research on similar problems from software engineering and provide evidence that the solutions adopted there can be transferred to the biological domain. We hope this paper can provoke new opportunities for further and profitable interdisciplinary research in the field.

  14. Synthesis, cytotoxicity and mechanistic evaluation of 4-oxoquinoline-3-carboxamide derivatives: finding new potential anticancer drugs.

    PubMed

    Forezi, Luana da S M; Tolentino, Nathalia M C; de Souza, Alessandra M T; Castro, Helena C; Montenegro, Raquel C; Dantas, Rafael F; Oliveira, Maria E I M; Silva, Floriano P; Barreto, Leilane H; Burbano, Rommel M R; Abrahim-Vieira, Bárbara; de Oliveira, Riethe; Ferreira, Vitor F; Cunha, Anna C; Boechat, Fernanda da C S; de Souza, Maria Cecília B V

    2014-05-22

    As part of a continuing search for new potential anticancer candidates, we describe the synthesis, cytotoxicity and mechanistic evaluation of a series of 4-oxoquinoline-3-carboxamide derivatives as novel anticancer agents. The inhibitory activity of compounds 10-18 was determined against three cancer cell lines using the MTT colorimetric assay. The screening revealed that derivatives 16b and 17b exhibited significant cytotoxic activity against the gastric cancer cell line but was not active against a normal cell line, in contrast to doxorubicin, a standard chemotherapeutic drug in clinical use. Interestingly, no hemolytical activity was observed when the toxicity of 16b and 17b was tested against blood cells. The in silico and in vitro mechanistic evaluation indicated the potential of 16b as a lead for the development of novel anticancer agents against gastric cancer cells.

  15. TOPICAL REVIEW: Mechanistically based probability modelling, life prediction and reliability assessment

    NASA Astrophysics Data System (ADS)

    Wei, Robert P.; Harlow, D. Gary

    2005-01-01

    Life prediction and reliability assessment are essential components for the life-cycle engineering and management (LCEM) of modern engineered systems. These systems can range from microelectronic and bio-medical devices to large machinery and structures. To be effective, the underlying approach to LCEM must be transformed to embody mechanistically based probability modelling, vis-à-vis the more traditional experientially based statistical modelling, for predicting damage evolution and distribution. In this paper, the probability and statistical approaches are compared and differentiated. The process of model development on the basis of mechanistic understanding derived from critical experiments is illustrated through selected examples. The efficacy of this approach is illustrated through an example of the evolution and distribution of corrosion and corrosion fatigue damage in aluminium alloys in relation to aircraft that had been in long-term service.

  16. Substrate inhibition in the heterogeneous catalyzed aldol condensation: A mechanistic study of supported organocatalysts

    SciTech Connect

    Kandel, Kapil; Althaus, Stacey M.; Peeraphatdit, Chorthip; Kobayashi, Takeshi; Trewyn, Brian G.; Pruski, Marek; Slowing, Igor I.

    2012-05-23

    In this study, we demonstrate how materials science can be combined with the established methods of organic chemistry to find mechanistic bottlenecks and redesign heterogeneous catalysts for improved performance. By using solid-state NMR, infrared spectroscopy, surface and kinetic analysis, we prove the existence of a substrate inhibition in the aldol condensation catalyzed by heterogeneous amines. We show that modifying the structure of the supported amines according to the proposed mechanism dramatically enhances the activity of the heterogeneous catalyst. We also provide evidence that the reaction benefits significantly from the surface chemistry of the silica support, which plays the role of a co-catalyst, giving activities up to two orders of magnitude larger than those of homogeneous amines. This study confirms that the optimization of a heterogeneous catalyst depends as much on obtaining organic mechanistic information as it does on controlling the structure of the support.

  17. Skin sensitization: reaction mechanistic applicability domains for structure-activity relationships.

    PubMed

    Aptula, Aynur O; Patlewicz, Grace; Roberts, David W

    2005-09-01

    The prediction of skin sensitization potential with minimum animal testing is currently of great importance in light of forthcoming legislation. A number of structure-activity relationships for skin sensitization have been published over the years, but their applicability has often been limited to structural classes. The concept of an applicability domain for a quantitative structure-activity relationship [(Q)SAR] is increasingly being viewed as key for the predictive application of (Q)SARs. This is particularly the case for skin sensitization if more widely applicable SARs are to be developed. In this paper, we analyze a recently published chemical data set for skin sensitization, apply reaction mechanistic criteria to domain classification, and evaluate the structure-activity trends observed within each of these mechanistic domains.

  18. Formalising a mechanistic linkage between heterotrophic feeding and thermal bleaching resistance

    NASA Astrophysics Data System (ADS)

    Wooldridge, Scott A.

    2014-12-01

    In this paper, I utilise the CO2 (sink) limitation model of coral bleaching to propose a new biochemical framework that explains how certain (well-adapted) coral species can utilise heterotrophic carbon acquisition to combat the damaging algal photoinhibition response sequence that underpins thermal bleaching, thereby increasing thermal bleaching resistance. This mechanistic linkage helps to clarify a number of previously challenging experimental responses arising from feeding (versus starved) temperature stress experiments, and isotope labelling (tracer) experiments with heterotrophic carbon sources (e.g., zooplankton). In an era of rapidly warming surface ocean temperatures, the conferred fitness benefits arising from such a mechanistic linkage are considerable. Yet, various ecological constraints are outlined which caution against the ultimate benefit of the mechanism for raising bleaching thresholds at the coral community (reef) scale. Future experiments are suggested that can strengthen these proposed arguments.

  19. Case study: the role of mechanistic network models in systems toxicology.

    PubMed

    Hoeng, Julia; Talikka, Marja; Martin, Florian; Sewer, Alain; Yang, Xiang; Iskandar, Anita; Schlage, Walter K; Peitsch, Manuel C

    2014-02-01

    Twenty first century systems toxicology approaches enable the discovery of biological pathways affected in response to active substances. Here, we briefly summarize current network approaches that facilitate the detailed mechanistic understanding of the impact of a given stimulus on a biological system. We also introduce our network-based method with two use cases and show how causal biological network models combined with computational methods provide quantitative mechanistic insights. Our approach provides a robust comparison of the transcriptional responses in different experimental systems and enables the identification of network-based biomarkers modulated in response to exposure. These advances can also be applied to pharmacology, where the understanding of disease mechanisms and adverse drug effects is imperative for the development of efficient and safe treatment options. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Current mechanistic insights into the roles of matrix metalloproteinases in tumour invasion and metastasis.

    PubMed

    Brown, Gordon T; Murray, Graeme I

    2015-11-01

    The purpose of this review is to highlight the recent mechanistic developments elucidating the role of matrix metalloproteinases (MMPs) in tumour invasion and metastasis. The ability of tumour cells to invade, migrate, and subsequently metastasize is a fundamental characteristic of cancer. Tumour invasion and metastasis are increasingly being characterized by the dynamic relationship between cancer cells and their microenvironment and developing a greater understanding of these basic pathological mechanisms is crucial. While MMPs have been strongly implicated in these processes as a result of extensive circumstantial evidence--for example, increased expression of individual MMPs in tumours and association of specific MMPs with prognosis--the underpinning mechanisms are only now being elucidated. Recent studies are now providing a mechanistic basis, highlighting and reinforcing the catalytic and non-catalytic roles of specific MMPs as key players in tumour invasion and metastasis. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  1. Mechanistic exploration of a bi-directional PDT-based combination in pancreatic cancer (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Huang, Huang-Chiao; Mallidi, Srivalleesha; Liu, Joyce; Chiang, Chun-Te; Mai, Zhiming; Goldschmidt, Ruth; Rizvi, Imran; Ebrahim-Zadeh, Neema; Hasan, Tayyaba

    2016-03-01

    It is increasingly evident that the most effective cancer treatments will involve interactive regimens that target multiple non-overlapping pathways, preferably such that each component enhances the others to improve outcomes while minimizing systemic toxicities. Toward this goal, we developed a combination of photodynamic therapy and irinotecan, which mechanistically cooperate with each other, beyond their individual tumor destruction pathways, to cause synergistic reduction in orthotopic pancreatic tumor burden. A three-way mechanistic basis of the observed the synergism will be discussed: (i) PDT downregulates drug efflux transporters to increase intracellular irinotecan levels. (ii) Irinotecan reduces the expression of hypoxia-induced marker, which is upregulated by PDT. (iii) PDT downregulates irinotecan-induced survivin expression to amplify the apoptotic and anti-proliferative effects. The clinical translation potential of the combination will also be highlighted.

  2. Revealing the electrophilicity of N-Ac indoles with FeCl3: a mechanistic study.

    PubMed

    Beaud, Rodolphe; Nandi, Raj Kumar; Perez-Luna, Alejandro; Guillot, Régis; Gori, Didier; Kouklovsky, Cyrille; Ghermani, Nour-Eddine; Gandon, Vincent; Vincent, Guillaume

    2017-05-30

    Herein, we report a mechanistic exploration of the unusual FeCl3-mediated hydroarylation of N-Ac indoles. Electron density topology analysis of a crystal, in situ IR monitoring, Hammett and Taft studies as well as DFT computations allowed us to determine that activation of acetyl with FeCl3 and of the C2[double bond, length as m-dash]C3 bond with a proton is involved.

  3. Microstructural and Mechanistic Study of Primary Creep in Titanium Alloys at Lower Temperatures.

    DTIC Science & Technology

    2007-11-02

    98- ata sources, spect of this 15 Jefferson 503. 1. AGENCY USE ONLY (Leave blank) | 2. REPORT DATE 5 June 1998 3. REPORT TYPE AND DATES...COVERED Final Technical Report 1 Feb 95 to 31 Jan 98 4. TITLE AND SUBTITLE Microstructural and Mechanistic Study of Primary Creep in titanium...alloys at Lower Temperatures 6. AUTHOR(S) Professor Michael J. Mills 5 . FUNDING NUMBERS F49620-95-1-0153 7. PERFORMING ORGANIZATION NAME(S) AND

  4. Quantitative assessment of biological impact using transcriptomic data and mechanistic network models

    SciTech Connect

    Thomson, Ty M.; Sewer, Alain; Martin, Florian; Belcastro, Vincenzo; Frushour, Brian P.; Gebel, Stephan; Park, Jennifer; Schlage, Walter K.; Talikka, Marja; Vasilyev, Dmitry M.; Westra, Jurjen W.; Hoeng, Julia; Peitsch, Manuel C.

    2013-11-01

    Exposure to biologically active substances such as therapeutic drugs or environmental toxicants can impact biological systems at various levels, affecting individual molecules, signaling pathways, and overall cellular processes. The ability to derive mechanistic insights from the resulting system responses requires the integration of experimental measures with a priori knowledge about the system and the interacting molecules therein. We developed a novel systems biology-based methodology that leverages mechanistic network models and transcriptomic data to quantitatively assess the biological impact of exposures to active substances. Hierarchically organized network models were first constructed to provide a coherent framework for investigating the impact of exposures at the molecular, pathway and process levels. We then validated our methodology using novel and previously published experiments. For both in vitro systems with simple exposure and in vivo systems with complex exposures, our methodology was able to recapitulate known biological responses matching expected or measured phenotypes. In addition, the quantitative results were in agreement with experimental endpoint data for many of the mechanistic effects that were assessed, providing further objective confirmation of the approach. We conclude that our methodology evaluates the biological impact of exposures in an objective, systematic, and quantifiable manner, enabling the computation of a systems-wide and pan-mechanistic biological impact measure for a given active substance or mixture. Our results suggest that various fields of human disease research, from drug development to consumer product testing and environmental impact analysis, could benefit from using this methodology. - Highlights: • The impact of biologically active substances is quantified at multiple levels. • The systems-level impact integrates the perturbations of individual networks. • The networks capture the relationships between

  5. N-Heterocyclic carbene-mediated oxidative esterification of aldehydes: ester formation and mechanistic studies.

    PubMed

    Maji, Biswajit; Vedachalan, Seenuvasan; Ge, Xin; Cai, Shuting; Liu, Xue-Wei

    2011-05-06

    An unexpected N-heterocyclic carbene-catalyzed esterification of α,β-unsaturated aldehydes including aromatic aldehydes with reactive cinnamyl bromides in the presence of air oxygen or MnO(2) as an oxidant is described. In the presence of oxygen, halogenated and electron-deficient aldehydes react smoothly to furnish esters in good yields. Great efforts have been made on mechanistic studies to deduce a plausible mechanism, based on the experimental results and isotopic labeling experiment.

  6. Exploiting the Imidazolium Effect in Base-free Ammonium Enolate Generation: Synthetic and Mechanistic Studies.

    PubMed

    Young, Claire M; Stark, Daniel G; West, Thomas H; Taylor, James E; Smith, Andrew D

    2016-11-07

    N-Acyl imidazoles and catalytic isothiourea hydrochloride salts function as ammonium enolate precursors in the absence of base. Enantioselective Michael addition-cyclization reactions using different α,β-unsaturated Michael acceptors have been performed to form dihydropyranones and dihydropyridinones with high stereoselectivity. Detailed mechanistic studies using RPKA have revealed the importance of the "imidazolium" effect in ammonium enolate formation and have highlighted key differences with traditional base-mediated processes.

  7. Mechanistic Oral Absorption Modeling and Simulation for Formulation Development and Bioequivalence Evaluation: Report of an FDA Public Workshop

    PubMed Central

    Duan, J; Kesisoglou, F; Novakovic, J; Amidon, GL; Jamei, M; Lukacova, V; Eissing, T; Tsakalozou, E; Zhao, L; Lionberger, R

    2017-01-01

    On May 19, 2016, the US Food and Drug Administration (FDA) hosted a public workshop, entitled “Mechanistic Oral Absorption Modeling and Simulation for Formulation Development and Bioequivalence Evaluation.”1 The topic of mechanistic oral absorption modeling, which is one of the major applications of physiologically based pharmacokinetic (PBPK) modeling and simulation, focuses on predicting oral absorption by mechanistically integrating gastrointestinal transit, dissolution, and permeation processes, incorporating systems, active pharmaceutical ingredient (API), and the drug product information, into a systemic mathematical whole‐body framework.2 PMID:28571121

  8. Fluence rate effect semi-mechanistic modelling on WWER-type RPV welds

    NASA Astrophysics Data System (ADS)

    Debarberis, L.; Acosta, B.; Sevini, F.; Chernobaeva, A.; Kryukov, A. M.

    2006-03-01

    Effort at JRC-IE is ongoing in order to develop a semi-mechanistic model to forecast radiation embrittlement. The understanding and the quantification of the influence of the fluence rate is of particular importance for the correct interpretation of data obtained in material testing reactors or in surveillance capsules, which are accelerated with respect to embrittlement of the reactor pressure vessel wall itself. To verify the applicability of the fluence rate as included in the semi-mechanistic model and tuning the model parameters various WWER-type vessel weld material have been studied. For the selected welds, copper ranges from 0.08 to 0.18 mass%, while phosphorus variation is from 0.013 to 0.036 mass%. The fluence range is up to 2 × 10 20 n cm -2 obtained at two fluence rates of 4 × 10 11 and 3.5 × 10 12 n cm -2 s -1, typical for WWER-440 surveillance positions. Significant fluence rate effect has been observed for the welds containing low copper and moderate phosphorus, and adaptation of the semi-mechanistic model's parameters for the high flux data is required. To verify the consistency and the limits of the findings other similar data coming from RPV surveillance programmes are also included in this analysis.

  9. Integration of QSAR and SAR methods for the mechanistic interpretation of predictive models for carcinogenicity

    PubMed Central

    Fjodorova, Natalja; Novič, Marjana

    2012-01-01

    The knowledge-based Toxtree expert system (SAR approach) was integrated with the statistically based counter propagation artificial neural network (CP ANN) model (QSAR approach) to contribute to a better mechanistic understanding of a carcinogenicity model for non-congeneric chemicals using Dragon descriptors and carcinogenic potency for rats as a response. The transparency of the CP ANN algorithm was demonstrated using intrinsic mapping technique specifically Kohonen maps. Chemical structures were represented by Dragon descriptors that express the structural and electronic features of molecules such as their shape and electronic surrounding related to reactivity of molecules. It was illustrated how the descriptors are correlated with particular structural alerts (SAs) for carcinogenicity with recognized mechanistic link to carcinogenic activity. Moreover, the Kohonen mapping technique enables one to examine the separation of carcinogens and non-carcinogens (for rats) within a family of chemicals with a particular SA for carcinogenicity. The mechanistic interpretation of models is important for the evaluation of safety of chemicals. PMID:24688639

  10. Adenosine as a probing tool for the mechanistic study of acupuncture treatment.

    PubMed

    Wang, Jia-You; Li, Hui; Zhang, Lei; Ma, Chun-Mei; Wang, Jia-Lu; Lai, Xin-Sheng; Zhou, Shu-Feng

    2014-11-01

    To date, acupuncture has been widely used despite a lack of solid clinical evidence in the East and West. However, there are few validated in vitro models for the mechanistic studies of acupuncture. We hypothesized that adenosine could be used as a probing tool in the mechanistic studies of acupuncture because of its critical role in the action of acupuncture. Subsequently, we tested this hypothesis using both in vitro and in vivo experiments. First, we found that adenosine stimulation mimicked the effect of acupuncture on microRNA profiling (including miR-339, miR-145 and miR-451) and protein level (including Sirt2) in nerve growth factor-induced differentiated PC12 cells. These miRNA and proteins have been found to be regulated by acupuncture treatment in the brain of spontaneously hypertensive rats. Next, we found that adenosine stimulation downregulated miR-339 expression through adenosine A1 receptor-mediated pathway. Finally, we showed that the concentration of adenosine was actually decreased in the brain of spontaneously hypertensive rats after acupuncture treatment at Taichong acupoint. Taken together, these findings suggest that adenosine could be used as a useful probing tool for acupuncture mechanistic studies, while more validation studies are certainly warranted. © 2014 Wiley Publishing Asia Pty Ltd.

  11. Mechanistic models of animal migration behaviour--their diversity, structure and use.

    PubMed

    Bauer, Silke; Klaassen, Marcel

    2013-05-01

    1. Migration is a widespread phenomenon in the animal kingdom, including many taxonomic groups and modes of locomotion. Developing an understanding of the proximate and ultimate causes for this behaviour not only addresses fundamental ecological questions but has relevance to many other fields, for example in relation to the spread of emerging zoonotic diseases, the proliferation of invasive species, aeronautical safety as well as the conservation of migrants. 2. Theoretical methods can make important contributions to our understanding of migration, by allowing us to integrate findings on this complex behaviour, identify caveats in our understanding and to guide future empirical research efforts. Various mechanistic models exist to date, but their applications seem to be scattered and far from evenly distributed across taxonomic units. 3. Therefore, we provide an overview of the major mechanistic modelling approaches used in the study of migration behaviour and characterize their fundamental features, assumptions and limitations and discuss their typical data requirements both for model parameterization and for scrutinizing model predictions. 4. Furthermore, we review 155 studies that have used mechanistic models to study animal migration and analyse them with regard to the approaches used and the focal species, and also explore their contribution to advancing current knowledge within six broad migration ecology research themes. 5. This identifies important gaps in our present knowledge, which should be tackled in future research using existing and to-be developed theoretical approaches. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

  12. Comparative evaluation of statistical and mechanistic models of Escherichia coli at beaches in southern Lake Michigan

    USGS Publications Warehouse

    Safaie, Ammar; Wendzel, Aaron; Ge, Zhongfu; Nevers, Meredith; Whitman, Richard L.; Corsi, Steven R.; Phanikumar, Mantha S.

    2016-01-01

    Statistical and mechanistic models are popular tools for predicting the levels of indicator bacteria at recreational beaches. Researchers tend to use one class of model or the other, and it is difficult to generalize statements about their relative performance due to differences in how the models are developed, tested, and used. We describe a cooperative modeling approach for freshwater beaches impacted by point sources in which insights derived from mechanistic modeling were used to further improve the statistical models and vice versa. The statistical models provided a basis for assessing the mechanistic models which were further improved using probability distributions to generate high-resolution time series data at the source, long-term “tracer” transport modeling based on observed electrical conductivity, better assimilation of meteorological data, and the use of unstructured-grids to better resolve nearshore features. This approach resulted in improved models of comparable performance for both classes including a parsimonious statistical model suitable for real-time predictions based on an easily measurable environmental variable (turbidity). The modeling approach outlined here can be used at other sites impacted by point sources and has the potential to improve water quality predictions resulting in more accurate estimates of beach closures.

  13. Exploiting Bioprocessing Fluctuations to Elicit the Mechanistics of De Novo Lipogenesis in Yarrowia lipolytica

    PubMed Central

    Silverman, Andrew M.; Stephanopoulos, Gregory

    2017-01-01

    Despite substantial achievements in elucidating the metabolic pathways of lipogenesis, a mechanistic representation of lipid accumulation and degradation has not been fully attained to-date. Recent evidence suggests that lipid accumulation can occur through increases of either the cytosolic copy-number of lipid droplets (LDs), or the LDs size. However, the prevailing phenotype, or how such mechanisms pertain to lipid degradation remain poorly understood. To address this shortcoming, we employed the–recently discovered–innate bioprocessing fluctuations in Yarrowia lipolytica, and performed single-cell fluctuation analysis using optical microscopy and microfluidics that generate a quasi-time invariant microenvironment. We report that lipid accumulation at early stationary phase in rich medium is substantially more likely to occur through variations in the LDs copy-number, rather than the LDs size. Critically, these mechanistics are also preserved during lipid degradation, as well as upon exposure to a protein translation inhibitor. The latter condition additionally induced a lipid accumulation phase, accompanied by the downregulation of lipid catabolism. Our results enable an in-depth mechanistic understanding of lipid biogenesis, and expand longitudinal single-cell fluctuation analyses from gene regulation to metabolism. PMID:28052085

  14. Mechanistic Modelling of DNA Repair and Cellular Survival Following Radiation-Induced DNA Damage

    NASA Astrophysics Data System (ADS)

    McMahon, Stephen J.; Schuemann, Jan; Paganetti, Harald; Prise, Kevin M.

    2016-09-01

    Characterising and predicting the effects of ionising radiation on cells remains challenging, with the lack of robust models of the underlying mechanism of radiation responses providing a significant limitation to the development of personalised radiotherapy. In this paper we present a mechanistic model of cellular response to radiation that incorporates the kinetics of different DNA repair processes, the spatial distribution of double strand breaks and the resulting probability and severity of misrepair. This model enables predictions to be made of a range of key biological endpoints (DNA repair kinetics, chromosome aberration and mutation formation, survival) across a range of cell types based on a set of 11 mechanistic fitting parameters that are common across all cells. Applying this model to cellular survival showed its capacity to stratify the radiosensitivity of cells based on aspects of their phenotype and experimental conditions such as cell cycle phase and plating delay (correlation between modelled and observed Mean Inactivation Doses R2 > 0.9). By explicitly incorporating underlying mechanistic factors, this model can integrate knowledge from a wide range of biological studies to provide robust predictions and may act as a foundation for future calculations of individualised radiosensitivity.

  15. Comparative Evaluation of Statistical and Mechanistic Models of Escherichia coli at Beaches in Southern Lake Michigan.

    PubMed

    Safaie, Ammar; Wendzel, Aaron; Ge, Zhongfu; Nevers, Meredith B; Whitman, Richard L; Corsi, Steven R; Phanikumar, Mantha S

    2016-03-01

    Statistical and mechanistic models are popular tools for predicting the levels of indicator bacteria at recreational beaches. Researchers tend to use one class of model or the other, and it is difficult to generalize statements about their relative performance due to differences in how the models are developed, tested, and used. We describe a cooperative modeling approach for freshwater beaches impacted by point sources in which insights derived from mechanistic modeling were used to further improve the statistical models and vice versa. The statistical models provided a basis for assessing the mechanistic models which were further improved using probability distributions to generate high-resolution time series data at the source, long-term "tracer" transport modeling based on observed electrical conductivity, better assimilation of meteorological data, and the use of unstructured-grids to better resolve nearshore features. This approach resulted in improved models of comparable performance for both classes including a parsimonious statistical model suitable for real-time predictions based on an easily measurable environmental variable (turbidity). The modeling approach outlined here can be used at other sites impacted by point sources and has the potential to improve water quality predictions resulting in more accurate estimates of beach closures.

  16. Emergent global patterns of ecosystem structure and function from a mechanistic general ecosystem model.

    PubMed

    Harfoot, Michael B J; Newbold, Tim; Tittensor, Derek P; Emmott, Stephen; Hutton, Jon; Lyutsarev, Vassily; Smith, Matthew J; Scharlemann, Jörn P W; Purves, Drew W

    2014-04-01

    Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures.

  17. Natural Variation of Plant Metabolism: Genetic Mechanisms, Interpretive Caveats, and Evolutionary and Mechanistic Insights1

    PubMed Central

    Soltis, Nicole E.; Kliebenstein, Daniel J.

    2015-01-01

    Combining quantitative genetics studies with metabolomics/metabolic profiling platforms, genomics, and transcriptomics is creating significant progress in identifying the causal genes controlling natural variation in metabolite accumulations and profiles. In this review, we discuss key mechanistic and evolutionary insights that are arising from these studies. This includes the potential role of transport and other processes in leading to a separation of the site of mechanistic causation and metabolic consequence. A reilluminated observation is the potential for genomic variation in the organelle to alter phenotypic variation alone and in epistatic interaction with the nuclear genetic variation. These studies are also highlighting new aspects of metabolic pleiotropy both in terms of the breadth of loci altering metabolic variation as well as the potential for broader effects on plant defense regulation of the metabolic variation than has previously been predicted. We also illustrate caveats that can be overlooked when translating quantitative genetics descriptors such as heritability and per-locus r2 to mechanistic or evolutionary interpretations. PMID:26272883

  18. Mechanistic models of animal migration behaviour – their diversity, structure and use

    PubMed Central

    Bauer, Silke; Klaassen, Marcel

    2013-01-01

    Migration is a wide-spread phenomenon in the animal kingdom, including many taxonomic groups and modes of locomotion. Developing an understanding of the proximate and ultimate causes for this behaviour not only addresses fundamental ecological questions but has relevance to many other fields, e.g. in relation to the spread of emerging zoonotic diseases, the proliferation of invasive species, aeronautical safety as well as the conservation of migrants.Theoretical methods can make important contributions to our understanding of migration, by allowing us to integrate findings on this complex behaviour, identify caveats in our understanding and guide future empirical research efforts. Various mechanistic models exist to date but their applications seem to be scattered and far from evenly distributed across taxonomic units.Therefore, we provide an overview of the major mechanistic modelling approaches used in the study of migration behaviour and characterise their fundamental features, assumptions and limitations, and discuss their typical data requirements both for model parameterisation and for scrutinizing model predictions.Furthermore, we review 155 studies that have used mechanistic models to study animal migration and analyse them with regard to the approaches used, focal species and also explore their contribution of advancing current knowledge within six broad migration ecology research themes.This identifies important gaps in our present knowledge, which should be tackled in future research using existing and to-be developed theoretical approaches. PMID:23373515

  19. Mechanistic analytical models for long-distance seed dispersal by wind.

    PubMed

    Katul, G G; Porporato, A; Nathan, R; Siqueira, M; Soons, M B; Poggi, D; Horn, H S; Levin, S A

    2005-09-01

    We introduce an analytical model, the Wald analytical long-distance dispersal (WALD) model, for estimating dispersal kernels of wind-dispersed seeds and their escape probability from the canopy. The model is based on simplifications to well-established three-dimensional Lagrangian stochastic approaches for turbulent scalar transport resulting in a two-parameter Wald (or inverse Gaussian) distribution. Unlike commonly used phenomenological models, WALD's parameters can be estimated from the key factors affecting wind dispersal--wind statistics, seed release height, and seed terminal velocity--determined independently of dispersal data. WALD's asymptotic power-law tail has an exponent of -3/2, a limiting value verified by a meta-analysis for a wide variety of measured dispersal kernels and larger than the exponent of the bivariate Student t-test (2Dt). We tested WALD using three dispersal data sets on forest trees, heathland shrubs, and grassland forbs and compared WALD's performance with that of other analytical mechanistic models (revised versions of the tilted Gaussian Plume model and the advection-diffusion equation), revealing fairest agreement between WALD predictions and measurements. Analytical mechanistic models, such as WALD, combine the advantages of simplicity and mechanistic understanding and are valuable tools for modeling large-scale, long-term plant population dynamics.

  20. Emergent Global Patterns of Ecosystem Structure and Function from a Mechanistic General Ecosystem Model

    PubMed Central

    Emmott, Stephen; Hutton, Jon; Lyutsarev, Vassily; Smith, Matthew J.; Scharlemann, Jörn P. W.; Purves, Drew W.

    2014-01-01

    Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures. PMID:24756001

  1. Model-free forecasting outperforms the correct mechanistic model for simulated and experimental data

    PubMed Central

    Perretti, Charles T.; Munch, Stephan B.; Sugihara, George

    2013-01-01

    Accurate predictions of species abundance remain one of the most vexing challenges in ecology. This observation is perhaps unsurprising, because population dynamics are often strongly forced and highly nonlinear. Recently, however, numerous statistical techniques have been proposed for fitting highly parameterized mechanistic models to complex time series, potentially providing the machinery necessary for generating useful predictions. Alternatively, there is a wide variety of comparatively simple model-free forecasting methods that could be used to predict abundance. Here we pose a rather conservative challenge and ask whether a correctly specified mechanistic model, fit with commonly used statistical techniques, can provide better forecasts than simple model-free methods for ecological systems with noisy nonlinear dynamics. Using four different control models and seven experimental time series of flour beetles, we found that Markov chain Monte Carlo procedures for fitting mechanistic models often converged on best-fit parameterizations far different from the known parameters. As a result, the correctly specified models provided inaccurate forecasts and incorrect inferences. In contrast, a model-free method based on state-space reconstruction gave the most accurate short-term forecasts, even while using only a single time series from the multivariate system. Considering the recent push for ecosystem-based management and the increasing call for ecological predictions, our results suggest that a flexible model-free approach may be the most promising way forward. PMID:23440207

  2. Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

    PubMed

    MacLeod, Miles; Nersessian, Nancy J

    2015-02-01

    In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding."

  3. The mechanistic-holistic divide revisited: The case of the lac operon.

    PubMed

    Racine, Valérie

    2016-10-01

    In this paper, I revisit the development of the repression model of genetic regulation in the lac operon to challenge a common application of a conceptual framework in the history of biology. I take Allen's (1978) account of the changes in the life sciences during the early and mid-twentieth century as an example of a common application of a framework based on the dichotomy between a mechanistic, or reductionist, approach to science and a holistic one. From this conceptual framework, Allen infers two general claims about the process of science and its goals: (1) that "mechanistic materialism" has often presented a more practical way to begin the study of complex phenomena in the life sciences, and (2) that the approach described as "holistic materialism" provides a more complete or accurate description of the natural world. The development of the lac operon model does not fit Allen's generalizations about scientific developments, and it can be used to cast some doubt on the scope of application of that conceptual framework. I argue that a better framework to interpret particular episodes in the history of molecular biology is to consider the ways in which biologists prioritize and track different aspects of the phenomena under study, rather than to focus on whether certain scientific practices are best described as developing from mechanistic to more holistic approaches. I end with some implications for the historiography of science by considering the appropriateness of different conceptual frameworks for different grains of resolution in the history of biology.

  4. Mechanistic models

    SciTech Connect

    Curtis, S.B.

    1990-09-01

    Several models and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the models, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) interaction'' of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in model development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL models is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to model the complex end point of radiation-induced carcinogenesis.

  5. Mechanistic models

    SciTech Connect

    Curtis, S.B.

    1990-09-01

    Several models and theories are reviewed that incorporate the idea of radiation-induced lesions (repairable and/or irreparable) that can be related to molecular lesions in the DNA molecule. Usually the DNA double-strand or chromatin break is suggested as the critical lesion. In the models, the shoulder on the low-LET survival curve is hypothesized as being due to one (or more) of the following three mechanisms: (1) ``interaction`` of lesions produced by statistically independent particle tracks; (2) nonlinear (i.e., linear-quadratic) increase in the yield of initial lesions, and (3) saturation of repair processes at high dose. Comparisons are made between the various approaches. Several significant advances in model development are discussed; in particular, a description of the matrix formulation of the Markov versions of the RMR and LPL models is given. The more advanced theories have incorporated statistical fluctuations in various aspects of the energy-loss and lesion-formation process. An important direction is the inclusion of physical and chemical processes into the formulations by incorporating relevant track structure theory (Monte Carlo track simulations) and chemical reactions of radiation-induced radicals. At the biological end, identification of repair genes and how they operate as well as a better understanding of how DNA misjoinings lead to lethal chromosome aberrations are needed for appropriate inclusion into the theories. More effort is necessary to model the complex end point of radiation-induced carcinogenesis.

  6. Deposited films with improved microstructures

    DOEpatents

    Patten, James W.; Moss, Ronald W.; McClanahan, Edwin D.

    1984-01-01

    Methods for improving microstructures of line-of-sight deposited films are described. Columnar growth defects ordinarily produced by geometrical shadowing during deposition of such films are eliminated without resorting to post-deposition thermal or mechanical treatments. The native, as-deposited coating qualities, including homogeneity, fine grain size, and high coating-to-substrate adherence, can thus be retained. The preferred method includes the steps of emitting material from a source toward a substrate to deposit a coating non-uniformly on the substrate surface, removing a portion of the coating uniformly over the surface, again depositing material onto the surface, but from a different direction, and repeating the foregoing steps. The quality of line-of-sight deposited films such as those produced by sputtering, progressively deteriorates as the angle of incidence between the flux and the surface becomes increasingly acute. Depositing non-uniformly, so that the coating becomes progressively thinner as quality deteriorates, followed by uniformly removing some of the coating, such as by resputtering, eliminates the poor quality portions, leaving only high quality portions of the coating. Subsequently sputtering from a different direction applies a high quality coating to other regions of the surface. Such steps can be performed either simultaneously or sequentially to apply coatings of a uniformly high quality, closed microstructure to three-dimensional or large planar surfaces.

  7. MODELING DEPOSITION OF INHALED PARTICLES

    EPA Science Inventory

    Modeling Deposition of Inhaled Particles: ABSTRACT

    The mathematical modeling of the deposition and distribution of inhaled aerosols within human lungs is an invaluable tool in predicting both the health risks associated with inhaled environmental aerosols and the therapeut...

  8. Variable temperature semiconductor film deposition

    DOEpatents

    Li, Xiaonan; Sheldon, Peter

    1998-01-01

    A method of depositing a semiconductor material on a substrate. The method sequentially comprises (a) providing the semiconductor material in a depositable state such as a vapor for deposition on the substrate; (b) depositing the semiconductor material on the substrate while heating the substrate to a first temperature sufficient to cause the semiconductor material to form a first film layer having a first grain size; (c) continually depositing the semiconductor material on the substrate while cooling the substrate to a second temperature sufficient to cause the semiconductor material to form a second film layer deposited on the first film layer and having a second grain size smaller than the first grain size; and (d) raising the substrate temperature, while either continuing or not continuing to deposit semiconductor material to form a third film layer, to thereby anneal the film layers into a single layer having favorable efficiency characteristics in photovoltaic applications. A preferred semiconductor material is cadmium telluride deposited on a glass/tin oxide substrate already having thereon a film layer of cadmium sulfide.

  9. Variable temperature semiconductor film deposition

    DOEpatents

    Li, X.; Sheldon, P.

    1998-01-27

    A method of depositing a semiconductor material on a substrate is disclosed. The method sequentially comprises (a) providing the semiconductor material in a depositable state such as a vapor for deposition on the substrate; (b) depositing the semiconductor material on the substrate while heating the substrate to a first temperature sufficient to cause the semiconductor material to form a first film layer having a first grain size; (c) continually depositing the semiconductor material on the substrate while cooling the substrate to a second temperature sufficient to cause the semiconductor material to form a second film layer deposited on the first film layer and having a second grain size smaller than the first grain size; and (d) raising the substrate temperature, while either continuing or not continuing to deposit semiconductor material to form a third film layer, to thereby anneal the film layers into a single layer having favorable efficiency characteristics in photovoltaic applications. A preferred semiconductor material is cadmium telluride deposited on a glass/tin oxide substrate already having thereon a film layer of cadmium sulfide.

  10. Particle Deposition in Granular Media

    SciTech Connect

    Tien, C.

    1992-01-01

    Objective is to understand aerosol deposition from gas streams flowing through granular media; this is important to the design of granular filtration systems. The following investigations were carried out: transient behavior of granular filtration of aerosols, and stochastic simulation of aerosol deposition in granular media.

  11. Geochemistry of sedimentary ore deposits

    SciTech Connect

    Maynard, J. B.

    1983-01-01

    A text providing a sedimentological treatment of a study on ore deposits, and especially as related to geochemistry. Excellently documented (about 5000 citations). Well indexed with the index of deposits and localities separated. Contents, Iron. Copper and silver. Aluminum and nickel. Manganese. Uranium. Lead and zinc. Volcanic-sedimentary ores. Appendix. Indexes.

  12. MODELING DEPOSITION OF INHALED PARTICLES

    EPA Science Inventory

    Modeling Deposition of Inhaled Particles: ABSTRACT

    The mathematical modeling of the deposition and distribution of inhaled aerosols within human lungs is an invaluable tool in predicting both the health risks associated with inhaled environmental aerosols and the therapeut...

  13. Vacuum vapor deposition

    NASA Technical Reports Server (NTRS)

    Poorman, Richard M. (Inventor); Weeks, Jack L. (Inventor)

    1995-01-01

    A method and apparatus is described for vapor deposition of a thin metallic film utilizing an ionized gas arc directed onto a source material spaced from a substrate to be coated in a substantial vacuum while providing a pressure differential between the source and the substrate so that, as a portion of the source is vaporized, the vapors are carried to the substrate. The apparatus includes a modified tungsten arc welding torch having a hollow electrode through which a gas, preferably inert, flows and an arc is struck between the electrode and the source. The torch, source, and substrate are confined within a chamber within which a vacuum is drawn. When the arc is struck, a portion of the source is vaporized and the vapors flow rapidly toward the substrate. A reflecting shield is positioned about the torch above the electrode and the source to ensure that the arc is struck between the electrode and the source at startup. The electrode and the source may be confined within a vapor guide housing having a duct opening toward the substrate for directing the vapors onto the substrate.

  14. Chemical vapor deposition growth

    NASA Technical Reports Server (NTRS)

    Ruth, R. P.; Manasevit, H. M.; Johnson, R. E.; Kenty, J. L.; Moudy, L. A.; Simpson, W. I.; Yang, J. J.

    1976-01-01

    A laboratory type CVD reactor system with a vertical deposition chamber and sample pedestal heated by an external RF coil has been extensively modified by installation of mass flow controllers, automatic process sequence timers, and special bellows-sealed air-operated valves for overall improved performance. Various film characterization procedures, including classical metallography, SEM analyses, X ray diffraction analyses, surface profilometry, and electrical measurements (resistivity, carrier concentration, mobility, spreading resistance profiles, and minority-carrier lifetime by the C-V-t method) area used to correlate Si sheet properties with CVD parameters and substrate properties. Evaluation procedures and measurements are given. Experimental solar cell structures were made both in epitaxial Si sheet (on sapphire substrates) and in polycrystalline material on alumina substrates, the former to provide an indication of what might be an upper limit on performance of the latter. Preliminary results are given, as obtained in cell structures not specially designed to allow for the unique properties of the sheet material, and fabricated in material known to be far from optimum for photovoltaic performance. Low power conversion efficiencies have been obtained in the epitaxial as well as the polycrystalline Si sheet.

  15. Chemical vapor deposition growth

    NASA Technical Reports Server (NTRS)

    Ruth, R. P.; Manasevit, H. M.; Campbell, A. G.; Johnson, R. E.; Kenty, J. L.; Moudy, L. A.; Shaw, G. L.; Simpson, W. I.; Yang, J. J.

    1978-01-01

    The objective was to investigate and develop chemical vapor deposition (CVD) techniques for the growth of large areas of Si sheet on inexpensive substrate materials, with resulting sheet properties suitable for fabricating solar cells that would meet the technical goals of the Low Cost Silicon Solar Array Project. The program involved six main technical tasks: (1) modification and test of an existing vertical-chamber CVD reactor system; (2) identification and/or development of suitable inexpensive substrate materials; (3) experimental investigation of CVD process parameters using various candidate substrate materials; (4) preparation of Si sheet samples for various special studies, including solar cell fabrication; (5) evaluation of the properties of the Si sheet material produced by the CVD process; and (6) fabrication and evaluation of experimental solar cell structures, using impurity diffusion and other standard and near-standard processing techniques supplemented late in the program by the in situ CVD growth of n(+)/p/p(+) sheet structures subsequently processed into experimental cells.

  16. Dense Deposit Disease

    PubMed Central

    Smith, Richard J.H; Harris, Claire L.; Pickering, Matthew C.

    2011-01-01

    Dense deposit disease (DDD) is an orphan disease that primarily affects children and young adults without sexual predilection. Studies of its pathophysiology have shown conclusively that it is caused by fluid-phase dysregulation of the alternative pathway of complement, however the role played by genetics and autoantibodies like C3 nephritic factors must be more thoroughly defined if we are to make an impact in the clinical management of this disease. There are currently no mechanism-directed therapies to offer affected patients, half of whom progress to end stage renal failure disease within 10 years of diagnosis. Transplant recipients face the dim prospect of disease recurrence in their allografts, half of which ultimately fail. More detailed genetic and complement studies of DDD patients may make it possible to identify protective factors prognostic for naïve kidney and transplant survival, or conversely risk factors associated with progression to renal failure and allograft loss. The pathophysiology of DDD suggests that a number of different treatments warrant consideration. As advances are made in these areas, there will be a need to increase healthcare provider awareness of DDD by making resources available to clinicians to optimize care for DDD patients. PMID:21601923

  17. Modeled Wet Nitrate Deposition

    EPA Pesticide Factsheets

    Modeled data on nitrate wet deposition was obtained from Dr. Jeff Grimm at Penn State Univ. Nitrate wet depostion causes acidification and eutrophication of surface water bodies. See below regarding decriptions on how original data was produced. These data will be part of future ReVA publications. The first, https://edg.epa.gov/data/Public/ORD/NERL/ReVA/ReVA_Data.zip, contains the variables used in this study (of which AGSL is one) and is freely available to the public. The second, www.waratah.com/region3edt is available to the general public to learn more about the ReVA program within EPA Region 3. The third, http://www.waratah.com/revanew/Welcome.asp, provides additional information about the tools and variables used in this program, but users must first obtain a user name and password to access it. A user name and password may be obtained from Vasu Kilaru at kilaru.vasu@epa.gov.

  18. Radioactive deposits of Nevada

    USGS Publications Warehouse

    Lovering, T.G.

    1954-01-01

    Thirty-five occurrences of radioactive rocks had been reported from Nevada prior to 1952. Twenty-five of these had been investigated by personnel of the U. S. Geological Surveyor of the U. S. Atomic Energy Commission. Of those investigated, uranium minerals were identified at 13 sites; two sites contained a thorium mineral (monazite); the source of radioactivity on nine properties was not ascertained, and one showed no abnormal radioactivity. Of the other reported occurrences, one is said to contain uraniferous hydrocarbons and nine are placers containing thorian monazite. Pitchblende occurs at two localities, the East Walker River area, and the Stalin's Present prospect, where it is sparsely disseminated in tabular bodies cutting granitic rocks. Other uranium minerals found in the state include: carnotite, tyuyamunite, autunite, torbernite, gummite, uranophane, kasolite, and an unidentified mineral which may be dumontite. Monazite is the only thorium mineral of possible economic importance that has been reported. From an economic standpoint, only four of the properties examined showed reserves of uranium ore in 1952; these are: the Green Monster mine, which shipped 5 tons of ore to Marysvale, Utah, during 1951; the Majuba Hill mine; the Stalin's Present prospect; and the West Willys claim in the Washington district. No estimate has been made of thorium reserves and no commercial deposits of thorium are known.

  19. Radioactive deposits of Nevada

    USGS Publications Warehouse

    Lovering, T.G.

    1953-01-01

    Thirty-five occurrences of radioactive rocks had been reported from Nevada prior to 1952. Twenty-five of these had been investigated by the U. S. Geological Survey and the U. S. Atomic Energy Commission. Of those investigated, uranium minerals were identified in 13; two contained a thorium mineral (monazite); the source of radioactivity on 7 properties was not ascertained; and one showed no abnormal radioactivity. Of the other reported occurrences, one is said to contain uraniferous hydrocarbons and 9 are placers containing thorian monazite. Pitchblende occurs at two localities; the East Walker River area, and the Stalin's Present prospect, where it is sparsely disseminated in tabular bodies cutting granitic rocks. Other uranium minerals found in the state include: carnotite, tyuyamunite, autunite, torbernite, gummite, uranophane, kasolite, and an unidentified mineral which may be dumontit. Monazite is the only thorium mineral of possible economic importance that has been reported. From an economic standpoint 9 only 4 of the properties examined showed reserves of uranium ore in 1952; these are: the Green Monster mine, which shipped 5 tons of ore to Marysvale, Utah, during 1951, the Majuba Hill mine, the Stalin's Present prospect, and the West Willys claim in the Washington district. Reserves of ore grade are small on all of these properties and probably cannot be developed commercially unless an ore-buying station is set up nearby. No estimate has been made of thorium reserves and no commercial deposits of thorium are known.

  20. Cerebrovascular lesions induce transient β-amyloid deposition

    PubMed Central

    Garcia-Alloza, Monica; Gregory, Julia; Kuchibhotla, Kishore V.; Fine, Sara; Wei, Ying; Ayata, Cenk; Frosch, Matthew P.; Greenberg, Steven M.

    2011-01-01

    Previous clinical studies have documented a close relationship between cerebrovascular disease and risk of Alzheimer's disease. We examined possible mechanistic interactions through use of experimental stroke models in a transgenic mouse model of β-amyloid deposition (APPswe/PS1dE9). Following middle cerebral artery occlusion, we observed a rapid increase in amyloid plaque burden in the region surrounding the infarction. In human tissue samples, however, we were unable to detect a localized increase in amyloid burden adjacent to cerebral infarcts. To resolve this discrepancy, we generated cerebral microstrokes in amyloid precursor protein mouse models with the photosensitive dye Rose bengal, and monitored plaque formation in real time using multiphoton microscopy. We observed a striking increase in the number of new plaques and amyloid angiopathy in the area immediately surrounding the infarcted area; however, the effect was transient, potentially resolving the discord between mouse and human tissue. We did not detect changes in candidate proteins related to β-amyloid generation or degradation such as β-amyloid-converting enzyme, amyloid precursor protein, presenilin 1, neprylisin or insulin-degrading enzyme. Together, these results demonstrate that strokes can trigger accelerated amyloid deposition, most likely through interference with amyloid clearance pathways. Additionally, this study indicates that focal ischaemia provides an experimental paradigm in which to study the mechanisms of plaque seeding and growth. PMID:22120142