Sample records for heterogeneous media molecular

  1. Molecular Mechanism of Heterogeneous Catalysis

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 6. Molecular Mechanism of Heterogeneous Catalysis - The 2007 Nobel Prize in Chemistry. R S Swathi K L Sebastian. General Article Volume 13 Issue 6 June 2008 pp 548-560 ...

  2. Snapshot wavefield decomposition for heterogeneous velocity media


    Holicki, M.E.; Wapenaar, C.P.A.


    We propose a novel directional decomposition operator for wavefield snapshots in heterogeneous-velocity media. The proposed operator demonstrates the link between the amplitude of pressure and particlevelocity plane waves in the wavenumber domain. The proposed operator requires two spatial Fourier transforms (one forward and one backward) per spatial dimension and time slice. To illustrate the operator we demonstrate its applicability to heterogeneous velocity models using a simple velocity-b...


    Energy Technology Data Exchange (ETDEWEB)

    C.T. Philip Chang; Changho Choi; Jeromy T. Hollenshead; Rudi Michalak; Jack Phan; Ramon Saavedra; John C. Slattery; Jinsoo Uh; Randi Valestrand; A. Ted Watson; Song Xue


    A critical and long-standing need within the petroleum industry is the specification of suitable petrophysical properties for mathematical simulation of fluid flow in petroleum reservoirs (i.e., reservoir characterization). The development of accurate reservoir characterizations is extremely challenging. Property variations may be described on many scales, and the information available from measurements reflect different scales. In fact, experiments on laboratory core samples, well-log data, well-test data, and reservoir-production data all represent information potentially valuable to reservoir characterization, yet they all reflect information about spatial variations of properties at different scales. Nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI) provide enormous potential for developing new descriptions and understandings of heterogeneous media. NMR has the rare capability to probe permeable media non-invasively, with spatial resolution, and it provides unique information about molecular motions and interactions that are sensitive to morphology. NMR well-logging provides the best opportunity ever to resolve permeability distributions within petroleum reservoirs. We develop MRI methods to determine, for the first time, spatially resolved distributions of porosity and permeability within permeable media samples that approach the intrinsic scale: the finest resolution of these macroscopic properties possible. To our knowledge, this is the first time that the permeability is actually resolved at a scale smaller than the sample. In order to do this, we have developed a robust method to determine of relaxation distributions from NMR experiments and a novel implementation and analysis of MRI experiments to determine the amount of fluid corresponding to imaging regions, which are in turn used to determine porosity and saturation distributions. We have developed a novel MRI experiment to determine velocity distributions within flowing experiments, and

  4. Snapshot wavefield decomposition for heterogeneous velocity media

    NARCIS (Netherlands)

    Holicki, M.E.; Wapenaar, C.P.A.


    We propose a novel directional decomposition operator for wavefield snapshots in heterogeneous-velocity media. The proposed operator demonstrates the link between the amplitude of pressure and particlevelocity plane waves in the wavenumber domain. The proposed operator requires two spatial Fourier

  5. Media Distribution in Heterogeneous Environments using IP-Multicast


    Parnes, Peter


    This document discusses problems and solutions around distribution of media in heterogeneous environments when using IP-multicast. This document discusses problems and solutions around distribution of media in heterogeneous environments when using IP-multicast.

  6. Modeling Endovascular Coils as Heterogeneous Porous Media (United States)

    Yadollahi Farsani, H.; Herrmann, M.; Chong, B.; Frakes, D.


    Minimally invasive surgeries are the stat-of-the-art treatments for many pathologies. Treating brain aneurysms is no exception; invasive neurovascular clipping is no longer the only option and endovascular coiling has introduced itself as the most common treatment. Coiling isolates the aneurysm from blood circulation by promoting thrombosis within the aneurysm. One approach to studying intra-aneurysmal hemodynamics consists of virtually deploying finite element coil models and then performing computational fluid dynamics. However, this approach is often computationally expensive and requires extensive resources to perform. The porous medium approach has been considered as an alternative to the conventional coil modeling approach because it lessens the complexities of computational fluid dynamics simulations by reducing the number of mesh elements needed to discretize the domain. There have been a limited number of attempts at treating the endovascular coils as homogeneous porous media. However, the heterogeneity associated with coil configurations requires a more accurately defined porous medium in which the porosity and permeability change throughout the domain. We implemented this approach by introducing a lattice of sample volumes and utilizing techniques available in the field of interactive computer graphics. We observed that the introduction of the heterogeneity assumption was associated with significant changes in simulated aneurysmal flow velocities as compared to the homogeneous assumption case. Moreover, as the sample volume size was decreased, the flow velocities approached an asymptotical value, showing the importance of the sample volume size selection. These results demonstrate that the homogeneous assumption for porous media that are inherently heterogeneous can lead to considerable errors. Additionally, this modeling approach allowed us to simulate post-treatment flows without considering the explicit geometry of a deployed endovascular coil mass

  7. Shock wave structure in heterogeneous reactive media

    Energy Technology Data Exchange (ETDEWEB)

    Baer, M.R.


    Continuum mixture theory and mesoscale modeling are applied to describe the behavior of shock-loaded heterogeneous media. One-dimensional simulations of gas-gun experiments demonstrate that the wave features are well described by mixture theory, including reflected wave behavior and conditions where significant reaction is initiated. Detailed wave fields are resolved in numerical simulations of impact on a lattice of discrete explosive {open_quotes}crystals{close_quotes}. It is shown that rapid distortion first occurs at material contact points; the nature of the dispersive fields includes large amplitude fluctuations of stress over several particle pathlengths. Localization of energy causes {open_quotes}hot-spots{close_quotes} due to shock focusing and plastic work as material flows into interstitial regions.

  8. A molecular view of heterogeneous catalysis

    DEFF Research Database (Denmark)

    Christensen, Claus H.; Nørskov, Jens Kehlet


    The establishment of a molecular view of heterogeneous catalysis has been hampered for a number of reasons. There are, however, recent developments, which show that we are now on the way towards reaching a molecular-scale picture of the way solids work as catalysts. By a combination of new...... by enabling a rational design of new catalysts. We illustrate this important development in heterogeneous catalysis by highlighting recent examples of catalyst systems for which it has been possible to achieve such a detailed understanding. In particular, we emphasize examples where this progress has made...

  9. Lanthanum(III)-catalyzed disproportionation of hydrogen peroxide: a heterogeneous generator of singlet molecular oxygen-1O2 (1Deltag)-in near-neutral aqueous and organic media for peroxidation of electron-rich substrates. (United States)

    Nardello, Véronique; Barbillat, Jacques; Marko, Jean; Witte, Peter T; Alsters, Paul L; Aubry, Jean-Marie


    The decomposition of hydrogen peroxide into singlet molecular oxygen-(1)O(2) ((1)Delta(g))-in the presence of lanthanum(iii) salts was studied by monitoring its characteristic IR luminescence at 1270 nm. The process was found to be heterogeneously catalyzed by La(III), provided that the heterogeneous catalyst is generated in situ. The yield of (1)O(2) generation was assessed as 45+/-5 % both in water and in methanol. The pH-dependence on the rate of (1)O(2) generation corresponds to a bell-shaped curve from pH 4.5 to 13 with a maximum around pH 8. The study of the influence of H(2)O(2) showed that the formation of (1)O(2) begins as soon as one equivalent of H(2)O(2) is introduced. It then increases drastically up to two equivalents and more smoothly above. Unlike all other metal salt catalyst systems known to date for H(2)O(2) disproportionation, this chemical source of (1)O(2) is able to generate (1)O(2) not only in basic media, but also under neutral and slightly acidic conditions. In addition, this La-based catalyst system has a very low tendency to induce unwanted oxygenating side reactions, such as epoxidation of alkenes. These two characteristics of the heterogeneous lanthanum catalyst system allow non-photochemical (i.e., "dark") singlet oxygenation of substrate classes that cannot be peroxidized successfully with conventional molybdate catalysts, such as allylic alcohols and alkenyl amines.

  10. Wave Scattering in Heterogeneous Media using the Finite Element Method (United States)


    AFRL-AFOSR-JP-TR-2016-0086 Wave Scattering in Heterogeneous Media using the Finite Element Method Chiruvai Vendhan INDIAN INSTITUTE OF TECHNOLOGY...Scattering in Heterogeneous Media using the Finite Element Method 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386-12-1-4026 5c.  PROGRAM ELEMENT NUMBER 61102F 6...heterogeneous ocean acoustic waveguide. 15.  SUBJECT TERMS Acoustics, Finite Element Methods , Wave propagation 16.  SECURITY CLASSIFICATION OF: 17

  11. Heterogeneity and Scaling in Geologic Media

    Energy Technology Data Exchange (ETDEWEB)

    Gregory N. Boitnott; Gilles Y. Bussod; Paul N. Hagin; Stephen R. Brown


    The accurate characterization and remediation of contaminated subsurface environments requires the detailed knowledge of subsurface structures and flow paths. Enormous resources are invested in scoping and characterizing sites using core sampling, 3-D geophysical surveys, well tests, etc.... Unfortunately, much of the information acquired is lost to compromises and simplifications made in constructing numerical grids for the simulators used to predict flow and transport from the contaminated area to the accessible environment. In rocks and soils, the bulk geophysical and transport properties of the matrix and of fracture systems are determined by the juxtaposition of geometric features at many length scales. In the interest of computational efficiency, recognized heterogeneities are simplified, averaged out, or entirely ignored in spite of recent studies that recognize that: (1) Structural and lithologic heterogeneities exist on all scales in rocks. (2) Small heterogeneities influence, and can control the physical and chemical properties of rocks. In this work we propose a physically based approach for the description and treatment of heterogeneities, that highlights the use of laboratory equipment designed to measure the effect on physical properties of fine scale heterogeneities observed in rocks and soils. We then discuss the development of an integration methodology that uses these measurements to develop and upscale flow and transport models. Predictive simulations are 'calibrated' to the measured heterogeneity data, and subsequently upscaled in a way that is consistent with the transport physics and the efficient use of environmental geophysics. This methodology provides a more accurate interpretation and representation of the subsurface for both environmental engineering and remediation. We show through examples, (i) the important influence of even subtle heterogeneity in the interpreting of geophysical data, and (ii) how physically based upscaling

  12. Heterogeneous self-assembled media for biopolymerization

    DEFF Research Database (Denmark)

    Monnard, Pierre-Alain


    compartments and lipid-bilayer lattices. Another kind of media is represented by self-assembled phases in the reaction medium, e.g., in water-ice matrices that are formed by two co-existing aqueous phases (a solid phase and a concentrated liquid phase) when an aqueous solution is cooled below its freezing...... point, but above the eutectic point. These media have the capacity to assemble chemical molecules or complex catalytic assemblies into unique configurations that are unstable or unavailable in bulk aqueous phases. Reactions can then proceed which do not readily occur in homogeneous solutions. To gauge...

  13. Reporting tumor molecular heterogeneity in histopathological diagnosis.

    Directory of Open Access Journals (Sweden)

    Andrea Mafficini

    Full Text Available Detection of molecular tumor heterogeneity has become of paramount importance with the advent of targeted therapies. Analysis for detection should be comprehensive, timely and based on routinely available tumor samples.To evaluate the diagnostic potential of targeted multigene next-generation sequencing (TM-NGS in characterizing gastrointestinal cancer molecular heterogeneity.35 gastrointestinal tract tumors, five of each intestinal type gastric carcinomas, pancreatic ductal adenocarcinomas, pancreatic intraductal papillary mucinous neoplasms, ampulla of Vater carcinomas, hepatocellular carcinomas, cholangiocarcinomas, pancreatic solid pseudopapillary tumors were assessed for mutations in 46 cancer-associated genes, using Ion Torrent semiconductor-based TM-NGS. One ampulla of Vater carcinoma cell line and one hepatic carcinosarcoma served to assess assay sensitivity. TP53, PIK3CA, KRAS, and BRAF mutations were validated by conventional Sanger sequencing.TM-NGS yielded overlapping results on matched fresh-frozen and formalin-fixed paraffin-embedded (FFPE tissues, with a mutation detection limit of 1% for fresh-frozen high molecular weight DNA and 2% for FFPE partially degraded DNA. At least one somatic mutation was observed in all tumors tested; multiple alterations were detected in 20/35 (57% tumors. Seven cancers displayed significant differences in allelic frequencies for distinct mutations, indicating the presence of intratumor molecular heterogeneity; this was confirmed on selected samples by immunohistochemistry of p53 and Smad4, showing concordance with mutational analysis.TM-NGS is able to detect and quantitate multiple gene alterations from limited amounts of DNA, moving one step closer to a next-generation histopathologic diagnosis that integrates morphologic, immunophenotypic, and multigene mutational analysis on routinely processed tissues, essential for personalized cancer therapy.

  14. Thermal non-equilibrium in heterogeneous media

    CERN Document Server

    de Lemos, Marcelo J S


    This book presents, in a self-contained fashion, a series of studies on flow and heat transfer in porous media, in which distinct energy balances are considered for the porous matrix and for the permeating fluid. Detailed mathematical modeling is presented considering both volume and time averaging operators simultaneously applied to the governing equations. System involving combustion in the gaseous phase, moving bed and double-diffusion mechanism are analyzed. Numerical results are presented for each case. In the end, this book contains the description of a tool that might benefit engineers in developing and designing more efficient thermal equipment.

  15. Plume dynamics in heterogeneous porous media (United States)

    Neufeld, Jerome A.; Huppert, Herbert E.


    Buoyancy driven flows in layered porous media are present in many geological settings and play an important role in the mixing of fluids, from the dispersal of pollutants in underground aquifers to enhanced oil recovery techniques and, of more recent importance, the sequestration of carbon dioxide (CO2). Seismic images of the rise of a buoyant CO2 plume at Sleipner in the North Sea indicate that these plumes are greatly influenced by a vertical array of thin lenses of relatively low permeability material. We model propagation of CO2 at each layer as a gravity current in a porous medium which propagates along, and drains through, a thin, low permeability seal. Drainage, driven both by hydrostatic pressure and the body force on the draining fluid, leads to an initial rapid advance followed by a gradual retreat of the current to a steady-state. By incorporating a vertical array of these single layer models we are able to capture the rise of the buoyant plume in layered reservoirs. We find that the plume is characterized by a broad head with a tail given by the steady state extent.

  16. Non-Enzymatic biopolymerization reactions supported by heterogeneous media

    DEFF Research Database (Denmark)

    Monnard, Pierre-Alain


    Heterogeneous media, such as micro-structured aqueous environments, could offer an alternative approach to the synthesis of biopolymers with novel functions. Structured media are here defined as specialized, self-assembled structures that are formed, e.g, by amphiphiles, such as liposomes, emulsion...... or unavailable in bulk aqueous phases. Reactions can then proceed which do not readily occur in homogeneous solutions. To gauge the potential of this idea, we have investigated the non-enzymatic polymerization of RNA from monomers in the presence of various catalysts....

  17. Inferring Molecular Processes Heterogeneity from Transcriptional Data. (United States)

    Gogolewski, Krzysztof; Wronowska, Weronika; Lech, Agnieszka; Lesyng, Bogdan; Gambin, Anna


    RNA microarrays and RNA-seq are nowadays standard technologies to study the transcriptional activity of cells. Most studies focus on tracking transcriptional changes caused by specific experimental conditions. Information referring to genes up- and downregulation is evaluated analyzing the behaviour of relatively large population of cells by averaging its properties. However, even assuming perfect sample homogeneity, different subpopulations of cells can exhibit diverse transcriptomic profiles, as they may follow different regulatory/signaling pathways. The purpose of this study is to provide a novel methodological scheme to account for possible internal, functional heterogeneity in homogeneous cell lines, including cancer ones. We propose a novel computational method to infer the proportion between subpopulations of cells that manifest various functional behaviour in a given sample. Our method was validated using two datasets from RNA microarray experiments. Both experiments aimed to examine cell viability in specific experimental conditions. The presented methodology can be easily extended to RNA-seq data as well as other molecular processes. Moreover, it complements standard tools to indicate most important networks from transcriptomic data and in particular could be useful in the analysis of cancer cell lines affected by biologically active compounds or drugs.

  18. Human Rights Event Detection from Heterogeneous Social Media Graphs. (United States)

    Chen, Feng; Neill, Daniel B


    Human rights organizations are increasingly monitoring social media for identification, verification, and documentation of human rights violations. Since manual extraction of events from the massive amount of online social network data is difficult and time-consuming, we propose an approach for automated, large-scale discovery and analysis of human rights-related events. We apply our recently developed Non-Parametric Heterogeneous Graph Scan (NPHGS), which models social media data such as Twitter as a heterogeneous network (with multiple different node types, features, and relationships) and detects emerging patterns in the network, to identify and characterize human rights events. NPHGS efficiently maximizes a nonparametric scan statistic (an aggregate measure of anomalousness) over connected subgraphs of the heterogeneous network to identify the most anomalous network clusters. It summarizes each event with information such as type of event, geographical locations, time, and participants, and provides documentation such as links to videos and news reports. Building on our previous work that demonstrates the utility of NPHGS for civil unrest prediction and rare disease outbreak detection, we present an analysis of human rights events detected by NPHGS using two years of Twitter data from Mexico. NPHGS was able to accurately detect relevant clusters of human rights-related tweets prior to international news sources, and in some cases, prior to local news reports. Analysis of social media using NPHGS could enhance the information-gathering missions of human rights organizations by pinpointing specific abuses, revealing events and details that may be blocked from traditional media sources, and providing evidence of emerging patterns of human rights violations. This could lead to more timely, targeted, and effective advocacy, as well as other potential interventions.

  19. Vorticity and upscaled dispersion in 3D heterogeneous porous media (United States)

    Di Dato, Mariaines; Chiogna, Gabriele; de Barros, Felipe; Bellin, Alberto; Fiori, Aldo


    Modeling flow in porous media is relevant for many environmental, energy and industrial applications. From an environmental perspective, the relevance of porous media flow becomes evident in subsurface hydrology. In general, flow in natural porous media is creeping, yet the large variability in the hydraulic conductivity values encountered in natural aquifers leads to highly heterogeneous flow fields. This natural variability in the conductivity field will affect both dilution rates of chemical species and reactive mixing. A physical consequence of this heterogeneity is also the presence of a various localized kinematical features such as straining, shearing and vorticity in aquifers, which will influence the shape of solute clouds and its fate and transport. This work aims in fundamentally characterizing the vorticity field in spatially heterogeneous flow fields as a function of their statistical properties in order to analyze the impact on transport processes. In our study, three-dimensional porous formations are constructed with an ensemble of N independent, non-overlapping spheroidal inclusions submerged into an homogeneous matrix, of conductivity K0. The inclusions are randomly located in a domain of volume W and are fully characterized by the geometry of spheroid (oblate or prolate), their conductivity K (random and drawn from a given probability density function fκ), the centroid location ¯x, the axes ratio e, the orientation of the rotational axis (α1,α2) and the volume w. Under the assumption of diluted medium, the flow problem is solved analitically by means of only two parameters: the conductivity contrast κ = K/K0 and the volume fraction n = Nw/W . Through the variation of these parameters of the problem, it is possible to approximate the structure of natural heterogeneous porous media. Using a random distribution of the orientation of the inclusions, we create media defined by the same global anisotropy f = Iz/Ix but different micro

  20. Molecular dynamics study on mechanism of preformed particle gel transporting through nanopores: Surface chemistry and heterogeneity (United States)

    Cui, Peng; Zhang, Heng; Ma, Ying; Hao, Qingquan; Liu, Gang; Sun, Jichao; Yuan, Shiling


    The translocation behavior of preformed particle gel (PPG) in porous media is crucial for its application in enhanced oil recovery. By means of non-equilibrium molecular dynamics simulation, the translocation mechanism of PPG confined in different silica nanopores were investigated. The influence of surface chemistry and chemical heterogeneity of silica nanopore on the translocation process was revealed. As the degree of surface hydroxylation increases and the heterogeneity decreases, the pulling force needed to drive PPG decreases. We infer that the nanopore's surface (i.e. surface chemistry and heterogeneity) affects the translocation of PPG indirectly by forming different hydration layers.

  1. Imaging multiple local changes in heterogeneous media with diffuse waves. (United States)

    Planès, Thomas; Larose, Eric; Rossetto, Vincent; Margerin, Ludovic


    This study focuses on imaging local changes in heterogeneous media. The method employed is demonstrated and validated using numerical experiments of acoustic wave propagation in a multiple scattering medium. Changes are simulated by adding new scatterers of different sizes at various positions in the medium, and the induced decorrelation of the diffuse (coda) waveforms is measured for different pairs of sensors. The spatial and temporal dependences of the decorrelation are modeled through a diffuse sensitivity kernel, based on the intensity transport in the medium. The inverse problem is then solved with a linear least square algorithm, which leads to a map of scattering cross section density of the changes.

  2. Multiscale analysis and computation for flows in heterogeneous media

    Energy Technology Data Exchange (ETDEWEB)

    Efendiev, Yalchin [Texas A & M Univ., College Station, TX (United States); Hou, T. Y. [California Inst. of Technology (CalTech), Pasadena, CA (United States); Durlofsky, L. J. [Stanford Univ., CA (United States); Tchelepi, H. [Stanford Univ., CA (United States)


    Our work in this project is aimed at making fundamental advances in multiscale methods for flow and transport in highly heterogeneous porous media. The main thrust of this research is to develop a systematic multiscale analysis and efficient coarse-scale models that can capture global effects and extend existing multiscale approaches to problems with additional physics and uncertainties. A key emphasis is on problems without an apparent scale separation. Multiscale solution methods are currently under active investigation for the simulation of subsurface flow in heterogeneous formations. These procedures capture the effects of fine-scale permeability variations through the calculation of specialized coarse-scale basis functions. Most of the multiscale techniques presented to date employ localization approximations in the calculation of these basis functions. For some highly correlated (e.g., channelized) formations, however, global effects are important and these may need to be incorporated into the multiscale basis functions. Other challenging issues facing multiscale simulations are the extension of existing multiscale techniques to problems with additional physics, such as compressibility, capillary effects, etc. In our project, we explore the improvement of multiscale methods through the incorporation of additional (single-phase flow) information and the development of a general multiscale framework for flows in the presence of uncertainties, compressible flow and heterogeneous transport, and geomechanics. We have considered (1) adaptive local-global multiscale methods, (2) multiscale methods for the transport equation, (3) operator-based multiscale methods and solvers, (4) multiscale methods in the presence of uncertainties and applications, (5) multiscale finite element methods for high contrast porous media and their generalizations, and (6) multiscale methods for geomechanics. Below, we present a brief overview of each of these contributions.

  3. Entrapment and dissolution of DNAPLs in heterogeneous porous media. (United States)

    Bradford, Scott A; Rathfelder, Klaus M; Lang, John; Abriola, Linda M


    Two-dimensional multiphase flow and transport simulators were refined and used to numerically investigate the entrapment and dissolution behavior of tetrachloroethylene (PCE) in heterogeneous porous media containing spatial variations in wettability. Measured hydraulic properties, residual saturations, and dissolution parameters were employed in these simulations. Entrapment was quantified using experimentally verified hydraulic property and residual saturation models that account for hysteresis and wettability variations. The nonequilibrium dissolution of PCE was modeled using independent estimates of the film mass transfer coefficient and interfacial area for entrapped and continuous (PCE pools or films) saturations. Flow simulations demonstrate that the spatial distribution of PCE is highly dependent on subsurface wettability characteristics that create differences in PCE retention mechanisms and the presence of subsurface capillary barriers. For a given soil texture, the maximum and minimum PCE infiltration depth was obtained when the sand had intermediate (an organic-wet mass fraction of 25%) and strong (water- or organic-wet) wettability conditions, respectively. In heterogeneous systems, subsurface wettability variations were also found to enhance or diminish the performance of soil texture-induced capillary barriers. The dissolution behavior of PCE was found to depend on the soil wettability and the spatial PCE distribution. Shorter dissolution times tended to occur when PCE was distributed over large regions due to an increased access of flowing water to the PCE. In heterogeneous systems, capillary barriers that produced high PCE saturations tended to exhibit longer dissolution times.

  4. Fundamental Problems of the Electrodynamics of Heterogeneous Media

    Directory of Open Access Journals (Sweden)

    N. N. Grinchik


    Full Text Available The consistent physic-mathematical model of propagation of an electromagnetic wave in a heterogeneous medium is constructed using the generalized wave equation and the Dirichlet theorem. Twelve conditions at the interfaces of adjacent media are obtained and justified without using a surface charge and surface current in explicit form. The conditions are fulfilled automatically in each section of counting schemes for calculations. A consistent physicomathematical model of interaction of nonstationaly electric and thermal fields in a layered medium with allowance or mass transfer is constructed. The model is based on the methods of thermodynamics and on the equations of an electromagnetic field and is formulated without explicit separation of the charge carriers and the charge of an electric double layer.

  5. Variational calculation of the effective fluid permeability of heterogeneous media (United States)

    Hristopulos, Dionissios T.; Christakos, George


    We evaluate the effective permeability of heterogeneous media with Gaussian local permeability disorder using the replica-variational approach. We obtain integral equations that determine the effective permeability kernel, and we study specific cases that admit analytical solutions. Specifically, in the case of homogeneous disorder we obtain a variational estimate for the uniform effective permeability. We compare the results of our analytical calculations with experimental and numerical data. Finally, we model the behavior of the effective permeability in the preasymptotic regime by means of momentum filters. Explicit finite-size expressions are obtained in terms of a support function that increases monotonically with the ratio of the support scale over the correlation length of the disorder. It is found that the asymptotic effective permeability is approached at a slower rate than expected.

  6. Heterogeneously Catalyzed Oxidation Reactions Using Molecular Oxygen

    DEFF Research Database (Denmark)

    Beier, Matthias Josef

    with a carboxylic acid resulting in TONs of up to 2000. In the absence of the carboxylic acid, ceria inhibited the reaction exhibiting radical scavenger properties. Contrary to p-xylene, neither ethylbenzene nor cumene conversion was promoted by ceria even in the presence of a carboxylic acid. Substantial leaching......Heterogeneously catalyzed selective oxidation reactions have attracted a lot of attention in recent time. The first part of the present thesis provides an overview over heterogeneous copper and silver catalysts for selective oxidations in the liquid phase and compared the performance and catalytic...... that both copper and silver can function as complementary catalyst materials to gold showing different catalytic properties and being more suitable for hydrocarbon oxidation reactions. Potential opportunities for future research were outlined. In an experimental study, the potential of silver as a catalyst...

  7. Flow of miscible and immiscible hydrocarbons in heterogeneous porous media

    Energy Technology Data Exchange (ETDEWEB)

    Butts, M.B.


    A series of large-scale two-dimensional physical model studies has been carried out in order to better understand and predict the multiphase flow of hydrocarbon contaminants and the release of the water-soluble fraction of such contaminants into the groundwater stream. The detailed measurements of the fluid saturations within the bulk hydrocarbon plume as well as the aqueous concentrations recorded downstream should provide a useful data set for testing and improving numerical models of both multiphase flow and transport. Predictions of a numerical model of immiscible multiphase flow developed in the petroleum industry were found to compare favourably with the observed oil plume for the case of an immiscible oil spill. Nevertheless, subtle layering within the experimental flume altered the long-term development of the oil plume in a manner not predicted by the numerical model. A stochastic model for three-dimensional, two-phase incompressible flow in heterogeneous soil and rock formations is developed. Analytical solutions for the resulting stochastic differential equations are derived for asymptotic flows using a perturbation approach. These solutions were used to derive general expressions for the large-scale (effective) properties for large-scale two-phase flow in porous media. An important observation from this analysis is that general large-scale flow in heterogeneous soils cannot be predicted on the basis of simple averages of the soil hydraulic properties alone. The large-scale capillary pressure saturation relation is evaluated for imbibition into a wet soil or rock formation. (EG) 194 refs.

  8. Transition Fronts in Time Heterogeneous and Random Media of Ignition Type


    Shen, Wenxian; Shen, Zhongwei


    The current paper is devoted to the investigation of wave propagation phenomenon in reaction-diffusion equations with ignition type nonlinearity in time heterogeneous and random media. It is proven that such equations in time heterogeneous media admit transition fronts or generalized traveling wave solutions with time dependent profiles and that such equations in time random media admit generalized traveling wave solutions with random profiles. Important properties of generalized traveling wa...

  9. Complexity Reduction of Multiphase Flows in Heterogeneous Porous Media

    KAUST Repository

    Ghommem, Mehdi


    In this paper, we apply mode decomposition and interpolatory projection methods to speed up simulations of two-phase flows in heterogeneous porous media. We propose intrusive and nonintrusive model-reduction approaches that enable a significant reduction in the size of the subsurface flow problem while capturing the behavior of the fully resolved solutions. In one approach, we use the dynamic mode decomposition. This approach does not require any modification of the reservoir simulation code but rather post-processes a set of global snapshots to identify the dynamically relevant structures associated with the flow behavior. In the second approach, we project the governing equations of the velocity and the pressure fields on the subspace spanned by their proper-orthogonal-decomposition modes. Furthermore, we use the discrete empirical interpolation method to approximate the mobility-related term in the global-system assembly and then reduce the online computational cost and make it independent of the fine grid. To show the effectiveness and usefulness of the aforementioned approaches, we consider the SPE-10 benchmark permeability field, and present a numerical example in two-phase flow. One can efficiently use the proposed model-reduction methods in the context of uncertainty quantification and production optimization.

  10. Flow and travel time statistics in highly heterogeneous porous media (United States)

    Gotovac, Hrvoje; Cvetkovic, Vladimir; Andricevic, Roko


    In this paper we present flow and travel time ensemble statistics based on a new simulation methodology, the adaptive Fup Monte Carlo method (AFMCM). As a benchmark case, we considered two-dimensional steady flow in a rectangular domain characterized by multi-Gaussian heterogeneity structure with an isotropic exponential correlation and lnK variance σY2 up to 8. Advective transport is investigated using the travel time framework where Lagrangian variables (e.g., velocity, transverse displacement, or travel time) depend on space rather than on time. We find that Eulerian and Lagrangian velocity distributions diverge for increasing lnK variance due to enhanced channeling. Transverse displacement is a nonnormal for all σY2 and control planes close to the injection area, but after xIY = 20 was found to be nearly normal even for high σY2. Travel time distribution deviates from the Fickian model for large lnK variance and exhibits increasing skewness and a power law tail for large lnK variance, the slope of which decreases for increasing distance from the source; no anomalous features are found. Second moment of advective transport is analyzed with respect to the covariance of two Lagrangian velocity variables: slowness and slope which are directly related to the travel time and transverse displacement variance, which are subsequently related to the longitudinal and transverse dispersion. We provide simple estimators for the Eulerian velocity variance, travel time variance, slowness, and longitudinal dispersivity as a practical contribution of this analysis. Both two-parameter models considered (the advection-dispersion equation and the lognormal model) provide relatively poor representations of the initial part of the travel time probability density function in highly heterogeneous porous media. We identify the need for further theoretical and experimental scrutiny of early arrival times, and the need for computing higher-order moments for a more accurate

  11. Molecular and prognostic heterogeneity of microsatellite-unstable colorectal cancer. (United States)

    Kim, Jung Ho; Kang, Gyeong Hoon


    Colorectal cancers (CRCs) with a high level of microsatellite instability (MSI-H) are clinicopathologically distinct tumors characterized by predominance in females, proximal colonic localization, poor differentiation, mucinous histology, tumor-infiltrating lymphocytes, a Crohn's-like lymphoid reaction and a favorable prognosis. In terms of their molecular features, MSI-H CRCs are heterogeneous tumors associated with various genetic and epigenetic alterations, including DNA mismatch repair deficiency, target microsatellite mutations, BRAF mutations, a CpG island methylator phenotype-high (CIMP-H) status, and a low level of genomic hypomethylation. The molecular heterogeneity of MSI-H CRCs also depends on ethnic differences; for example, in Eastern Asian countries, relatively low frequencies of CIMP-H and BRAF mutations have been observed in MSI-H CRCs compared to Western countries. Although the prognostic features of MSI-H CRCs include a favorable survival of patients and low benefit of adjuvant chemotherapy, there may be prognostic differences based on the molecular heterogeneity of MSI-H CRCs. Here, we have reviewed and discussed the molecular and prognostic features of MSI-H CRCs, as well as several putative prognostic or predictive molecular markers, including HSP110 expression, beta2-microglobulin mutations, myosin 1a expression, CDX2/CK20 expression, SMAD4 expression, CIMP status and LINE-1 methylation levels.

  12. Overcoming tumor heterogeneity in the molecular diagnosis of urological cancers. (United States)

    Donovan, Michael J; Cordon-Cardo, Carlos


    Our understanding of tumor heterogeneity and impact on treatment response is still in its infancy, presenting significant challenges to the molecular pathologist, treating physician and ultimately for the patient. Given that tumor recurrence due to treatment resistance is the most common cause of cancer death, there remains a critical unmet need to change the current paradigm. The mechanisms which underlie tumor heterogeneity can be broadly divided into genomic instability and non-mutational processes, including stochastic variations in cellular responses, modulation by tumor microenvironment and or phenotypic/ functional plasticity relating to cancer stem cells. We believe that these biological mechanisms are not mutually exclusive and emphasize the need for more suitable methodologies to exploit the spatiotemporal patterns of intratumoral heterogeneity using novel approaches such as quantitative tissue-based biomarker assessment and systemic fluid analytics. Generating a comprehensive patient-centric phenotypic disease profile should generate a 'codex' which can be employed to change the current treatment decision process.

  13. Mass media and heterogeneous bounds of confidence in continuous opinion dynamics


    Pineda, M.; Buendia, G. M.


    This work focus on the effects of an external mass media on continuous opinion dynamics with heterogeneous bounds of confidence. We modified the original Deffuant et al. and Hegselmann and Krause models to incorporate both, an external mass media and a heterogeneous distribution of confidence levels. We analysed two cases, one where only two bounds of confidence are taken into account, and other were each individual of the system has her/his own characteristic level of confidence. We found th...

  14. Compositional multiphase flow and transport in heterogeneous porous media

    Energy Technology Data Exchange (ETDEWEB)

    Huber, R.U.


    This work first treats the conceptual models for the description of multiphase flow processes in porous media. The thermodynamic laws are explained and the description and quantification of multi-fluid equilibria are discussed in order to account for fluid composition. The fully and weakly coupled approaches for the mathematical description of such flow processes with respect to systems consisting of two and three fluid phases as well as with respect to compositional single and multiphase systems are assessed. For the discretization of the two-phase flow equations node- and cell-centered finite volume methods and mixed and mixed-hybrid finite element approaches are applied. Based upon these methods five solution algorithms are developed. Four of these algorithms are based on the simultaneous solution of the discretized equations in combination with the Newton-Raphson technique. Methods 1 and 2 treat two- three-phase flow processes, Method 3 applies to the solution of partially miscible three-component systems while Method 4 is created for three-phase three-component systems. The latter method uses a variable substitution dependent on the local presence of the fluid phases. Method 5 is based on the IMPES/IMPESC concept. The time-implicit pressure equation is discretized with the mixed-hybrid finite element method. The saturation and concentration equations, respectively, are solved with a cell-centered finite volume scheme. The developed algorithms are applied to the two- and three-phase Buckley-Leverett problems. A partitioning interwell tracer test is simulated. The propagation behavior of nonaqueous phase liquids (NAPLs) in the saturated and unsaturated ground zone under the influence of heterogeneities are examined. In addition, a larger-scale experiment is simulated, which involves an injection of trichloroethylene into the subsurface and the subsequent distribution. Here, the development of a dissolved contaminant plume as well as the behavior of organic

  15. The molecular and cellular heterogeneity of pancreatic ductal adenocarcinoma. (United States)

    Samuel, Nardin; Hudson, Thomas J


    Current standard therapies for pancreatic ductal adenocarcinoma have failed to attenuate the aggressiveness of this disease or confer notable improvements in survival. Previous molecular research into pancreatic cancers, along with advances in sequencing technologies, have identified many altered genes in patients with pancreatic cancer and revealed the marked genetic heterogeneity of individual tumors. Thus, the lack of success of conventional empiric therapy can be partly attributed to the underlying heterogeneity of pancreatic tumors. The genetic alterations that have been detected in pancreatic cancer range from simple mutations at the level of base pairs to complex chromosomal structural changes and rearrangements. The identification of molecular changes that are unique to an individual patient's tumors, and the subsequent development of strategies to target the tumors in a personalized approach to therapeutics, is a necessary advance to improve therapy for patients with this disease.

  16. Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes (United States)

    Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten


    Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

  17. Local sparse bump hunting reveals molecular heterogeneity of colon tumors. (United States)

    Dazard, Jean-Eudes; Rao, J Sunil; Markowitz, Sanford


    The question of molecular heterogeneity and of tumoral phenotype in cancer remains unresolved. To understand the underlying molecular basis of this phenomenon, we analyzed genome-wide expression data of colon cancer metastasis samples, as these tumors are the most advanced and hence would be anticipated to be the most likely heterogeneous group of tumors, potentially exhibiting the maximum amount of genetic heterogeneity. Casting a statistical net around such a complex problem proves difficult because of the high dimensionality and multicollinearity of the gene expression space, combined with the fact that genes act in concert with one another and that not all genes surveyed might be involved. We devise a strategy to identify distinct subgroups of samples and determine the genetic/molecular signature that defines them. This involves use of the local sparse bump hunting algorithm, which provides a much more optimal and biologically faithful transformed space within which to search for bumps. In addition, thanks to the variable selection feature of the algorithm, we derived a novel sparse gene expression signature, which appears to divide all colon cancer patients into two populations: a population whose expression pattern can be molecularly encompassed within the bump and an outlier population that cannot be. Although all patients within any given stage of the disease, including the metastatic group, appear clinically homogeneous, our procedure revealed two subgroups in each stage with distinct genetic/molecular profiles. We also discuss implications of such a finding in terms of early detection, diagnosis and prognosis. Copyright © 2011 John Wiley & Sons, Ltd.

  18. Analytical and experimental analysis of solute transport in heterogeneous porous media. (United States)

    Wu, Lei; Gao, Bin; Tian, Yuan; Muñoz-Carpena, Rafael


    Knowledge of solute transport in heterogeneous porous media is crucial to monitor contaminant fate and transport in soil and groundwater systems. In this study, we present new findings from experimental and mathematical analysis to improve current understanding of solute transport in structured heterogeneous porous media. Three saturated columns packed with different sand combinations were used to examine the breakthrough behavior of bromide, a conservative tracer. Experimental results showed that bromide had different breakthrough responses in the three types of sand combinations, indicating that heterogeneity in hydraulic conductivity has a significant effect on the solute transport in structured heterogeneous porous media. Simulations from analytical solutions of a two-domain solute transport model matched experimental breakthrough data well for all the experimental conditions tested. Experimental and model results show that under saturated flow conditions, advection dominates solute transport in both fast-flow and slow-flow domains. The sand with larger hydraulic conductivity provided a preferential flow path for solute transport (fast-flow domain) that dominates the mass transfer in the heterogeneous porous media. Importantly, the transport in the slow-flow domain and mass exchange between the domains also contribute to the flow and solute transport processes and thus must be considered when investigating contaminant transport in heterogeneous porous media.

  19. Colloid interaction energies for physically and chemically heterogeneous porous media (United States)

    The mean and variance of the colloid interaction energy (phi*) as a function of separation distance (h) were calculated on physically and/or chemically heterogeneous solid surfaces at the representative elementary area (REA) scale. Nanoscale roughness was demonstrated to have a significant influence...

  20. Ultrasonic wave propagation in heterogeneous elastic and poroelastic media

    NARCIS (Netherlands)

    Jocker, J.


    The influence of small- and large-scale heterogeneities on an incident wavefield was investigated in ultrasonic experiments. The field generated by conventional piezoelectric transducers was investigated separately. It was confirmed that the far-field diffraction was correctly predicted by

  1. A numerical homogenization method for heterogeneous, anisotropic elastic media based on multiscale theory

    KAUST Repository

    Gao, Kai


    The development of reliable methods for upscaling fine-scale models of elastic media has long been an important topic for rock physics and applied seismology. Several effective medium theories have been developed to provide elastic parameters for materials such as finely layered media or randomly oriented or aligned fractures. In such cases, the analytic solutions for upscaled properties can be used for accurate prediction of wave propagation. However, such theories cannot be applied directly to homogenize elastic media with more complex, arbitrary spatial heterogeneity. Therefore, we have proposed a numerical homogenization algorithm based on multiscale finite-element methods for simulating elastic wave propagation in heterogeneous, anisotropic elastic media. Specifically, our method used multiscale basis functions obtained from a local linear elasticity problem with appropriately defined boundary conditions. Homogenized, effective medium parameters were then computed using these basis functions, and the approach applied a numerical discretization that was similar to the rotated staggered-grid finite-difference scheme. Comparisons of the results from our method and from conventional, analytical approaches for finely layered media showed that the homogenization reliably estimated elastic parameters for this simple geometry. Additional tests examined anisotropic models with arbitrary spatial heterogeneity in which the average size of the heterogeneities ranged from several centimeters to several meters, and the ratio between the dominant wavelength and the average size of the arbitrary heterogeneities ranged from 10 to 100. Comparisons to finite-difference simulations proved that the numerical homogenization was equally accurate for these complex cases.

  2. Mass media and heterogeneous bounds of confidence in continuous opinion dynamics (United States)

    Pineda, M.; Buendía, G. M.


    This work focuses on the effects of an external mass media on continuous opinion dynamics with heterogeneous bounds of confidence. We modified the original Deffuant et al. and Hegselmann and Krause models to incorporate both, an external mass media and a heterogeneous distribution of confidence levels. We analysed two cases, one where only two bounds of confidence are taken into account, and other where each individual of the system has her/his own characteristic level of confidence. We found that, in the absence of mass media, diversity of bounds of confidence can improve the capacity of the systems to reach consensus. We show that the persuasion capacity of the external message is optimal for intermediate levels of heterogeneity. Our simulations also show the existence, for certain parameter values, of a counter-intuitive effect in which the persuasion capacity of the mass media decreases if the mass media intensity is too large. We discuss similarities and differences between the two heterogeneous versions of these continuous opinion dynamic models under the influence of mass media.

  3. Deflection range of water in heterogeneous permeable media | Alabi ...

    African Journals Online (AJOL)

    Knowledge of mode of transport of fluid in soil is the basis for soil environmental engineering especially in transport of contaminants in groundwater. The study investigates the possible minimum and maximum angle of deflection of water through media of different porosities for the purpose of environmental pollution control.

  4. Experimental design of diffusion and desorption of contaminant in heterogeneous media. (United States)

    Jiang, Guannan; Crimi, Michelle; Fowler, Kathleen; Fu, Xiaojing


    Storage of contaminants in low permeability media (LPM) presents a great challenge for prediction of remediation effectiveness and efficiency. The reason lies in the contaminants' complex behaviors within heterogeneous media. Both interparticle and intraparticle diffusion contribute to the difficulty of precise site assessment. Sorption of contaminants--especially within LPM--may sequester the contaminants from active treatment, while desorption over a long period of time leads to contaminant release from storage and consequent re-contamination. Research has been conducted toward better understanding of contaminant diffusion and sorption/desorption processes to better predict contaminant response to site treatment. However, most of the research has been carried out within homogeneous media, while real scenarios in environmental problems feature media whose permeability and other characteristics vary significantly over the treatment volume. Further, few efforts have combined the interparticle/intraparticle diffusion and sorption/desorption processes together. This research aims at a feasible experimental design of diffusion and desorption of contaminant in heterogeneous media to address the gaps in previous research. A 2-D experimental system was designed to evaluate interparticle/intraparticle diffusion processes of trichloroethylene (TCE) in heterogeneous media. The 2-D system was modified to include organic matter in media for simulation of sorption/desorption processes. Results of the research will improve the understanding of how these different transport processes act together within heterogeneous media. Results will also allow for the evaluation of the impact of contaminant mass transport from within low permeability media at a potential treatment site and can support the development of mathematical tools/models combining interparticle/intraparticle and sorption/desorption processes. Such a model will promote more accurate site assessment and provide more

  5. Secure Media Independent Handover Message Transport in Heterogeneous Networks

    Directory of Open Access Journals (Sweden)

    Cho Choong-Ho


    Full Text Available The IEEE 802.21 framework for Media Independent Handover (MIH provides seamless vertical handover support for multimode mobile terminals. MIH messages are exchanged over various wireless media between mobile terminals and access networks to facilitate seamless handover. This calls for the need to secure MIH messages against network security threats in the wireless medium. In this paper, we first analyze IPSec/IKEv2 and DTLS security solution for secure MIH message transport. We show that handover latency can be an impediment to the use of IPSec and DTLS solutions. To overcome the handover overhead and hence minimize authentication time, a new secure MIH message transport solution, referred as MIHSec in this paper, is proposed. Experimental results are obtained for MIH between WLAN and Ethernet networks and the impacts of MIH message security on the handover latency are evaluated for IPSec, DTLS, and MIHSec security solutions. The effectiveness of MIHSec is demonstrated.

  6. Molecular heterogeneity of XY sex reversal in horses. (United States)

    Raudsepp, T; Durkin, K; Lear, T L; Das, P J; Avila, F; Kachroo, P; Chowdhary, B P


    Male-to-female 64,XY sex reversal is a frequently reported chromosome abnormality in horses. Despite this, the molecular causes of the condition are as yet poorly understood. This is partially because only limited molecular information is available for the horse Y chromosome (ECAY). Here, we used the recently developed ECAY map and carried out the first comprehensive study of the Y chromosome in XY mares (n=18). The integrity of the ECAY in XY females was studied by FISH and PCR using markers evenly distributed along the euchromatic region. The results showed that the XY sex reversal condition in horses has two molecularly distinct forms: (i) a Y-linked form that is characterized by Y chromosome deletions and (ii) a non-Y-linked form where the Y chromosome of affected females is molecularly the same as in normal males. Further analysis of the Y-linked form (13 cases) showed that the condition is molecularly heterogeneous: the smallest deletions spanned about 21 kb, while the largest involved the entire euchromatic region. Regardless of the size, all deletions included the SRY gene. We show that the deletions were likely caused by inter-chromatid recombination events between repeated sequences in ECAY. Further, we hypothesize that the occurrence of SRY-negative XY females in some species (horse, human) but not in others (pig, dog) is because of differences in the organization of the Y chromosome. Finally, in contrast to the Y-linked SRY-negative form of equine XY sex reversal, the molecular causes of SRY-positive XY mares (5 cases) remain as yet undefined. © 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.

  7. A mathematical framework for inverse wave problems in heterogeneous media (United States)

    Blazek, Kirk D.; Stolk, Christiaan; Symes, William W.


    This paper provides a theoretical foundation for some common formulations of inverse problems in wave propagation, based on hyperbolic systems of linear integro-differential equations with bounded and measurable coefficients. The coefficients of these time-dependent partial differential equations represent parametrically the spatially varying mechanical properties of materials. Rocks, manufactured materials, and other wave propagation environments often exhibit spatial heterogeneity in mechanical properties at a wide variety of scales, and coefficient functions representing these properties must mimic this heterogeneity. We show how to choose domains (classes of nonsmooth coefficient functions) and data definitions (traces of weak solutions) so that optimization formulations of inverse wave problems satisfy some of the prerequisites for application of Newton’s method and its relatives. These results follow from the properties of a class of abstract first-order evolution systems, of which various physical wave systems appear as concrete instances. Finite speed of propagation for linear waves with bounded, measurable mechanical parameter fields is one of the by-products of this theory.

  8. A heterogeneous model for gas transport in carbon molecular sieves. (United States)

    Ding, L P; Yuan, Y X; Farooq, S; Bhatia, S K


    A dual resistance model with distribution of either barrier or pore diffusional activation energy is proposed in this work for gas transport in carbon molecular sieve (CMS) micropores. This is a novel approach in which the equilibrium is homogeneous, but the kinetics is heterogeneous. The model seems to provide a possible explanation for the concentration dependence of the thermodynamically corrected barrier and pore diffusion coefficients observed in previous studies from this laboratory on gas diffusion in CMS. The energy distribution is assumed to follow the gamma distribution function. It is shown that the energy distribution model can fully capture the behavior described by the empirical model established in earlier studies to account for the concentration dependence of thermodynamically corrected barrier and pore diffusion coefficients. A methodology is proposed for extracting energy distribution parameters, and it is further shown that the extracted energy distribution parameters can effectively predict integral uptake and column breakthrough profiles over a wide range of operating pressures.

  9. Prostate cancer heterogeneity: Discovering novel molecular targets for therapy. (United States)

    Ciccarese, Chiara; Massari, Francesco; Iacovelli, Roberto; Fiorentino, Michelangelo; Montironi, Rodolfo; Di Nunno, Vincenzo; Giunchi, Francesca; Brunelli, Matteo; Tortora, Giampaolo


    Prostate cancer (PCa) shows a broad spectrum of biological and clinical behavior, which represents the epiphenomenon of an extreme genetic heterogeneity. Recent genomic profiling studies have deeply improved the knowledge of the genomic landscape of localized and metastatic PCa. The AR and PI3K/Akt/mTOR signaling pathways are the two most frequently altered, representing therefore interestingly targets for therapy. Moreover, somatic or germline aberrations of DNA repair genes (DRGs) have been observed at high frequency, supporting the potential role of platinum derivatives and PARP inhibitors as effective therapeutic strategies. In the future, the identification of driver mutations present at a specific stage of the disease, the classification PCa based on specific molecular alterations, and the selection of the most appropriate therapy based on biomarkers predictors of response represent the foundations for an increasingly more accurate personalized medicine. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Stretched and Filtered Transport Precondititioning of Sn Problems Part 2: Heterogeneous Media

    Energy Technology Data Exchange (ETDEWEB)

    Hanshaw, H L; Nowak, P; Larsen, E W


    In [1], we presented the stretched filtered transport synthetic acceleration method (SFTSA) for homogeneous media. Both SFTSA and SFTSA preconditioned Krylov were shown to be effective iterative schemes in homogeneous media due to the predictable structure of the iteration eigenvalues. In heterogeneous media or on non-uniform grids, the eigenvalue structure is unpredictable for general problems, making the filter strength a for optimal SFTSA extremely problem dependent. Leaving Q set to the optimal value (in each cell by table lookup) predicted by homogeneous media theory can make SFTSA divergent, even for relatively mild heterogeneities. Thus, SFTSA is more fragile than DSA in the sense that most DSA schemes break down only for much more severe heterogeneities. Fortunately, breakdown of SFTSA occurs with large negative eigenvalues, and Krylov methods preconditioned with SFTSA remain effective for such problems. Therefore, with a Krylov scheme ''wrapped around'' SFTSA, the resulting method is relatively insensitive to the filter strength, and a user may achieve reasonably good performance, if not optimal, with a fixed a over a wide range of heterogeneous problems.

  11. Frequency-Domain Green's Functions for Radar Waves in Heterogeneous 2.5D Media (United States)

    Green’s functions for radar waves propagating in heterogeneous media may be calculated in the frequency domain using a hybrid of two numerical methods. The model is defined in the Cartesian coordinate system, and its electromagnetic properties may vary in the x and z directions, ...

  12. Computer simulation of microwave propagation in heterogeneous and fractal media (United States)

    Korvin, Gabor; Khachaturov, Ruben V.; Oleschko, Klaudia; Ronquillo, Gerardo; Correa López, María de jesús; García, Juan-josé


    Maxwell's equations (MEs) are the starting point for all calculations involving surface or borehole electromagnetic (EM) methods in Petroleum Industry. In well-log analysis numerical modeling of resistivity and induction tool responses has became an indispensable step of interpretation. We developed a new method to numerically simulate electromagnetic wave propagation through heterogeneous and fractal slabs taking into account multiple scattering in the direction of normal incidence. In simulation, the gray-scale image of the porous medium is explored by monochromatic waves. The gray-tone of each pixel can be related to the dielectric permittivity of the medium at that point by two different equations (linear dependence, and fractal or power law dependence). The wave equation is solved in second order difference approximation, using a modified sweep technique. Examples will be shown for simulated EM waves in carbonate rocks imaged at different scales by electron microscopy and optical photography. The method has wide ranging applications in remote sensing, borehole scanning and Ground Penetrating Radar (GPR) exploration.

  13. Dynamics of Coupled Contaminant and Microbial Transport in Heterogeneous Porous Media: Purdue Component

    Energy Technology Data Exchange (ETDEWEB)

    Cushman, J.H.


    Dynamic microbial attachment/detachment occurs in subsurface systems in response to changing environmental conditions caused by contaminant movement and degradation. Understanding the environmental conditions and mechanisms by which anaerobic bacteria partition between aqueous and solid phases is a critical requirement for designing and evaluating in situ bioremediation efforts. This interdisciplinary research project, of which we report only the Purdue contribution, provides fundamental information on the attachment/detachment dynamics of bacteria in heterogeneous porous media. Fundamental results from the Purdue collaboration are: (a) development of a matched-index method for obtaining 3-D Lagrangian trajectories of microbial sized particles transporting within porous media or microflow cells, (b) application of advanced numerical methods to optimally design a microflow cell for studying anaerobic bacterial attachment/detachment phenomena, (c) development of two types of models for simulating bacterial movement and attachment/detachment in microflow cells and natural porous media, (d) application of stochastic analysis to upscale pore scale microbial attachment/detachment models to natural heterogeneous porous media, and (e) evaluation of the role nonlocality plays in microbial dynamics in heterogeneous porous media.

  14. Dynamics of Coupled Contaminant and Microbial Transport in Heterogeneous Porous Media: Purdue Component

    Energy Technology Data Exchange (ETDEWEB)

    Cushman, J.H.; Madilyn Fletcher


    Dynamic microbial attachment/detachment occurs in subsurface systems in response to changing environmental conditions caused by contaminant movement and degradation. Understanding the environmental conditions and mechanisms by which anaerobic bacteria partition between aqueous and solid phases is a critical requirement for designing and evaluating in situ bioremediation efforts. This interdisciplinary research project, of which we report only the Purdue contribution, provides fundamental information on the attachment/detachment dynamics of bacteria in heterogeneous porous media. Fundamental results from the Purdue collaboration are: (a) development of a matched-index method for obtaining 3-D Lagrangian trajectories of microbial sized particles transporting within porous media or microflow cells, (b) application of advanced numerical methods to optimally design a microflow cell for studying anaerobic bacterial attachment/detachment phenomena, (c) development of two types of models for simulating bacterial movement and attachment/detachment in microflow cells and natural porous media, (d) application of stochastic analysis to upscale pore scale microbial attachment/detachment models to natural heterogeneous porous media, and (e) evaluation of the role nonlocality plays in microbial dynamics in heterogeneous porous media

  15. Stochastic Diagrammatic Analysis of Groundwater Flow in Heterogeneous Porous Media (United States)

    Christakos, G.; Hristopulos, D. T.; Miller, C. T.


    The diagrammatic approach is an alternative to standard analytical methods for solving stochastic differential equations governing groundwater flow with spatially variable hydraulic conductivity. This approach uses diagrams instead of abstract symbols to visualize complex multifold integrals that appear in the perturbative expansion of the stochastic flow solution and reduces the original flow problem to a closed set of equations for the mean and the covariance functions. Diagrammatic analysis provides an improved formulation of the flow problem over conventional first-order series approximations, which are based on assumptions such as constant mean hydraulic gradient, infinite flow domain, and neglect of cross correlation terms. This formulation includes simple schemes, like finite-order diagrammatic perturbations that account for mean gradient trends and boundary condition effects, as well as more advanced schemes, like diagrammatic porous media description operators which contain infinite-order correlations. In other words, diagrammatic analysis covers not only the cases where low-order diagrams lead to good approximations of flow, but also those situations where low-order perturbation is insufficient and a more sophisticated analysis is needed. Diagrams lead to a nonlocal equation for the mean hydraulic gradient in terms of which necessary conditions are formulated for the existence of an effective hydraulic conductivity. Three-dimensional flow in an isotropic bounded domain with Dirichlet boundary conditions is considered, and an integral equation for the mean hydraulic head is derived by means of diagrams. This formulation provides an explicit expression for the boundary effects within the three-dimensional flow domain. In addition to these theoretical results, the numerical performance of the diagrammatic approach is tested, and useful insight is obtained by means of one-dimensional flow examples where the exact stochastic solutions are available.

  16. An upscaled rate law for magnesite dissolution in heterogeneous porous media (United States)

    Wen, Hang; Li, Li


    Spatial heterogeneity in natural subsurface systems governs water fluxes and residence time in reactive zones and therefore determines effective rates of mineral dissolution. Extensive studies have documented mineral dissolution rates in natural systems, although a general rate law has remain elusive. Here we fill this gap by answering two questions: (1) how and to what extent does spatial heterogeneity affect water residence time and effectively-dissolving surface area? (2) what is the upscaled rate law that quantifies effective dissolution rates in natural, heterogeneous media? With data constraints from experimental work, 240 Monte-Carlo numerical experiments of magnesite dissolution within quartz matrix were run with spatial distributions characterized by a range of permeability variance σ2lnκ (0.5-6.0) and correlation length (2-50 cm). Although the total surface area and global residence time (τa) are the same in all experiments, the water fluxes through reactive magnesite zones varies between 0.7 and 72.8% of the total water fluxes. Highly heterogeneous media with large σ2lnκ and long λ divert water mostly into non-reactive preferential flow paths, therefore bypassing and minimizing flow in low permeability magnesite zones. As a result, the water residence time in magnesite zones (i.e., reactive residence time τa,r) is long and magnesite dissolution quickly reaches local equilibrium, which leads to small effective surface area and low dissolution rates. Magnesite dissolution rates in heterogeneous media vary from 2.7 to 100% of the rates in the equivalent homogeneous media, with effectively-dissolving surface area varying from 0.18 to 6.83 m2 (out of 51.71 m2 total magnesite surface area). Based on 240 numerical experiments and 45 column experiments, a general upscaled rate law in heterogeneous media, RMgCO3,ht =kAe,hm(1 - exp(-τa/τa,r))α , was derived to quantify effective dissolution rates. The dissolution rates in heterogeneous media are a

  17. A continuous time random walk model for Darcy-scale anomalous transport in heterogeneous porous media. (United States)

    Comolli, Alessandro; Hakoun, Vivien; Dentz, Marco


    Achieving the understanding of the process of solute transport in heterogeneous porous media is of crucial importance for several environmental and social purposes, ranging from aquifers contamination and remediation, to risk assessment in nuclear waste repositories. The complexity of this aim is mainly ascribable to the heterogeneity of natural media, which can be observed at all the scales of interest, from pore scale to catchment scale. In fact, the intrinsic heterogeneity of porous media is responsible for the arising of the well-known non-Fickian footprints of transport, including heavy-tailed breakthrough curves, non-Gaussian spatial density profiles and the non-linear growth of the mean squared displacement. Several studies investigated the processes through which heterogeneity impacts the transport properties, which include local modifications to the advective-dispersive motion of solutes, mass exchanges between some mobile and immobile phases (e.g. sorption/desorption reactions or diffusion into solid matrix) and spatial correlation of the flow field. In the last decades, the continuous time random walk (CTRW) model has often been used to describe solute transport in heterogenous conditions and to quantify the impact of point heterogeneity, spatial correlation and mass transfer on the average transport properties [1]. Open issues regarding this approach are the possibility to relate measurable properties of the medium to the parameters of the model, as well as its capability to provide predictive information. In a recent work [2] the authors have shed new light on understanding the relationship between Lagrangian and Eulerian dynamics as well as on their evolution from arbitrary initial conditions. On the basis of these results, we derive a CTRW model for the description of Darcy-scale transport in d-dimensional media characterized by spatially random permeability fields. The CTRW approach models particle velocities as a spatial Markov process, which is

  18. Molecular-Level Design of Heterogeneous Chiral Catalysis

    Energy Technology Data Exchange (ETDEWEB)

    Francisco Zaera


    , and the development of ways to imprint chiral centers on achiral solid surfaces. Chiral catalysis is not only a problem of great importance in its own right, but also the ultimate test of how to control selectivity in catalysis. The time is ripe for fundamental work in heterogeneous chiral catalysis to provide the U.S. with a leadership role in developing the next generation of catalytic processes for medicinal and agrochemical manufacturing. Our team provides the required expertise for a synergistic and comprehensive integration of physical and chemical experimentation with solid state and molecular reactivity theories to solve this problem.

  19. Three-phase flow in heterogeneous wettability porous media; Deplacements triphasiques en milieux poreux de mouillabilite heterogene

    Energy Technology Data Exchange (ETDEWEB)

    Jaffrennou-Laroche, C.


    Better understanding and modelling of three-phase flow through porous media is of great interest, especially for improved oil recovery methods such as gas injection processes. Early theoretical and experimental studies have already demonstrated that the wettability characteristics of the solid surface and the spreading characteristics of the fluid system hold the key roles. This observation is confirmed by our theoretical results using DLP theory on the stability and the thickness of static oil films. In most of the works related to three-phase flow processes, homogeneous wettability is assumed. There exist only a few studies demonstrating the tremendous impact of the wettability heterogeneities on gas injection. The objective of the present work is twofold: to demonstrate the effect of small scale wettability heterogeneities on gas injection efficiency, and to develop a tool to predict this impact for various patterns and spatial distributions. To this end an experimental investigation in transparent glass micro-models is performed and a theoretical simulator is developed. Secondary and tertiary gas injections are performed for different heterogeneity patterns obtained by selective silane grafting. Displacement sequences are video-recorded and fluid saturations are determined by image analysis. Visualization of the displacement mechanisms provides the network model with the basic rules for water/oil and water/oil/gas motion. In water/oil displacement, drainage and imbibition occur according to the local wettability. Three-phase displacement is dominated by drainage mechanisms. The simulator allows the flow of oil through wetting films in the oil-wet regions and through spreading films on water in the water-wet regions. The effect of the wettability heterogeneities on: displacement mechanisms, sweep efficiency, and fluid distribution in three-phase gas injection is clearly demonstrated and successfully described by the network simulator. (author) 175 refs.

  20. Continuous-time random-walk model of transport in variably saturated heterogeneous porous media. (United States)

    Zoia, Andrea; Néel, Marie-Christine; Cortis, Andrea


    We propose a unified physical framework for transport in variably saturated porous media. This approach allows fluid flow and solute migration to be treated as ensemble averages of fluid and solute particles, respectively. We consider the cases of homogeneous and heterogeneous porous materials. Within a fractal mobile-immobile continuous time random-walk framework, the heterogeneity will be characterized by algebraically decaying particle retention times. We derive the corresponding (nonlinear) continuum-limit partial differential equations and we compare their solutions to Monte Carlo simulation results. The proposed methodology is fairly general and can be used to track fluid and solutes particles trajectories for a variety of initial and boundary conditions.

  1. Multi-level adaptive simulation of transient two-phase flow in heterogeneous porous media

    KAUST Repository

    Chueh, C.C.


    An implicit pressure and explicit saturation (IMPES) finite element method (FEM) incorporating a multi-level shock-type adaptive refinement technique is presented and applied to investigate transient two-phase flow in porous media. Local adaptive mesh refinement is implemented seamlessly with state-of-the-art artificial diffusion stabilization allowing simulations that achieve both high resolution and high accuracy. Two benchmark problems, modelling a single crack and a random porous medium, are used to demonstrate the robustness of the method and illustrate the capabilities of the adaptive refinement technique in resolving the saturation field and the complex interaction (transport phenomena) between two fluids in heterogeneous media. © 2010 Elsevier Ltd.

  2. Two-dimensional gas flows under heterogeneous combustion of solid porous media (United States)

    Levin, V. A.; Lutsenko, N. A.


    Two-dimensional unsteady gas flows in porous media with heterogeneous-combustion centers are investigated under forced filtration and free convection. With the use of numerical methods, it is shown that complex gas flows including vortex ones can arise under the combustion of solid porous media. In the case of forced filtration, the gas tends to flow around the heated portion of an object preferring to flow along cold regions. Under natural convection, the vortex gas flows, which can exist for a reasonably long time and strongly affect the oxidizer inflow into the reaction zone, arise at the initial moment of the process in the combustion zone and in its vicinities.

  3. Simulation of DNAPL migration in heterogeneous translucent porous media based on estimation of representative elementary volume (United States)

    Wu, Ming; Wu, Jianfeng; Wu, Jichun


    When the dense nonaqueous phase liquid (DNAPL) comes into the subsurface environment, its migration behavior is crucially affected by the permeability and entry pressure of subsurface porous media. A prerequisite for accurately simulating DNAPL migration in aquifers is then the determination of the permeability, entry pressure and corresponding representative elementary volumes (REV) of porous media. However, the permeability, entry pressure and corresponding representative elementary volumes (REV) are hard to determine clearly. This study utilizes the light transmission micro-tomography (LTM) method to determine the permeability and entry pressure of two dimensional (2D) translucent porous media and integrates the LTM with a criterion of relative gradient error to quantify the corresponding REV of porous media. As a result, the DNAPL migration in porous media might be accurately simulated by discretizing the model at the REV dimension. To validate the quantification methods, an experiment of perchloroethylene (PCE) migration is conducted in a two-dimensional heterogeneous bench-scale aquifer cell. Based on the quantifications of permeability, entry pressure and REV scales of 2D porous media determined by the LTM and relative gradient error, different models with different sizes of discretization grid are used to simulate the PCE migration. It is shown that the model based on REV size agrees well with the experimental results over the entire migration period including calibration, verification and validation processes. This helps to better understand the microstructures of porous media and achieve accurately simulating DNAPL migration in aquifers based on the REV estimation.

  4. Frame accurate media synchronization of heterogeneous media sources in an HBB context

    NARCIS (Netherlands)

    Veenhuizen, A.T.; Brandenburg, R. van


    Next generation HbbTV applications promise exciting new possibilities with respect to heterogeneous content sources synchronization, like multi-angle picture-in-picture video rendering and . Frame accurate synchronization is required in order to achieve these new possibilities. In this study, as

  5. Convergence of Discontinuous Galerkin Methods for Incompressible Two-Phase Flow in Heterogeneous Media

    KAUST Repository

    Kou, Jisheng


    A class of discontinuous Galerkin methods with interior penalties is presented for incompressible two-phase flow in heterogeneous porous media with capillary pressures. The semidiscrete approximate schemes for fully coupled system of two-phase flow are formulated. In highly heterogeneous permeable media, the saturation is discontinuous due to different capillary pressures, and therefore, the proposed methods incorporate the capillary pressures in the pressure equation instead of saturation equation. By introducing a coupling approach for stability and error estimates instead of the conventional separate analysis for pressure and saturation, the stability of the schemes in space and time and a priori hp error estimates are presented in the L2(H 1) for pressure and in the L∞(L2) and L2(H1) for saturation. Two time discretization schemes are introduced for effectively computing the discrete solutions. © 2013 Societ y for Industrial and Applied Mathematics.

  6. A discontinuous control volume finite element method for multi-phase flow in heterogeneous porous media (United States)

    Salinas, P.; Pavlidis, D.; Xie, Z.; Osman, H.; Pain, C. C.; Jackson, M. D.


    We present a new, high-order, control-volume-finite-element (CVFE) method for multiphase porous media flow with discontinuous 1st-order representation for pressure and discontinuous 2nd-order representation for velocity. The method has been implemented using unstructured tetrahedral meshes to discretize space. The method locally and globally conserves mass. However, unlike conventional CVFE formulations, the method presented here does not require the use of control volumes (CVs) that span the boundaries between domains with differing material properties. We demonstrate that the approach accurately preserves discontinuous saturation changes caused by permeability variations across such boundaries, allowing efficient simulation of flow in highly heterogeneous models. Moreover, accurate solutions are obtained at significantly lower computational cost than using conventional CVFE methods. We resolve a long-standing problem associated with the use of classical CVFE methods to model flow in highly heterogeneous porous media.

  7. Spectroscopy in heterogenous media and applications for bioprocess and environmental monitoring


    Frank Schael; Oliver Reich; Sonja Engelhard


    Diffuse reflectance measurements and photon migration studies with near infrared (NIR) diode lasers were employed to elucidate experimental methods for determining absorption and scattering coefficients and species concentrations in heterogenous media. Measurements were performed at a number of wavelengths utilizing several laser sources some of which were widely tunable. In order to establish the applicability of simple photon migration models derived from radiation transport theory and to c...

  8. Molecular-level Design of Heterogeneous Chiral Catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Gellman, Andrew John [Carnegie Mellon University; Sholl, David S. [Georgia Institute of Technology; Tysoe, Wilfred T. [University of Wisconsin - Milwaukee; Zaera, Francisco [University of California at Riverside


    Understanding and controlling selectivity is one of the key challenges in heterogeneous catalysis. Among problems in catalytic selectivity enantioselectivity is perhaps the most the most challenging. The primary goal of the project on “Molecular-level Design of Heterogeneous Chiral Catalysts” is to understand the origins of enantioselectivity on chiral heterogeneous surfaces and catalysts. The efforts of the project team include preparation of chiral surfaces, characterization of chiral surfaces, experimental detection of enantioselectivity on such surfaces and computational modeling of the interactions of chiral probe molecules with chiral surfaces. Over the course of the project period the team of PI’s has made some of the most detailed and insightful studies of enantioselective chemistry on chiral surfaces. This includes the measurement of fundamental interactions and reaction mechanisms of chiral molecules on chiral surfaces and leads all the way to rationale design and synthesis of chiral surfaces and materials for enantioselective surface chemistry. The PI’s have designed and prepared new materials for enantioselective adsorption and catalysis. Naturally Chiral Surfaces • Completion of a systematic study of the enantiospecific desorption kinetics of R-3-methylcyclohexanone (R-3-MCHO) on 9 achiral and 7 enantiomeric pairs of chiral Cu surfaces with orientations that span the stereographic triangle. • Discovery of super-enantioselective tartaric acid (TA) and aspartic acid (Asp) decomposition as a result of a surface explosion mechanism on Cu(643)R&S. Systematic study of super-enantiospecific TA and Asp decomposition on five enantiomeric pairs of chiral Cu surfaces. • Initial observation of the enantiospecific desorption of R- and S-propylene oxide (PO) from Cu(100) imprinted with {3,1,17} facets by L-lysine adsorption. Templated Chiral Surfaces • Initial observation of the enantiospecific desorption of R- and S-PO from Pt(111) and Pd(111

  9. A Context-Aware Adaptive Streaming Media Distribution System in a Heterogeneous Network with Multiple Terminals

    Directory of Open Access Journals (Sweden)

    Yepeng Ni


    Full Text Available We consider the problem of streaming media transmission in a heterogeneous network from a multisource server to home multiple terminals. In wired network, the transmission performance is limited by network state (e.g., the bandwidth variation, jitter, and packet loss. In wireless network, the multiple user terminals can cause bandwidth competition. Thus, the streaming media distribution in a heterogeneous network becomes a severe challenge which is critical for QoS guarantee. In this paper, we propose a context-aware adaptive streaming media distribution system (CAASS, which implements the context-aware module to perceive the environment parameters and use the strategy analysis (SA module to deduce the most suitable service level. This approach is able to improve the video quality for guarantying streaming QoS. We formulate the optimization problem of QoS relationship with the environment parameters based on the QoS testing algorithm for IPTV in ITU-T G.1070. We evaluate the performance of the proposed CAASS through 12 types of experimental environments using a prototype system. Experimental results show that CAASS can dynamically adjust the service level according to the environment variation (e.g., network state and terminal performances and outperforms the existing streaming approaches in adaptive streaming media distribution according to peak signal-to-noise ratio (PSNR.

  10. Hemoglobin Variants in Northern Thailand: Prevalence, Heterogeneity and Molecular Characteristics. (United States)

    Panyasai, Sitthichai; Fucharoen, Goonnapa; Fucharoen, Supan


    There are limited data on hemoglobin (Hb) variants among peoples of northern Thailand. Hence, we determined the prevalence of Hb variants among a large cohort from this region. A study was done on 23,914 subjects recruited from eight provinces during June 2012-January 2014. Hb was analyzed by high performance liquid chromatography (HPLC) and capillary electrophoresis, and corresponding mutations were identified by polymerase chain reaction. Among 23,914 subjects examined, 211 (0.88%) were found to carry 14 different Hb variants. Five α-globin chain variants were identified: Hb Q-Thailand (n = 40; 19.0%), Hb Hekinan (n = 8, 3.8%), Hb Siam (n = 2, 0.9%), Hb Beijing (n = 1, 0.5%), and Hb Kawachi (n = 1, 0.5%), not previously described in the Thai population. Seven β-globin variants, including Hb Hope, Hb Tak, Hb S, Hb J-Bangkok, Hb G-Makassar, Hb C, and Hb Korle-Bu, were found in 115 (54.5%), 30 (14.2%), 3 (1.4%), 3 (1.4%), 1 (0.5%), 1 (0.5%), and 1 (0.5%) subjects, respectively. The remaining five subjects (2.4%) were carriers of two different δ-globin chain variants. A different spectrum and frequencies of Hb variants were noted compared to other geographical areas. Haplotype analysis demonstrated multiple origins for Hbs Hope and Tak and confirmed a non-African origin of Hb C. Several genetic interactions between these variants with other hemoglobinopathies were encountered. Associated hematological phenotypes and novel Hb derivatives formed were presented. The prevalence and molecular heterogeneities of the Hb variants found in this large cohort of the northern Thai people's should prove useful in developing a screening program, and for the performance of additional population genetics studies of hemoglobinopathy in the region.

  11. Multiregion gene expression profiling reveals heterogeneity in molecular subtypes and immunotherapy response signatures in lung cancer. (United States)

    Lee, Won-Chul; Diao, Lixia; Wang, Jing; Zhang, Jianhua; Roarty, Emily B; Varghese, Susan; Chow, Chi-Wan; Fujimoto, Junya; Behrens, Carmen; Cascone, Tina; Peng, Weiyi; Kalhor, Neda; Moran, Cesar A; Weissferdt, Annikka; Johnson, Faye M; William, William N; Swisher, Stephen G; Lee, J Jack; Hong, Waun Ki; Heymach, John V; Wistuba, Ignacio I; Futreal, P Andrew; Zhang, Jianjun


    Intra-tumor heterogeneity may be present at all molecular levels. Genomic intra-tumor heterogeneity at the exome level has been reported in many cancer types, but comprehensive gene expression intra-tumor heterogeneity has not been well studied. Here, we delineated the gene expression intra-tumor heterogeneity by exploring gene expression profiles of 35 tumor regions from 10 non-small cell lung cancer tumors (three or four regions/tumor), including adenocarcinoma, squamous cell carcinoma, large-cell carcinoma, and pleomorphic carcinoma of the lung. Using Affymetrix Gene 1.0 ST arrays, we generated the gene expression data for every sample. Inter-tumor heterogeneity was generally higher than intra-tumor heterogeneity, but some tumors showed a substantial level of intra-tumor heterogeneity. The analysis of various clinically relevant gene expression signatures including molecular subtype, epithelial-to-mesenchymal transition, and anti-PD-1 resistance signatures also revealed heterogeneity between different regions of the same tumor. The gene expression intra-tumor heterogeneity we observed was associated with heterogeneous tumor microenvironments represented by stromal and immune cells infiltrated. Our data suggest that RNA-based prognostic or predictive molecular tests should be carefully conducted in consideration of the gene expression intra-tumor heterogeneity.

  12. Lagrangian scheme to model subgrid-scale mixing and spreading in heterogeneous porous media (United States)

    Herrera, P. A.; Cortínez, J. M.; Valocchi, A. J.


    Small-scale heterogeneity of permeability controls spreading, dilution, and mixing of solute plumes at large scale. However, conventional numerical simulations of solute transport are unable to resolve scales of heterogeneity below the grid scale. We propose a Lagrangian numerical approach to implement closure models to account for subgrid-scale spreading and mixing in Darcy-scale numerical simulations of solute transport in mildly heterogeneous porous media. The novelty of the proposed approach is that it considers two different dispersion coefficients to account for advective spreading mechanisms and local-scale dispersion. Using results of benchmark numerical simulations, we demonstrate that the proposed approach is able to model subgrid-scale spreading and mixing provided there is a correct choice of block-scale dispersion coefficient. We also demonstrate that for short travel times it is only possible to account for spreading or mixing using a single block-scale dispersion coefficient. Moreover, we show that it is necessary to use time-dependent dispersion coefficients to obtain correct mixing rates. On the contrary, for travel times that are large in comparison to the typical dispersive time scale, it is possible to use a single expression to compute the block-dispersion coefficient, which is equal to the asymptotic limit of the block-scale macrodispersion coefficient proposed by Rubin et al. (1999). Our approach provides a flexible and efficient way to model subgrid-scale mixing in numerical models of large-scale solute transport in heterogeneous aquifers. We expect that these findings will help to better understand the applicability of the advection-dispersion-equation (ADE) to simulate solute transport at the Darcy scale in heterogeneous porous media.

  13. Clinical and Molecular Heterogeneity of RTEL1 Deficiency

    Directory of Open Access Journals (Sweden)

    Marcin W. Wlodarski


    Full Text Available Typical features of dyskeratosis congenita (DC resulting from excessive telomere shortening include bone marrow failure (BMF, mucosal fragility, and pulmonary or liver fibrosis. In more severe cases, immune deficiency and recurring infections can add to disease severity. RTEL1 deficiency has recently been described as a major genetic etiology, but the molecular basis and clinical consequences of RTEL1-associated DC are incompletely characterized. We report our observations in a cohort of six patients: five with novel biallelic RTEL1 mutations p.Trp456Cys, p.Ile425Thr, p.Cys1244ProfsX17, p.Pro884_Gln885ins53X13, and one with novel heterozygous mutation p.Val796AlafsX4. The most unifying features were hypocellular BMF in 6/6 and B-/NK-cell lymphopenia in 5/6 patients. In addition, three patients with homozygous mutations p.Trp456Cys or p.Ile425Thr also suffered from immunodeficiency, cerebellar hypoplasia, and enteropathy, consistent with Hoyeraal-Hreidarsson syndrome. Chromosomal breakage resembling a homologous recombination defect was detected in patient-derived fibroblasts but not in hematopoietic compartment. Notably, in both cellular compartments, differential expression of 1243aa and 1219/1300aa RTEL1 isoforms was observed. In fibroblasts, response to ionizing irradiation and non-homologous end joining were not impaired. Telomeric circles did not accumulate in patient-derived primary cells and lymphoblastoid cell lines, implying alternative pathomechanisms for telomeric loss. Overall, RTEL1-deficient cells exhibited a phenotype of replicative exhaustion, spontaneous apoptosis and senescence. Specifically, CD34+ cells failed to expand in vitro, B-cell development was compromised, and T-cells did not proliferate in long-term culture. Finally, we report on the natural history and outcome of our patients. While two patients died from infections, hematopoietic stem cell transplantation (HSCT resulted in sustained engraftment in two patients

  14. Applications of TOUGH2 to infiltration of liquids in media with strong heterogeneity

    Energy Technology Data Exchange (ETDEWEB)

    Pruess, K.; Antunez, E.


    Much hydrogeological research during the last decade has focused on the heterogeneity of natural geologic media on different scales. Most of this work has dealt with flow and transport in single-phase, isothermal conditions. The present paper is concerned with multiphase and nonisothermal flows in strongly heterogeneous media. A primary driver of our studies is the hydrogeological system at Yucca Mountain, which is currently being evaluated by the Department of Energy for its suitability as the site of the first geologic repository for civilian high-level nuclear wastes in the US Yucca Mountain is located in the and Southwest, near the Nevada-California border. Going from large scale to small, formation heterogeneities at Yucca Mountain include (i) alternating tilting layers of welded and non-welded tuffs with different matrix permeability and variable degree of fracturing, (ii) major fault systems, (iii) well-connected and permeable fracture networks in low-permeability rocks, and (iv) individual fractures with highly variable apertures.

  15. Rupture dynamics and ground motions from earthquakes in 2-D heterogeneous media

    KAUST Repository

    Bydlon, Samuel A.


    ©2015. American Geophysical Union. All Rights Reserved. We perform 2-D simulations of earthquakes on rough faults in media with random heterogeneities (with von Karman distribution) to study the effects of geometric and material heterogeneity on the rupture process and resulting high-frequency ground motions in the near-fault region (out to ∼20km). Variations in slip and rupture velocity can arise from material heterogeneity alone but are dominantly controlled by fault roughness. Scattering effects become appreciable beyond ∼3km from the fault. Near-fault scattering extends the duration of incoherent, high-frequency ground motions and, at least in our 2-D simulations, elevates root-mean-square accelerations (i.e., Arias intensity) with negligible reduction in peak velocities. We also demonstrate that near-fault scattering typically occurs in the power law tail of the power spectral density function, quantified by the Hurst exponent and another parameter combining standard deviation and correlation length. Key Points Fault roughness, not material heterogeneity, dominates rupture process Introduce parameter that can be used to quantify near-fault scattering Scattering affects the duration and amplitude of high-frequency ground motions

  16. Exact asymptotic relations for the effective response of linear viscoelastic heterogeneous media (United States)

    Gallican, Valentin; Brenner, Renald; Suquet, Pierre


    This article addresses the asymptotic response of viscoelastic heterogeneous media in the frequency domain, at high and low frequencies, for different types of elementary linear viscoelastic constituents. By resorting to stationary principles for complex viscoelasticity and adopting a classification of the viscoelastic behaviours based on the nature of their asymptotic regimes, either elastic or viscous, four exact relations are obtained on the overall viscoelastic complex moduli in each case. Two relations are related to the asymptotic uncoupled heterogeneous problems, while the two remaining ones result from the viscoelastic coupling that manifests itself in the transient regime. These results also provide exact conditions on certain integrals in time of the effective relaxation spectrum. This general setting encompasses the results obtained in preceding studies on mixtures of Maxwell constituents [1,2]. xml:lang="fr"

  17. Transverse mixing in three-dimensional nonstationary anisotropic heterogeneous porous media

    DEFF Research Database (Denmark)

    Cirpka, Olaf; Chiogna, Gabriele; Rolle, Massimo


    that nonstationary anisotropy in the correlation structure has a significant impact on transverse plume deformation and mixing. In natural sediments, contaminant plumes most likely mix more effectively in the transverse directions than predicted by models that neglect the nonstationarity of anisotropy.......Groundwater plumes originating from continuously emitting sources are typically controlled by transverse mixing between the plume and reactants in the ambient solution. In two-dimensional domains, heterogeneity causes only weak enhancement of transverse mixing in steady-state flows. In three......-dimensional domains, more complex flow patterns are possible because streamlines can twist. In particular, spatially varying orientation of anisotropy can cause steady-state groundwater whirls. We analyze steady-state solute transport in three-dimensional locally isotropic heterogeneous porous media with blockwise...

  18. Grayscale lattice Boltzmann model for multiphase heterogeneous flow through porous media. (United States)

    Pereira, Gerald G


    The grayscale lattice Boltzmann (LB) model has been recently developed to model single-phase fluid flow through heterogeneous porous media. Flow is allowed in each voxel but the degree of flow depends on that voxel's resistivity to fluid motion. Here we extend the grayscale LB model to multiphase, immiscible flow. The new model is outlined and then applied to a number of test cases, which show good agreement with theory. This method is subsequently used to model the important case where each voxel may have a different resistance to each particular fluid that is passing through it. Finally, the method is applied to model fluid flow through real porous media to demonstrate its capability. Both the capillary and viscous flow regimes are recovered in these simulations.

  19. Modeling Dynamics of Diffusion Across Heterogeneous Social Networks: News Diffusion in Social Media

    Directory of Open Access Journals (Sweden)

    Peter Christen


    Full Text Available Diverse online social networks are becoming increasingly interconnected by sharing information. Accordingly, emergent macro-level phenomena have been observed, such as the synchronous spread of information across different types of social media. Attempting to analyze the emergent global behavior is impossible from the examination of a single social platform, and dynamic influences between different social networks are not negligible. Furthermore, the underlying structural property of networks is important, as it drives the diffusion process in a stochastic way. In this paper, we propose a macro-level diffusion model with a probabilistic approach by combining both the heterogeneity and structural connectivity of social networks. As real-world phenomena, we explore instances of news diffusion across different social media platforms from a dataset that contains over 386 million web documents covering a one-month period in early 2011. We find that influence between different media types is varied by the context of information. News media are the most influential in the arts and economy categories, while social networking sites (SNS and blog media are in the politics and culture categories, respectively. Furthermore, controversial topics, such as political protests and multiculturalism failure, tend to spread concurrently across social media, while entertainment topics, such as film releases and celebrities, are more likely driven by interactions within single social platforms. We expect that the proposed model applies to a wider class of diffusion phenomena in diverse fields and that it provides a way of interpreting the dynamics of diffusion in terms of the strength and directionality of influences among populations.

  20. Carbon fiber composite molecular sieve electrically regenerable air filter media (United States)

    Wilson, Kirk A.; Burchell, Timothy D.; Judkins, Roddie R.


    An electrically regenerable gas filter system includes a carbon fiber composite molecular sieve (CFCMS) filter medium. After a separate medium-efficiency pre-filter removes particulate from the supply airstream, the CFCMS filter sorbs gaseous air pollutants before the air is recirculated to the space. When saturated, the CFCMS media is regenerated utilizing a low-voltage current that is caused to pass through the filter medium.

  1. Effects of incomplete mixing on reactive transport in flows through heterogeneous porous media (United States)

    Wright, Elise E.; Richter, David H.; Bolster, Diogo


    The phenomenon of incomplete mixing reduces bulk effective reaction rates in reactive transport. Many existing models do not account for these effects, resulting in the overestimation of reaction rates in laboratory and field settings. To date, most studies on incomplete mixing have focused on diffusive systems; here, we extend these to explore the role that flow heterogeneity has on incomplete mixing. To do this, we examine reactive transport using a Lagrangian reactive particle tracking algorithm in two-dimensional idealized heterogeneous porous media. Contingent on the nondimensional Peclet and Damköhler numbers in the system, it was found that near well-mixed behavior could be observed at late times in the heterogeneous flow field simulations. We look at three common flow deformation metrics that describe the enhancement of mixing in the flow due to velocity gradients: the Okubo-Weiss parameter (θ ), the largest eigenvalue of the Cauchy-Green strain tensor (λC), and the finite-time Lyapunov exponent (Λ ). Strong mixing regions in the heterogeneous flow field identified by these metrics were found to correspond to regions with higher numbers of reactions, but the infrequency of these regions compared to the large numbers of reactions occurring elsewhere in the domain imply that these strong mixing regions are insufficient in explaining the observed near well-mixed behavior. Since it was found that reactive transport in these heterogeneous flows could overcome the effects of incomplete mixing, we also search for a closure for the mean concentration. The conservative quantity u2¯, where u =CA-CB , was found to predict the late time scaling of the mean concentration, i.e., Ci¯˜u2¯ .

  2. An ensemble heterogeneous classification methodology for discovering health-related knowledge in social media messages. (United States)

    Tuarob, Suppawong; Tucker, Conrad S; Salathe, Marcel; Ram, Nilam


    The role of social media as a source of timely and massive information has become more apparent since the era of Web 2.0.Multiple studies illustrated the use of information in social media to discover biomedical and health-related knowledge.Most methods proposed in the literature employ traditional document classification techniques that represent a document as a bag of words.These techniques work well when documents are rich in text and conform to standard English; however, they are not optimal for social media data where sparsity and noise are norms.This paper aims to address the limitations posed by the traditional bag-of-word based methods and propose to use heterogeneous features in combination with ensemble machine learning techniques to discover health-related information, which could prove to be useful to multiple biomedical applications, especially those needing to discover health-related knowledge in large scale social media data.Furthermore, the proposed methodology could be generalized to discover different types of information in various kinds of textual data. Social media data is characterized by an abundance of short social-oriented messages that do not conform to standard languages, both grammatically and syntactically.The problem of discovering health-related knowledge in social media data streams is then transformed into a text classification problem, where a text is identified as positive if it is health-related and negative otherwise.We first identify the limitations of the traditional methods which train machines with N-gram word features, then propose to overcome such limitations by utilizing the collaboration of machine learning based classifiers, each of which is trained to learn a semantically different aspect of the data.The parameter analysis for tuning each classifier is also reported. Three data sets are used in this research.The first data set comprises of approximately 5000 hand-labeled tweets, and is used for cross validation of the

  3. Large-scale model of flow in heterogeneous and hierarchical porous media (United States)

    Chabanon, Morgan; Valdés-Parada, Francisco J.; Ochoa-Tapia, J. Alberto; Goyeau, Benoît


    Heterogeneous porous structures are very often encountered in natural environments, bioremediation processes among many others. Reliable models for momentum transport are crucial whenever mass transport or convective heat occurs in these systems. In this work, we derive a large-scale average model for incompressible single-phase flow in heterogeneous and hierarchical soil porous media composed of two distinct porous regions embedding a solid impermeable structure. The model, based on the local mechanical equilibrium assumption between the porous regions, results in a unique momentum transport equation where the global effective permeability naturally depends on the permeabilities at the intermediate mesoscopic scales and therefore includes the complex hierarchical structure of the soil. The associated closure problem is numerically solved for various configurations and properties of the heterogeneous medium. The results clearly show that the effective permeability increases with the volume fraction of the most permeable porous region. It is also shown that the effective permeability is sensitive to the dimensionality spatial arrangement of the porous regions and in particular depends on the contact between the impermeable solid and the two porous regions.

  4. Fluid-driven fracture propagation in heterogeneous media: Probability distributions of fracture trajectories (United States)

    Santillán, David; Mosquera, Juan-Carlos; Cueto-Felgueroso, Luis


    Hydraulic fracture trajectories in rocks and other materials are highly affected by spatial heterogeneity in their mechanical properties. Understanding the complexity and structure of fluid-driven fractures and their deviation from the predictions of homogenized theories is a practical problem in engineering and geoscience. We conduct a Monte Carlo simulation study to characterize the influence of heterogeneous mechanical properties on the trajectories of hydraulic fractures propagating in elastic media. We generate a large number of random fields of mechanical properties and simulate pressure-driven fracture propagation using a phase-field model. We model the mechanical response of the material as that of an elastic isotropic material with heterogeneous Young modulus and Griffith energy release rate, assuming that fractures propagate in the toughness-dominated regime. Our study shows that the variance and the spatial covariance of the mechanical properties are controlling factors in the tortuousness of the fracture paths. We characterize the deviation of fracture paths from the homogenous case statistically, and conclude that the maximum deviation grows linearly with the distance from the injection point. Additionally, fracture path deviations seem to be normally distributed, suggesting that fracture propagation in the toughness-dominated regime may be described as a random walk.

  5. An emotional contagion model for heterogeneous social media with multiple behaviors (United States)

    Xiong, Xi; Li, Yuanyuan; Qiao, Shaojie; Han, Nan; Wu, Yue; Peng, Jing; Li, Binyong


    The emotion varies and propagates with the spatial and temporal information of individuals through social media, which uncovers several interaction mechanisms and features the community structure in order to facilitate individuals' communication and emotional contagion in social networks. Aiming to show the detailed process and characteristics of emotional contagion within social media, we propose an emotional independent cascade model in which individual emotion can affect the subsequent emotion of his/her friends. The transmissibility is introduced to measure the capability of propagating emotion with respect to an individual in social networks. By analyzing the patterns of emotional contagion on Twitter data, we find that the value of transmissibility differs on different layers and on different community structures. Extensive experiments were conducted and the results reveal that, the polar emotion of hub users can lead to the disappearance of opposite emotion, and the transmissibility makes no sense. The final emotional distribution depends on the initial emotional distribution and the transmissibilities. Individuals from a small community are more likely to change their mood by the influence of community leaders. In addition, we compared the proposed model with two other models, the emotion-based spreader-ignorant-stifler model and the standard independent cascade model. The results demonstrate that the proposed model can reflect the real-world situation of emotional contagion for heterogeneous social media while the computational complexities of all these three models are similar.

  6. A perfectly matched layer for the time-dependent wave equation in heterogeneous and layered media

    KAUST Repository

    Duru, Kenneth


    A mathematical analysis of the perfectly matched layer (PML) for the time-dependent wave equation in heterogeneous and layered media is presented. We prove the stability of the PML for discontinuous media with piecewise constant coefficients, and derive energy estimates for discontinuous media with piecewise smooth coefficients. We consider a computational setup consisting of smaller structured subdomains that are discretized using high order accurate finite difference operators for approximating spatial derivatives. The subdomains are then patched together into a global domain by a weak enforcement of interface conditions using penalties. In order to ensure the stability of the discrete PML, it is necessary to transform the interface conditions to include the auxiliary variables. In the discrete setting, the transformed interface conditions are crucial in deriving discrete energy estimates analogous to the continuous energy estimates, thus proving stability and convergence of the numerical method. Finally, we present numerical experiments demonstrating the stability of the PML in a layered medium and high order accuracy of the proposed interface conditions. © 2013 Elsevier Inc.

  7. Pore-scale simulations of concentration tails in heterogeneous porous media (United States)

    Di Palma, Paolo Roberto; Parmigiani, Andrea; Huber, Christian; Guyennon, Nicolas; Viotti, Paolo


    The retention of contaminants in the finest and less-conductive regions of natural aquifer is known to strongly affect the decontamination of polluted aquifers. In fact, contaminant transfer from low to high mobility regions at the back end of a contaminant plume (i.e. back diffusion) is responsible for the long-term release of contaminants during remediation operation. In this paper, we perform pore-scale calculations for the transport of contaminant through heterogeneous porous media composed of low and high mobility regions with two objectives: (i) study the effect of permeability contrast and solute transport conditions on the exchange of solutes between mobile and immobile regions and (ii) estimate the mass of contaminants sequestered in low mobility regions based on concentration breakthrough curves.

  8. Boundary effects on effective conductivity of random heterogeneous media with spherical inclusions (United States)

    Rabinovich, A.; Dagan, G.; Miloh, T.


    It is common to determine the effective conductivity of heterogeneous media by assuming stationarity of the random local properties. This assumption is not obeyed in a boundary layer of a body of finite size. The effect of different types of boundaries is examined for a two-phase medium with spherical inclusions of given conductivity distributed randomly in a matrix of a different conductivity. Exact solutions are derived for the apparent conductivity and the boundary layer thickness. The interaction between the spheres and the boundaries is fully incorporated in the solutions using a spherical harmonics expansion and the method of images. As applications, the corrections for the effective conductivity are given for two cases of finite bodies: the Maxwell sphere and a cylinder of flow parallel to the axis.

  9. Multiscale Lattice Boltzmann method for flow simulations in highly heterogenous porous media

    KAUST Repository

    Li, Jun


    A lattice Boltzmann method (LBM) for flow simulations in highly heterogeneous porous media at both pore and Darcy scales is proposed in the paper. In the pore scale simulations, flow of two phases (e.g., oil and gas) or two immiscible fluids (e.g., water and oil) are modeled using cohesive or repulsive forces, respectively. The relative permeability can be computed using pore-scale simulations and seamlessly applied for intermediate and Darcy-scale simulations. A multiscale LBM that can reduce the computational complexity of existing LBM and transfer the information between different scales is implemented. The results of coarse-grid, reduced-order, simulations agree very well with the averaged results obtained using fine grid.

  10. A domain decomposed finite element method for solving Darcian velocity in heterogeneous porous media (United States)

    Xie, Yifan; Wu, Jichun; Xue, Yuqun; Xie, Chunhong; Ji, Haifeng


    This paper proposes a domain decomposed finite element method (DDFEM) for groundwater flow velocity simulation, which can effectively and efficiently deal with arbitrarily oriented or intersected material interfaces in heterogeneous porous media. The main idea of this problem is to employ domain decompose technique to break the velocity problem down to subproblems by material interfaces, thereby achieving high accuracy at interface nodes and improving the velocity computation efficiency. By solving the global flow field by FEM before velocity computation, this method can capture the global information of the whole study region so as to ensure the subproblem solution accuracy by Yeh's model. After one subproblem has been solved, the DDFEM employs refraction law to obtain the Dirichlet boundary velocities of the adjacent subdomains. Numerical examples have been done to demonstrate the applicability and accuracy of the proposed method. Comparison between the DDFEM and two classical methods shows that the DDFEM can indeed save much computational cost, while achieving high accuracy.

  11. Solute mixing regulates heterogeneity of mineral precipitation in porous media: Effect of Solute Mixing on Precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Cil, Mehmet B.; Xie, Minwei; Packman, Aaron I.; Buscarnera, Giuseppe (NWU); (HKUST-- China)


    Synchrotron X-ray microtomography was used to track the spatiotemporal evolution of mineral precipitation and the consequent alteration of the pore structure. Column experiments were conducted by injecting CaCl2 and NaHCO3 solutions into granular porous media either as a premixed supersaturated solution (external mixing) or as separate solutions that mixed within the specimen (internal mixing). The two mixing modes produced distinct mineral growth patterns. While internal mixing promoted transverse heterogeneity with precipitation at the mixing zone, external mixing favored relatively homogeneous precipitation along the flow direction. The impact of precipitation on pore water flow and permeability was assessed via 3-D flow simulations, which indicated anisotropic permeability evolution for both mixing modes. Under both mixing modes, precipitation decreased the median pore size and increased the skewness of the pore size distribution. Such similar pore-scale evolution patterns suggest that the clogging of individual pores depends primarily on local supersaturation state and pore geometry.

  12. Migration of buoyant non-wetting fluids in heterogeneous porous media (United States)

    Huber, C.; Parmigiani, A.; Faroughi, S. A.; Bachmann, O.; Karani, H.


    The buoyant migration of a non-wetting fluid in porous media occurs in several natural contexts, such as during CO2 sequestration, methane in cold seeps, DNAPLs infiltration in groundwater, oil recovery and magma chambers. In this study, we use numerical modeling and laboratory experiments to investigate the migration of buoyant non-wetting fluids in time-dependent (reactive) or spatially heterogeneous porous media. We find that the stress balance at the pore scale greatly influences the migration dynamics and regime of viscous energy dissipation of the flow (low Re) and therefore impacts the transport of non-wetting fluid even at the field scale. We consider two complementary pore-scale studies. In the first case, the migration of the non-wetting fluid is impacted by the concurrent dissolution of the porous medium because of the reactivity of the buoyant invading fluid. In the second scenario a chemically inert buoyant non-wetting fluid migrates across an heterogeneous medium, from a low porosity (and permeability) layer into a high porosity (high permeability) layer. We find that these two cases lead to a similar and counter-intuitive outcome: the migration of the buoyant non-wetting fluid is reduced at high porosity/permeability. These counter-intuitive results stem from the effect of confinement of the non-wetting fluid (volume available for invasion) and viscosity ratio between the immiscible fluids on the fluid migration at the pore scale. An important solid confinement (low porosity) stabilizes fingering pathways and promotes efficient transport, while high porosity promotes the formation of an emulsion with discrete bubbles or slugs of non-wetting fluids.

  13. Multiphase flow in heterogeneous porous media from a stochastic differential geometry viewpoint (United States)

    Christakos, George; Hristopulos, Dionissios T.; Li, Xinyang


    Multiphase flow of immiscible fluids is studied by means of a stochastic flow path approach. This approach is based on a differential geometric formulation that replaces the partial differential equations (PDEs) of flow by a set of ordinary differential equations (ODEs) that determine the flow paths and impose conservation of flux. It is shown that flux conservation along the flow paths involves a space transform. Other formulations of the multiphase flow equations involve Jacobian mappings. Flow realizations as well as statistical flow moments can be derived by means of the stochastic flow path method. Advantages of the stochastic flow path method include: reduction of a PDE to an ODE system, independence from perturbation approximations and Green's functions, and the freedom to use random initial conditions at the boundary. Using the stochastic flow path method, closed-form expressions are obtained for two-phase flow in uniaxially heterogeneous media. Two-phase flow in a heterogeneous two-dimensional medium is also investigated using numerical simulations.

  14. Gaussian process emulators for quantifying uncertainty in CO2 spreading predictions in heterogeneous media (United States)

    Tian, Liang; Wilkinson, Richard; Yang, Zhibing; Power, Henry; Fagerlund, Fritjof; Niemi, Auli


    We explore the use of Gaussian process emulators (GPE) in the numerical simulation of CO2 injection into a deep heterogeneous aquifer. The model domain is a two-dimensional, log-normally distributed stochastic permeability field. We first estimate the cumulative distribution functions (CDFs) of the CO2 breakthrough time and the total CO2 mass using a computationally expensive Monte Carlo (MC) simulation. We then show that we can accurately reproduce these CDF estimates with a GPE, using only a small fraction of the computational cost required by traditional MC simulation. In order to build a GPE that can predict the simulator output from a permeability field consisting of 1000s of values, we use a truncated Karhunen-Loève (K-L) expansion of the permeability field, which enables the application of the Bayesian functional regression approach. We perform a cross-validation exercise to give an insight of the optimization of the experiment design for selected scenarios: we find that it is sufficient to use 100s values for the size of training set and that it is adequate to use as few as 15 K-L components. Our work demonstrates that GPE with truncated K-L expansion can be effectively applied to uncertainty analysis associated with modelling of multiphase flow and transport processes in heterogeneous media.

  15. Factors affecting gas migration and contaminant redistribution in heterogeneous porous media subject to electrical resistance heating. (United States)

    Munholland, Jonah L; Mumford, Kevin G; Kueper, Bernard H


    A series of intermediate-scale laboratory experiments were completed in a two-dimensional flow cell to investigate gas production and migration during the application of electrical resistance heating (ERH) for the removal of dense non-aqueous phase liquids (DNAPLs). Experiments consisted of heating water in homogeneous silica sand and heating 270 mL of trichloroethene (TCE) and chloroform (CF) DNAPL pools in heterogeneous silica sands, both under flowing groundwater conditions. Spatial and temporal distributions of temperature were measured using thermocouples and observations of gas production and migration were collected using front-face image capture throughout the experiments. Post-treatment soil samples were collected and analyzed to assess DNAPL removal. Results of experiments performed in homogeneous sand subject to different groundwater flow rates showed that high groundwater velocities can limit subsurface heating rates. In the DNAPL pool experiments, temperatures increased to achieve DNAPL-water co-boiling, creating estimated gas volumes of 131 and 114 L that originated from the TCE and CF pools, respectively. Produced gas migrated vertically, entered a coarse sand lens and subsequently migrated laterally beneath an overlying capillary barrier to outside the heated treatment zone where 31-56% of the original DNAPL condensed back into a DNAPL phase. These findings demonstrate that layered heterogeneity can potentially facilitate the transport of contaminants outside the treatment zone by mobilization and condensation of gas phases during ERH applications. This underscores the need for vapor phase recovery and/or control mechanisms below the water table during application of ERH in heterogeneous porous media during the co-boiling stage, which occurs prior to reaching the boiling point of water. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Algebraic dynamic multilevel method for compositional flow in heterogeneous porous media (United States)

    Cusini, Matteo; Fryer, Barnaby; van Kruijsdijk, Cor; Hajibeygi, Hadi


    This paper presents the algebraic dynamic multilevel method (ADM) for compositional flow in three dimensional heterogeneous porous media in presence of capillary and gravitational effects. As a significant advancement compared to the ADM for immiscible flows (Cusini et al., 2016) [33], here, mass conservation equations are solved along with k-value based thermodynamic equilibrium equations using a fully-implicit (FIM) coupling strategy. Two different fine-scale compositional formulations are considered: (1) the natural variables and (2) the overall-compositions formulation. At each Newton's iteration the fine-scale FIM Jacobian system is mapped to a dynamically defined (in space and time) multilevel nested grid. The appropriate grid resolution is chosen based on the contrast of user-defined fluid properties and on the presence of specific features (e.g., well source terms). Consistent mapping between different resolutions is performed by the means of sequences of restriction and prolongation operators. While finite-volume restriction operators are employed to ensure mass conservation at all resolutions, various prolongation operators are considered. In particular, different interpolation strategies can be used for the different primary variables, and multiscale basis functions are chosen as pressure interpolators so that fine scale heterogeneities are accurately accounted for across different resolutions. Several numerical experiments are conducted to analyse the accuracy, efficiency and robustness of the method for both 2D and 3D domains. Results show that ADM provides accurate solutions by employing only a fraction of the number of grid-cells employed in fine-scale simulations. As such, it presents a promising approach for large-scale simulations of multiphase flow in heterogeneous reservoirs with complex non-linear fluid physics.

  17. Solute transport in periodical heterogeneous porous media: Importance of observation scale and experimental sampling (United States)

    Majdalani, S.; Chazarin, J. P.; Delenne, C.; Guinot, V.


    This paper focuses on the effects of the observation scale and sampling on the dispersion of tracers in periodical heterogeneous porous media. A Model Heterogeneous Porous Medium (MHPM) with a high degree of heterogeneity was built. It consists of a preferential flow path surrounded by glass beads. 44 tracer experiments were carried out on several series of periodic MHPM to investigate the effect of the observation scale on solute dispersion. Each series was replicated several times, allowing for a statistical description of the unit transfer function of the MHPM. No significant trend was found for the dispersion coefficient as a function of the size of the MHPM. However, given the variability of the breakthrough curves from one experiment replicate to another, under-sampling might easily lead to conclude that the dispersion coefficient is variable with distance. Depending on the samples used, it would be as easy to (wrongly) detect an increasing trend as to detect a decreasing one. A confidence interval analysis of the experimental breakthrough curves in the Laplace space shows that (i) there exists a model with scale independent parameters that can describe the experimental breakthrough curves within the limits of experimental uncertainty, (ii) this model is not the advection-dispersion (AD) model, (iii) the modelling error of the AD model decreases with the number of periods, (iv) the size of the Reference Elementary Volume for the dispersion coefficient is between 10 and 20 periods. The effects of sampling prove to override those of scaling. This, with the invalidity of the AD model, leads to question attempts to calibrate and/or identify trends in the dispersion coefficient at intermediate scales from a limited number of experiment replicates.

  18. Global-local nonlinear model reduction for flows in heterogeneous porous media

    KAUST Repository

    AlOtaibi, Manal


    In this paper, we combine discrete empirical interpolation techniques, global mode decomposition methods, and local multiscale methods, such as the Generalized Multiscale Finite Element Method (GMsFEM), to reduce the computational complexity associated with nonlinear flows in highly-heterogeneous porous media. To solve the nonlinear governing equations, we employ the GMsFEM to represent the solution on a coarse grid with multiscale basis functions and apply proper orthogonal decomposition on a coarse grid. Computing the GMsFEM solution involves calculating the residual and the Jacobian on a fine grid. As such, we use local and global empirical interpolation concepts to circumvent performing these computations on the fine grid. The resulting reduced-order approach significantly reduces the flow problem size while accurately capturing the behavior of fully-resolved solutions. We consider several numerical examples of nonlinear multiscale partial differential equations that are numerically integrated using fully-implicit time marching schemes to demonstrate the capability of the proposed model reduction approach to speed up simulations of nonlinear flows in high-contrast porous media.

  19. Bayesian and variational Bayesian approaches for flows in heterogeneous random media (United States)

    Yang, Keren; Guha, Nilabja; Efendiev, Yalchin; Mallick, Bani K.


    In this paper, we study porous media flows in heterogeneous stochastic media. We propose an efficient forward simulation technique that is tailored for variational Bayesian inversion. As a starting point, the proposed forward simulation technique decomposes the solution into the sum of separable functions (with respect to randomness and the space), where each term is calculated based on a variational approach. This is similar to Proper Generalized Decomposition (PGD). Next, we apply a multiscale technique to solve for each term (as in [1]) and, further, decompose the random function into 1D fields. As a result, our proposed method provides an approximation hierarchy for the solution as we increase the number of terms in the expansion and, also, increase the spatial resolution of each term. We use the hierarchical solution distributions in a variational Bayesian approximation to perform uncertainty quantification in the inverse problem. We conduct a detailed numerical study to explore the performance of the proposed uncertainty quantification technique and show the theoretical posterior concentration.

  20. A note on variational multiscale methods for high-contrast heterogeneous porous media flows with rough source terms

    KAUST Repository

    Calo, Victor M.


    In this short note, we discuss variational multiscale methods for solving porous media flows in high-contrast heterogeneous media with rough source terms. Our objective is to separate, as much as possible, subgrid effects induced by the media properties from those due to heterogeneous source terms. For this reason, enriched coarse spaces designed for high-contrast multiscale problems are used to represent the effects of heterogeneities of the media. Furthermore, rough source terms are captured via auxiliary correction equations that appear in the formulation of variational multiscale methods [23]. These auxiliary equations are localized and one can use additive or multiplicative constructions for the subgrid corrections as discussed in the current paper. Our preliminary numerical results show that one can capture the effects due to both spatial heterogeneities in the coefficients (such as permeability field) and source terms (e.g., due to singular well terms) in one iteration. We test the cases for both smooth source terms and rough source terms and show that with the multiplicative correction, the numerical approximations are more accurate compared to the additive correction. © 2010 Elsevier Ltd.

  1. Sensitivity of Effective Thermal Conductivity Models on Temperature Distribution of Heterogeneous media of Fully Ceramic Micro-encapsulated Fuel

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Hyuk; Kim, S. J.; Hwang, D. H.; Lee, W. J. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)


    A TRISO fuel particle consists of a spherical fuel kernel with four coating layers such as buffer, Inner PyC, SiC, Outer PyC. A FCM fuel pellet contains randomly distributed 36 in a SiC matrix. Such heterogeneous and complicated structure adds difficulty in calculating the realistic temperature distributions in the FCM fuel. General practice is to use a homogenized model using an effective thermal conductivity model. For these difficulties, a realistic temperature profile on a heterogeneous media is generally calculated on a homogenization model. In this study, we investigate the influence of effective thermal conductivity models on the temperature distribution in a heterogeneous media on FCM fuel pellet. Feasibility of Single Domain Homogenization(SDH) model has been estimated for a heterogeneous media like FCM fuel. From the study, it is found that the effective thermal conductivity is a crucial parameter in analyzing the temperature distributions in SDH approach. Sensitivity of the effective thermal conductivity models indicates that the Maxwell model or an optimized conductivity models are adequate in modeling the heterogeneous FCM fuel.

  2. Endogenous molecular network reveals two mechanisms of heterogeneity within gastric cancer (United States)

    Li, Site; Zhu, Xiaomei; Liu, Bingya; Wang, Gaowei; Ao, Ping


    Intratumor heterogeneity is a common phenomenon and impedes cancer therapy and research. Gastric cancer (GC) cells have generally been classified into two heterogeneous cellular phenotypes, the gastric and intestinal types, yet the mechanisms of maintaining two phenotypes and controlling phenotypic transition are largely unknown. A qualitative systematic framework, the endogenous molecular network hypothesis, has recently been proposed to understand cancer genesis and progression. Here, a minimal network corresponding to such framework was found for GC and was quantified via a stochastic nonlinear dynamical system. We then further extended the framework to address the important question of intratumor heterogeneity quantitatively. The working network characterized main known features of normal gastric epithelial and GC cell phenotypes. Our results demonstrated that four positive feedback loops in the network are critical for GC cell phenotypes. Moreover, two mechanisms that contribute to GC cell heterogeneity were identified: particular positive feedback loops are responsible for the maintenance of intestinal and gastric phenotypes; GC cell progression routes that were revealed by the dynamical behaviors of individual key components are heterogeneous. In this work, we constructed an endogenous molecular network of GC that can be expanded in the future and would broaden the known mechanisms of intratumor heterogeneity. PMID:25962957

  3. First-principles modeling of electromagnetic scattering by discrete and discretely heterogeneous random media

    Energy Technology Data Exchange (ETDEWEB)

    Mishchenko, Michael I., E-mail: [NASA Goddard Institute for Space Studies, 2880 Broadway, New York, NY 10025 (United States); Dlugach, Janna M. [Main Astronomical Observatory of the National Academy of Sciences of Ukraine, 27 Zabolotny Str., 03680, Kyiv (Ukraine); Yurkin, Maxim A. [Voevodsky Institute of Chemical Kinetics and Combustion, SB RAS, Institutskaya str. 3, 630090 Novosibirsk (Russian Federation); Novosibirsk State University, Pirogova 2, 630090 Novosibirsk (Russian Federation); Bi, Lei [Department of Atmospheric Sciences, Texas A& M University, College Station, TX 77843 (United States); Cairns, Brian [NASA Goddard Institute for Space Studies, 2880 Broadway, New York, NY 10025 (United States); Liu, Li [NASA Goddard Institute for Space Studies, 2880 Broadway, New York, NY 10025 (United States); Columbia University, 2880 Broadway, New York, NY 10025 (United States); Panetta, R. Lee [Department of Atmospheric Sciences, Texas A& M University, College Station, TX 77843 (United States); Travis, Larry D. [NASA Goddard Institute for Space Studies, 2880 Broadway, New York, NY 10025 (United States); Yang, Ping [Department of Atmospheric Sciences, Texas A& M University, College Station, TX 77843 (United States); Zakharova, Nadezhda T. [Trinnovim LLC, 2880 Broadway, New York, NY 10025 (United States)


    A discrete random medium is an object in the form of a finite volume of a vacuum or a homogeneous material medium filled with quasi-randomly and quasi-uniformly distributed discrete macroscopic impurities called small particles. Such objects are ubiquitous in natural and artificial environments. They are often characterized by analyzing theoretically the results of laboratory, in situ, or remote-sensing measurements of the scattering of light and other electromagnetic radiation. Electromagnetic scattering and absorption by particles can also affect the energy budget of a discrete random medium and hence various ambient physical and chemical processes. In either case electromagnetic scattering must be modeled in terms of appropriate optical observables, i.e., quadratic or bilinear forms in the field that quantify the reading of a relevant optical instrument or the electromagnetic energy budget. It is generally believed that time-harmonic Maxwell’s equations can accurately describe elastic electromagnetic scattering by macroscopic particulate media that change in time much more slowly than the incident electromagnetic field. However, direct solutions of these equations for discrete random media had been impracticable until quite recently. This has led to a widespread use of various phenomenological approaches in situations when their very applicability can be questioned. Recently, however, a new branch of physical optics has emerged wherein electromagnetic scattering by discrete and discretely heterogeneous random media is modeled directly by using analytical or numerically exact computer solutions of the Maxwell equations. Therefore, the main objective of this Report is to formulate the general theoretical framework of electromagnetic scattering by discrete random media rooted in the Maxwell–Lorentz electromagnetics and discuss its immediate analytical and numerical consequences. Starting from the microscopic Maxwell–Lorentz equations, we trace the development

  4. Molecular Heterogeneity in Primary Breast Carcinomas and Axillary Lymph Node Metastases Assessed by Genomic Fingerprinting Analysis

    Directory of Open Access Journals (Sweden)

    Rachel E. Ellsworth


    Full Text Available Molecular heterogeneity within primary breast carcinomas and among axillary lymph node (LN metastases may impact diagnosis and confound treatment. In this study, we used short tandem repeated sequences to assess genomic heterogeneity and to determine hereditary relationships among primary tumor areas and regional metastases from 30 breast cancer patients. We found that primary carcinomas were genetically heterogeneous and sampling multiple areas was necessary to adequately assess genomic variability. LN metastases appeared to originate at different time periods during disease progression from different sites of the primary tumor and the extent of genomic divergence among regional metastases was associated with a less favorable patient outcome ( P = 0.009. In conclusion, metastasis is a complex process influenced by primary tumor heterogeneity and variability in the timing of dissemination. Genomic variation in primary breast tumors and regional metastases may negatively impact clinical diagnostics and contribute to therapeutic resistance.

  5. Tumor Heterogeneity: Mechanisms and Bases for a Reliable Application of Molecular Marker Design (United States)

    Diaz-Cano, Salvador J.


    Tumor heterogeneity is a confusing finding in the assessment of neoplasms, potentially resulting in inaccurate diagnostic, prognostic and predictive tests. This tumor heterogeneity is not always a random and unpredictable phenomenon, whose knowledge helps designing better tests. The biologic reasons for this intratumoral heterogeneity would then be important to understand both the natural history of neoplasms and the selection of test samples for reliable analysis. The main factors contributing to intratumoral heterogeneity inducing gene abnormalities or modifying its expression include: the gradient ischemic level within neoplasms, the action of tumor microenvironment (bidirectional interaction between tumor cells and stroma), mechanisms of intercellular transference of genetic information (exosomes), and differential mechanisms of sequence-independent modifications of genetic material and proteins. The intratumoral heterogeneity is at the origin of tumor progression and it is also the byproduct of the selection process during progression. Any analysis of heterogeneity mechanisms must be integrated within the process of segregation of genetic changes in tumor cells during the clonal expansion and progression of neoplasms. The evaluation of these mechanisms must also consider the redundancy and pleiotropism of molecular pathways, for which appropriate surrogate markers would support the presence or not of heterogeneous genetics and the main mechanisms responsible. This knowledge would constitute a solid scientific background for future therapeutic planning. PMID:22408433

  6. Time-lapse monitoring of localized changes within heterogeneous media with scattered waves (United States)

    Chinaemerem, Kanu

    travel-time changes or decorrelation estimated from the time-lapse coda waves. The imaging algorithm is defined to invert for the location and magnitude of changes within both statistically homogeneous and statistically heterogeneous scattering media. The imaging of the localized change requires an appropriate computation of the sensitivity of the scattered waves to the monitored change. I develop a novel approach to compute the sensitivity kernel needed to image localized changes present within a scattering medium. I compute the sensitivity kernel, using an a-priori scattering model that has similar statistical properties as the actual medium, by computing the intensity of the scattered waves generated at both the source and the receiver locations. This approach of the kernel computation allows one to compute the sensitivity kernel for any heterogeneous scattering medium with a prescribed boundary condition. Generating the kernel with the a priori model prevents one from invoking a homogeneity assumption of the scattering model. I apply the imaging algorithm on both numerical and laboratory experiments. The numerical experiment provides an opportunity to evaluate the resolution of the monitored change for each coda lapse time. In the laboratory experiment, I accurately resolve the change induced within two concrete blocks due to localize stress and heat changes. I also monitored velocity changes present within the subsurface beneath the Eastern section of the Basin and Range Province, Western US. Time-lapse monitoring with coda waves, generated with repeating active sources, over a period of four months suggests of the presence of a maximum velocity change of approximately 0.2% with the Eastern section of the Basin and Range Province. This observed velocity change are likely induced by the deformation within the Basin and Range Province.

  7. Sensitivity and type curves of cross-borehole flowmeter tests: application to heterogeneous fractured media. (United States)

    Ruelleu, S.; Bour, O.; Le Borgne, T.


    Crystalline rocks aquifers are very difficult to characterize since flow is mainly localized in few fractures or faults. In most cases, the large-scale hydraulic properties of such media strongly depend on the connectivity of few permeable fractures. To image and quantify the properties of such features, borehole flowmetry can be a very useful and efficient method that is also suitable when boreholes are screened. The methodology is based on the measurements of vertical flow both for single and cross-borehole configurations. In this study, we investigate through a numerical model the sensitivity of cross-borehole flowmeter tests to the geometry and properties of main permeable pathways. To model transient flow in heterogeneous media, we used a finite element method code where we reproduce few fractures and two boreholes. In each fracture, the diffusivity equation is solved. We considered different geometrical cases : a single fracture connecting two boreholes, two parallel fractures, and two intersecting fractures with a variable angle between the fractures. In the pumping well and in the observation borehole, we implemented borehole storage. For each geometry, we varied the hydraulic parameters and established cross-borehole flowmeters type curve as the typical variation of flow measured in an observation well in response to a pumping in an adjacent well. In most cases, our results appear very sensitive to the modelling of wellbore storage that affects the data especially in the early times, and for low fracture storativity. Nevertheless we do observe different shapes of type-curves depending on the geometrical connexion between fractures and boreholes. We also defined a new methodology more appropriate to identify the fracture connexions. However, our results show also that in some cases, one cannot distinguish the different type curves. Thus, uniqueness of the flow response is questioned. These results are compared with field examples obtained on the Ploemeur

  8. Heterogeneous Molecular Catalysis of Electrochemical Reactions: Volcano Plots and Catalytic Tafel Plots. (United States)

    Costentin, Cyrille; Savéant, Jean-Michel


    We analyze here, in the framework of heterogeneous molecular catalysis, the reasons for the occurrence or nonoccurrence of volcanoes upon plotting the kinetics of the catalytic reaction versus the stabilization free energy of the primary intermediate of the catalytic process. As in the case of homogeneous molecular catalysis or catalysis by surface-active metallic sites, a strong motivation of such studies relates to modern energy challenges, particularly those involving small molecules, such as water, hydrogen, oxygen, proton, and carbon dioxide. This motivation is particularly pertinent for what concerns heterogeneous molecular catalysis, since it is commonly preferred to homogeneous molecular catalysis by the same molecules if only for chemical separation purposes and electrolytic cell architecture. As with the two other catalysis modes, the main drawback of the volcano plot approach is the basic assumption that the kinetic responses depend on a single descriptor, viz., the stabilization free energy of the primary intermediate. More comprehensive approaches, investigating the responses to the maximal number of experimental factors, and conveniently expressed as catalytic Tafel plots, should clearly be preferred. This is more so in the case of heterogeneous molecular catalysis in that additional transport factors in the supporting film may additionally affect the current-potential responses. This is attested by the noteworthy presence of maxima in catalytic Tafel plots as well as their dependence upon the cyclic voltammetric scan rate.

  9. Space-time mesh adaptation for solute transport in randomly heterogeneous porous media. (United States)

    Dell'Oca, Aronne; Porta, Giovanni Michele; Guadagnini, Alberto; Riva, Monica


    We assess the impact of an anisotropic space and time grid adaptation technique on our ability to solve numerically solute transport in heterogeneous porous media. Heterogeneity is characterized in terms of the spatial distribution of hydraulic conductivity, whose natural logarithm, Y, is treated as a second-order stationary random process. We consider nonreactive transport of dissolved chemicals to be governed by an Advection Dispersion Equation at the continuum scale. The flow field, which provides the advective component of transport, is obtained through the numerical solution of Darcy's law. A suitable recovery-based error estimator is analyzed to guide the adaptive discretization. We investigate two diverse strategies guiding the (space-time) anisotropic mesh adaptation. These are respectively grounded on the definition of the guiding error estimator through the spatial gradients of: (i) the concentration field only; (ii) both concentration and velocity components. We test the approach for two-dimensional computational scenarios with moderate and high levels of heterogeneity, the latter being expressed in terms of the variance of Y. As quantities of interest, we key our analysis towards the time evolution of section-averaged and point-wise solute breakthrough curves, second centered spatial moment of concentration, and scalar dissipation rate. As a reference against which we test our results, we consider corresponding solutions associated with uniform space-time grids whose level of refinement is established through a detailed convergence study. We find a satisfactory comparison between results for the adaptive methodologies and such reference solutions, our adaptive technique being associated with a markedly reduced computational cost. Comparison of the two adaptive strategies tested suggests that: (i) defining the error estimator relying solely on concentration fields yields some advantages in grasping the key features of solute transport taking place within

  10. Frequency-domain Green's functions for radar waves in heterogeneous 2.5D media (United States)

    Ellefsen, K.J.; Croize, D.; Mazzella, A.T.; McKenna, J.R.


    Green's functions for radar waves propagating in heterogeneous 2.5D media might be calculated in the frequency domain using a hybrid method. The model is defined in the Cartesian coordinate system, and its electromagnetic properties might vary in the x- and z-directions, but not in the y-direction. Wave propagation in the x- and z-directions is simulated with the finite-difference method, and wave propagation in the y-direction is simulated with an analytic function. The absorbing boundaries on the finite-difference grid are perfectly matched layers that have been modified to make them compatible with the hybrid method. The accuracy of these numerical Greens functions is assessed by comparing them with independently calculated Green's functions. For a homogeneous model, the magnitude errors range from -4.16% through 0.44%, and the phase errors range from -0.06% through 4.86%. For a layered model, the magnitude errors range from -2.60% through 2.06%, and the phase errors range from -0.49% through 2.73%. These numerical Green's functions might be used for forward modeling and full waveform inversion. ?? 2009 Society of Exploration Geophysicists. All rights reserved.

  11. Upscaled Lattice Boltzmann Method for Simulations of Flows in Heterogeneous Porous Media

    KAUST Repository

    Li, Jun


    An upscaled Lattice Boltzmann Method (LBM) for flow simulations in heterogeneous porous media at the Darcy scale is proposed in this paper. In the Darcy-scale simulations, the Shan-Chen force model is used to simplify the algorithm. The proposed upscaled LBM uses coarser grids to represent the average effects of the fine-grid simulations. In the upscaled LBM, each coarse grid represents a subdomain of the fine-grid discretization and the effective permeability with the reduced-order models is proposed as we coarsen the grid. The effective permeability is computed using solutions of local problems (e.g., by performing local LBM simulations on the fine grids using the original permeability distribution) and used on the coarse grids in the upscaled simulations. The upscaled LBM that can reduce the computational cost of existing LBM and transfer the information between different scales is implemented. The results of coarse-grid, reduced-order, simulations agree very well with averaged results obtained using a fine grid.

  12. Robust Multiscale Iterative Solvers for Nonlinear Flows in Highly Heterogeneous Media

    KAUST Repository

    Efendiev, Y.


    In this paper, we study robust iterative solvers for finite element systems resulting in approximation of steady-state Richards\\' equation in porous media with highly heterogeneous conductivity fields. It is known that in such cases the contrast, ratio between the highest and lowest values of the conductivity, can adversely affect the performance of the preconditioners and, consequently, a design of robust preconditioners is important for many practical applications. The proposed iterative solvers consist of two kinds of iterations, outer and inner iterations. Outer iterations are designed to handle nonlinearities by linearizing the equation around the previous solution state. As a result of the linearization, a large-scale linear system needs to be solved. This linear system is solved iteratively (called inner iterations), and since it can have large variations in the coefficients, a robust preconditioner is needed. First, we show that under some assumptions the number of outer iterations is independent of the contrast. Second, based on the recently developed iterative methods, we construct a class of preconditioners that yields convergence rate that is independent of the contrast. Thus, the proposed iterative solvers are optimal with respect to the large variation in the physical parameters. Since the same preconditioner can be reused in every outer iteration, this provides an additional computational savings in the overall solution process. Numerical tests are presented to confirm the theoretical results. © 2012 Global-Science Press.

  13. Complexity reduction of multi-phase flows in heterogeneous porous media

    KAUST Repository

    Ghommem, Mehdi


    In this paper, we apply mode decomposition and interpolatory projection methods to speed up simulations of two-phase flows in highly heterogeneous porous media. We propose intrusive and non-intrusive model reduction approaches that enable a significant reduction in the dimension of the flow problem size while capturing the behavior of the fully-resolved solutions. In one approach, we employ the dynamic mode decomposition (DMD) and the discrete empirical interpolation method (DEIM). This approach does not require any modification of the reservoir simulation code but rather postprocesses a set of global snapshots to identify the dynamically-relevant structures associated with the flow behavior. In a second approach, we project the governing equations of the velocity and the pressure fields on the subspace spanned by their proper orthogonal decomposition (POD) modes. Furthermore, we use DEIM to approximate the mobility related term in the global system assembly and then reduce the online computational cost and make it independent of the fine grid. To show the effectiveness and usefulness of the aforementioned approaches, we consider the SPE 10 benchmark permeability field and present a variety of numerical examples of two-phase flow and transport. The proposed model reduction methods can be efficiently used when performing uncertainty quantification or optimization studies and history matching.

  14. Crack deflection in brittle media with heterogeneous interfaces and its application in shale fracking (United States)

    Zeng, Xiaguang; Wei, Yujie

    Driven by the rapid progress in exploiting unconventional energy resources such as shale gas, there is growing interest in hydraulic fracture of brittle yet heterogeneous shales. In particular, how hydraulic cracks interact with natural weak zones in sedimentary rocks to form permeable cracking networks is of significance in engineering practice. Such a process is typically influenced by crack deflection, material anisotropy, crack-surface friction, crustal stresses, and so on. In this work, we extend the He-Hutchinson theory (He and Hutchinson, 1989) to give the closed-form formulae of the strain energy release rate of a hydraulic crack with arbitrary angles with respect to the crustal stress. The critical conditions in which the hydraulic crack deflects into weak interfaces and exhibits a dependence on crack-surface friction and crustal stress anisotropy are given in explicit formulae. We reveal analytically that, with increasing pressure, hydraulic fracture in shales may sequentially undergo friction locking, mode II fracture, and mixed mode fracture. Mode II fracture dominates the hydraulic fracturing process and the impinging angle between the hydraulic crack and the weak interface is the determining factor that accounts for crack deflection; the lower friction coefficient between cracked planes and the greater crustal stress difference favor hydraulic fracturing. In addition to shale fracking, the analytical solution of crack deflection could be used in failure analysis of other brittle media.

  15. Upscaled Lattice Boltzmann Method for Simulations of Flows in Heterogeneous Porous Media

    Directory of Open Access Journals (Sweden)

    Jun Li


    Full Text Available An upscaled Lattice Boltzmann Method (LBM for flow simulations in heterogeneous porous media at the Darcy scale is proposed in this paper. In the Darcy-scale simulations, the Shan-Chen force model is used to simplify the algorithm. The proposed upscaled LBM uses coarser grids to represent the average effects of the fine-grid simulations. In the upscaled LBM, each coarse grid represents a subdomain of the fine-grid discretization and the effective permeability with the reduced-order models is proposed as we coarsen the grid. The effective permeability is computed using solutions of local problems (e.g., by performing local LBM simulations on the fine grids using the original permeability distribution and used on the coarse grids in the upscaled simulations. The upscaled LBM that can reduce the computational cost of existing LBM and transfer the information between different scales is implemented. The results of coarse-grid, reduced-order, simulations agree very well with averaged results obtained using a fine grid.

  16. Physical heterogeneity increases biofilm resource use and its molecular diversity in stream mesocosms.

    Directory of Open Access Journals (Sweden)

    Gabriel Singer

    Full Text Available BACKGROUND: Evidence increasingly shows that stream ecosystems greatly contribute to global carbon fluxes. This involves a tight coupling between biofilms, the dominant form of microbial life in streams, and dissolved organic carbon (DOC, a very significant pool of organic carbon on Earth. Yet, the interactions between microbial biodiversity and the molecular diversity of resource use are poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: Using six 40-m-long streamside flumes, we created a gradient of streambed landscapes with increasing spatial flow heterogeneity to assess how physical heterogeneity, inherent to streams, affects biofilm diversity and DOC use. We determined bacterial biodiversity in all six landscapes using 16S-rRNA fingerprinting and measured carbon uptake from glucose and DOC experimentally injected to all six flumes. The diversity of DOC molecules removed from the water was determined from ultrahigh-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS. Bacterial beta diversity, glucose and DOC uptake, and the molecular diversity of DOC use all increased with increasing flow heterogeneity. Causal modeling and path analyses of the experimental data revealed that the uptake of glucose was largely driven by physical processes related to flow heterogeneity, whereas biodiversity effects, such as complementarity, most likely contributed to the enhanced uptake of putatively recalcitrant DOC compounds in the streambeds with higher flow heterogeneity. CONCLUSIONS/SIGNIFICANCE: Our results suggest biophysical mechanisms, including hydrodynamics and microbial complementarity effects, through which physical heterogeneity induces changes of resource use and carbon fluxes in streams. These findings highlight the importance of fine-scale streambed heterogeneity for microbial biodiversity and ecosystem functioning in streams, where homogenization and loss of habitats increasingly reduce biodiversity.

  17. Physical Heterogeneity Increases Biofilm Resource Use and Its Molecular Diversity in Stream Mesocosms (United States)

    Singer, Gabriel; Besemer, Katharina; Schmitt-Kopplin, Philippe; Hödl, Iris; Battin, Tom J.


    Background Evidence increasingly shows that stream ecosystems greatly contribute to global carbon fluxes. This involves a tight coupling between biofilms, the dominant form of microbial life in streams, and dissolved organic carbon (DOC), a very significant pool of organic carbon on Earth. Yet, the interactions between microbial biodiversity and the molecular diversity of resource use are poorly understood. Methodology/Principal Findings Using six 40-m-long streamside flumes, we created a gradient of streambed landscapes with increasing spatial flow heterogeneity to assess how physical heterogeneity, inherent to streams, affects biofilm diversity and DOC use. We determined bacterial biodiversity in all six landscapes using 16S-rRNA fingerprinting and measured carbon uptake from glucose and DOC experimentally injected to all six flumes. The diversity of DOC molecules removed from the water was determined from ultrahigh-resolution Fourier Transform Ion Cyclotron Resonance mass spectrometry (FTICR-MS). Bacterial beta diversity, glucose and DOC uptake, and the molecular diversity of DOC use all increased with increasing flow heterogeneity. Causal modeling and path analyses of the experimental data revealed that the uptake of glucose was largely driven by physical processes related to flow heterogeneity, whereas biodiversity effects, such as complementarity, most likely contributed to the enhanced uptake of putatively recalcitrant DOC compounds in the streambeds with higher flow heterogeneity. Conclusions/Significance Our results suggest biophysical mechanisms, including hydrodynamics and microbial complementarity effects, through which physical heterogeneity induces changes of resource use and carbon fluxes in streams. These findings highlight the importance of fine-scale streambed heterogeneity for microbial biodiversity and ecosystem functioning in streams, where homogenization and loss of habitats increasingly reduce biodiversity. PMID:20376323

  18. XML-based approaches for the integration of heterogeneous bio-molecular data. (United States)

    Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David


    The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

  19. User recommendation in healthcare social media by assessing user similarity in heterogeneous network. (United States)

    Jiang, Ling; Yang, Christopher C


    The rapid growth of online health social websites has captured a vast amount of healthcare information and made the information easy to access for health consumers. E-patients often use these social websites for informational and emotional support. However, health consumers could be easily overwhelmed by the overloaded information. Healthcare information searching can be very difficult for consumers, not to mention most of them are not skilled information searcher. In this work, we investigate the approaches for measuring user similarity in online health social websites. By recommending similar users to consumers, we can help them to seek informational and emotional support in a more efficient way. We propose to represent the healthcare social media data as a heterogeneous healthcare information network and introduce the local and global structural approaches for measuring user similarity in a heterogeneous network. We compare the proposed structural approaches with the content-based approach. Experiments were conducted on a dataset collected from a popular online health social website, and the results showed that content-based approach performed better for inactive users, while structural approaches performed better for active users. Moreover, global structural approach outperformed local structural approach for all user groups. In addition, we conducted experiments on local and global structural approaches using different weight schemas for the edges in the network. Leverage performed the best for both local and global approaches. Finally, we integrated different approaches and demonstrated that hybrid method yielded better performance than the individual approach. The results indicate that content-based methods can effectively capture the similarity of inactive users who usually have focused interests, while structural methods can achieve better performance when rich structural information is available. Local structural approach only considers direct connections

  20. Up scaling two-phase flow in heterogeneous porous media; Mise a l'echelle des ecoulements diphasiques dans les milieux poreux heterogenes

    Energy Technology Data Exchange (ETDEWEB)

    Artus, V.


    For two-phase flow in heterogeneous media, the emergence of different flow regimes at large-scale is driven by local interactions between the viscous coupling and the heterogeneity. In particular, when the viscosity ratio is favorable, viscous effects induce a transverse flow that stabilizes the front while flooding. However, most of recent stochastic models neglect the influence of the viscous coupling. We developed a stochastic model for the dynamics of the front, taking the viscous coupling into account. For stable cases, this model relates the statistical properties of the front to the statistical properties of the permeability field. For stable flow in stratified media, we show that the front is stationary by parts in the reservoir. These parts can be identified as large-scale hydrodynamic layers and separately coarsened in the large-scale simulation model. For flows with favorable viscosity ratios in isotropic reservoirs, we show that a stationary front occurs, in a statistical sense. For unfavorable viscosity ratios, the flow is driven by the development of viscous fingering. These different regimes lead to different large-scale saturation profiles that can be matched with a macro-dispersion equation, if the effective convective flux is modified to take into account stabilizing or destabilizing viscous effects. (author)

  1. Online Adaptive Local-Global Model Reduction for Flows in Heterogeneous Porous Media

    KAUST Repository

    Efendiev, Yalchin R.


    We propose an online adaptive local-global POD-DEIM model reduction method for flows in heterogeneous porous media. The main idea of the proposed method is to use local online indicators to decide on the global update, which is performed via reduced cost local multiscale basis functions. This unique local-global online combination allows (1) developing local indicators that are used for both local and global updates (2) computing global online modes via local multiscale basis functions. The multiscale basis functions consist of offline and some online local basis functions. The approach used for constructing a global reduced system is based on Proper Orthogonal Decomposition (POD) Galerkin projection. The nonlinearities are approximated by the Discrete Empirical Interpolation Method (DEIM). The online adaption is performed by incorporating new data, which become available at the online stage. Once the criterion for updates is satisfied, we adapt the reduced system online by changing the POD subspace and the DEIM approximation of the nonlinear functions. The main contribution of the paper is that the criterion for adaption and the construction of the global online modes are based on local error indicators and local multiscale basis function which can be cheaply computed. Since the adaption is performed infrequently, the new methodology does not add significant computational overhead associated with when and how to adapt the reduced basis. Our approach is particularly useful for situations where it is desired to solve the reduced system for inputs or controls that result in a solution outside the span of the snapshots generated in the offline stage. Our method also offers an alternative of constructing a robust reduced system even if a potential initial poor choice of snapshots is used. Applications to single-phase and two-phase flow problems demonstrate the efficiency of our method.

  2. Generalized Multiscale Finite Element Methods for Wave Propagation in Heterogeneous Media

    KAUST Repository

    Chung, Eric T.


    Numerical modeling of wave propagation in heterogeneous media is important in many applications. Due to their complex nature, direct numerical simulations on the fine grid are prohibitively expensive. It is therefore important to develop efficient and accurate methods that allow the use of coarse grids. In this paper, we present a multiscale finite element method for wave propagation on a coarse grid. The proposed method is based on the generalized multiscale finite element method (GMsFEM) (see [Y. Efendiev, J. Galvis, and T. Hou, J. Comput. Phys., 251 (2012), pp. 116--135]). To construct multiscale basis functions, we start with two snapshot spaces in each coarse-grid block, where one represents the degrees of freedom on the boundary and the other represents the degrees of freedom in the interior. We use local spectral problems to identify important modes in each snapshot space. These local spectral problems are different from each other and their formulations are based on the analysis. To the best of knowledge, this is the first time that multiple snapshot spaces and multiple spectral problems are used and necessary for efficient computations. Using the dominant modes from local spectral problems, multiscale basis functions are constructed to represent the solution space locally within each coarse block. These multiscale basis functions are coupled via the symmetric interior penalty discontinuous Galerkin method which provides a block diagonal mass matrix and, consequently, results in fast computations in an explicit time discretization. Our methods\\' stability and spectral convergence are rigorously analyzed. Numerical examples are presented to show our methods\\' performance. We also test oversampling strategies. In particular, we discuss how the modes from different snapshot spaces can affect the proposed methods\\' accuracy.

  3. Micro-scale displacement of NAPL by surfactant and microemulsion in heterogeneous porous media (United States)

    Javanbakht, Gina; Arshadi, Maziar; Qin, Tianzhu; Goual, Lamia


    Industrial processes such as remediation of oil-contaminated aquifers and enhanced oil recovery (EOR) often utilize chemical additives to increase the removal of non-aqueous phase liquids (NAPLs) from subsurface formations. Although the majority of crude oils are classified as LNAPLs, they often contain heavy molecules (DNAPLs) such as asphaltenes that tend to adsorb on minerals and alter their wettability. Effective additives are therefore those that can reduce the threshold capillary pressure, thus mobilizing LNAPL inside pore spaces and solubilizing DNAPL from rock surfaces. Nonionic surfactants in brine have often been injected to oil or contaminated aquifer formations in order to enhance NAPL displacement through IFT reduction. Recent studies revealed that surfactant-based microemulsions have a higher tendency to alter the wettability of surfaces, compared to surfactants alone, leading to more effective NAPL removal. However, the impact of these additives on pore-scale displacement mechanisms and multi-phase fluid occupancy in porous media is, to date, still unclear. In this study, x-ray microtomography experiments were performed to investigate the impact of surfactants and microemulsions on the mobilization and solubilization of NAPL in heterogeneous rocks. Saturation profiles indicated that an incremental NAPL removal was attained by addition of microemulsion to brine, compared with surfactant. Residual cluster size distributions revealed that microemulsions could break up large clusters into smaller disconnected ones, improving their mobilization in the rock. In-situ contact angle measurements showed that microemulsions could reverse the wettability of rough contaminated surfaces to a higher extent than surfactants. Unlike surfactant alone, the surfactant-solvent blend in the carrier fluid of microemulsions was able to penetrate rough grain surfaces, particularly those of dolomite cement, and desorb asphaltenes in the form of small-emulsified NAPL droplets

  4. Simulation of heterogeneous molecular delivery in tumours using μCT reconstructions and MRI validation. (United States)

    Wittenborn, Thomas Rea; Nielsen, Thomas; Thomsen, Jesper Skovhus; Horsman, Michael Robert; Nygaard, Jens Vinge


    Utilizing the detailed vascular network obtained from micro-computed tomography (μCT) to establish a mathematical model of the temporal molecular distribution within a murine C3H mammary carcinoma. Female CDF1 mice with a C3H mammary carcinoma on the right rear foot were used in this study. Dynamic information for each tumour was achieved by Dynamic Contrast Enhanced-Magnetic Resonance Imaging (DCE-MRI) on a 16.4 T system. Detailed morphologic information on the tumour vasculature was obtained by ex vivo μCT and compared to CD34 immunohistochemical staining of tissue sections. The reconstructed vascular network served as origin for the diffusion (described by the apparent diffusion coefficient) within the tumour (the restricted volume described by the interstitial volume fraction derived from DCE-MRI). The resulting partial differential equation was solved using Finite-Element and a combined mathematical graph describing molecular distribution within the tumour was obtained. The established molecular distribution model predicted a heterogeneous distribution throughout the tumour related to the layout of the vascular network. Central tumour section concentration-time curves estimated from the established molecular distribution model were compared with physical measurements obtained by DCE-MRI of the same tumours and showed excellent correlation. A mathematical model describing temporal molecular distribution based on detailed vascular network structures was established and compared to DCE-MRI. The improved morphological insight will enhance future studies of heterogeneous tumours. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Mesoporous molecular sieve MCM-41 synthesis from fluoride media

    Directory of Open Access Journals (Sweden)

    F. S. Bastos


    Full Text Available A study of the synthesis of MCM-41 mesoporous molecular sieves in fluoride media, having no alkaline metal ions, was performed by changing the gel composition and crystallization temperature and time. X-ray diffraction and nitrogen adsorption analyses showed that highly ordered MCM-41 samples were obtained from gels with a NH4OH/SiO2 molar ratio in the 3.25-4.3 range (room temperature synthesis or in the 4.3-20 range (24 hours at 373 K. During calcination, unit cell shrinkage, caused by high temperature polycondensation of the SiOH groups, was observed for all samples. The samples synthesized at high temperature (373 K or using low pH gels (7.5 underwent lower unit cell shrinkage than those obtained at room temperature or high pH (9.0, indicating that the former samples had lower SiOH groups content than the latter. These highly-ordered samples showed large surface area (ca. 1100 m²/g and pore volume (ca. 0.80 cm³/g, also presenting a narrow pore size distribution. Due to higher silicate polycondensation and a thicker pore wall, the samples synthesized at 373 K were more hydrothermally stable than those obtained at room temperature.

  6. Heterogeneity revealed by integrated genomic analysis uncovers a molecular switch in malignant uveal melanoma. (United States)

    de Lange, Mark J; van Pelt, Sake I; Versluis, Mieke; Jordanova, Ekaterina S; Kroes, Wilma G M; Ruivenkamp, Claudia; van der Burg, Sjoerd H; Luyten, Grégorius P M; van Hall, Thorbald; Jager, Martine J; van der Velden, Pieter A


    Gene expression profiles as well as genomic imbalances are correlated with disease progression in uveal melanoma (UM). We integrated expression and genomic profiles to obtain insight into the oncogenic mechanisms in development and progression of UM. We used tumor tissue from 64 enucleated eyes of UM patients for profiling. Mutations and genomic imbalances were quantified with digital PCR to study tumor heterogeneity and molecular pathogenesis. Gene expression analysis divided the UM panel into three classes. Class I presented tumors with a good prognosis and a distinct genomic make up that is characterized by 6p gain. The UM with a bad prognosis were subdivided into class IIa and class IIb. These classes presented similar survival risks but could be distinguished by tumor heterogeneity. Class IIa presented homogeneous tumors while class IIb tumors, on average, contained 30% of non-mutant cells. Tumor heterogeneity coincided with expression of a set of immune genes revealing an extensive immune infiltrate in class IIb tumors. Molecularly, class IIa and IIb presented the same genomic configuration and could only be distinguished by 8q copy number. Moreover, UM establish in the void of the immune privileged eye indicating that in IIb tumors the infiltrate is attracted by the UM. Combined our data show that chromosome 8q contains the locus that causes the immune phentotype of UM. UM thereby provides an unique opportunity to study immune attraction by tumors.

  7. Hybrid finite volume scheme for a two-phase flow in heterogeneous porous media*

    Directory of Open Access Journals (Sweden)

    Brenner Konstantin


    Full Text Available We propose a finite volume method on general meshes for the numerical simulation of an incompressible and immiscible two-phase flow in porous media. We consider the case that can be written as a coupled system involving a degenerate parabolic convection-diffusion equation for the saturation together with a uniformly elliptic equation for the global pressure. The numerical scheme, which is implicit in time, allows computations in the case of a heterogeneous and anisotropic permeability tensor. The convective fluxes, which are non monotone with respect to the unknown saturation and discontinuous with respect to the space variables, are discretized by means of a special Godunov scheme. We prove the existence of a discrete solution which converges, along a subsequence, to a solution of the continuous problem. We present a number of numerical results in space dimension two, which confirm the efficiency of the numerical method. Nous proposons un schéma de volumes finis hybrides pour la discrétisation d’un problème d’écoulement diphasique incompressible et immiscible en milieu poreux. On suppose que ce problème a la forme d’une équation parabolique dégénérée de convection-diffusion en saturation couplée à une équation uniformément elliptique en pression. On considère un schéma implicite en temps, où les flux diffusifs sont discrétisés par la méthode des volumes finis hybride, ce qui permet de pouvoir traiter le cas d’un tenseur de perméabilité anisotrope et hétérogène sur un maillage très général, et l’on s’appuie sur un schéma de Godunov pour la discrétisation des flux convectifs, qui peuvent être non monotones et discontinus par rapport aux variables spatiales. On démontre l’existence d’une solution discrète, dont une sous-suite converge vers une solution faible du problème continu. On présente finalement des cas test bidimensionnels.

  8. Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach. (United States)

    Scott, Milcah C; Sarver, Aaron L; Gavin, Katherine J; Thayanithy, Venugopal; Getzy, David M; Newman, Robert A; Cutter, Gary R; Lindblad-Toh, Kerstin; Kisseberth, William C; Hunter, Lawrence E; Subramanian, Subbaya; Breen, Matthew; Modiano, Jaime F


    The heterogeneous and chaotic nature of osteosarcoma has confounded accurate molecular classification, prognosis, and prediction for this tumor. The occurrence of spontaneous osteosarcoma is largely confined to humans and dogs. While the clinical features are remarkably similar in both species, the organization of dogs into defined breeds provides a more homogeneous genetic background that may increase the likelihood to uncover molecular subtypes for this complex disease. We thus hypothesized that molecular profiles derived from canine osteosarcoma would aid in molecular subclassification of this disease when applied to humans. To test the hypothesis, we performed genome wide gene expression profiling in a cohort of dogs with osteosarcoma, primarily from high-risk breeds. To further reduce inter-sample heterogeneity, we assessed tumor-intrinsic properties through use of an extensive panel of osteosarcoma-derived cell lines. We observed strong differential gene expression that segregated samples into two groups with differential survival probabilities. Groupings were characterized by the inversely correlated expression of genes associated with 'G2/M transition and DNA damage checkpoint' and 'microenvironment-interaction' categories. This signature was preserved in data from whole tumor samples of three independent dog osteosarcoma cohorts, with stratification into the two expected groups. Significantly, this restricted signature partially overlapped a previously defined, predictive signature for soft tissue sarcomas, and it unmasked orthologous molecular subtypes and their corresponding natural histories in five independent data sets from human patients with osteosarcoma. Our results indicate that the narrower genetic diversity of dogs can be utilized to group complex human osteosarcoma into biologically and clinically relevant molecular subtypes. This in turn may enhance prognosis and prediction, and identify relevant therapeutic targets. Copyright © 2011 Elsevier

  9. Bias and Uncertainty in Regression-Calibrated Models of Groundwater Flow in Heterogeneous Media

    DEFF Research Database (Denmark)

    Cooley, R.L.; Christensen, Steen


    Groundwater models need to account for detailed but generally unknown spatial variability (heterogeneity) of the hydrogeologic model inputs. To address this problem we replace the large, m-dimensional stochastic vector β that reflects both small and large scales of heterogeneity in the inputs...

  10. Transport and deposition of polymer-modified Fe0 nanoparticles in 2-D heterogeneous porous media: effects of particle concentration, Fe0 content, and coatings. (United States)

    Phenrat, Tanapon; Cihan, Abdullah; Kim, Hye-Jin; Mital, Menka; Illangasekare, Tissa; Lowry, Gregory V


    Concentrated suspensions of polymer-modified Fe(0) nanoparticles (NZVI) are injected into heterogeneous porous media for groundwater remediation. This study evaluated the effect of porous media heterogeneity and the dispersion properties including particle concentration, Fe(0) content, and adsorbed polymer mass and layer thickness which are expected to affect the delivery and emplacement of NZVI in heterogeneous porous media in a two-dimensional (2-D) cell. Heterogeneity in hydraulic conductivity had a significant impact on the deposition of NZVI. Polymer modified NZVI followed preferential flow paths and deposited in the regions where fluid shear is insufficient to prevent NZVI agglomeration and deposition. NZVI transported in heterogeneous porous media better at low particle concentration (0.3 g/L) than at high particle concentrations (3 and 6 g/L) due to greater particle agglomeration at high concentration. High Fe(0) content decreased transport during injection due to agglomeration promoted by magnetic attraction. NZVI with a flat adsorbed polymeric layer (thickness ∼30 nm) could not be transported effectively due to pore clogging and deposition near the inlet, while NZVI with a more extended adsorbed layer thickness (i.e., ∼70 nm) were mobile in porous media. This study indicates the importance of characterizing porous media heterogeneity and NZVI dispersion properties as part of the design of a robust delivery strategy for NZVI in the subsurface.

  11. A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments. (United States)

    Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Mikkelsen, Kurt V; Ågren, Hans


    We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

  12. The use of laboratory experiments for the study of conservative solute transport in heterogeneous porous media (United States)

    Silliman, S. E.; Zheng, L.; Conwell, P.

    Laboratory experiments on heterogeneous porous media (otherwise known as intermediate scale experiments, or ISEs) have been increasingly relied upon by hydrogeologists for the study of saturated and unsaturated groundwater systems. Among the many ongoing applications of ISEs is the study of fluid flow and the transport of conservative solutes in correlated permeability fields. Recent advances in ISE design have provided the capability of creating correlated permeability fields in the laboratory. This capability is important in the application of ISEs for the assessment of recent stochastic theories. In addition, pressure-transducer technology and visualization methods have provided the potential for ISEs to be used in characterizing the spatial distributions of both hydraulic head and local water velocity within correlated permeability fields. Finally, various methods are available for characterizing temporal variations in the spatial distribution (and, thereby, the spatial moments) of solute concentrations within ISEs. It is concluded, therefore, that recent developments in experimental techniques have provided an opportunity to use ISEs as important tools in the continuing study of fluid flow and the transport of conservative solutes in heterogeneous, saturated porous media. Résumé Les hydrogéologues se sont progressivement appuyés sur des expériences de laboratoire sur des milieux poreux hétérogènes (connus aussi par l'expression "Expériences àéchelle intermédiaire", ISE) pour étudier les zones saturées et non saturées des aquifères. Parmi les nombreuses applications en cours des ISE, il faut noter l'étude de l'écoulement de fluide et le transport de solutés conservatifs dans des champs aux perméabilités corrélées. Les récents progrès du protocole des ISE ont donné la possibilité de créer des champs de perméabilités corrélées au laboratoire. Cette possibilité est importante dans l'application des ISE pour l'évaluation des th

  13. Structural Variation of Chondroitin Sulfate Chains Contributes to the Molecular Heterogeneity of Perineuronal Nets

    Directory of Open Access Journals (Sweden)

    Shinji Miyata


    Full Text Available Aggrecan, a chondroitin sulfate (CS proteoglycan, forms lattice-like extracellular matrix structures called perineuronal nets (PNNs. Neocortical PNNs primarily ensheath parvalbumin-expressing inhibitory neurons (parvalbumin, PV cells late in brain development. Emerging evidence indicates that PNNs promote the maturation of PV cells by enhancing the incorporation of homeobox protein Otx2 and regulating experience-dependent neural plasticity. Wisteria floribunda agglutinin (WFA, an N-acetylgalactosamine-specific plant lectin, binds to the CS chains of aggrecan and has been widely used to visualize PNNs. Although PNNs show substantial molecular heterogeneity, the importance of this heterogeneity in neural plasticity remains unknown. Here, in addition to WFA lectin, we used the two monoclonal antibodies Cat315 and Cat316, both of which recognize the glycan structures of aggrecan, to investigate the molecular heterogeneity of PNNs. WFA detected the highest number of PNNs in all cortical layers, whereas Cat315 and Cat316 labeled only a subset of PNNs. WFA+, Cat315+, and Cat316+ PNNs showed different laminar distributions in the adult visual cortex. WFA, Cat315 and Cat316 detected distinct, but partially overlapping, populations of PNNs. Based on the reactivities of these probes, we categorized PNNs into four groups. We found that two subpopulation of PNNs, one with higher and one with lower WFA-staining are differentially labeled by Cat316 and Cat315, respectively. CS chains recognized by Cat316 were diminished in mice deficient in an enzyme involved in the initiation of CS-biosynthesis. Furthermore, WFA+ and Cat316+ aggrecan were spatially segregated and formed microdomains in a single PNN. Otx2 co-localized with Cat316+ but not with WFA+ aggrecan in PNNs. Our results suggest that the heterogeneity of PNNs around PV cells may affect the functional maturation of these cells.

  14. Probing the surface profile and friction behavior of heterogeneous polymers: a molecular dynamics study (United States)

    Dai, L.; Sorkin, V.; Zhang, Y. W.


    We perform molecular dynamics simulations to investigate molecular structure alternation and friction behavior of heterogeneous polymer (perfluoropolyether) surfaces using a nanoscale probing tip (tetrahedral amorphous carbon). It is found that depending on the magnitude of the applied normal force, three regimes exist: the shallow depth-sensing (SDS), deep depth-sensing (DDS), and transitional depth-sensing (TDS) regimes; TDS is between SDS and DDS. In SDS, the tip is floating on the polymer surface and there is insignificant permanent alternation in the polymer structure due to largely recoverable atomic deformations, and the surface roughness profile can be accurately measured. In DDS, the tip is plowing through the polymer surface and there is significant permanent alternation in the molecular structure. In this regime, the lateral friction force rises sharply and fluctuates violently when overcoming surface pile-ups. In SDS, the friction can be described by a modified Amonton’s law including the adhesion effect; meanwhile, in DDS, the adhesion effect is negligible but the friction coefficient is significantly higher. The underlying reason for the difference in these regimes rests upon different contributions by the repulsion and attraction forces between the tip and polymer surfaces to the friction force. Our findings here reveal important insights into lateral depth-sensing on heterogeneous polymer surfaces and may help improve the precision of depth-sensing devices.

  15. Multiscale Adapted Time-Splitting Technique for Nonisothermal Two-Phase Flow and Nanoparticles Transport in Heterogenous Porous Media

    KAUST Repository

    El-Amin, Mohamed F.


    This paper is devoted to study the problem of nonisothermal two-phase flow with nanoparticles transport in heterogenous porous media, numerically. For this purpose, we introduce a multiscale adapted time-splitting technique to simulate the problem under consideration. The mathematical model consists of equations of pressure, saturation, heat, nanoparticles concentration in the water–phase, deposited nanoparticles concentration on the pore–walls, and entrapped nanoparticles concentration in the pore–throats. We propose a multiscale time splitting IMplicit Pressure Explicit Saturation–IMplicit Temperature Concentration (IMPES-IMTC) scheme to solve the system of governing equations. The time step-size adaptation is achieved by satisfying the stability Courant–Friedrichs–Lewy (CFL<1) condition. Moreover, numerical test of a highly heterogeneous porous medium is provided and the water saturation, the temperature, the nanoparticles concentration, the deposited nanoparticles concentration, and the permeability are presented in graphs.

  16. Elucidation of molecular and functional heterogeneity through differential expression network analyses of discrete tumor subsets (United States)

    Naik, Rutika R.; Gardi, Nilesh L.; Bapat, Sharmila A.


    Intratumor heterogeneity presents a major hurdle in cancer therapy. Most current research studies consider tumors as single entities and overlook molecular diversity between heterogeneous state(s) of different cells assumed to be homogenous. The present approach was designed for fluorescence-activated cell sorting-based resolution of heterogeneity arising from cancer stem cell (CSC) hierarchies and genetic instability in ovarian tumors, followed by microarray-based expression profiling of sorted fractions. Through weighted gene correlation network analyses, we could assign enriched modules of co-regulated genes to each fraction. Such gene modules often correlate with biological functions; one such specific association was the enrichment of CD53 expression in CSCs, functional validation indicated CD53 to be a tumor-initiating cell- rather than quiescent CSC-marker. Another association defined a state of poise for stress-induced metastases in aneuploid cells. Our results thus emphasize the need for studying cell-specific functionalities relevant to regeneration, drug resistance and disease progression in discrete tumor cell fractions. PMID:27140846

  17. Heterogeneity and frequency of BRAF mutations in primary melanoma: Comparison between molecular methods and immunohistochemistry. (United States)

    Bruno, William; Martinuzzi, Claudia; Andreotti, Virginia; Pastorino, Lorenza; Spagnolo, Francesco; Dalmasso, Bruna; Cabiddu, Francesco; Gualco, Marina; Ballestrero, Alberto; Bianchi-Scarrà, Giovanna; Queirolo, Paola; Grillo, Federica; Mastracci, Luca; Ghiorzo, Paola


    Finding the best technique to identify BRAF mutations with a high sensitivity and specificity is mandatory for accurate patient selection for target therapy. BRAF mutation frequency ranges from 40 to 60% depending on melanoma clinical characteristics and detection technique used.Intertumoral heterogeneity could lead to misinterpretation of BRAF mutational status; this is especially important if testing is performed on primary specimens, when metastatic lesions are unavailable.Aim of this study was to identify the best combination of methods for detecting BRAF mutations (among peptide nucleic acid - PNA-clamping real-time PCR, immunohistochemistry and capillary sequencing) and investigate BRAF mutation heterogeneity in a series of 100 primary melanomas and a subset of 25 matched metastatic samples.Overall, we obtained a BRAF mutation frequency of 62%, based on the combination of at least two techniques. Concordance between mutation status in primary and metastatic tumor was good but not complete (67%), when agreement of at least two techniques were considered. Next generation sequencing was used to quantify the threshold of detected mutant alleles in discordant samples. Combining different methods excludes that the observed heterogeneity is technique-based. We propose an algorithm for BRAF mutation testing based on agreement between immunohistochemistry and PNA; a third molecular method could be added in case of discordance of the results. Testing the primary tumor when the metastatic sample is unavailable is a good option if at least two methods of detection are used, however the presence of intertumoral heterogeneity or the occurrence of additional primaries should be carefully considered.

  18. Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media

    KAUST Repository

    Gao, Kai


    It is important to develop fast yet accurate numerical methods for seismic wave propagation to characterize complex geological structures and oil and gas reservoirs. However, the computational cost of conventional numerical modeling methods, such as finite-difference method and finite-element method, becomes prohibitively expensive when applied to very large models. We propose a Generalized Multiscale Generalized Multiscale Finite-Element Method (GMsFEM) for elastic wave propagation in heterogeneous, anisotropic media, where we construct basis functions from multiple local problems for both boundaries and the interior of a coarse node support or coarse element. The application of multiscale basis functions can capture the fine scale medium property variations, and allows us to greatly reduce the degrees of freedom that are required to implement the modeling compared with conventional finite-element method for wave equation, while restricting the error to low values. We formulate the continuous Galerkin and discontinuous Galerkin formulation of the multiscale method, both of which have pros and cons. Applications of the multiscale method to three heterogeneous models show that our multiscale method can effectively model the elastic wave propagation in anisotropic media with a significant reduction in the degrees of freedom in the modeling system.

  19. Heterogeneous porous media permeability field characterization from fluid displacement data; Integration de donnees de deplacements de fluides dans la caracterisation de milieux poreux heterogenes

    Energy Technology Data Exchange (ETDEWEB)

    Kretz, V.


    The prediction of oil recovery or pollutant dispersion requires an accurate knowledge of the permeability field distribution. Available data are usually measurements in well bores, and, since a few years, 4D-seismic data (seismic mappings repeated in time). Such measurements allow to evaluate fluids displacements fronts evolution. The purpose of the thesis is to evaluate the possibility to determinate permeability fields from fluid displacement measurements in heterogeneous porous media. At the laboratory scale, experimental studies are made on a model and on numerical simulations. The system uses blocks of granular materials whose individual geometries and permeabilities are controlled. The fluids displacements are detected with an acoustical. The key parameters of the study are the size and spatial correlation of the permeability heterogeneity distribution, and the influence of viscosity and gravity contrasts between the injected ant displaced fluid. Then the inverse problem - evaluating the permeability field from concentration fronts evolution - is approached. At the reservoir scale, the work will mainly be focused on the integration of 4D-seismic data into inversion programs on a 3D synthetic case. A particular importance will be given to the calculation of gradients, in order to obtain a complementary information about the sensitivity of data. The information provided by 4D-seismic data consists in maps showing the vertical average of oil saturation or the presence of gas. The purpose is to integrate this qualitative information in the inversion process and to evaluate the impact on the reservoir characterization. Comparative studies - with or without 4D-seismic data - will be realized on a synthetic case. (author)

  20. A theoretical analysis of colloid attachment and straining in chemically heterogeneous porous media (United States)

    A balance of applied hydrodynamic (TH) and resisting adhesive (TA) torques was conducted over a chemically heterogeneous porous medium that contained random roughness of height hr to determine the fraction of the solid surface area that contributes to colloid immobilization (Sf*) under unfavorable a...

  1. On the potential of uneven heating in heterogeneous food media with dielectric heating

    NARCIS (Netherlands)

    Veen, van der M.E.; Goot, van der A.J.; Vriezinga, C.A.; Meester, de J.W.G.; Boom, R.M.


    A dynamic model was developed describing dielectric heating dynamics of a heterogeneous material, in which the dispersed phase heats more quickly than the surrounding phase. The model includes effects of scattering by small particles, absorption and differences in thermal and conduction properties,

  2. Influence of surface heterogeneities on reversibility of fullerene (nC60) nanoparticle attachment in saturated porous media. (United States)

    Shen, Chongyang; Zhang, Mengjia; Zhang, Shuzhen; Wang, Zhan; Zhang, Hongyan; Li, Baoguo; Huang, Yuanfang


    This study systematically investigated influence of surface roughness and surface chemical heterogeneity on attachment and detachment of nC60 nanoparticles in saturated porous media by conducting laboratory column experiments. Sand and glass beads were employed as a model collectors to represent a different surface roughness. The two collectors were treated by washing with only deionized water or by using acids to extensively remove chemical heterogeneities. Results show that both attachment and detachment were more in the acid-treated sand than those in the acid-treated glass beads. The greater attachment and detachment were attributed to the reason that sand surfaces have much more nanoscale asperities, which facilitates particle attachment atop of them at primary minima and subsequent detachment upon reduction of ionic strength. No detachment was observed if the water-washed collectors were employed, demonstrating that the couple of chemical heterogeneity with nanoscale roughness causes irreversible attachment in primary minima. Whereas existing studies frequently represented surface rough asperities as regular geometries (e.g., hemisphere, cone, pillar) for estimating influence of surface roughness on Derjaguin-Landau-Verwey-Overbeek (DLVO) interaction energies, our theoretical calculations indicate that the assumptions could underestimate both attachment and detachment because these geometries cannot account for surface curvature effects. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Evolving Spatial Heterogeneity Induced by Preferential Carbonate Dissolution in Fractured Media (United States)

    Wen, H.; Li, L.; Crandall, D.; Hakala, A.


    Spatial heterogeneity plays a key role in determining physical and geochemical processes in geological systems. In reactive fractures, mineral reactions also can alter fracture properties locally, therefore leading to evolving spatial heterogeneity. Here we use two-dimensional (2D) reactive transport modeling to 1) understand the evolving spatial heterogeneity due to the preferential dissolution of carbonate and 2) quantify the dependence of calcite dissolution on characteristics of spatial heterogeneity, including fracture roughness (i.e., aperture standard derivation, surface parameter and fractal dimension), flow connectivity (i.e., ratio of effective permeability keff over geometric mean of local permeability kG), and transport connectivity indicators (e.g., ratio of late 5% arrival time tlate5% over average arrival time tave). The fractured core samples from Brady's Hot Springs geothermal field are composed of primarily carbonate, clay, and quartz. The computational domains were set up using fracture images obtained from CT scanning at the resolution of 31.6 μm. The two samples have similar initial average aperture, porosity, permeability, and mineralogical composition. They differ in the spatial patterns: one has narrow large-aperture zones distributed widely (AD sample); the other has a major large-aperture zone in the middle of the sample (AC sample). Simulation results show that highly connected flow path forms quickly in the AD sample, leading to an increase of average chemical aperture, effective permeability, and flow velocity by five times after 75 days of injecting salt water. In contrast, these properties remain constant in the AC sample. Other parameters that quantitatively characterize the spatial heterogeneity, including connectivity and the tail slope of the breakthrough curves, also change dramatically, indicating major alteration in fracture properties due to calcite dissolution.

  4. Molecular Mixed-Metal Manganese Oxido Cubanes as Precursors to Heterogeneous Oxygen Evolution Catalysts. (United States)

    Suseno, Sandy; McCrory, Charles C L; Tran, Rosalie; Gul, Sheraz; Yano, Junko; Agapie, Theodor


    Well-defined mixed-metal [CoMn3 O4 ] and [NiMn3 O4 ] cubane complexes were synthesized and used as precursors for heterogeneous oxygen evolution reaction (OER) electrocatalysts. The discrete clusters were dropcasted onto glassy carbon (GC) and indium tin oxide (ITO) electrodes, and the OER activities of the resulting films were evaluated. The catalytic surfaces were analyzed by various techniques to gain insight into the structure-function relationships of the electrocatalysts' heterometallic composition. Depending on preparation conditions, the Co-Mn oxide was found to change metal composition during catalysis, while the Ni-Mn oxides maintained the NiMn3 ratio. XAS studies provided structural insights indicating that the electrocatalysts are different from the molecular precursors, but that the original NiMn3 O4 cubane-like geometry was maintained in the absence of thermal treatment (2-Ni). In contrast, the thermally generated 3-Ni develops an oxide-like extended structure. Both 2-Ni and 3-Ni undergo structural changes upon electrolysis, but they do not convert into the same material. The observed structural motifs in these heterogeneous electrocatalysts are reminiscent of the biological oxygen-evolving complex in Photosystem II, including the MMn3 O4 cubane moiety. The reported studies demonstrate the use of discrete heterometallic oxide clusters as precursors for heterogeneous water oxidation catalysts of novel composition and the distinct behavior of two sets of mixed metal oxides. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Characterization of Cellular and Molecular Heterogeneity of Bone Marrow Stromal Cells

    Directory of Open Access Journals (Sweden)

    Mona Elsafadi


    Full Text Available Human bone marrow-derived stromal stem cells (hBMSC exhibit multiple functions, including differentiation into skeletal cells (progenitor function, hematopoiesis support, and immune regulation (nonprogenitor function. We have previously demonstrated the presence of morphological and functional heterogeneity of hBMSC cultures. In the present study, we characterized in detail two hTERT-BMSC clonal cell populations termed here CL1 and CL2 that represent an opposing phenotype with respect to morphology, markers expression: alkaline phosphatase (ALP and CD146, and ex vivo differentiation potential. CL1 differentiated readily to osteoblasts, adipocytes, and chondrocytes as shown by expression of lineage specific genes and proteins. Whole genome transcriptome profiling of CL1 versus CL2 revealed enrichment in CL1 of bone-, mineralization-, and skeletal muscle-related genes, for example, ALP, POSTN, IGFBP5 BMP4, and CXCL12. On the other hand, CL2 transcriptome was enriched in immune modulatory genes, for example, CD14, CD99, NOTCH3, CXCL6, CFB, and CFI. Furthermore, gene expression microarray analysis of osteoblast differentiated CL1 versus CL2 showed significant upregulation in CL1 of bone development and osteoblast differentiation genes which included several homeobox genes: TBX15, HOXA2 and HOXA10, and IGF1, FGFR3, BMP6, MCAM, ITGA10, IGFBP5, and ALP. siRNA-based downregulation of the ALP gene in CL1 impaired osteoblastic and adipocytic differentiation. Our studies demonstrate the existence of molecular and functional heterogeneity in cultured hBMSC. ALP can be employed to identify osteoblastic and adipocytic progenitor cells in the heterogeneous hBMSC cultures.

  6. A Theoretical Analysis of Colloid Attachment and Straining in Chemically Heterogeneous Porous Media

    DEFF Research Database (Denmark)

    Bradford, Scott A.; Torkzaban, Saeed; Shapiro, Alexander


    A balance of applied hydrodynamic (TH) and resisting adhesive (TA) torques was conducted over a chemically heterogeneous porous medium that contained random roughness of height hr to determine the fraction of the solid surface area that contributes to colloid immobilization (Sf*) under unfavorable...... of physicochemical properties to gain insight into mechanisms and factors influencing colloid immobilization. Colloid attachment processes were demonstrated to depend on solution ionic strength (IS), the colloid radius (rc), the Young’s modulus (K), the amount of chemical heterogeneity (P+), and the Darcy velocity...... (q). Colloid immobilization was also demonstrated to occur on a rough surface in the absence of attachment. In this case, Sf* depended on IS, rc, the roughness fraction (f), hr, and q. Roughness tended to enhance TA and diminish TH. Consequently, the effect of IS on Sf* was enhanced by hr relative...

  7. Dosimetric verification of a high dose rate brachytherapy treatment planning system in homogeneous and heterogeneous media. (United States)

    Uniyal, S C; Sharma, S D; Naithani, U C


    To verify the dosimetric accuracy of treatment plans in high dose rate (HDR) brachytherapy by using Gafchromic EBT2 film and to demonstrate the adequacy of dose calculations of a commercial treatment planning system (TPS) in a heterogeneous medium. Absorbed doses at chosen points in anatomically different tissue equivalent phantoms were measured using Gafchromic EBT2 film. In one case, tandem ovoid brachytherapy was performed in a homogeneous cervix phantom, whereas in the other, organ heterogeneities were introduced in a phantom to replicate the upper thorax for esophageal brachytherapy treatment. A commercially available TPS was used to perform treatment planning in each case and the EBT2 films were irradiated with the HDR Ir-192 brachytherapy source. Film measurements in the cervix phantom were found to agree with the TPS calculated values within 3% in the clinically relevant volume. In the thorax phantom, the presence of surrounding heterogeneities was not seen to affect the dose distribution in the volume being treated, whereas, a little dose perturbation was observed at the lung surface. Doses to the spinal cord and to the sternum bone were overestimated and underestimated by 14.6% and 16.5% respectively by the TPS relative to the film measurements. At the trachea wall facing the esophagus, a dose reduction of 10% was noticed in the measurements. The dose calculation accuracy of the TPS was confirmed in homogeneous medium, whereas, it was proved inadequate to produce correct dosimetric results in conditions of tissue heterogeneity. Copyright © 2012 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  8. A theoretical framework for modeling dilution enhancement of non-reactive solutes in heterogeneous porous media. (United States)

    de Barros, F P J; Fiori, A; Boso, F; Bellin, A


    Spatial heterogeneity of the hydraulic properties of geological porous formations leads to erratically shaped solute clouds, thus increasing the edge area of the solute body and augmenting the dilution rate. In this study, we provide a theoretical framework to quantify dilution of a non-reactive solute within a steady state flow as affected by the spatial variability of the hydraulic conductivity. Embracing the Lagrangian concentration framework, we obtain explicit semi-analytical expressions for the dilution index as a function of the structural parameters of the random hydraulic conductivity field, under the assumptions of uniform-in-the-average flow, small injection source and weak-to-mild heterogeneity. Results show how the dilution enhancement of the solute cloud is strongly dependent on both the statistical anisotropy ratio and the heterogeneity level of the porous medium. The explicit semi-analytical solution also captures the temporal evolution of the dilution rate; for the early- and late-time limits, the proposed solution recovers previous results from the literature, while at intermediate times it reflects the increasing interplay between large-scale advection and local-scale dispersion. The performance of the theoretical framework is verified with high resolution numerical results and successfully tested against the Cape Cod field data. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Modeling Dynamics of Diffusion Across Heterogeneous Social Networks: News Diffusion in Social Media


    Peter Christen; David Newth; Minkyoung Kim


    Diverse online social networks are becoming increasingly interconnected by sharing information. Accordingly, emergent macro-level phenomena have been observed, such as the synchronous spread of information across different types of social media. Attempting to analyze the emergent global behavior is impossible from the examination of a single social platform, and dynamic influences between different social networks are not negligible. Furthermore, the underlying structural property of networks...

  10. Coulombic interactions and multicomponent ionic dispersion during transport of charged species in heterogeneous porous media

    DEFF Research Database (Denmark)

    Muniruzzaman, Muhammad; Rolle, Massimo

    the capability of the proposed two-dimensional multicomponent approach to describe transport of charged species and to accurately capture the Coulombic interactions between the ions, which are clearly observed in the flow-through experiments. Furthermore, the model allowed us to directly quantify and visualize...... the ionic interactions by mapping the Coulombic cross-coupling between the dispersive fluxes of the charged species in the heterogeneous domains. The outcomes of this study are important in many subsurface applications including migration of contaminants and propagation of reaction fronts....

  11. Membraneless flow battery leveraging flow-through heterogeneous porous media for improved power density and reduced crossover

    CERN Document Server

    Suss, Matthew E; Gilson, Laura; Buie, Cullen R; Bazant, Martin Z


    A key factor preventing the market penetration of renewable, intermittent energy sources, such as solar, wind and wave, is the lack of cost-effective energy storage options to counteract intermittency. Here, we propose and demonstrate a novel flow battery architecture that replaces traditional ion-exchange membranes with less expensive heterogeneous flow-through porous media. We present an experimentally-validated model which demonstrates that our architecture promises reduced crossover of reactive species compared to typical membraneless systems employing co-laminar flows in open channels. In addition, our prototype battery exhibits significantly improved power density (0.925 W/cm2) and maximum current density (3 A/cm2) compared to previous membraneless systems.

  12. Multilevel and quasi-Monte Carlo methods for uncertainty quantification in particle travel times through random heterogeneous porous media. (United States)

    Crevillén-García, D; Power, H


    In this study, we apply four Monte Carlo simulation methods, namely, Monte Carlo, quasi-Monte Carlo, multilevel Monte Carlo and multilevel quasi-Monte Carlo to the problem of uncertainty quantification in the estimation of the average travel time during the transport of particles through random heterogeneous porous media. We apply the four methodologies to a model problem where the only input parameter, the hydraulic conductivity, is modelled as a log-Gaussian random field by using direct Karhunen-Loéve decompositions. The random terms in such expansions represent the coefficients in the equations. Numerical calculations demonstrating the effectiveness of each of the methods are presented. A comparison of the computational cost incurred by each of the methods for three different tolerances is provided. The accuracy of the approaches is quantified via the mean square error.

  13. Finite volume approximation of the three-dimensional flow equation in axisymmetric, heterogeneous porous media based on local analytical solution

    KAUST Repository

    Salama, Amgad


    In this work the problem of flow in three-dimensional, axisymmetric, heterogeneous porous medium domain is investigated numerically. For this system, it is natural to use cylindrical coordinate system, which is useful in describing phenomena that have some rotational symmetry about the longitudinal axis. This can happen in porous media, for example, in the vicinity of production/injection wells. The basic feature of this system is the fact that the flux component (volume flow rate per unit area) in the radial direction is changing because of the continuous change of the area. In this case, variables change rapidly closer to the axis of symmetry and this requires the mesh to be denser. In this work, we generalize a methodology that allows coarser mesh to be used and yet yields accurate results. This method is based on constructing local analytical solution in each cell in the radial direction and moves the derivatives in the other directions to the source term. A new expression for the harmonic mean of the hydraulic conductivity in the radial direction is developed. Apparently, this approach conforms to the analytical solution for uni-directional flows in radial direction in homogeneous porous media. For the case when the porous medium is heterogeneous or the boundary conditions is more complex, comparing with the mesh-independent solution, this approach requires only coarser mesh to arrive at this solution while the traditional methods require more denser mesh. Comparisons for different hydraulic conductivity scenarios and boundary conditions have also been introduced. © 2013 Elsevier B.V.

  14. Direct molecular-level characterization of different heterogeneous freezing modes on mica – Part 1

    Directory of Open Access Journals (Sweden)

    A. Abdelmonem


    Full Text Available The mechanisms behind heterogeneous ice nucleation are of fundamental importance to the prediction of the occurrence and properties of many cloud types, which influence climate and precipitation. Aerosol particles act as cloud condensation and freezing nuclei. The surface–water interaction of an ice nucleation particle plays a major, not well explored, role in its ice nucleation ability. This paper presents a real-time molecular-level comparison of different freezing modes on the surface of an atmospherically relevant mineral surface (mica under varying supersaturation conditions using second-harmonic generation spectroscopy. Two sub-deposition nucleation modes were identified (one- and two-stage freezing. The nonlinear signal at the water–mica interface was found to drop following the formation of a thin film on the surface regardless of (1 the formed phase (liquid or ice and (2 the freezing path (one or two step, indicating similar molecular structuring. The results also revealed a transient phase of ice at water–mica interfaces during freezing, which has a lifetime of around 1 min. Such information will have a significant impact on climate change, weather modification, and the tracing of water in hydrosphere studies.

  15. Direct molecular-level characterization of different heterogeneous freezing modes on mica - Part 1 (United States)

    Abdelmonem, Ahmed


    The mechanisms behind heterogeneous ice nucleation are of fundamental importance to the prediction of the occurrence and properties of many cloud types, which influence climate and precipitation. Aerosol particles act as cloud condensation and freezing nuclei. The surface-water interaction of an ice nucleation particle plays a major, not well explored, role in its ice nucleation ability. This paper presents a real-time molecular-level comparison of different freezing modes on the surface of an atmospherically relevant mineral surface (mica) under varying supersaturation conditions using second-harmonic generation spectroscopy. Two sub-deposition nucleation modes were identified (one- and two-stage freezing). The nonlinear signal at the water-mica interface was found to drop following the formation of a thin film on the surface regardless of (1) the formed phase (liquid or ice) and (2) the freezing path (one or two step), indicating similar molecular structuring. The results also revealed a transient phase of ice at water-mica interfaces during freezing, which has a lifetime of around 1 min. Such information will have a significant impact on climate change, weather modification, and the tracing of water in hydrosphere studies.

  16. Molecular Heterogeneity of Ewing Sarcoma as Detected by Ion Torrent Sequencing. (United States)

    Zhang, Nana; Liu, Haijing; Yue, Guanjun; Zhang, Yan; You, Jiangfeng; Wang, Hua


    Ewing sarcoma (ES) is the second most common malignant bone and soft tissue tumor in children and adolescents. Despite advances in comprehensive treatment, patients with ES metastases still suffer poor outcomes, thus, emphasizing the need for detailed genetic profiles of ES patients to identify suitable molecular biomarkers for improved prognosis and development of effective and targeted therapies. In this study, the next generation sequencing Ion AmpliSeq™ Cancer Hotspot Panel v2 was used to identify cancer-related gene mutations in the tissue samples from 20 ES patients. This platform targeted 207 amplicons of 2800 loci in 50 cancer-related genes. Among the 20 tissue specimens, 62 nonsynonymous hotspot mutations were identified in 26 cancer-related genes, revealing the molecular heterogeneity of ES. Among these, five novel mutations in cancer-related genes (KDR, STK11, MLH1, KRAS, and PTPN11) were detected in ES, and these mutations were confirmed with traditional Sanger sequencing. ES patients with KDR, STK11, and MLH1 mutations had higher Ki-67 proliferation indices than the ES patients lacking such mutations. Notably, more than half of the ES patients harbored one or two possible 'druggable' mutations that have been previously linked to a clinical cancer treatment option. Our results provided the foundation to not only elucidate possible mechanisms involved in ES pathogenesis but also indicated the utility of Ion Torrent sequencing as a sensitive and cost-effective tool to screen key oncogenes and tumor suppressors in order to develop personalized therapy for ES patients.

  17. Synthesis and Self-Assembly of Chiral Cylindrical Molecular Complexes: Functional Heterogeneous Liquid-Solid Materials Formed by Helicene Oligomers

    Directory of Open Access Journals (Sweden)

    Nozomi Saito


    Full Text Available Chiral cylindrical molecular complexes of homo- and hetero-double-helices derived from helicene oligomers self-assemble in solution, providing functional heterogeneous liquid-solid materials. Gels and liotropic liquid crystals are formed by fibril self-assembly in solution; molecular monolayers and fibril films are formed by self-assembly on solid surfaces; gels containing gold nanoparticles emit light; silica nanoparticles aggregate and adsorb double-helices. Notable dynamics appears during self-assembly, including multistep self-assembly, solid surface catalyzed double-helix formation, sigmoidal and stairwise kinetics, molecular recognition of nanoparticles, discontinuous self-assembly, materials clocking, chiral symmetry breaking and homogeneous-heterogeneous transitions. These phenomena are derived from strong intercomplex interactions of chiral cylindrical molecular complexes.

  18. 332 Molecular Characteristics of Tumor Infiltrating Front in Glioblastoma: Insights Into Molecular Heterogeneity and Implications on Targeted Therapy. (United States)

    Arimappamagan, Arivazhagan; Kruthika; Dawn, Rose; Paturu, Kondaiah; Santosh, Vani


    Molecular heterogeneity in glioblastoma (GBM) is a novel area of research recently. Because tumor infiltrating front in GBM is often left behind following tumor decompression, knowledge of its genetic makeup can improve the rationale of potential molecular targets. MRI localized biopsies of the tumor core and peritumoral brain zone (PBZ) were obtained from 25 GBM patients. The PBZ samples containing 15% to 30% tumor cells and core samples with predominantly tumor cells along with 8 nonneoplastic brain tissues were selected for a whole Genome Gene Expression Microarray. The list of differentially expressed genes between the tumor core and PBZ compared with nonneoplastic brain tissue was identified using R Bioconductor. Selected genes were validated using quantitative real-time polymerase chain reaction (PCR) and immunohistochemistry (IHC). Unsupervised hierarchical clustering of the genes revealed that the tumor core and PBZ samples showed a varied gene expression profile and clustered into 2 distinct groups. Approximately 7123, 5188, and 991 genes were differentially expressed in Core vs Normal, PBZ vs Normal and PBZ vs Core. Novel genes like PBK (role in cell cycle), MELK (stem cell marker), and TOP2A (proliferation marker) were upregulated in PBZ and tumor core compared with normal brain and robustly validated on IHC. Pathways involved in cell cycle, immune response, cell-cell adhesion, cell-matrix interaction, etc, were commonly enriched in periphery and tumor core compared with normal brain. Some of the novel markers were validated by real-time PCR and IHC. We demonstrate that the key genes involved in tumor cell proliferation, invasion, migration, response to immune system, and stemness markers are highly enriched in the PBZ. These genes, probably contribute to the resistance of PBZ cells to standard adjuvant therapy, resulting in tumor recurrence.

  19. Bayesian Uncertainty Quantification in Predictions of Flows in Highly Heterogeneous Media and Its Applications to the CO2 Sequestration

    Energy Technology Data Exchange (ETDEWEB)

    Efendiev, Yalchin [Texas A & M Univ., College Station, TX (United States); Datta-Gupta, Akhil [Texas A & M Univ., College Station, TX (United States); Jafarpour, Behnam [Texas A & M Univ., College Station, TX (United States); Mallick, Bani [Texas A & M Univ., College Station, TX (United States); Vassilevski, Panayot [Texas A & M Univ., College Station, TX (United States)


    In this proposal, we have worked on Bayesian uncertainty quantification for predictions of fows in highly heterogeneous media. The research in this proposal is broad and includes: prior modeling for heterogeneous permeability fields; effective parametrization of heterogeneous spatial priors; efficient ensemble- level solution techniques; efficient multiscale approximation techniques; study of the regularity of complex posterior distribution and the error estimates due to parameter reduction; efficient sampling techniques; applications to multi-phase ow and transport. We list our publications below and describe some of our main research activities. Our multi-disciplinary team includes experts from the areas of multiscale modeling, multilevel solvers, Bayesian statistics, spatial permeability modeling, and the application domain.

  20. Phylogenetical and ontogenetical studies on the molecular weight heterogeneity of bovine serum transferrin. (United States)

    Tsuji, S; Kato, H; Matsuoka, Y; Fukushima, T; Nanjoh, I; Amano, T; Namikawa, T


    Antitransferrin (Tf) rabbit serum was highly specific: it reacted with Tfs of ruminants, such as European breeds and Zebu breeds of cattle, Bali cattle, banteng, swamp and river types of water buffalo, anoa, goat, sheep, deer, antelope, camel, and giraffe, but did not react with serum of other non-ruminant species, such as pig, wild boar, hippopotamus, horse, rabbit, rat, chicken, etc. Electrophoresis of Tf and immunoglobulin G (IgG) complexes was carried out using sodium dodecyl sulfate--polyacrylamide gel electrophoresis (SDS-PAGE). Within ruminants, the following species showed two Tf molecules on SDS-PAGE; European and Zebu cattle, Bali cattle, banteng, two types of water buffalo, and two species of anoa. Other ruminants, sheep, goat, deer, antelope, camel, and giraffe, etc., showed only one Tf molecule. The Tf heterogeneity in molecular weight was, thus, restricted to Bos, Bubalus, and Anoa. The molecular weight of Tf of water buffalo was slightly larger than that of cattle on the gel. The peptide pattern from cyanogen bromide cleavage of Tf of the water buffalo differed clearly from that of cattle. Fetal Tf showed only one molecule during development, but a newborn calf has two Tf molecules, (one large and one small) within 18 hr after birth. We suggest, therefore, that the small molecules formed during the last month of gestation. The peptide patterns of adult and fetal Tfs cleaved by cyanogen bromide differed with regard to the two large peptides; fetal Tf, lacking the second-largest peptide, had twice the amount of the largest peptide compared with adult Tf. From these results, we suggest that a change in peptide sequence occurs from the last month of gestation, when the largest peptide is degraded to the second largest. However, a Tf-like protein detected in the liver microsomal fraction has only one molecular size, both in adult and in fetal livers.

  1. Development and Evaluation of an Open-Source Software Package “CGITA” for Quantifying Tumor Heterogeneity with Molecular Images

    Directory of Open Access Journals (Sweden)

    Yu-Hua Dean Fang


    Full Text Available Background. The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA toolbox, and provide it to the research community as a free, open-source project. Methods. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC cancer patients treated with definitive radiotherapies. Results. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmean for outcome prediction in the ROC analysis with a higher area under curve (AUC. Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmean and TLG (0.6 and 0.52, resp.. Conclusions. CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use at

  2. Development and evaluation of an open-source software package "CGITA" for quantifying tumor heterogeneity with molecular images. (United States)

    Fang, Yu-Hua Dean; Lin, Chien-Yu; Shih, Meng-Jung; Wang, Hung-Ming; Ho, Tsung-Ying; Liao, Chun-Ta; Yen, Tzu-Chen


    The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA) toolbox, and provide it to the research community as a free, open-source project. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC) cancer patients treated with definitive radiotherapies. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmean for outcome prediction in the ROC analysis with a higher area under curve (AUC). Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmean and TLG (0.6 and 0.52, resp.). CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use at

  3. Micro-macro model for prediction of local temperature distribution in heterogeneous and two-phase media

    Directory of Open Access Journals (Sweden)

    Furmański Piotr


    Full Text Available Heat flow in heterogeneous media with complex microstructure follows tortuous path and therefore determination of temperature distribution in them is a challenging task. Two-scales, micro-macro model of heat conduction with phase change in such media was considered in the paper. A relation between temperature distribution on the microscopic level, i.e., on the level of details of microstructure, and the temperature distribution on the macroscopic level, i.e., on the level where the properties were homogenized and treated as effective, was derived. The expansion applied to this relation allowed to obtain its more simplified, approximate form corresponding to separation of micro- and macro-scales. Then the validity of this model was checked by performing calculations for 2D microstructure of a composite made of two constituents. The range of application of the proposed micro-macro model was considered in transient states of heat conduction both for the case when the phase change in the material is present and when it is absent. Variation of the effective thermal conductivity with time was considered and a criterion was found for which application of the considered model is justified.

  4. Effect of Pore-Scale Heterogeneity and Capillary-Viscous Fingering on Commingled Waterflood Oil Recovery in Stratified Porous Media

    Directory of Open Access Journals (Sweden)

    Emad W. Al-Shalabi


    Full Text Available Oil recovery prediction and field pilot implements require basic understanding and estimation of displacement efficiency. Corefloods and glass micromodels are two of the commonly used experimental methods to achieve this. In this paper, waterflood recovery is investigated using layered etched glass micromodel and Berea sandstone core plugs with large permeability contrasts. This study focuses mainly on the effect of permeability (heterogeneity in stratified porous media with no cross-flow. Three experimental setups were designed to represent uniformly stratified oil reservoir with vertical discontinuity in permeability. Waterflood recovery to residual oil saturation (Sor is measured through glass micromodel (to aid visual observation, linear coreflood, and forced drainage-imbibition processes by ultracentrifuge. Six oil samples of low-to-medium viscosity and porous media of widely different permeability (darcy and millidarcy ranges were chosen for the study. The results showed that waterflood displacement efficiencies are consistent in both permeability ranges, namely, glass micromodel and Berea sandstone core plugs. Interestingly, the experimental results show that the low permeability zones resulted in higher ultimate oil recovery compared to high permeability zones. At Sor microheterogeneity and fingering are attributed for this phenomenon. In light of the findings, conformance control is discussed for better sweep efficiency. This paper may be of help to field operators to gain more insight into microheterogeneity and fingering phenomena and their impact on waterflood recovery estimation.

  5. Statistics of highly heterogeneous flow fields confined to three-dimensional random porous media (United States)

    Jin, C.; Langston, P. A.; Pavlovskaya, G. E.; Hall, M. R.; Rigby, S. P.


    We present a strong relationship between the microstructural characteristics of, and the fluid velocity fields confined to, three-dimensional random porous materials. The relationship is revealed through simultaneously extracting correlation functions Ru u(r ) of the spatial (Eulerian) velocity fields and microstructural two-point correlation functions S2(r ) of the random porous heterogeneous materials. This demonstrates that the effective physical transport properties depend on the characteristics of complex pore structure owing to the relationship between Ru u(r ) and S2(r ) revealed in this study. Further, the mean excess plot was used to investigate the right tail of the streamwise velocity component that was found to obey light-tail distributions. Based on the mean excess plot, a generalized Pareto distribution can be used to approximate the positive streamwise velocity distribution.

  6. Evaluating the assumption of power-law late time scaling of breakthrough curves in highly heterogeneous media (United States)

    Pedretti, Daniele


    Power-law (PL) distributions are widely adopted to define the late-time scaling of solute breakthrough curves (BTCs) during transport experiments in highly heterogeneous media. However, from a statistical perspective, distinguishing between a PL distribution and another tailed distribution is difficult, particularly when a qualitative assessment based on visual analysis of double-logarithmic plotting is used. This presentation aims to discuss the results from a recent analysis where a suite of statistical tools was applied to evaluate rigorously the scaling of BTCs from experiments that generate tailed distributions typically described as PL at late time. To this end, a set of BTCs from numerical simulations in highly heterogeneous media were generated using a transition probability approach (T-PROGS) coupled to a finite different numerical solver of the flow equation (MODFLOW) and a random walk particle tracking approach for Lagrangian transport (RW3D). The T-PROGS fields assumed randomly distributed hydraulic heterogeneities with long correlation scales creating solute channeling and anomalous transport. For simplicity, transport was simulated as purely advective. This combination of tools generates strongly non-symmetric BTCs visually resembling PL distributions at late time when plotted in double log scales. Unlike other combination of modeling parameters and boundary conditions (e.g. matrix diffusion in fractures), at late time no direct link exists between the mathematical functions describing scaling of these curves and physical parameters controlling transport. The results suggest that the statistical tests fail to describe the majority of curves as PL distributed. Moreover, they suggest that PL or lognormal distributions have the same likelihood to represent parametrically the shape of the tails. It is noticeable that forcing a model to reproduce the tail as PL functions results in a distribution of PL slopes comprised between 1.2 and 4, which are the

  7. Bias and uncertainty in regression-calibrated models of groundwater flow in heterogeneous media (United States)

    Cooley, R.L.; Christensen, S.


    Groundwater models need to account for detailed but generally unknown spatial variability (heterogeneity) of the hydrogeologic model inputs. To address this problem we replace the large, m-dimensional stochastic vector ?? that reflects both small and large scales of heterogeneity in the inputs by a lumped or smoothed m-dimensional approximation ????*, where ?? is an interpolation matrix and ??* is a stochastic vector of parameters. Vector ??* has small enough dimension to allow its estimation with the available data. The consequence of the replacement is that model function f(????*) written in terms of the approximate inputs is in error with respect to the same model function written in terms of ??, ??,f(??), which is assumed to be nearly exact. The difference f(??) - f(????*), termed model error, is spatially correlated, generates prediction biases, and causes standard confidence and prediction intervals to be too small. Model error is accounted for in the weighted nonlinear regression methodology developed to estimate ??* and assess model uncertainties by incorporating the second-moment matrix of the model errors into the weight matrix. Techniques developed by statisticians to analyze classical nonlinear regression methods are extended to analyze the revised method. The analysis develops analytical expressions for bias terms reflecting the interaction of model nonlinearity and model error, for correction factors needed to adjust the sizes of confidence and prediction intervals for this interaction, and for correction factors needed to adjust the sizes of confidence and prediction intervals for possible use of a diagonal weight matrix in place of the correct one. If terms expressing the degree of intrinsic nonlinearity for f(??) and f(????*) are small, then most of the biases are small and the correction factors are reduced in magnitude. Biases, correction factors, and confidence and prediction intervals were obtained for a test problem for which model error is

  8. Molecular analysis reveals heterogeneity of mouse mammary tumors conditionally mutant for Brca1

    Directory of Open Access Journals (Sweden)

    Anver Miriam R


    Full Text Available Abstract Background Development of therapies for patients with BRCA1 mutations has been hampered by lack of readily available in vitro and in vivo models. We recently showed that transplantation of transgenic mammary tumors as cell suspensions into naïve recipients generates reproducible tumors with remarkable stability of gene expression profile. We examined the expression profiles of original and serially transplanted mammary tumors from Brca1 deficient mice, and tumor derived cell lines to validate their use for preclinical testing and studies of tumor biology. Methods Original tumors, serially transplanted and multiple cell lines derived from Brca1 mammary tumors were characterized by morphology, gene and protein expression, and cell surface markers. Results Gene expression among Brca1 tumors showed more heterogeneity than among previously characterized tumors from MMTV-PyMT and -Wnt1 models. Gene expression data segregated Brca1 tumors into 3 distinct types: basal, mixed luminal, and tumors with epithelial-to-mesenchymal transition (EMT. Serial transplantation of individual tumors and multiple cell lines derived from the original tumors recapitulated the molecular characteristics of each tumor of origin. One tumor had distinct features of EMT and gave rise to cell lines that contained a distinct CD44+/CD24-/low population that may correlate with human breast cancer stem cells. Conclusion Although individual tumors expanded by transplantation maintain the genomic profile of the original tumors, the heterogeneity among Brca1 tumors limits the extent of their use for preclinical testing. However, cell lines offer a robust material for understanding tumor biology and response to therapies driven by BRCA1 deficiency.

  9. Molecular isotopic heterogeneity of fossil organic matter: implications for δ13Cbiomass and δ13Cpalaeoatmosphere proxies

    NARCIS (Netherlands)

    Poole, I.J.; Bergen, P.F. van; Kool, J.; Schouten, S.; Cantrill, David J.


    The degree of isotopic variation in fossil organic matter renders bulk δ13C signatures strongly influenced by molecular isotopic heterogeneity. For example, in fossil wood the relative abundance of less depleted 13C moieties, i.e. preserved 13C enriched polysaccharides versus the relatively 13C

  10. Laser control of molecular excitations in stochastic dissipative media. (United States)

    Tremblay, Jean Christophe


    In the present work, ideas for controlling photochemical reactions in dissipative environments using shaped laser pulses are presented. New time-local control algorithms for the stochastic Schrödinger equation are introduced and compared to their reduced density matrix analog. The numerical schemes rely on time-dependent targets for guiding the reaction along a preferred path. The methods are tested on the vibrational control of adsorbates at metallic surfaces and on the ultrafast electron dynamics in a strong dissipative medium. The selective excitation of the specific states is achieved with improved yield when using the new algorithms. Both methods exhibit similar convergence behavior and results compare well with those obtained using local optimal control for the reduced density matrix. The favorable scaling of the methods allows to tackle larger systems and to control photochemical reactions in dissipative media of molecules with many more degrees of freedom.

  11. Approaches to large scale unsaturated flow in heterogeneous, stratified, and fractured geologic media

    Energy Technology Data Exchange (ETDEWEB)

    Ababou, R.


    This report develops a broad review and assessment of quantitative modeling approaches and data requirements for large-scale subsurface flow in radioactive waste geologic repository. The data review includes discussions of controlled field experiments, existing contamination sites, and site-specific hydrogeologic conditions at Yucca Mountain. Local-scale constitutive models for the unsaturated hydrodynamic properties of geologic media are analyzed, with particular emphasis on the effect of structural characteristics of the medium. The report further reviews and analyzes large-scale hydrogeologic spatial variability from aquifer data, unsaturated soil data, and fracture network data gathered from the literature. Finally, various modeling strategies toward large-scale flow simulations are assessed, including direct high-resolution simulation, and coarse-scale simulation based on auxiliary hydrodynamic models such as single equivalent continuum and dual-porosity continuum. The roles of anisotropy, fracturing, and broad-band spatial variability are emphasized. 252 refs.

  12. Extracting the Green's function of attenuating heterogeneous acoustic media from uncorrelated waves. (United States)

    Snieder, Roel


    The Green's function of acoustic or elastic wave propagation can, for loss-less media, be retrieved by correlating the wave field that is excited by random sources and is recorded at two locations. Here the generalization of this idea to attenuating acoustic waves in an inhomogeneous medium is addressed, and it is shown that the Green's function can be retrieved from waves that are excited throughout the volume by spatially uncorrelated injection sources with a power spectrum that is proportional to the local dissipation rate. For a finite volume, one needs both volume sources and sources at the bounding surface for the extraction of the Green's functions. For the special case of a homogeneous attenuating medium defined over a finite volume, the phase and geometrical spreading of the Green's function is correctly retrieved when the volume sources are ignored, but the attenuation is not.

  13. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)


    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

  14. Overcoming intratumoural heterogeneity for reproducible molecular risk stratification: a case study in advanced kidney cancer. (United States)

    Lubbock, Alexander L R; Stewart, Grant D; O'Mahony, Fiach C; Laird, Alexander; Mullen, Peter; O'Donnell, Marie; Powles, Thomas; Harrison, David J; Overton, Ian M


    Metastatic clear cell renal cell cancer (mccRCC) portends a poor prognosis and urgently requires better clinical tools for prognostication as well as for prediction of response to treatment. Considerable investment in molecular risk stratification has sought to overcome the performance ceiling encountered by methods restricted to traditional clinical parameters. However, replication of results has proven challenging, and intratumoural heterogeneity (ITH) may confound attempts at tissue-based stratification. We investigated the influence of confounding ITH on the performance of a novel molecular prognostic model, enabled by pathologist-guided multiregion sampling (n = 183) of geographically separated mccRCC cohorts from the SuMR trial (development, n = 22) and the SCOTRRCC study (validation, n = 22). Tumour protein levels quantified by reverse phase protein array (RPPA) were investigated alongside clinical variables. Regularised wrapper selection identified features for Cox multivariate analysis with overall survival as the primary endpoint. The optimal subset of variables in the final stratification model consisted of N-cadherin, EPCAM, Age, mTOR (NEAT). Risk groups from NEAT had a markedly different prognosis in the validation cohort (log-rank p = 7.62 × 10-7; hazard ratio (HR) 37.9, 95% confidence interval 4.1-353.8) and 2-year survival rates (accuracy = 82%, Matthews correlation coefficient = 0.62). Comparisons with established clinico-pathological scores suggest favourable performance for NEAT (Net reclassification improvement 7.1% vs International Metastatic Database Consortium score, 25.4% vs Memorial Sloan Kettering Cancer Center score). Limitations include the relatively small cohorts and associated wide confidence intervals on predictive performance. Our multiregion sampling approach enabled investigation of NEAT validation when limiting the number of samples analysed per tumour, which significantly degraded performance. Indeed

  15. Organizing the Cellular and Molecular Heterogeneity in High-Grade Serous Ovarian Cancer by Mass Cytometry (United States)

    Tumor heterogeneity in high grade serous ovarian cancer (HG-SOC) represents a significant barrier for successful therapeutic intervention. To further...understand the cell types contributing to this heterogeneity we performed a comprehensive phenotypic characterization of 22 primary ovarian tumor...also showed greater overall phenotypic heterogeneity quantified by Simpsons Diversity Index. Importantly the novel cell types identified have the

  16. Tumor microvascular changes in antiangiogenic treatment : Assessment by magnetic resonance contrast media of different molecular weights

    NARCIS (Netherlands)

    Turetschek, K; Preda, A; Novikov, [No Value; Brasch, RC; Weinmann, HJ; Wunderbaldinger, P; Roberts, TPL

    Purpose: To test magnetic resonance (MR) contrast media of different molecular weights (MWs) for their potential to characterize noninvasively microvascular changes in an experimental tumor treatment model. Materials and Methods: MD-MBA-435, a poorly differentiated human breast cancer cell line, was

  17. The larmor frequency shift in magnetically heterogeneous media depends on their mesoscopic structure. (United States)

    Ruh, Alexander; Scherer, Harald; Kiselev, Valerij G


    Recent studies have addressed the determination of the NMR precession frequency in biological tissues containing magnetic susceptibility differences between cell types. The purpose of this study is to investigate the dependence of the precession frequency on medium microstructure using a simple physical model. This dependence is governed by diffusion of NMR-visible molecules in magnetically heterogeneous microenvironments. In the limit of fast diffusion, the precession frequency is determined by the average susceptibility-induced magnetic field, whereas in the limit of slow diffusion it is determined by the average local phase factor of precessing spins. The main method used is Monte Carlo simulation of isotropic suspensions of impermeable magnetized spheres. In addition, NMR spectroscopy was performed in aqueous suspensions of polystyrene microbeads. The precession frequency depends on the structural organization of magnetized objects in the medium. Monte Carlo simulations demonstrated a nonmonotonic transition between the regimes of fast and slow diffusion. NMR experiments confirmed the transition, but were unable to confirm its precise form. Results for a given pattern of structural organization obey a scaling law. The NMR precession frequency exhibits a complex dependence on medium structure. Our results suggest that the commonly assumed limit of fast water diffusion holds for biological tissues with small cells. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  18. Structure and dynamical intra-molecular heterogeneity of star polymer melts above glass transition temperature (United States)

    Chremos, Alexandros; Glynos, Emmanouil; Green, Peter F.


    Structural and dynamical properties of star melts have been investigated with molecular dynamics simulations of a bead-spring model. Star polymers are known to be heterogeneous, but a systematic simulation study of their properties in melt conditions near the glass transition temperature was lacking. To probe their properties, we have expanded from linear to star polymers the applicability of Dobkowski's chain-length dependence correlation function [Z. Dobkowski, Eur. Polym. J. 18, 563 (1982)]. The density and the isokinetic temperature, based on the canonical definition of the laboratory glass-transition, can be described well by the correlation function and a subtle behavior manifests as the architecture becomes more complex. For linear polymer chains and low functionality star polymers, we find that an increase of the arm length would result in an increase of the density and the isokinetic temperature, but high functionality star polymers have the opposite behavior. The effect between low and high functionalities is more pronounced for short arm lengths. Complementary results such as the specific volume and number of neighbors in contact provide further insights on the subtle relation between structure and dynamics. The findings would be valuable to polymer, colloidal, and nanocomposites fields for the design of materials in absence of solution with the desired properties.

  19. 369 TFlop/s molecular dynamics simulations on the Roadrunner general-purpose heterogeneous supercomputer

    Energy Technology Data Exchange (ETDEWEB)

    Swaminarayan, Sriram [Los Alamos National Laboratory; Germann, Timothy C [Los Alamos National Laboratory; Kadau, Kai [Los Alamos National Laboratory; Fossum, Gordon C [IBM CORPORATION


    The authors present timing and performance numbers for a short-range parallel molecular dynamics (MD) code, SPaSM, that has been rewritten for the heterogeneous Roadrunner supercomputer. Each Roadrunner compute node consists of two AMD Opteron dual-core microprocessors and four PowerXCell 8i enhanced Cell microprocessors, so that there are four MPI ranks per node, each with one Opteron and one Cell. The interatomic forces are computed on the Cells (each with one PPU and eight SPU cores), while the Opterons are used to direct inter-rank communication and perform I/O-heavy periodic analysis, visualization, and checkpointing tasks. The performance measured for our initial implementation of a standard Lennard-Jones pair potential benchmark reached a peak of 369 Tflop/s double-precision floating-point performance on the full Roadrunner system (27.7% of peak), corresponding to 124 MFlop/Watt/s at a price of approximately 3.69 MFlops/dollar. They demonstrate an initial target application, the jetting and ejection of material from a shocked surface.

  20. Molecular heterogeneity of beta-thalassaemia in Malaysia: a practical approach to diagnosis. (United States)

    Thong, M K; Law, H Y; Ng, I S


    The beta-thalassaemia mutations in 20 Malaysian children with beta-thalassaemia major were characterised by using a multi-modal approach, consisting of a slot-blot hybridisation with selected allele-specific oligonucleotides (ASO), followed by reverse dot-blot assay (RDB), amplification refractory mutation system (ARMS) and genomic sequencing. This strategy yielded a 94.4% mutation detection rate. The 6 most common mutations were codons 41/42 (-TTCT), IVS II nt 654(C --> T), IVS I nt 5(G --> C), IVS I nt 1(G -->T), codon 35 (-C) and codon 19 (A --> G), which accounted for 83.3% of all mutations detected. A strategy of initial screening with the above 6 selected ASOs for slot-blot hybridisation followed by RDB assay for the less common Asian mutations would give a mutation identification of 91.7%. Another feasible approach would be to analyse alleles from a particular racial group, by a judicious selection of 4 ASOs common to that particular subpopulation and then supplement this with RDB assay. This could yield a 100% coverage for the Chinese subpopulation in Malaysia. With these strategies, a practical approach has been identified to overcome the pitfalls posed by the molecular heterogeneity of beta-thalassaemia to enable prenatal diagnosis and carrier screening to be carried out. Regional collaborative studies are to be encouraged as an indispensable tool in providing better health care services to our patients.

  1. Compensation of optical heterogeneity-induced artifacts in fluorescence molecular tomography: theory and in vivo validation. (United States)

    Mohajerani, Pouyan; Adibi, Ali; Kempner, Joshua; Yared, Wael


    We present a method for reduction of image artifacts induced by the optical heterogeneities of tissue in fluorescence molecular tomography (FMT) through identification and compensation of image regions that evidence propagation of emission light through thin or low-absorption tunnels in tissue. The light tunneled as such contributes to the emission image as spurious components that might substantially overwhelm the desirable fluorescence emanating from the targeted lesions. The proposed method makes use of the strong spatial correlation between the emission and excitation images to estimate the tunneled components and yield a residual image that mainly consists of the signal due to the desirable fluorescence. This residual image is further refined using a coincidence mask constructed for each excitation-emission image pair. The coincidence mask is essentially a map of the "hot spots" that occur in both excitation and emission images, as such areas are often associated with tunneled emission. In vivo studies are performed on a human colon adenocarcinoma xenograft tumor model with subcutaneous tumors and a murine breast adenocarcinoma model with aggressive tumor cell metastasis and growth in the lungs. Results demonstrate significant improvements in the reconstructions achieved by the proposed method.

  2. Comparison of iterative methods and preconditioners for the solution of miscible two-phase flow in heterogeneous porous media (United States)

    Büsing, Henrik


    calculation of mutual solubilities from 12 to 100 °C and up to 600 bar, Geochimica et Cosmochimica Acta, 67(16), 3015-3031. [2] Huber, R. & Helmig, R., 2000. Node-centered finite volume discretizations for the numerical simulation of multiphase flow in heterogeneous porous media, Computational Geosciences, 4, 141-164. [3] Griewank, A. & Walther, A., 2008. Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation, SIAM, Philadelphia, PA, 2nd edn. [4] Büsing, H., Willkomm, J., Bischof, C. H., & Clauser, C., 2012. Using exact Jacobians in an implicit Newton method for solving multiphase flow in porous media, International Journal for Computational Science and Engineering, (to appear). [5] Pape, H., Clauser, C., & Iffland, J., 2000. Variation of permeability with porosity in sandstone diagenesis interpreted with a fractal pore space model, Pure and Applied Geophysics, 157, 603-619.

  3. Molecular Optical Simulation Environment (MOSE): A Platform for the Simulation of Light Propagation in Turbid Media (United States)

    Ren, Shenghan; Chen, Xueli; Wang, Hailong; Qu, Xiaochao; Wang, Ge; Liang, Jimin; Tian, Jie


    The study of light propagation in turbid media has attracted extensive attention in the field of biomedical optical molecular imaging. In this paper, we present a software platform for the simulation of light propagation in turbid media named the “Molecular Optical Simulation Environment (MOSE)”. Based on the gold standard of the Monte Carlo method, MOSE simulates light propagation both in tissues with complicated structures and through free-space. In particular, MOSE synthesizes realistic data for bioluminescence tomography (BLT), fluorescence molecular tomography (FMT), and diffuse optical tomography (DOT). The user-friendly interface and powerful visualization tools facilitate data analysis and system evaluation. As a major measure for resource sharing and reproducible research, MOSE aims to provide freeware for research and educational institutions, which can be downloaded at PMID:23577215

  4. Experimental Investigation of Heterogeneous Power Systems on the Basis of Lyophobic Liquids and Porous Media

    Directory of Open Access Journals (Sweden)

    V. D. Borman


    Full Text Available The use of non-traditional ways for energy accumulation (absorption is a reserve to increase efficiency of accumulating and damping devices. The work is aimed at experimental and theoretical verification of possibility to create the accumulating and energy damping devices based on the heterogeneous systems (HS. The HS includes a couple i.e. a porous body (silochromes with pore diameter from 20 nm to 360 nm and a lyophobic (non-wetting liquid (Wood's alloy. The paper briefly presents provisions of the theory of processes in HS based on the kinetics of percolation transition that allows us to calculate power, power and temporary characteristics of devices and prove the methods for choosing the couples for HS with the specified characteristics. It explains effect of hysteresis function of changing liquid volume that fills a porous body and outflows from it under the differential pressure, as well as conditions to realize effect of non-outflowing liquid after removal of the differential pressure thanks to which energy accumulation in HS is possible. The stand diagram, device parameters to study static and dynamic processes in HS, and measurement system characteristics are provided. Research results of static processes to fill (outflow pores of various silochromes with Wood's alloy are presented. It is shown that among considered HS the most efficient one is the HS possessing S-120 silochrome, hexamethyldisilazane-modified. The certain filling pores specific energy of HS made 71 J/g, while the outflow specific energy was 28 J/g. The paper presents a scheme of device model damping a force impact on the support. Test results of spring and hydraulic dampers and the model, as well, with HS based on silochromes with various lyophobic liquids are given. High HS efficiency that allows the 4 times less impact value is shown. Further researches concern a development of engineering techniques to design and optimize the HS parameters and a choice of the most

  5. Pore-network model of evaporation-induced salt precipitation in porous media: The effect of correlations and heterogeneity (United States)

    Dashtian, Hassan; Shokri, Nima; Sahimi, Muhammad


    Salt transport and precipitation in porous media constitute a set of complex and fascinating phenomena that are of considerable interest to several important problems, ranging from storage of CO2 in geological formations, to soil fertility, and protection of pavements and roads, as well as historical monuments. The phenomena occur at the pore scale and are greatly influenced by the heterogeneity of the pore space morphology. We present a pore-network (PN) model to study the phenomena. Vapor diffusion, capillary effect at the brine-vapor interface, flow of brine, and transport of salt and its precipitation in the pores that plug the pores partially or completely are all accounted for. The drying process is modeled by the invasion percolation, while transport of salt in brine is accounted for by the convective-diffusion equation. We demonstrate that the drying patterns, the clustering and connectivity of the pore throats in which salt precipitation occurs, the saturation distribution, and the drying rate are all strongly dependent upon the pore-size distribution, the correlations among the pore sizes, and the anisotropy of the pore space caused by stratification that most natural porous media contain. In particular, if the strata are more or less parallel to the direction of injection of the gas that dries out the pore space (air, for example) and/or causes salt precipitation (CO2, for example), the drying rate increases significantly. Moreover, salt tends to precipitate in clusters of neighboring pores that are parallel to the open surface of the porous medium.

  6. Prevalence and molecular heterogeneity of Bartonella bovis in cattle and Haemaphysalis bispinosa ticks in Peninsular Malaysia. (United States)

    Kho, Kai-Ling; Koh, Fui-Xian; Jaafar, Tariq; Nizam, Quaza Nizamuddin Hassan; Tay, Sun-Tee


    Bartonellosis is an emerging zoonotic infection responsible for a variety of clinical syndromes in humans and animals. Members of the genus Bartonella exhibit high degrees of genetic diversity and ecologic plasticity. The infection is usually transmitted to animals and humans through blood-feeding arthropod vectors such as fleas, lice, ticks and sandflies. This study was conducted to investigate the prevalence of Bartonella species in 184 beef cattle, 40 dairy cattle, 40 sheep and 40 goats in eight animal farms across Peninsular Malaysia. Bartonella-specific PCR assays and sequence analysis of partial fragments of the citrate synthase gene were used for detection and identification of B. bovis. Isolation of B. bovis was attempted from PCR-positive blood samples. Molecular heterogeneity of the isolates was investigated based on sequence analysis of gltA, ITS, rpoB genes, ERIC-PCR, as well as using an established multilocus sequence typing (MLST) method. The carriage rate of B. bovis in ticks was also determined in this study. B. bovis was detected using Bartonella gltA-PCR assays from ten (4.5 %) of 224 cattle blood samples, of which three (1.3 %) were from beef cattle and seven (3.1 %) were from dairy cattle. None of the blood samples from the sheep and goats understudied were positive for B. bovis. Haemaphysalis bispinosa and Rhipicephalus (Boophilus) microplus were the predominant tick species identified in this study. B. bovis was detected from eight of 200 H. bispinosa ticks and none from the R. microplus ticks. Isolation of B. bovis was successful from all PCR-positive cattle blood samples, except one. Strain differentiation of B. bovis isolates was attempted based on sequence analysis of gltA, ITS, rpoB, and ERIC-PCR assay. B. bovis isolates were differentiated into six genotypes using the approach. The genetic heterogeneity of the isolates was confirmed using MLST method. Of the six MLST sequence types identified, five were designated new sequence types (ST

  7. Numerical study of compositional compressible degenerate two-phase flow in saturated–unsaturated heterogeneous porous media

    KAUST Repository

    Saad, Ali S.


    We study the convergence of a combined finite volume-nonconforming finite element scheme on general meshes for a partially miscible two-phase flow model in anisotropic porous media. This model includes capillary effects and exchange between the phases. The diffusion term, which can be anisotropic and heterogeneous, is discretized by piecewise linear nonconforming triangular finite elements. The other terms are discretized by means of a cell-centered finite volume scheme on a dual mesh. The relative permeability of each phase is decentered according to the sign of the velocity at the dual interface. The convergence of the scheme is proved thanks to an estimate on the two pressures which allows to show estimates on the discrete time and compactness results in the case of degenerate relative permeabilities. A key point in the scheme is to use particular averaging formula for the dissolution function arising in the diffusion term. We show also a simulation of hydrogen production in nuclear waste management. Numerical results are obtained by in-house numerical code. © 2015 Elsevier Ltd.

  8. Bayesian uncertainty quantification for flows in heterogeneous porous media using reversible jump Markov chain Monte Carlo methods

    KAUST Repository

    Mondal, A.


    In this paper, we study the uncertainty quantification in inverse problems for flows in heterogeneous porous media. Reversible jump Markov chain Monte Carlo algorithms (MCMC) are used for hierarchical modeling of channelized permeability fields. Within each channel, the permeability is assumed to have a lognormal distribution. Uncertainty quantification in history matching is carried out hierarchically by constructing geologic facies boundaries as well as permeability fields within each facies using dynamic data such as production data. The search with Metropolis-Hastings algorithm results in very low acceptance rate, and consequently, the computations are CPU demanding. To speed-up the computations, we use a two-stage MCMC that utilizes upscaled models to screen the proposals. In our numerical results, we assume that the channels intersect the wells and the intersection locations are known. Our results show that the proposed algorithms are capable of capturing the channel boundaries and describe the permeability variations within the channels using dynamic production history at the wells. © 2009 Elsevier Ltd. All rights reserved.

  9. Adaptive Mesh Refinement for a Finite Volume Method for Flow and Transport of Radionuclides in Heterogeneous Porous Media

    Directory of Open Access Journals (Sweden)

    Amaziane Brahim


    Full Text Available In this paper, we consider adaptive numerical simulation of miscible displacement problems in porous media, which are modeled by single phase flow equations. A vertex-centred finite volume method is employed to discretize the coupled system: the Darcy flow equation and the diffusion-convection concentration equation. The convection term is approximated with a Godunov scheme over the dual finite volume mesh, whereas the diffusion-dispersion term is discretized by piecewise linear conforming finite elements. We introduce two kinds of indicators, both of them of residual type. The first one is related to time discretization and is local with respect to the time discretization: thus, at each time, it provides an appropriate information for the choice of the next time step. The second is related to space discretization and is local with respect to both the time and space variable and the idea is that at each time it is an efficient tool for mesh adaptivity. An error estimation procedure evaluates where additional refinement is needed and grid generation procedures dynamically create or remove fine-grid patches as resolution requirements change. The method was implemented in the software MELODIE, developed by the French Institute for Radiological Protection and Nuclear Safety (IRSN, Institut de Radioprotection et de Sûreté Nucléaire. The algorithm is then used to simulate the evolution of radionuclide migration from the waste packages through a heterogeneous disposal, demonstrating its capability to capture complex behavior of the resulting flow.

  10. Improving degradation of emerging organic compounds by applying chaotic advection in Managed Aquifer Recharge in randomly heterogeneous porous media (United States)

    Rodríguez-Escales, P.; Fernà ndez-Garcia, D.; Drechsel, J.; Folch, A.; Sanchez-Vila, X.


    Improving degradation rates of emerging organic compounds (EOCs) in groundwater is still a challenge. Although their degradation is not fully understood, it has been observed that some substances are preferably degraded under specific redox conditions. The coupling of Managed Aquifer Recharge with soil aquifer remediation treatment, by placing a reactive layer containing organic matter at the bottom of the infiltration pond, is a promising technology to improve the rate of degradation of EOCs. Its success is based on assuming that recharged water and groundwater get well mixed, which is not always true. It has been demonstrated that mixing can be enhanced by inducing chaotic advection through extraction-injection-engineering. In this work, we analyze how chaotic advection might enhance the spreading of redox conditions with the final aim of improving degradation of a mix of benzotriazoles: benzotriazole, 5-methyl-benzotriazole, and 5-chloro-benzotriazole. The degradation of the first two compounds was fastest under aerobic conditions whereas the third compound was best degraded under denitrification conditions. We developed a reactive transport model that describes how a recharged water rich in organic matter mixes with groundwater, how this organic matter is oxidized by different electron acceptors, and how the benzotriazoles are degraded attending for the redox state. The model was tested in different scenarios of recharge, both in homogenous and in heterogenous media. It was found that chaotic flow increases the spreading of the plume of recharged water. Consequently, different redox conditions coexist at a given time, facilitating the degradation of EOCs.

  11. Nonideal transport of reactive contaminants in heterogeneous porous media: 7. distributed-domain model incorporating immiscible-liquid dissolution and rate-limited sorption/desorption. (United States)

    Zhang, Zhihui; Brusseau, Mark L


    The purpose of this work is to present a distributed-domain mathematical model incorporating the primary mass-transfer processes that mediate the transport of immiscible organic liquid constituents in water-saturated, locally heterogeneous porous media. Specifically, the impact of grain/pore-scale heterogeneity on immiscible-liquid dissolution and sorption/desorption is represented in the model by describing the system as comprising a continuous distribution of mass-transfer domains. With this conceptualization, the distributions of the initial dissolution rate coefficient and the sorption/desorption rate coefficient are represented as probability density functions. Several sets of numerical experiments are conducted to examine the effects of heterogeneous dissolution and sorption/desorption on contaminant transport and elution. Four scenarios with different combinations of uniform/heterogeneous rate-limited dissolution and uniform/heterogeneous rate-limited sorption/desorption are evaluated. The results show that both heterogeneous rate-limited sorption/desorption and heterogeneous rate-limited dissolution can significantly increase the time or pore volumes required to elute immiscible-liquid constituents from a contaminated porous medium. However, sorption/desorption has minimal influence on elution behavior until essentially all of the immiscible liquid has been removed. For typical immiscible-liquid constituents that have relatively low sorption, the asymptotic elution tailing produced by heterogeneous rate-limited sorption/desorption begins at effluent concentrations that are several orders of magnitude below the initial steady-state concentrations associated with dissolution of the immiscible liquid. Conversely, the enhanced elution tailing associated with heterogeneous rate-limited dissolution begins at concentrations that are approximately one-tenth of the initial steady-state concentrations. Hence, dissolution may generally control elution behavior of

  12. Some current methods to represent the heterogeneity of natural media in hydrogeology (United States)

    de Marsily, G.; Delay, F.; Teles, V.; Schafmeister, M. T.

    We have known for a long time that the material properties of the subsurface are highly variable in space. We have learned that this variability is due to the extreme complexity and variation with time of processes responsible for the formation of the earth's crust, from plate tectonics to erosion, sediment transport, and deposition, as well as to mechanical, climatic, and diagenetic effects. As geologists, we learned how to "read" this complex history in the rocks and how to try to extrapolate in space what we have understood. As physicists, we then learned that to study flow processes in such media we must apply the laws of continuum mechanics. As mathematicians using analytical methods, we learned that we must simplify by dividing this complex continuum into a small number of units, such as aquifers and aquitards, and describe their properties by (constant) equivalent values. In recent years, as numerical modelers, we learned that we now have the freedom to "discretize" this complex reality and describe it as an ensemble of small homogeneous boxes of continuous media, each of which can have different properties. How do we use this freedom? Is there a need for it? If the answer is "yes," how can we assign different rock-property values to thousands or even millions of such little boxes in our models, to best represent reality, and include confidence levels for each selected rock property? As a tribute to Professor Eugene S. Simpson, with whom the first author of this paper often discussed these questions, we present an overview of three techniques that focus on one property, the rock permeability. We explain the motivation for describing spatial variability and illustrate how to do so by the geostatistical method, the Boolean method, and the genetic method. We discuss their advantages and disadvantages and indicate their present state of development. This is an active field of research and space is limited, so the review is certain to be incomplete, but we hope

  13. Molecular- and nm-scale Investigation of the Structure and Compositional Heterogeneity of Naturally Occurring Ferrihydrite (United States)

    Cismasu, C.; Michel, F. M.; Stebbins, J. F.; Tcaciuc, A. P.; Brown, G. E.


    methods to study such naturally occurring nanomaterials, both at the molecular- and nm-scale. This work provides structural information at the short-, medium- and long- range, as well as evidence of compositional heterogeneity, and mineral/organic matter associations.

  14. Molecular isotopic heterogeneity of fossil organic matter: implications for δ13Cbiomass and δ13Cpalaeoatmosphere proxies


    Poole, I.J.; Bergen, P.F. van; Kool, J.; Schouten, S.; Cantrill, David J.


    The degree of isotopic variation in fossil organic matter renders bulk δ13C signatures strongly influenced by molecular isotopic heterogeneity. For example, in fossil wood the relative abundance of less depleted 13C moieties, i.e. preserved 13C enriched polysaccharides versus the relatively 13C depleted lignin moieties, can be seen to significantly bias δ13Cfossil wood values. Moreover the variation in δ13C values of specific compounds within fossil material are themselves highly variable and...

  15. Panel 4: Recent advances in otitis media in molecular biology, biochemistry, genetics, and animal models. (United States)

    Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F; Bakaletz, Lauren O; Brown, Steve D; Cheeseman, Michael T; Juhn, Steven K; Jung, Timothy T K; Lim, David J; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J Christopher


    Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications.

  16. Media optimization for elevated molecular weight and mass production of pigment-free pullulan. (United States)

    Yu, Xiaoliu; Wang, Yulei; Wei, Gongyuan; Dong, Yingying


    In this study, an Aureobasidium pullulans SZU 1001 mutant, deficient in pigment production, was screened by complex UV and γ-ray mutagenesis. Medium composition optimization for increased pullulan molecular weight and production was conducted using this mutant. Six nutrients: yeast extract, (NH4)2SO4, K2HPO4, NaCl, MgSO4·7H2O and CaCl2 were detected within pullulan production in flasks. It is shown that NaCl and K2HPO4 have significant influences on molecular weight of pullulan, while yeast extract and (NH4)2SO4 significantly affect pullulan yield. To achieve a higher molecular weight and more efficient pullulan production, a response surface methodology approach was introduced to predict an optimal nutrient combination. A molecular weight of 5.74 × 10(6) and pullulan yield on glucose of 51.30% were obtained under batch pullulan fermentation with the optimized media, which increased molecular weight and pullulan production by 97.25% and 11.04%, respectively compared with the control media. Copyright © 2012 Elsevier Ltd. All rights reserved.



    Marble, J. C.; DiFilippo, E. L.; Zhang, Z.; Tick, G. R.; Brusseau, M. L.


    The use of a lumped-process mathematical model to simulate the complete dissolution of immiscible liquid non-uniformly distributed in physically heterogeneous porous-media systems was investigated. The study focused specifically on systems wherein immiscible liquid was poorly accessible to flowing water. Two representative, idealized scenarios were examined, one wherein immiscible liquid at residual saturation exists within a lower-permeability unit residing in a higher-permeability matrix, a...

  18. Adaptive mixed-hybrid and penalty discontinuous Galerkin method for two-phase flow in heterogeneous media

    KAUST Repository

    Hou, Jiangyong


    In this paper, we present a hybrid method, which consists of a mixed-hybrid finite element method and a penalty discontinuous Galerkin method, for the approximation of a fractional flow formulation of a two-phase flow problem in heterogeneous media with discontinuous capillary pressure. The fractional flow formulation is comprised of a wetting phase pressure equation and a wetting phase saturation equation which are coupled through a total velocity and the saturation affected coefficients. For the wetting phase pressure equation, the continuous mixed-hybrid finite element method space can be utilized due to a fundamental property that the wetting phase pressure is continuous. While it can reduce the computational cost by using less degrees of freedom and avoiding the post-processing of velocity reconstruction, this method can also keep several good properties of the discontinuous Galerkin method, which are important to the fractional flow formulation, such as the local mass balance, continuous normal flux and capability of handling the discontinuous capillary pressure. For the wetting phase saturation equation, the penalty discontinuous Galerkin method is utilized due to its capability of handling the discontinuous jump of the wetting phase saturation. Furthermore, an adaptive algorithm for the hybrid method together with the centroidal Voronoi Delaunay triangulation technique is proposed. Five numerical examples are presented to illustrate the features of proposed numerical method, such as the optimal convergence order, the accurate and efficient velocity approximation, and the applicability to the simulation of water flooding in oil field and the oil-trapping or barrier effect phenomena.

  19. Modelling radionuclide transport in highly heterogeneous media and under variable hydrochemical conditions using a "dynamic Kd" approach (United States)

    Trinchero, Paolo; Painter, Scott; Ebrahimi, Hedieh; Koskinen, Lasse; Molinero, jorge; Selroos, Jan-Olof


    Due to the high heterogeneity of fractured media and the ubiquitous lack of a complete site characterization, deterministic simulations of radionuclide transport in fractured rocks are notoriously highly uncertain. This uncertainty is usually addressed using stochastic methods; e.g. the connectivity structure of the medium is described using multiple realizations of Discrete Fracture Networks (DFN), which are then combined to particle tracking simulations. In these formulations, many complex geochemical retention processes are typically lumped into a single parameter: the distribution coefficient (Kd). This approach relies on an important assumption: the Kd values are constant in time. This hypothesis is critical under long-term geochemical changes as it is known that the distribution coefficient depends on the pH, redox conditions and major chemistry of the system. In this work, we present a novel methodology that combines the robustness of stochastic methods with an explicit description of water-solute-rock interaction processes. The reconciliation of all these is achieved by using a dynamic Kd approach. The hydrogeochemical evolution of the site of study is first computed using long-term and large-scale mechanistic reactive transport simulations. The simulated hydrochemical conditions are then used to generate a complete database of Kd values, which represent the hydrochemical conditions in every position and time of the model domain. Then, MARFA (Painter and Mancillas, 2009) is used to carry out Time Domain Random Walk (TDRW) simulations of radionuclide transport. In these simulations, Kd values are dynamically updated using the afore-mentioned database. The results (i.e. radionuclide breakthrough curves) bring the signature of the underlying changes in the background geochemistry.

  20. Surface heterogeneity on hemispheres-in-cell model yields all experimentally-observed non-straining colloid retention mechanisms in porous media in the presence of energy barriers. (United States)

    Ma, Huilian; Pazmino, Eddy; Johnson, William P


    Many mechanisms of colloid retention in porous media under unfavorable conditions have been identified from experiments or theory, such as attachment at surface heterogeneities, wedging at grain to grain contacts, retention via secondary energy minimum association in zones of low flow drag, and straining in pore throats too small to pass. However, no previously published model is capable of representing all of these mechanisms of colloid retention. In this work, we demonstrate that incorporation of surface heterogeneity into our hemispheres-in-cell model yields all experimentally observed non-straining retention mechanisms in porous media under unfavorable conditions. We also demonstrate that the predominance of any given retention mechanism depends on the coupled colloid-collector-flow interactions that are governed by parameters such as the size and spatial frequency of heterogeneous attractive domains, colloid size, and solution ionic strength. The force/torque balance-simulated retention is shown to decrease gradually with decreasing solution ionic strength, in agreement with experimental observations. This gradual decrease stands in sharp contrast to predictions from mean field theory that does not account for discrete surface heterogeneity. © 2011 American Chemical Society

  1. Molecular dynamics in porous media studied by nuclear magnetic resonance techniques

    Energy Technology Data Exchange (ETDEWEB)

    Mattea, C.


    Field cycling NMR relaxometry was used to study dynamics of fluids under confinement in different scenarios: fluids flowing through porous media, fluids partially filling porous media and polymer melts in nanoscopic pores. Diffusion in partially filled porous media was also studied with the aid of an NMR diffusometry technique. It is shown that hydrodynamic flow influences the spin-lattice relaxation rate of water confined in mesoscopic porous media under certain conditions. The effect is predicted by an analytical theory and Monte Carlo simulations, and confirmed experimentally by field-cycling NMR relaxometry. Field-cycling NMR relaxometry has been applied to polar and non polar adsorbates in partially filled silica porous glasses. The dependence of the spin-lattice relaxation rate on the filling degree shows that limits for slow and fast exchange between different phases can be distinguished and identified depending on the pore size and polarity of the solvents. Diffusion in the same unsaturated systems was studied with the aid of NMR diffusometry technique. The effective diffusion coefficient of solvents with different polarities displays opposite tendencies as a function of the liquid content. A two-phase fast exchange model including Knudsen and ordinary diffusion and different effective tortuosities is presented accounting for these phenomena. In the case of polymer melts confined in narrow artificial tubes of a porous solid matrix with variable diameter (9 to 57 nm), the characteristics of reptation were experimentally verified using proton field cycling NMR relaxometry technique. This observation is independent of the molecular mass and pore size. In bulk, the same polymer melts show either Rouse or renormalized Rouse dynamics, depending on the molecular mass. The polymers under confinement show features specific for reptation even with a pore diameter 15 times larger than the Flory radius while bulk melts of the same polymers do not. (orig.)

  2. Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models (United States)

    Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher


    Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

  3. Media

    National Research Council Canada - National Science Library

    Emily Wexler


    .... Tradigital allows us to use online behaviour to track the effectiveness of online and offline media, not simply the correlation of TV airings with search activity, but also by employing a bevy...

  4. A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics. (United States)

    Perry, John D


    In the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, including Pseudomonas aeruginosa, group B streptococci, Clostridium difficile, Campylobacter spp., and Yersinia enterocolitica. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistant Acinetobacter spp., and Enterobacteriaceae with extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics. © Crown copyright 2017.

  5. Hierarchical and Heterogeneous Bioinspired Composites-Merging Molecular Self-Assembly with Additive Manufacturing. (United States)

    Rajasekharan, Anand K; Bordes, Romain; Sandström, Carl; Ekh, Magnus; Andersson, Martin


    Biological composites display exceptional mechanical properties owing to a highly organized, heterogeneous architecture spanning several length scales. It is challenging to translate this ordered and multiscale structural organization in synthetic, bulk composites. Herein, a combination of top-down and bottom-up approach is demonstrated, to form a polymer-ceramic composite by macroscopically aligning the self-assembled nanostructure of polymerizable lyotropic liquid crystals via 3D printing. The polymer matrix is then uniformly reinforced with bone-like apatite via in situ biomimetic mineralization. The combinatorial method enables the formation of macrosized, heterogeneous composites where the nanostructure and chemical composition is locally tuned over microscopic distances. This enables precise control over the mechanics in specific directions and regions, with a unique intrinsic-extrinsic toughening mechanism. As a proof-of-concept, the method is used to form large-scale composites mimicking the local nanostructure, compositional gradients and directional mechanical properties of heterogeneous tissues like the bone-cartilage interface, for mechanically stable osteochondral plugs. This work demonstrates the possibility to create hierarchical and complex structured composites using weak starting components, thus opening new routes for efficient synthesis of high-performance materials ranging from biomaterials to structural nanocomposites. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Simulating propagation of decomposed elastic waves using low-rank approximate mixed-domain integral operators for heterogeneous transversely isotropic media

    KAUST Repository

    Cheng, Jiubing


    In elastic imaging, the extrapolated vector fields are decomposed into pure wave modes, such that the imaging condition produces interpretable images, which characterize reflectivity of different reflection types. Conventionally, wavefield decomposition in anisotropic media is costly as the operators involved is dependent on the velocity, and thus not stationary. In this abstract, we propose an efficient approach to directly extrapolate the decomposed elastic waves using lowrank approximate mixed space/wavenumber domain integral operators for heterogeneous transverse isotropic (TI) media. The low-rank approximation is, thus, applied to the pseudospectral extrapolation and decomposition at the same time. The pseudo-spectral implementation also allows for relatively large time steps in which the low-rank approximation is applied. Synthetic examples show that it can yield dispersionfree extrapolation of the decomposed quasi-P (qP) and quasi- SV (qSV) modes, which can be used for imaging, as well as the total elastic wavefields.

  7. Genetic and molecular mechanisms in multiple myeloma: a route to better understand disease pathogenesis and heterogeneity

    Directory of Open Access Journals (Sweden)

    Marie-Christine Kyrtsonis


    Full Text Available Marie-Christine Kyrtsonis1,2, Vassiliki Bartzis1,2, Xenophon Papanikolaou1, Efstathios Koulieris1,2, George Georgiou2, Maria Dimou2, Tatiana Tzenou1,2, Panayiotis Panayiotidis21First Department of Propedeutic Internal Medicine, 2Department of Hematology, National and Kapodistrian University of Athens, Laikon Hospital, GreeceAbstract: Multiple myeloma (MM is a heterogeneous plasma cell neoplasm presenting with a wide range of clinical manifestations. In spite of the availability of very performing treatment modalities, survival is highly varying, ranging from a few months to several years. Underlying genetic and microenvironmental mechanisms are thought to be responsible for clinical heterogeneity. Disease etiology is unknown but progresses in the understanding of its pathogenesis have shown that MM precursor cell transformation into a malignant one occurs in a multistep process. Possibly during class switch recombination a primary genetic event takes place. With the occurrence of additional events and the support of bone marrow microenvironmental cells, neoplastic plasma cells actively proliferate and disease behavior may change. Recurrent translocations involving the IgH locus (11q13, 4p16, 16q23, 21q12, and 6p21, deletions of chromosome 13, trisomies of chromosomes 3, 5, 9, 11, 15, 19, and 21, and dysregulated expression of cyclin D genes, are considered initiating or primary events. Alterations related to further disease transformation and adverse prognosis are deletion of 17p13, c-myc translocations, and gains of chromosome 1q21. In relation to the underlying genetic defects, disease subgroups are recognized. Accordingly treatment effectiveness may differ among groups. Intense research is ongoing in this field.Keywords: myeloma, pathogenesis, genetic abnormalities, heterogeneity, prognosis

  8. Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study. (United States)

    Städler, Nicolas; Dondelinger, Frank; Hill, Steven M; Akbani, Rehan; Lu, Yiling; Mills, Gordon B; Mukherjee, Sach


    Molecular pathways and networks play a key role in basic and disease biology. An emerging notion is that networks encoding patterns of molecular interplay may themselves differ between contexts, such as cell type, tissue or disease (sub)type. However, while statistical testing of differences in mean expression levels has been extensively studied, testing of network differences remains challenging. Furthermore, since network differences could provide important and biologically interpretable information to identify molecular subgroups, there is a need to consider the unsupervised task of learning subgroups and networks that define them. This is a nontrivial clustering problem, with neither subgroups nor subgroup-specific networks known at the outset. We leverage recent ideas from high-dimensional statistics for testing and clustering in the network biology setting. The methods we describe can be applied directly to most continuous molecular measurements and networks do not need to be specified beforehand. We illustrate the ideas and methods in a case study using protein data from The Cancer Genome Atlas (TCGA). This provides evidence that patterns of interplay between signalling proteins differ significantly between cancer types. Furthermore, we show how the proposed approaches can be used to learn subtypes and the molecular networks that define them. As the Bioconductor package nethet. or Supplementary data are available at Bioinformatics online.

  9. Molecular portraits revealing the heterogeneity of breast tumor subtypes defined using immunohistochemistry markers. (United States)

    Dai, Xiaofeng; Li, Yang; Bai, Zhonghu; Tang, Xu-Qing


    Breast cancer is highly heterogeneous. The subtypes defined using immunohistochemistry markers and gene expression profilings (GEP) are related but not equivalent, with inter-connections under investigated. Our previous study revealed a set of differentially expressed genes (diff-genes), containing 1015 mRNAs and 69 miRNAs, which characterize the immunohistochemistry-defined breast tumor subtypes at the GEP level. However, they may convey redundant information due to the large amount of genes included. By reducing the dimension of the diff-genes, we identified 119 mRNAs and 20 miRNAs best explaining breast tumor heterogeneity with the most succinct number of genes found using hierarchical clustering and nearest-to-center principle. The final signature panel contains 119 mRNAs, whose superiority over diff-genes was replicated in two independent public datasets. The comparison of our signature with two pioneering signatures, the Sorlie's signature and PAM50, suggests a novel marker, FOXA1, in breast cancer classification. Subtype-specific feature genes are reported to characterize each immunohistochemistry-defined subgroup. Pathway and network analysis reveal the critical roles of Notch signalings in [ER+|PR+]HER2- and cell cycle in [ER+|PR+]HER2+ tumors. Our study reveals the primary differences among the four immunohistochemistry-defined breast tumors at the mRNA and miRNA levels, and proposes a novel signature for breast tumor subtyping given GEP data.

  10. Resolution of Disulfide Heterogeneity in Nogo Receptor 1 Fusion Proteins by Molecular Engineering

    Energy Technology Data Exchange (ETDEWEB)

    P Weinreb; D Wen; F Qian; C Wildes; E Garber; L Walus; M Jung; J Wang; J Relton; et al.


    NgRI (Nogo-66 receptor) is part of a signalling complex that inhibits axon regeneration in the central nervous system. Truncated soluble versions of NgRI have been used successfully to promote axon regeneration in animal models of spinal-cord injury, raising interest in this protein as a potential therapeutic target. The LRR (leucine-rich repeat) regions in NgRI are flanked by N- and C-terminal disulfide-containing 'cap' domains (LRRNT and LRRCT respectively). In the present work we show that, although functionally active, the NgRI(310)-Fc fusion protein contains mislinked and heterogeneous disulfide patterns in the LRRCT domain, and we report the generation of a series of variant molecules specifically designed to prevent this heterogeneity. Using these variants we explored the effects of modifying the NgRI truncation site or the spacing between the NgRI and Fc domains, or replacing cysteines within the NgRI or IgG hinge regions. One variant, which incorporates replacements of Cys{sup 266} and Cys{sup 309} with alanine residues, completely eliminated disulfide scrambling while maintaining functional in vitro and in vivo efficacy. This modified NgRI-Fc molecule represents a significantly improved candidate for further pharmaceutical development, and may serve as a useful model for the optimization of other IgG fusion proteins made from LRR proteins.

  11. Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis (United States)

    Der, Evan; Ranabothu, Saritha; Suryawanshi, Hemant; Akat, Kemal M.; Clancy, Robert; Kustagi, Manjunath; Czuppa, Mareike; Izmirly, Peter; Belmont, H. Michael; Wang, Tao; Jordan, Nicole; Bornkamp, Nicole; Nwaukoni, Janet; Martinez, July; Buyon, Jill P.; Tuschl, Thomas


    Lupus nephritis is a leading cause of mortality among systemic lupus erythematosus (SLE) patients, and its heterogeneous nature poses a significant challenge to the development of effective diagnostics and treatments. Single cell RNA sequencing (scRNA-seq) offers a potential solution to dissect the heterogeneity of the disease and enables the study of similar cell types distant from the site of renal injury to identify novel biomarkers. We applied scRNA-seq to human renal and skin biopsy tissues and demonstrated that scRNA-seq can be performed on samples obtained during routine care. Chronicity index, IgG deposition, and quantity of proteinuria correlated with a transcriptomic-based score composed of IFN-inducible genes in renal tubular cells. Furthermore, analysis of cumulative expression profiles of single cell keratinocytes dissociated from nonlesional, non–sun-exposed skin of patients with lupus nephritis also revealed upregulation of IFN-inducible genes compared with keratinocytes isolated from healthy controls. This indicates the possible use of scRNA-seq analysis of skin biopsies as a biomarker of renal disease. These data support the potential utility of scRNA-seq to provide new insights into the pathogenesis of lupus nephritis and pave the way for exploiting a readily accessible tissue to reflect injury in the kidney. PMID:28469080

  12. Multi-scale Modeling of Compressible Single-phase Flow in Porous Media using Molecular Simulation

    KAUST Repository

    Saad, Ahmed Mohamed


    In this study, an efficient coupling between Monte Carlo (MC) molecular simulation and Darcy-scale flow in porous media is presented. The cell-centered finite difference method with a non-uniform rectangular mesh were used to discretize the simulation domain and solve the governing equations. To speed up the MC simulations, we implemented a recently developed scheme that quickly generates MC Markov chains out of pre-computed ones, based on the reweighting and reconstruction algorithm. This method astonishingly reduces the required computational time by MC simulations from hours to seconds. In addition, the reweighting and reconstruction scheme, which was originally designed to work with the LJ potential model, is extended to work with a potential model that accounts for the molecular quadrupole moment of fluids with non-spherical molecules such as CO2. The potential model was used to simulate the thermodynamic equilibrium properties for single-phase and two-phase systems using the canonical ensemble and the Gibbs ensemble, respectively. Comparing the simulation results with the experimental data showed that the implemented model has an excellent fit outperforming the standard LJ model. To demonstrate the strength of the proposed coupling in terms of computational time efficiency and numerical accuracy in fluid properties, various numerical experiments covering different compressible single-phase flow scenarios were conducted. The novelty in the introduced scheme is in allowing an efficient coupling of the molecular scale and Darcy scale in reservoir simulators. This leads to an accurate description of the thermodynamic behavior of the simulated reservoir fluids; consequently enhancing the confidence in the flow predictions in porous media.

  13. Characterization of Cellular and Molecular Heterogeneity of Bone Marrow Stromal Cells

    DEFF Research Database (Denmark)

    Elsafadi, Mona; Manikandan, Muthurangan; Atteya, Muhammad


    and osteoblast differentiation genes which included several homeobox genes: TBX15, HOXA2 and HOXA10, and IGF1, FGFR3, BMP6, MCAM, ITGA10, IGFBP5, and ALP. siRNA-based downregulation of the ALP gene in CL1 impaired osteoblastic and adipocytic differentiation. Our studies demonstrate the existence of molecular...

  14. Clinical Features, Molecular Heterogeneity, and Prognostic Implications in YARS2-Related Mitochondrial Myopathy

    NARCIS (Netherlands)

    Sommerville, Ewen W.; Ng, Yi Shiau; Alston, Charlotte L.; Dallabona, Cristina; Gilberti, Micol; He, Langping; Knowles, Charlotte; Chin, Sophie L.; Schaefer, Andrew M.; Falkous, Gavin; Murdoch, David; Longman, Cheryl; de Visser, Marianne; Bindoff, Laurence A.; Rawles, John M.; Dean, John C. S.; Petty, Richard K.; Farrugia, Maria E.; Haack, Tobias B.; Prokisch, Holger; McFarland, Robert; Turnbull, Douglass M.; Donnini, Claudia; Taylor, Robert W.; Gorman, Gráinne S.


    YARS2 mutations have been associated with a clinical triad of myopathy, lactic acidosis, and sideroblastic anemia in predominantly Middle Eastern populations. However, the identification of new patients expands the clinical and molecular spectrum of mitochondrial disorders. To review the clinical,

  15. Local electric fields and molecular properties in heterogeneous environments through polarizable embedding

    DEFF Research Database (Denmark)

    List, Nanna Holmgaard; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob


    the additional effective external field effect, i.e., the manifestations of the environment polarization induced by the external field, which allows for the calculation of properties defined in terms of the external field. Within a response framework, we report calculations of the one- and two-photon absorption......In spectroscopies, the local field experienced by a molecule embedded in an environment will be different from the externally applied electromagnetic field, and this difference may significantly alter the response and transition properties of the molecule. The polarizable embedding (PE) model has...... previously been developed to model the local field contribution stemming from the direct molecule-environment coupling of the electromagnetic response properties of molecules in solution as well as in heterogeneous environments, such as proteins. Here we present an extension of this approach to address...

  16. Molecular Catalysis of O2 Reduction by Iron Porphyrins in Water: Heterogeneous versus Homogeneous Pathways. (United States)

    Costentin, Cyrille; Dridi, Hachem; Savéant, Jean-Michel


    Despite decades of active attention, important problems remain pending in the catalysis of dioxygen reduction by iron porphyrins in water in terms of selectivity and mechanisms. This is what happens, for example, for the distinction between heterogeneous and homogeneous catalysis for soluble porphyrins, for the estimation of H2O2/H2O product selectivity, and for the determination of the reaction mechanism in the two situations. With water-soluble iron tetrakis(N-methyl-4-pyridyl)porphyrin as an example, procedures are described that allow one to operate this distinction and determine the H2O2/H2O product ratio in each case separately. It is noteworthy that, despite the weak adsorption of the iron(II) porphyrin on the glassy carbon electrode, the contribution of the adsorbed complex to catalysis rivals that of its solution counterpart. Depending on the electrode potential, two successive catalytic pathways have been identified and characterized in terms of current-potential responses and H2O2/H2O selectivity. These observations are interpreted in the framework of the commonly accepted mechanism for catalytic reduction of dioxygen by iron porphyrins, after checking its compatibility with a change of oxygen concentration and pH. The difference in intrinsic catalytic reactivity between the catalyst in the adsorbed state and in solution is also discussed. The role of heterogeneous catalysis with iron tetrakis(N-methyl-4-pyridyl)porphyrin has been overlooked in previous studies because of its water solubility. The main objective of the present contribution is therefore to call attention, by means of this emblematic example, to such possibilities to reach a correct identification of the catalyst, its performances, and reaction mechanism. This is a question of general interest, so that reduction of dioxygen remains a topic of high importance in the context of contemporary energy challenges.

  17. Histopathological and molecular heterogeneity among individuals with dementia associated with Presenilin mutations

    Directory of Open Access Journals (Sweden)

    Kalback Walter M


    Full Text Available Abstract Background Mutations in the presenilin (PSEN genes are associated with early-onset familial Alzheimer's disease (FAD. Biochemical characterizations and comparisons have revealed that many PSEN mutations alter γ-secretase activity to promote accumulation of toxic Aβ42 peptides. In this study, we compared the histopathologic and biochemical profiles of ten FAD cases expressing independent PSEN mutations and determined the degradation patterns of amyloid-β precursor protein (AβPP, Notch, N-cadherin and Erb-B4 by γ-secretase. In addition, the levels of Aβ40/42 peptides were quantified by ELISA. Results We observed a wide variation in type, number and distribution of amyloid deposits and neurofibrillary tangles. Four of the ten cases examined exhibited a substantial enrichment in the relative proportions of Aβ40 over Aβ42. The AβPP N-terminal and C-terminal fragments and Tau species, assessed by Western blots and scanning densitometry, also demonstrated a wide variation. The Notch-1 intracellular domain was negligible by Western blotting in seven PSEN cases. There was significant N-cadherin and Erb-B4 peptide heterogeneity among the different PSEN mutations. Conclusion These observations imply that missense mutations in PSEN genes can alter a range of key γ-secretase activities to produce an array of subtly different biochemical, neuropathological and clinical manifestations. Beyond the broad common features of dementia, plaques and tangles, the various PSEN mutations resulted in a wide heterogeneity and complexity and differed from sporadic AD.

  18. Shocking of metallic glass to induce microstructure heterogeneity: A molecular dynamics study (United States)

    Ma, Chi; Wang, Guo-Xiang; Ye, Chang; Dong, Yalin


    Surface severe plastic deformation (SSPD) has been demonstrated to improve the ductility of metallic glass. The physical interpretation, however, remains on the phenomenological level. In this study, a molecular dynamics (MD) simulation is carried out to elucidate the molecular mechanisms underlying the improvement in ductility. MD simulation reveals that shock waves resulting from SSPD can induce pre-deformed atoms, which are randomly embedded in the matrix of the metallic glass. The pre-deformed atoms have similar stress distribution and short-order structure as the matrix atoms, but with a larger atomic volume. When subjected to tensile or compressive stress, more shear bands are promoted by the pre-deformed atoms in the shock-treated sample as compared to the untreated one. The randomly distributed shear bands were found to experience more interactions, which delayed the catastrophic fracture, leading to increased ductility.

  19. A gas aggregation source for the production of heterogeneous molecular clusters (United States)

    Braud, I.; Zamith, S.; L'Hermite, J.-M.


    We present the design of a versatile gas aggregation source that allows producing molecular beams of charged clusters containing a controlled amount of chosen impurities. Several examples of clusters production using this source characterized by time of flight mass spectrometry are presented here. We demonstrate the source ability to produce homogeneous clusters, such as pure protonated water and alcohol clusters, as well as inhomogeneous ones such as water clusters containing a few units of uracil, glycine, sulfuric acid, or pyrene.

  20. A molecular dynamics simulations study on the relations between dynamical heterogeneity, structural relaxation, and self-diffusion in viscous liquids. (United States)

    Henritzi, Patrick; Bormuth, André; Klameth, Felix; Vogel, Michael


    We perform molecular dynamics simulations for viscous liquids to study the relations between dynamical heterogeneity, structural (α) relaxation, and self-diffusion. For atomistic models of supercooled water, polymer melts, and an ionic liquid, we characterize the space-time characteristics of dynamical heterogeneity by the degree of deviations from Gaussian displacement statistics (α2), the size of clusters comprising highly mobile particles (S(w)), and the length of strings consisting of cooperatively moving particles (L(w)). Comparison of our findings with previous simulation results for a large variety of viscous liquids, ranging from monoatomic liquids to silica melt, reveals a nearly universal decoupling between the time scales of maximum non-Gaussian parameter (τ(α2)) and the time constant of the α relaxation (τ(α)) upon cooling, explicitly, τ(α2) ∝τ(α)(3/4). Such uniform relation was not observed between the peak times of S(w) or L(w) and τ(α). On the other hand, the temperature-dependent time scale of maximum string length (τ(L)) follows the inverse of the self-diffusion coefficient (D) for various systems at sufficiently low temperatures, i.e., τ(L) ∝ D(-1). These observations are discussed in view of a breakdown of the Stokes-Einstein relation for the studied systems. It is found that the degree of deviation from this relation is correlated with the stretching of the α relaxation.

  1. Stereodirection of an α-ketoester at sub-molecular sites on chirally modified Pt(111): heterogeneous asymmetric catalysis. (United States)

    Demers-Carpentier, Vincent; Rasmussen, Anton M H; Goubert, Guillaume; Ferrighi, Lara; Dong, Yi; Lemay, Jean-Christian; Masini, Federico; Zeng, Yang; Hammer, Bjørk; McBreen, Peter H


    Chirally modified Pt catalysts are used in the heterogeneous asymmetric hydrogenation of α-ketoesters. Stereoinduction is believed to occur through the formation of chemisorbed modifier-substrate complexes. In this study, the formation of diastereomeric complexes by coadsorbed methyl 3,3,3-trifluoropyruvate, MTFP, and (R)-(+)-1-(1-naphthyl)ethylamine, (R)-NEA, on Pt(111) was studied using scanning tunneling microscopy and density functional theory methods. Individual complexes were imaged with sub-molecular resolution at 260 K and at room temperature. The calculations find that the most stable complex isolated in room-temperature experiments is formed by the minority rotamer of (R)-NEA and pro-S MTFP. The stereodirecting forces in this complex are identified as a combination of site-specific chemisorption of MTFP and multiple non-covalent attractive interactions between the carbonyl groups of MTFP and the amine and aromatic groups of (R)-NEA.

  2. Nail-Patella Syndrome: clinical and molecular data in 55 families raising the hypothesis of a genetic heterogeneity. (United States)

    Ghoumid, Jamal; Petit, Florence; Holder-Espinasse, Muriel; Jourdain, Anne-Sophie; Guerra, José; Dieux-Coeslier, Anne; Figeac, Martin; Porchet, Nicole; Manouvrier-Hanu, Sylvie; Escande, Fabienne


    Nail-Patella Syndrome (NPS) is a rare autosomal dominant condition comprising nail and skeletal anomalies. Skeletal features include dysplastic patellae and iliac horns, as well as scapula and elbow dysplasia. Nephropathy and glaucoma or intra-ocular hypertension can sometimes be present. NPS is due to variants affecting function in LMX1B, which encodes a LIM-homeodomain protein critical for limb, kidney and eye development. We describe the phenotype and the molecular data of 55 index patients and their 39 relatives presenting with typical NPS. We identified 38 different LMX1B anomalies, 19 of which were not reported before. In our series, 9% of families are not carriers of a LMX1B genomic alteration after extensive study of the coding and non-coding regions of the gene. One of the families showed no linkage to the LMX1B locus, raising the hypothesis of a genetic heterogeneity.

  3. Coupled Enzyme Reactions Performed in Heterogeneous Reaction Media: Experiments and Modeling for Glucose Oxidase and Horseradish Peroxidase in a PEG/Citrate Aqueous Two-Phase System (United States)


    The intracellular environment in which biological reactions occur is crowded with macromolecules and subdivided into microenvironments that differ in both physical properties and chemical composition. The work described here combines experimental and computational model systems to help understand the consequences of this heterogeneous reaction media on the outcome of coupled enzyme reactions. Our experimental model system for solution heterogeneity is a biphasic polyethylene glycol (PEG)/sodium citrate aqueous mixture that provides coexisting PEG-rich and citrate-rich phases. Reaction kinetics for the coupled enzyme reaction between glucose oxidase (GOX) and horseradish peroxidase (HRP) were measured in the PEG/citrate aqueous two-phase system (ATPS). Enzyme kinetics differed between the two phases, particularly for the HRP. Both enzymes, as well as the substrates glucose and H2O2, partitioned to the citrate-rich phase; however, the Amplex Red substrate necessary to complete the sequential reaction partitioned strongly to the PEG-rich phase. Reactions in ATPS were quantitatively described by a mathematical model that incorporated measured partitioning and kinetic parameters. The model was then extended to new reaction conditions, i.e., higher enzyme concentration. Both experimental and computational results suggest mass transfer across the interface is vital to maintain the observed rate of product formation, which may be a means of metabolic regulation in vivo. Although outcomes for a specific system will depend on the particulars of the enzyme reactions and the microenvironments, this work demonstrates how coupled enzymatic reactions in complex, heterogeneous media can be understood in terms of a mathematical model. PMID:24517887

  4. Gravity-destabilized nonwetting phase invasion in macro-heterogeneous porous media: Experimental observations of invasion dynamics and scale analysis

    Energy Technology Data Exchange (ETDEWEB)



    The authors designed and conducted experiments in a heterogeneous sand pack where gravity-destabilized nonwetting phase invasion (CO{sub 2} and TCE) could be recorded using high resolution light transmission methods. The heterogeneity structure was designed to be reminiscent of fluvial channel lag cut-and-fill architecture and contain a series of capillary barriers. As invasion progressed, nonwetting phase structure developed a series of fingers and pools; behind the growing front they found nonwetting phase saturation to pulsate in certain regions when viscous forces were low. Through a scale analysis, they derive a series of length scales that describe finger diameter, pool height and width, and regions where pulsation occurs within a heterogeneous porous medium. In all cases, they find that the intrinsic pore scale nature of the invasion process and resulting structure must be incorporated into the analysis to explain experimental results. The authors propose a simple macro-scale structural growth model that assembles length scales for sub-structures to delineate nonwetting phase migration from a source into a heterogeneous domain. For such a model applied at the field scale for DNAPL migration, they expect capillary and gravity forces within the complex subsurface lithology to play the primary roles with viscous forces forming a perturbation on the inviscid phase structure.

  5. Monte Carlo simulation of the Leksell Gamma Knife{sup TM}: II. Effects of heterogeneous versus homogeneous media for stereotactic radiosurgery

    Energy Technology Data Exchange (ETDEWEB)

    Moskvin, Vadim; Timmerman, Robert; DesRosiers, Colleen; Randall, Marcus; DesRosiers, Paul; Dittmer, Phil; Papiez, Lech [Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, 535 Barnhill Dr, RT041, IN 46202-5289 (United States)


    The absence of electronic equilibrium in the vicinity of bone-tissue or air-tissue heterogeneity in the head can misrepresent deposited dose with treatment planning algorithms that assume all treatment volume as homogeneous media. In this paper, Monte Carlo simulation (PENELOPE) and measurements with a specially designed heterogeneous phantom were applied to investigate the effect of air-tissue and bone-tissue heterogeneity on dose perturbation with the Leksell Gamma Knife{sup TM}. The dose fall-off near the air-tissue interface caused by secondary electron disequilibrium leads to overestimation of dose by the vendor supplied treatment planning software (GammaPlan{sup TM}) at up to 4 mm from an interface. The dose delivered to the target area away from an air-tissue interface may be underestimated by up to 7% by GammaPlan{sup TM} due to overestimation of attenuation of photon beams passing through air cavities. While the underdosing near the air-tissue interface cannot be eliminated with any plug pattern, the overdosage due to under-attenuation of the photon beams in air cavities can be eliminated by plugging the sources whose beams intersect the air cavity. Little perturbation was observed next to bone-tissue interfaces. Monte Carlo results were confirmed by measurements. This study shows that the employed Monte Carlo treatment planning is more accurate for precise dosimetry of stereotactic radiosurgery with the Leksell Gamma Knife{sup TM} for targets in the vicinity of air-filled cavities.

  6. Molecular heterogeneity assessment by next-generation sequencing and response to gefitinib of EGFR mutant advanced lung adenocarcinoma. (United States)

    Bria, Emilio; Pilotto, Sara; Amato, Eliana; Fassan, Matteo; Novello, Silvia; Peretti, Umberto; Vavalà, Tiziana; Kinspergher, Stefania; Righi, Luisella; Santo, Antonio; Brunelli, Matteo; Corbo, Vincenzo; Giglioli, Eliana; Sperduti, Isabella; Milella, Michele; Chilosi, Marco; Scarpa, Aldo; Tortora, Giampaolo


    Cancer molecular heterogeneity might explain the variable response of EGFR mutant lung adenocarcinomas to tyrosine kinase inhibitors (TKIs). We assessed the mutational status of 22 cancer genes by next-generation sequencing (NGS) in poor, intermediate or good responders to first-line gefitinib. Clinical outcome was correlated with Additional Coexisting Mutations (ACMs) and the EGFR Proportion of Mutated Alleles (PMA). Thirteen ACMs were found in 10/17 patients: TP53 (n=6), KRAS (n=2), CTNNB1 (n=2), PIK3CA, SMAD4 and MET (n=1 each). TP53 mutations were exclusive of poor/intermediate responders (66.7% versus 0, p=0.009). Presence of ACMs significantly affected both PFS (median 3.0 versus 12.3 months, p=0.03) and survival (3.6 months versus not reached, p=0.03). TP53 mutation was the strongest negative modifier (median PFS 4.0 versus 14.0 months). Higher EGFR PMA was present in good versus poor/intermediate responders. Median PFS and survival were longer in patients with EGFR PMA ≥0.36 (12.0 versus 4.0 months, p=0.31; not reached versus 18.0 months, p=0.59). Patients with an EGFR PMA ≥0.36 and no ACMs fared significantly better (p=0.03), with a trend towards increased survival (p=0.06). Our exploratory data suggest that a quantitative (PMA) and qualitative (ACMs) molecular heterogeneity assessment using NGS might be useful for a better selection of patients.

  7. Molecular epidemiology of cutaneous leishmaniasis and heterogeneity of Leishmania major strains in Iran. (United States)

    Mahmoudzadeh-Niknam, Hamid; Ajdary, Soheila; Riazi-Rad, Farhad; Mirzadegan, Ebrahim; Rezaeian, Abdolhossein; Khaze, Vahid; Djadid, Navid D; Alimohammadian, Mohammad H


    To determine the geographical distribution of Leishmania species causing cutaneous leishmaniasis (CL) and to study the genetic heterogeneity of Leishmania major isolates from different endemic areas of Iran. A total of 341 isolates from lesions of patients living in 11 provinces of Iran were grown in culture medium and inoculated to BALB/c mice to detect possible visceralisation. The species were identified by isoenzyme analysis using a battery of six enzymes and kinetoplast (k) DNA-PCR technique. Genetic variation among L. major isolates was analysed by random amplified polymorphic DNA (RAPD) technique. Of the total 341 isolates, 283 isolates were L. major and 58 isolates were Leishmania tropica. In rural areas, the causative agent of CL was mainly L. major (95%L. major vs. 5%L. tropica), in urban areas it was L. tropica (65%L. tropica vs. 35%L. major). All isolates of L. major and 8.6% of L. tropica isolates showed visceralisation in BALB/c mice. There is considerable genetic diversity between L. major strains from different endemic areas and even between some isolates of the same endemic area. Leishmania major is the most frequent species in the endemic areas of CL in eleven provinces of Iran, and genetic diversity is a common feature of L. major in the country. © 2012 Blackwell Publishing Ltd.

  8. Single thyroid tumour showing multiple differentiated morphological patterns and intramorphological molecular genetic heterogeneity. (United States)

    Schopper, Heather K; Stence, Aaron; Ma, Deqin; Pagedar, Nitin A; Robinson, Robert A


    A 49-year-old man presented with a single thyroid tumour that showed a combination of conventional papillary carcinoma, follicular variant of papillary carcinoma, clear cell papillary carcinoma, columnar cell carcinoma and poorly differentiated carcinoma. As all of the morphologies have been associated with papillary carcinoma in the literature, we wished to determine if they contained identical or different molecular abnormalities. Targeted next generation sequencing (NGS) of each morphological component and metastases was performed. NGS revealed a BRAF p.K601E mutation in both the clear cell papillary carcinoma and poorly differentiated carcinoma and a KRAS p.G12R mutation in the papillary carcinoma, follicular variant. Two different areas of columnar cell variant were tested, with one showing a KRAS p.G12D mutation but no mutation in the other area. A KRAS p.G12R mutation was seen in the metastatic clear cell variant. Two different lymph nodes had metastatic columnar cell carcinoma, one negative for mutations but the other with a compound KRAS p.G12R and KRAS p.G12V mutation on different alleles. No mutations including BRAF and KRAS were seen in the conventional papillary carcinoma. Although all of the morphological patterns in this tumour have been reported as having aetiological or other association with one another, there was only partial concordance with their molecular signatures. There was significant molecular discordance, however, even with identical morphologies. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to

  9. Molecular heterogeneity of Malassezia pachydermatis through RAPD-PCR = Heterogeneidade molecular da Malassezia pachydermatis através de RAPD-PCR

    Directory of Open Access Journals (Sweden)

    Patrícia da Silva Nascente


    Full Text Available Several methodologies in molecular biology have been used in theinvestigation of Malassezia pachydermatis and its differentiation into subtypes. Recent molecular research of this species includes the use of samples isolated from canine otitis externa and dermatitis, as well as from healthy animals, having in view an epidemiologicalstudy of the yeast. The aim of this study was to identify molecular differences in M. pachydermatis samples isolated from dogs with otitis externa. The M. pachydermatis strains were analyzed by means of the Random Amplification Primer DNA - Polimerase Chain Reaction (RAPD–PCR for molecular heterogeneity research. DNA extraction was carried out with phenol-chloroform and the RAPD technique using the AGAATCCGCC primer. A variation was observed in the number and arrangement of the bands among the 49 studied isolates, grouped into nine patterns. Isolate groupings were not found to be related to animal breed, age or sex. It was concluded that M. pachydermatis has differences in its molecular profile, as shown by the molecular technique (RAPD – PCR, which allows isolates to be classified into nine subtypes.Várias metodologias em biologia molecular têm sido aplicadas para estudar a M. pachydermatis diferenciando-a em subgrupos. Recentemente utiliza-se a investigação molecular desta espécie isolada de otite externa e dermatite, e também de isolados da mesma de animais hígidos, para um estudo epidemiológico da levedura. O objetivo deste trabalho foi identificar diferenças moleculares entre isolados de M. pachydermatis obtidos de casos de otite externa canina. Para isto, amostras da levedura provenientes de cães com esta enfermidade foram estudadas através da técnica de Polimorfismo de DNA Amplificado aoAcaso - Reação da Polimerase em Cadeia (RAPD–PCR para pesquisa de heterogeneidade molecular. A extração de DNA foi realizada no processo fenol-cloroformio e a técnica de RAPD foi estudada com o primer

  10. Finite-Difference Modeling of Seismic Wave Scattering in 3D Heterogeneous Media: Generation of Tangential Motion from an Explosion Source (United States)

    Hirakawa, E. T.; Pitarka, A.; Mellors, R. J.


    Evan Hirakawa, Arben Pitarka, and Robert Mellors One challenging task in explosion seismology is development of physical models for explaining the generation of S-waves during underground explosions. Pitarka et al. (2015) used finite difference simulations of SPE-3 (part of Source Physics Experiment, SPE, an ongoing series of underground chemical explosions at the Nevada National Security Site) and found that while a large component of shear motion was generated directly at the source, additional scattering from heterogeneous velocity structure and topography are necessary to better match the data. Large-scale features in the velocity model used in the SPE simulations are well constrained, however, small-scale heterogeneity is poorly constrained. In our study we used a stochastic representation of small-scale variability in order to produce additional high-frequency scattering. Two methods for generating the distributions of random scatterers are tested. The first is done in the spatial domain by essentially smoothing a set of random numbers over an ellipsoidal volume using a Gaussian weighting function. The second method consists of filtering a set of random numbers in the wavenumber domain to obtain a set of heterogeneities with a desired statistical distribution (Frankel and Clayton, 1986). This method is capable of generating distributions with either Gaussian or von Karman autocorrelation functions. The key parameters that affect scattering are the correlation length, the standard deviation of velocity for the heterogeneities, and the Hurst exponent, which is only present in the von Karman media. Overall, we find that shorter correlation lengths as well as higher standard deviations result in increased tangential motion in the frequency band of interest (0 - 10 Hz). This occurs partially through S-wave refraction, but mostly by P-S and Rg-S waves conversions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore

  11. A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett's Esophagus.

    Directory of Open Access Journals (Sweden)

    Kit Curtius


    Full Text Available Biomarkers that drift differentially with age between normal and premalignant tissues, such as Barrett's esophagus (BE, have the potential to improve the assessment of a patient's cancer risk by providing quantitative information about how long a patient has lived with the precursor (i.e., dwell time. In the case of BE, which is a metaplastic precursor to esophageal adenocarcinoma (EAC, such biomarkers would be particularly useful because EAC risk may change with BE dwell time and it is generally not known how long a patient has lived with BE when a patient is first diagnosed with this condition. In this study we first describe a statistical analysis of DNA methylation data (both cross-sectional and longitudinal derived from tissue samples from 50 BE patients to identify and validate a set of 67 CpG dinucleotides in 51 CpG islands that undergo age-related methylomic drift. Next, we describe how this information can be used to estimate a patient's BE dwell time. We introduce a Bayesian model that incorporates longitudinal methylomic drift rates, patient age, and methylation data from individually paired BE and normal squamous tissue samples to estimate patient-specific BE onset times. Our application of the model to 30 sporadic BE patients' methylomic profiles first exposes a wide heterogeneity in patient-specific BE onset times. Furthermore, independent application of this method to a cohort of 22 familial BE (FBE patients reveals significantly earlier mean BE onset times. Our analysis supports the conjecture that differential methylomic drift occurs in BE (relative to normal squamous tissue and hence allows quantitative estimation of the time that a BE patient has lived with BE.

  12. Observed Dependence of Colloid Detachment on the Concentration of Initially Attached Colloids and Collector Surface Heterogeneity in Porous Media. (United States)

    Li, Tiantian; Jin, Yan; Huang, Yuanfang; Li, Baoguo; Shen, Chongyang


    Sand column experiments were conducted to examine the effects of the concentration of attached colloids (CAC) on their subsequent detachment upon decreasing solution ionic strength (IS). Different pore volumes of latex microparticle suspensions were injected into the columns to allow different amounts of colloids to attach at ISs of 0.001, 0.01, and 0.2 M. Then, deionized water was introduced to release the attached colloids. Results show that the fraction of attachments that were reversible to reduction of IS (FRA) increased with increasing CAC at a given IS if the sand was extensively treated using acids to reduce surface charge heterogeneity. This indicates that colloids were preferentially immobilized in sites favoring irreversible attachment and then gradually occupied reversible sites. In contrast, the FRA decreased with increasing CAC at 0.001 M in sand without the acid treatment, illustrating the opposite attachment sequence. Scanning electron microscope examinations reveal that the concave regions favored irreversible colloid attachment. Reversible attachment is likely due to immobilization on flat surfaces with charge heterogeneities, retention in stagnation point regions via secondary minimum association, ripening in the acid-treated sand, and capture of colloids by protruding asperities with charge heterogeneity in the untreated sand. At ISs of 0.01 and 0.2 M, the FRA was essentially independent of CAC in the untreated sand because the colloids were randomly attached on the sand surfaces over time.

  13. Real-space investigation of energy transfer in heterogeneous molecular dimers (United States)

    Imada, Hiroshi; Miwa, Kuniyuki; Imai-Imada, Miyabi; Kawahara, Shota; Kimura, Kensuke; Kim, Yousoo


    Given its central role in photosynthesis and artificial energy-harvesting devices, energy transfer has been widely studied using optical spectroscopy to monitor excitation dynamics and probe the molecular-level control of energy transfer between coupled molecules. However, the spatial resolution of conventional optical spectroscopy is limited to a few hundred nanometres and thus cannot reveal the nanoscale spatial features associated with such processes. In contrast, scanning tunnelling luminescence spectroscopy has revealed the energy dynamics associated with phenomena ranging from single-molecule electroluminescence, absorption of localized plasmons and quantum interference effects to energy delocalization and intervalley electron scattering with submolecular spatial resolution in real space. Here we apply this technique to individual molecular dimers that comprise a magnesium phthalocyanine and a free-base phthalocyanine (MgPc and H2Pc) and find that locally exciting MgPc with the tunnelling current of the scanning tunnelling microscope generates a luminescence signal from a nearby H2Pc molecule as a result of resonance energy transfer from the former to the latter. A reciprocating resonance energy transfer is observed when exciting the second singlet state (S2) of H2Pc, which results in energy transfer to the first singlet state (S1) of MgPc and final funnelling to the S1 state of H2Pc. We also show that tautomerization of H2Pc changes the energy transfer characteristics within the dimer system, which essentially makes H2Pc a single-molecule energy transfer valve device that manifests itself by blinking resonance energy transfer behaviour.

  14. Three-dimensional visualization of membrane phospholipid distributions in Arabidopsis thaliana seeds: A spatial perspective of molecular heterogeneity. (United States)

    Sturtevant, Drew; Dueñas, Maria Emilia; Lee, Young-Jin; Chapman, Kent D


    Arabidopsis thaliana has been widely used as a model plant to study acyl lipid metabolism. Seeds of A. thaliana are quite small (approximately 500×300μm and weigh ~20μg), making lipid compositional analyses of single seeds difficult to achieve. Here we have used matrix assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to map and visualize the three-dimensional spatial distributions of two common membrane phospholipid classes, phosphatidylcholine (PC) and phosphatidylinositol (PI), in single A. thaliana seeds. The 3D images revealed distinct differences in distribution of several molecular species of both phospholipids among different seed tissues. Using data from these 3D reconstructions, the PC and PI mol% lipid profiles were calculated for the embryonic axis, cotyledons, and peripheral endosperm, and these data agreed well with overall quantification of these lipids in bulk seed extracts analyzed by conventional electrospray ionization-mass spectrometry (ESI-MS). In addition, MALDI-MSI was used to profile PC and PI molecular species in seeds of wild type, fad2-1, fad3-2, fad6-1, and fae1-1 acyl lipid mutants. The resulting distributions revealed previously unobserved changes in spatial distribution of several lipid molecular species, and were used to suggest new insights into biochemical heterogeneity of seed lipid metabolism. These studies highlight the value of mass spectrometry imaging to provide unprecedented spatial and chemical resolution of metabolites directly in samples even as small as a single A. thaliana seeds, and allow for expanded imaging of plant metabolites to improve our understanding of plant lipid metabolism from a spatial perspective. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Clinical Features, Molecular Heterogeneity, and Prognostic Implications in YARS2-Related Mitochondrial Myopathy. (United States)

    Sommerville, Ewen W; Ng, Yi Shiau; Alston, Charlotte L; Dallabona, Cristina; Gilberti, Micol; He, Langping; Knowles, Charlotte; Chin, Sophie L; Schaefer, Andrew M; Falkous, Gavin; Murdoch, David; Longman, Cheryl; de Visser, Marianne; Bindoff, Laurence A; Rawles, John M; Dean, John C S; Petty, Richard K; Farrugia, Maria E; Haack, Tobias B; Prokisch, Holger; McFarland, Robert; Turnbull, Douglass M; Donnini, Claudia; Taylor, Robert W; Gorman, Gráinne S


    YARS2 mutations have been associated with a clinical triad of myopathy, lactic acidosis, and sideroblastic anemia in predominantly Middle Eastern populations. However, the identification of new patients expands the clinical and molecular spectrum of mitochondrial disorders. To review the clinical, molecular, and genetic features of YARS2-related mitochondrial disease and to demonstrate a new Scottish founder variant. An observational case series study was conducted at a national diagnostic center for mitochondrial disease in Newcastle upon Tyne, England, and review of cases published in the literature. Six adults in a well-defined mitochondrial disease cohort and 11 additional cases described in the literature were identified with YARS2 variants between January 1, 2000, and January 31, 2015. The spectrum of clinical features and disease progression in unreported and reported patients with pathogenic YARS2 variants. Seventeen patients (median [interquartile range] age at onset, 1.5 [9.8] years) with YARS2-related mitochondrial myopathy were identified. Fifteen individuals (88%) exhibited an elevated blood lactate level accompanied by generalized myopathy; only 12 patients (71%) manifested with sideroblastic anemia. Hypertrophic cardiomyopathy (9 [53%]) and respiratory insufficiency (8 [47%]) were also prominent clinical features. Central nervous system involvement was rare. Muscle studies showed global cytochrome-c oxidase deficiency in all patients tested and severe, combined respiratory chain complex activity deficiencies. Microsatellite genotyping demonstrated a common founder effect shared between 3 Scottish patients with a p.Leu392Ser variant. Immunoblotting from fibroblasts and myoblasts of an affected Scottish patient showed normal YARS2 protein levels and mild respiratory chain complex defects. Yeast modeling of novel missense YARS2 variants closely correlated with the severity of clinical phenotypes. The p.Leu392Ser variant is likely a newly identified

  16. Destabilization, Propagation, and Generation of Surfactant-Stabilized Foam during Crude Oil Displacement in Heterogeneous Model Porous Media. (United States)

    Xiao, Siyang; Zeng, Yongchao; Vavra, Eric D; He, Peng; Puerto, Maura; Hirasaki, George J; Biswal, Sibani L


    Foam flooding in porous media is of increasing interest due to its numerous applications such as enhanced oil recovery, aquifer remediation, and hydraulic fracturing. However, the mechanisms of oil-foam interactions have yet to be fully understood at the pore level. Here, we present three characteristic zones identified in experiments involving the displacement of crude oil from model porous media via surfactant-stabilized foam, and we describe a series of pore-level dynamics in these zones which were not observed in experiments involving paraffin oil. In the displacement front zone, foam coalesces upon initial contact with crude oil, which is known to destabilize the liquid lamellae of the foam. Directly upstream, a transition zone occurs where surface wettability is altered from oil-wet to water-wet. After this transition takes place, a strong foam bank zone exists where foam is generated within the porous media. We visualized each zone using a microfluidic platform, and we discuss the unique physicochemical phenomena that define each zone. In our analysis, we also provide an updated mechanistic understanding of the "smart rheology" of foam which builds upon simple "phase separation" observations in the literature.

  17. Incorporation of Molecular Catalysts in Metal-Organic Frameworks for Highly Efficient Heterogeneous Catalysis. (United States)

    Wu, Chuan-De; Zhao, Min


    Porous metal-organic frameworks (MOFs) are built from periodically alternate organic moieties and metal ions/clusters. The unique features of the open framework structures, the high surface areas, the permanent porosity, and the appropriate hydrophilic and hydrophobic pore nature mean that MOF materials are a class of ideal host matrices for immobilization of molecular catalysts. The emerging porous materials can not only retain but are also able to enhance the catalytic functions of the single individuals. MOF catalysts have the following super characters: i) uniformly dispersed catalytic sites on the pore surfaces to improve the utility, ii) appropriate hydrophilic and hydrophobic pore nature to facilitate the recognition and transportation of reactant and product molecules, iii) a collaborative microenvironment to realize synergistic catalysis, and iv) simple separation and recovery for long-term usage. Accompanying the development of the synthetic strategies and the technologies for the characterization of MOF materials, MOF catalysis has undergone an upsurge, which has transcended the stage of opportunism. Here, the rational design and synthesis of MOF catalysts are discussed, along with the key factors of active sites, microenvironments, and transmission channels that lead to the distinct catalytic properties of MOF catalysts. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Heterogeneous nucleation of solid Al from the melt by Al 3 Ti : Molecular dynamics simulations

    KAUST Repository

    Wang, Junsheng


    It has been known experimentally for some time that Al3 Ti is a powerful nucleant for the solidification of aluminum from the melt; however, a full microscopic understanding is still lacking. To develop this understanding, we have performed molecular dynamics simulations of the nucleation and early stages of growth using published embedded atom method potentials for Al-Ti, but modified by us to stabilize the D 022 structure. We discover that Al3 Ti can indeed be very effective in promoting the growth of solid Al but the manner in which growth takes place depends sensitively on the surface on which the Al nucleates. In particular, complete growth of solid Al from the liquid on the (001) and (110) surfaces of Al3 Ti occurs at a lower temperature than on the (112) surface. This anisotropy agrees with observations in previous experiments. We explain this observation in terms of interfacial energies. On the preferential (111) surface of Al the solid-liquid interfacial energy is highest while the solid-vacuum energy is lowest. Our simulations also show that the extent of ordering taking place in liquid Al close to the Al 3 Ti substrate above the melting point correlates well with the effectiveness of the substrate as a nucleant below the melting temperature: this could provide a computationally efficient scheme to identify good nucleants. © 2010 The American Physical Society.

  19. Molecular System Dynamics for Self-Organization in Heterogeneous Wireless Networks

    Directory of Open Access Journals (Sweden)

    Milner StuartD


    Full Text Available We have been looking at the properties of physical configurations that occur in nature in order to characterize, predict, and control network robustness in dynamic communication networks. Our framework is based on the definition of a potential energy function to characterize robustness in communication networks and the study of first- and second-order variations of the potential energy to provide prediction and control strategies for network-performance optimization. This paper describes novel investigations within this framework that draw from molecular system dynamics. The Morse potential, which governs the energy stored in bonds within molecules, is considered for the characterization of the potential energy of communication links in the presence of physical constraints such as the power available at the transmitters in a network. The inclusion of the Morse potential translates into improved control strategies, where forces on network nodes drive the release, retention, or reconfiguration of communication links based on their role within the network architecture. The performance of the proposed approach is measured in terms of the number of source-to-destination connections that have an end-to-end communications path. Simulation results show the effectiveness of our control mechanism, where the physical topology reorganizes to maximize the number of source-to-destination communicating pairs. The algorithms developed are completely distributed, show constant time complexity and produce optimal solutions from local interactions, thus preserving the system's self-organizing capability.

  20. Molecular heterogeneity in major urinary proteins of Mus musculus subspecies: potential candidates involved in speciation. (United States)

    Hurst, Jane L; Beynon, Robert J; Armstrong, Stuart D; Davidson, Amanda J; Roberts, Sarah A; Gómez-Baena, Guadalupe; Smadja, Carole M; Ganem, Guila


    When hybridisation carries a cost, natural selection is predicted to favour evolution of traits that allow assortative mating (reinforcement). Incipient speciation between the two European house mouse subspecies, Mus musculus domesticus and M.m.musculus, sharing a hybrid zone, provides an opportunity to understand evolution of assortative mating at a molecular level. Mouse urine odours allow subspecific mate discrimination, with assortative preferences evident in the hybrid zone but not in allopatry. Here we assess the potential of MUPs (major urinary proteins) as candidates for signal divergence by comparing MUP expression in urine samples from the Danish hybrid zone border (contact) and from allopatric populations. Mass spectrometric characterisation identified novel MUPs in both subspecies involving mostly new combinations of amino acid changes previously observed in M.m.domesticus. The subspecies expressed distinct MUP signatures, with most MUPs expressed by only one subspecies. Expression of at least eight MUPs showed significant subspecies divergence both in allopatry and contact zone. Another seven MUPs showed divergence in expression between the subspecies only in the contact zone, consistent with divergence by reinforcement. These proteins are candidates for the semiochemical barrier to hybridisation, providing an opportunity to characterise the nature and evolution of a putative species recognition signal.

  1. The Impact of DNAPL Source-Zone Architecture on Contaminant Mass Flux and Plume Evolution in Heterogeneous Porous Media (United States)


    M.D.; Jawitz, J.W. 2008. Laboratory investigation of flux reduction from dense non-aqueous phase liquid (DNAPL) partial source zone remediation by...project was designed to accomplish a systematic study of the mass-transfer behavior of chlorinated-solvent immiscible liquids in heterogeneous porous...5.1.3-1b Summary of experimental conditions……………………………………… 43 Tables 5.3.1-1 Summary of miscible -displacement experiments…………………………… 63 Table 5.3.1

  2. Gravity destabilized non-wetting phase invasion in macro-heterogeneous porous media: Near pore scale macro modified invasion percolation simulation of experiments

    Energy Technology Data Exchange (ETDEWEB)



    The authors reconceptualize macro modified invasion percolation (MMIP) at the near pore (NP) scale and apply it to simulate the non-wetting phase invasion experiments of Glass et al [in review] conducted in macro-heterogeneous porous media. For experiments where viscous forces were non-negligible, they redefine the total pore filling pressure to include viscous losses within the invading phase as well as the viscous influence to decrease randomness imposed by capillary forces at the front. NP-MMIP exhibits the complex invasion order seen experimentally with characteristic alternations between periods of gravity stabilized and destabilized invasion growth controlled by capillary barriers. The breaching of these barriers and subsequent pore scale fingering of the non-wetting phase is represented extremely well as is the saturation field evolution, and total volume invaded.

  3. Inverse radiative transfer problems in two-dimensional heterogeneous media; Problemas inversos em transferencia radiativa em meios heterogeneos bidimensionais

    Energy Technology Data Exchange (ETDEWEB)

    Tito, Mariella Janette Berrocal


    The analysis of inverse problems in participating media where emission, absorption and scattering take place has several relevant applications in engineering and medicine. Some of the techniques developed for the solution of inverse problems have as a first step the solution of the direct problem. In this work the discrete ordinates method has been used for the solution of the linearized Boltzmann equation in two dimensional cartesian geometry. The Levenberg - Marquardt method has been used for the solution of the inverse problem of internal source and absorption and scattering coefficient estimation. (author)

  4. Rules for Flight Paths and Time of Flight for Flows in Porous Media with Heterogeneous Permeability and Porosity

    Directory of Open Access Journals (Sweden)

    Lihua Zuo


    Full Text Available Porous media like hydrocarbon reservoirs may be composed of a wide variety of rocks with different porosity and permeability. Our study shows in algorithms and in synthetic numerical simulations that the flow pattern of any particular porous medium, assuming constant fluid properties and standardized boundary and initial conditions, is not affected by any spatial porosity changes but will vary only according to spatial permeability changes. In contrast, the time of flight along the streamline will be affected by both the permeability and porosity, albeit in opposite directions. A theoretical framework is presented with evidence from flow visualizations. A series of strategically chosen streamline simulations, including systematic spatial variations of porosity and permeability, visualizes the respective effects on the flight path and time of flight. Two practical rules are formulated. Rule  1 states that an increase in permeability decreases the time of flight, whereas an increase in porosity increases the time of flight. Rule  2 states that the permeability uniquely controls the flight path of fluid flow in porous media; local porosity variations do not affect the streamline path. The two rules are essential for understanding fluid transport mechanisms, and their rigorous validation therefore is merited.

  5. Conduction and Reactivity in Heterogeneous-Molecular Catalysis: New Insights in Water Oxidation Catalysis by Phosphate Cobalt Oxide Films. (United States)

    Costentin, Cyrille; Porter, Thomas R; Savéant, Jean-Michel


    Cyclic voltammetry of phosphate cobalt oxide (CoPi) films catalyzing O2-evolution from water oxidation as a function of scan rate, phosphate concentration and film thickness allowed for new insights into the coupling between charge transport and catalysis. At pH = 7 and low buffer concentrations, the film is insulating below 0.8 (V vs SHE) but becomes conductive above 0.9 (V vs SHE). Between 1.0 to 1.3 (V vs SHE), the mesoporous structure of the film gives rise to a large thickness-dependent capacitance. At higher buffer concentrations, two reversible proton-coupled redox couples appear over the capacitive response with 0.94 and 1.19 (V vs SHE) pH = 7 standard potentials. The latter is, at most, very weakly catalytic and not responsible for the large catalytic current observed at higher potentials. CV-response analysis showed that the amount of redox-active cobalt-species in the film is small, less than 10% of total. The catalytic process involves a further proton-coupled-electron-transfer and is so fast that it is controlled by diffusion of phosphate, the catalyst cofactor. CV-analysis with newly derived relationships led to a combination of the catalyst standard potential with the catalytic rate constant and a lower-limit estimation of these parameters. The large currents resulting from the fast catalytic reaction result in significant potential losses related to charge transport through the film. CoPi films appear to combine molecular catalysis with semiconductor-type charge transport. This mode of heterogeneous molecular catalysis is likely to occur in many other catalytic films.

  6. The influence of molecular structure and aerosol phase on the heterogeneous oxidation of normal and branched alkanes by OH. (United States)

    Ruehl, Christopher R; Nah, Theodora; Isaacman, Gabriel; Worton, David R; Chan, Arthur W H; Kolesar, Katheryn R; Cappa, Christopher D; Goldstein, Allen H; Wilson, Kevin R


    Insights into the influence of molecular structure and thermodynamic phase on the chemical mechanisms of hydroxyl radical-initiated heterogeneous oxidation are obtained by identifying reaction products of submicrometer particles composed of either n-octacosane (C28H58, a linear alkane) or squalane (C30H62, a highly branched alkane) and OH. A common pattern is observed in the positional isomers of octacosanone and octacosanol, with functionalization enhanced toward the end of the molecule. This suggests that relatively large linear alkanes are structured in submicrometer particles such that their ends are oriented toward the surface. For squalane, positional isomers of first-generation ketones and alcohols also form in distinct patterns. Ketones are favored on carbons adjacent to tertiary carbons, while hydroxyl groups are primarily found on tertiary carbons but also tend to form toward the end of the molecule. Some first-generation products, viz., hydroxycarbonyls and diols, contain two oxygen atoms. These results suggest that alkoxy radicals are important intermediates and undergo both intramolecular (isomerization) and intermolecular (chain propagation) hydrogen abstraction reactions. Oxidation products with carbon number less than the parent alkane's are observed to a much greater extent for squalane than for n-octacosane oxidation and can be explained by the preferential cleavage of bonds involving tertiary carbons.

  7. A numerical study of super-resolution through fast 3D wideband algorithm for scattering in highly-heterogeneous media

    KAUST Repository

    Létourneau, Pierre-David


    We present a wideband fast algorithm capable of accurately computing the full numerical solution of the problem of acoustic scattering of waves by multiple finite-sized bodies such as spherical scatterers in three dimensions. By full solution, we mean that no assumption (e.g. Rayleigh scattering, geometrical optics, weak scattering, Born single scattering, etc.) is necessary regarding the properties of the scatterers, their distribution or the background medium. The algorithm is also fast in the sense that it scales linearly with the number of unknowns. We use this algorithm to study the phenomenon of super-resolution in time-reversal refocusing in highly-scattering media recently observed experimentally (Lemoult et al., 2011), and provide numerical arguments towards the fact that such a phenomenon can be explained through a homogenization theory.

  8. Modeling of Electromagnetic Scattering by Discrete and Discretely Heterogeneous Random Media by Using Numerically Exact Solutions of the Maxwell Equations (United States)

    Dlugach, Janna M.; Mishchenko, Michael I.


    In this paper, we discuss some aspects of numerical modeling of electromagnetic scattering by discrete random medium by using numerically exact solutions of the macroscopic Maxwell equations. Typical examples of such media are clouds of interstellar dust, clouds of interplanetary dust in the Solar system, dusty atmospheres of comets, particulate planetary rings, clouds in planetary atmospheres, aerosol particles with numerous inclusions and so on. Our study is based on the results of extensive computations of different characteristics of electromagnetic scattering obtained by using the superposition T-matrix method which represents a direct computer solver of the macroscopic Maxwell equations for an arbitrary multisphere configuration. As a result, in particular, we clarify the range of applicability of the low-density theories of radiative transfer and coherent backscattering as well as of widely used effective-medium approximations.

  9. Correspondence Between One- and Two-Equation Models for Solute Transport in Two-Region Heterogeneous Porous Media

    KAUST Repository

    Davit, Y.


    In this work, we study the transient behavior of homogenized models for solute transport in two-region porous media. We focus on the following three models: (1) a time non-local, two-equation model (2eq-nlt). This model does not rely on time constraints and, therefore, is particularly useful in the short-time regime, when the timescale of interest (t) is smaller than the characteristic time (τ 1) for the relaxation of the effective macroscale parameters (i. e., when t ≤ τ 1); (2) a time local, two-equation model (2eq). This model can be adopted when (t) is significantly larger than (τ 1) (i.e., when t≫τ 1); and (3) a one-equation, time-asymptotic formulation (1eq ∞). This model can be adopted when (t) is significantly larger than the timescale (τ 2) associated with exchange processes between the two regions (i. e., when t≫τ 2). In order to obtain insight into this transient behavior, we combine a theoretical approach based on the analysis of spatial moments with numerical and analytical results in several simple cases. The main result of this paper is to show that there is only a weak asymptotic convergence of the solution of (2eq) towards the solution of (1eq ∞) in terms of standardized moments but, interestingly, not in terms of centered moments. The physical interpretation of this result is that deviations from the Fickian situation persist in the limit of long times but that the spreading of the solute is eventually dominating these higher order effects. © 2012 Springer Science+Business Media B.V.

  10. Spatial and molecular resolution of diffuse malignant mesothelioma heterogeneity by integrating label-free FTIR imaging, laser capture microdissection and proteomics (United States)

    Großerueschkamp, Frederik; Bracht, Thilo; Diehl, Hanna C.; Kuepper, Claus; Ahrens, Maike; Kallenbach-Thieltges, Angela; Mosig, Axel; Eisenacher, Martin; Marcus, Katrin; Behrens, Thomas; Brüning, Thomas; Theegarten, Dirk; Sitek, Barbara; Gerwert, Klaus


    Diffuse malignant mesothelioma (DMM) is a heterogeneous malignant neoplasia manifesting with three subtypes: epithelioid, sarcomatoid and biphasic. DMM exhibit a high degree of spatial heterogeneity that complicates a thorough understanding of the underlying different molecular processes in each subtype. We present a novel approach to spatially resolve the heterogeneity of a tumour in a label-free manner by integrating FTIR imaging and laser capture microdissection (LCM). Subsequent proteome analysis of the dissected homogenous samples provides in addition molecular resolution. FTIR imaging resolves tumour subtypes within tissue thin-sections in an automated and label-free manner with accuracy of about 85% for DMM subtypes. Even in highly heterogeneous tissue structures, our label-free approach can identify small regions of interest, which can be dissected as homogeneous samples using LCM. Subsequent proteome analysis provides a location specific molecular characterization. Applied to DMM subtypes, we identify 142 differentially expressed proteins, including five protein biomarkers commonly used in DMM immunohistochemistry panels. Thus, FTIR imaging resolves not only morphological alteration within tissue but it resolves even alterations at the level of single proteins in tumour subtypes. Our fully automated workflow FTIR-guided LCM opens new avenues collecting homogeneous samples for precise and predictive biomarkers from omics studies.

  11. Lapse-time-dependent coda-wave depth sensitivity to local velocity perturbations in 3-D heterogeneous elastic media (United States)

    Obermann, Anne; Planès, Thomas; Hadziioannou, Céline; Campillo, Michel


    In the context of seismic monitoring, recent studies made successful use of seismic coda waves to locate medium changes on the horizontal plane. Locating the depth of the changes, however, remains a challenge. In this paper, we use 3-D wavefield simulations to address two problems: first, we evaluate the contribution of surface- and body-wave sensitivity to a change at depth. We introduce a thin layer with a perturbed velocity at different depths and measure the apparent relative velocity changes due to this layer at different times in the coda and for different degrees of heterogeneity of the model. We show that the depth sensitivity can be modelled as a linear combination of body- and surface-wave sensitivity. The lapse-time-dependent sensitivity ratio of body waves and surface waves can be used to build 3-D sensitivity kernels for imaging purposes. Second, we compare the lapse-time behaviour in the presence of a perturbation in horizontal and vertical slabs to address, for instance, the origin of the velocity changes detected after large earthquakes.

  12. A time domain finite-difference technique for oblique incidence of antiplane waves in heterogeneous dissipative media

    Directory of Open Access Journals (Sweden)

    A. Caserta


    Full Text Available This paper deals with the antiplane wave propagation in a 2D heterogeneous dissipative medium with complex layer interfaces and irregular topography. The initial boundary value problem which represents the viscoelastic dynamics driving 2D antiplane wave propagation is formulated. The discretization scheme is based on the finite-difference technique. Our approach presents some innovative features. First, the introduction of the forcing term into the equation of motion offers the advantage of an easier handling of different inputs such as general functions of spatial coordinates and time. Second, in the case of a straight-line source, the symmetry of the incident plane wave allows us to solve the problem of oblique incidence simply by rotating the 2D model. This artifice reduces the oblique incidence to the vertical one. Third, the conventional rheological model of the generalized Maxwell body has been extended to include the stress-free boundary condition. For this reason we solve explicitly the stress-free boundary condition, not following the most popular technique called vacuum formalism. Finally, our numerical code has been constructed to model the seismic response of complex geological structures: real geological interfaces are automatically digitized and easily introduced in the input model. Three numerical applications are discussed. To validate our numerical model, the first test compares the results of our code with others shown in the literature. The second application rotates the input model to simulate the oblique incidence. The third one deals with a real high-complexity 2D geological structure.

  13. An $h$-Adaptive Operator Splitting Method for Two-Phase Flow in 3D Heterogeneous Porous Media

    KAUST Repository

    Chueh, Chih-Che


    The simulation of multiphase flow in porous media is a ubiquitous problem in a wide variety of fields, such as fuel cell modeling, oil reservoir simulation, magma dynamics, and tumor modeling. However, it is computationally expensive. This paper presents an interconnected set of algorithms which we show can accelerate computations by more than two orders of magnitude compared to traditional techniques, yet retains the high accuracy necessary for practical applications. Specifically, we base our approach on a new adaptive operator splitting technique driven by an a posteriori criterion to separate the flow from the transport equations, adaptive meshing to reduce the size of the discretized problem, efficient block preconditioned solver techniques for fast solution of the discrete equations, and a recently developed artificial diffusion strategy to stabilize the numerical solution of the transport equation. We demonstrate the accuracy and efficiency of our approach using numerical experiments in one, two, and three dimensions using a program that is made available as part of a large open source library. © 2013 Society for Industrial and Applied Mathematics.

  14. Control of biologically active degradation zones by vertical heterogeneity: Applications in fractured media. 1997 annual progress report

    Energy Technology Data Exchange (ETDEWEB)

    Colwell, F.S.; Smith, R.W.; McKinley, J.; Fredrickson, J.; Onstott, T.C.; Reysenbach, A.L.


    'The objective of this research is to determine the relationship between of biologically active contaminant degradation zones in a fractured, subsurface medium and vertical geological heterogeneities. The research is being performed on samples collected from the Test Area North (TAN) site at the Idaho National Engineering and Environmental Laboratory (INEEL) where a dissolved trichloroethylene (TCE) plume is migrating in the basalts and interbed sediments of the Eastern Snake River Plain (ESRP) aquifer. Research results are leading to an enhanced understanding of the constraints that the geochemical and hydrological environment place on the activities and distribution of TCE-degrading organisms in this fractured subsurface medium. Enhanced understanding allows better decisions to be made regarding the use of remedial technologies such as natural attenuation and in situ bioremediation at geologically complex waste sites. Through this research, investigations conducted by the Subsurface Science Program (SSP) at TAN are being extended in order to develop a mechanistic understanding of the coupled geomicrobial and hydrogeochemical processes that are necessary to predict the field-scale intrinsic degradation rates of TCE. The research objective is being accomplished by characterizing paired cores and water samples from boreholes located in differing geochemical and flow environments within the plume. Analysis of these samples will allow the determination of the spatial correlation and microbial characterization. The results presented in this report consist primarily of TAN-33 data as many of those analyses have been completed. Nearly all of the TAN-37 data has yet to be acquired. It should be noted that most of the cores were collected from zones that consist of relatively competent, massive basalt. This was because the authors were doubtful about the quality of samples obtained from rubble zones due to potential alteration by the drilling fluids. Thus

  15. An efficient algorithm for double-difference tomography and location in heterogeneous media, with an application to the Kilauea volcano (United States)

    Monteiller, V.; Got, J.-L.; Virieux, J.; Okubo, P.


    Improving our understanding of crustal processes requires a better knowledge of the geometry and the position of geological bodies. In this study we have designed a method based upon double-difference relocation and tomography to image, as accurately as possible, a heterogeneous medium containing seismogenic objects. Our approach consisted not only of incorporating double difference in tomography but also partly in revisiting tomographic schemes for choosing accurate and stable numerical strategies, adapted to the use of cross-spectral time delays. We used a finite difference solution to the eikonal equation for travel time computation and a Tarantola-Valette approach for both the classical and double-difference three-dimensional tomographic inversion to find accurate earthquake locations and seismic velocity estimates. We estimated efficiently the square root of the inverse model's covariance matrix in the case of a Gaussian correlation function. It allows the use of correlation length and a priori model variance criteria to determine the optimal solution. Double-difference relocation of similar earthquakes is performed in the optimal velocity model, making absolute and relative locations less biased by the velocity model. Double-difference tomography is achieved by using high-accuracy time delay measurements. These algorithms have been applied to earthquake data recorded in the vicinity of Kilauea and Mauna Loa volcanoes for imaging the volcanic structures. Stable and detailed velocity models are obtained: the regional tomography unambiguously highlights the structure of the island of Hawaii and the double-difference tomography shows a detailed image of the southern Kilauea caldera-upper east rift zone magmatic complex. Copyright 2005 by the American Geophysical Union.

  16. Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity (United States)

    Xu, Ning; Cui, Jinrui; Mengesha, Emebet; Chen, Yii-Der I.; Taylor, Kent D.; Azziz, Ricardo; Goodarzi, Mark O.


    Genome wide association studies (GWAS) have revealed 11 independent risk loci for polycystic ovary syndrome (PCOS), a common disorder in young women characterized by androgen excess and oligomenorrhea. To put these risk loci and the single nucleotide polymorphisms (SNPs) therein into functional context, we measured DNA methylation and gene expression in subcutaneous adipose tissue biopsies to identify PCOS-specific alterations. Two genes from the LHCGR region, STON1-GTF2A1L and LHCGR, were overexpressed in PCOS. In analysis stratified by obesity, LHCGR was overexpressed only in non-obese PCOS women. Although not differentially expressed in the entire PCOS group, INSR was underexpressed in obese PCOS subjects only. Alterations in gene expression in the LHCGR, RAB5B and INSR regions suggest that SNPs in these loci may be functional and could affect gene expression directly or indirectly via epigenetic alterations. We identified reduced methylation in the LHCGR locus and increased methylation in the INSR locus, changes that are concordant with the altered gene expression profiles. Complex patterns of meQTL and eQTL were identified in these loci, suggesting that local genetic variation plays an important role in gene regulation. We propose that non-obese PCOS women possess significant alterations in LH receptor expression, which drives excess androgen secretion from the ovary. Alternatively, obese women with PCOS possess alterations in insulin receptor expression, with underexpression in metabolic tissues and overexpression in the ovary, resulting in peripheral insulin resistance and excess ovarian androgen production. These studies provide a genetic and molecular basis for the reported clinical heterogeneity of PCOS. PMID:26305227

  17. Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity.

    Directory of Open Access Journals (Sweden)

    Michelle R Jones


    Full Text Available Genome wide association studies (GWAS have revealed 11 independent risk loci for polycystic ovary syndrome (PCOS, a common disorder in young women characterized by androgen excess and oligomenorrhea. To put these risk loci and the single nucleotide polymorphisms (SNPs therein into functional context, we measured DNA methylation and gene expression in subcutaneous adipose tissue biopsies to identify PCOS-specific alterations. Two genes from the LHCGR region, STON1-GTF2A1L and LHCGR, were overexpressed in PCOS. In analysis stratified by obesity, LHCGR was overexpressed only in non-obese PCOS women. Although not differentially expressed in the entire PCOS group, INSR was underexpressed in obese PCOS subjects only. Alterations in gene expression in the LHCGR, RAB5B and INSR regions suggest that SNPs in these loci may be functional and could affect gene expression directly or indirectly via epigenetic alterations. We identified reduced methylation in the LHCGR locus and increased methylation in the INSR locus, changes that are concordant with the altered gene expression profiles. Complex patterns of meQTL and eQTL were identified in these loci, suggesting that local genetic variation plays an important role in gene regulation. We propose that non-obese PCOS women possess significant alterations in LH receptor expression, which drives excess androgen secretion from the ovary. Alternatively, obese women with PCOS possess alterations in insulin receptor expression, with underexpression in metabolic tissues and overexpression in the ovary, resulting in peripheral insulin resistance and excess ovarian androgen production. These studies provide a genetic and molecular basis for the reported clinical heterogeneity of PCOS.

  18. Diffusion-weighted imaging features of breast tumours and the surrounding stroma reflect intrinsic heterogeneous characteristics of molecular subtypes in breast cancer

    KAUST Repository

    Fan, Ming


    Breast cancer heterogeneity is the main obstacle preventing the identification of patients with breast cancer with poor prognoses and treatment responses; however, such heterogeneity has not been well characterized. The purpose of this retrospective study was to reveal heterogeneous patterns in the apparent diffusion coefficient (ADC) signals in tumours and the surrounding stroma to predict molecular subtypes of breast cancer. A dataset of 126 patients with breast cancer, who underwent preoperative diffusion-weighted imaging (DWI) on a 3.0-T image system, was collected. Breast images were segmented into regions comprising the tumour and surrounding stromal shells in which features that reflect heterogeneous ADC signal distribution were extracted. For each region, imaging features were computed, including the mean, minimum, variance, interquartile range (IQR), range, skewness, kurtosis and entropy of ADC values. Univariate and stepwise multivariate logistic regression modelling was performed to identify the magnetic resonance imaging features that optimally discriminate luminal A, luminal B, human epidermal growth factor 2 (HER2)-enriched and basal-like molecular subtypes. The performance of the predictive models was evaluated using the area under the receiver operating characteristic curve (AUC). Univariate logistic regression analysis showed that the skewness in the tumour boundary achieved an AUC of 0.718 for discrimination between luminal A and non-luminal A tumours, whereas the IQR of the ADC value in the tumour boundary had an AUC of 0.703 for classification of the HER2-enriched subtype. Imaging features in the tumour boundary and the proximal peritumoral stroma corresponded to a higher overall prediction performance than those in other regions. A multivariate logistic regression model combining features in all the regions achieved an overall AUC of 0.800 for the classification of the four tumour subtypes. These findings suggest that features in the tumour

  19. OpenSWPC: an open-source integrated parallel simulation code for modeling seismic wave propagation in 3D heterogeneous viscoelastic media (United States)

    Maeda, Takuto; Takemura, Shunsuke; Furumura, Takashi


    We have developed an open-source software package, Open-source Seismic Wave Propagation Code (OpenSWPC), for parallel numerical simulations of seismic wave propagation in 3D and 2D (P-SV and SH) viscoelastic media based on the finite difference method in local-to-regional scales. This code is equipped with a frequency-independent attenuation model based on the generalized Zener body and an efficient perfectly matched layer for absorbing boundary condition. A hybrid-style programming using OpenMP and the Message Passing Interface (MPI) is adopted for efficient parallel computation. OpenSWPC has wide applicability for seismological studies and great portability to allowing excellent performance from PC clusters to supercomputers. Without modifying the code, users can conduct seismic wave propagation simulations using their own velocity structure models and the necessary source representations by specifying them in an input parameter file. The code has various modes for different types of velocity structure model input and different source representations such as single force, moment tensor and plane-wave incidence, which can easily be selected via the input parameters. Widely used binary data formats, the Network Common Data Form (NetCDF) and the Seismic Analysis Code (SAC) are adopted for the input of the heterogeneous structure model and the outputs of the simulation results, so users can easily handle the input/output datasets. All codes are written in Fortran 2003 and are available with detailed documents in a public repository.[Figure not available: see fulltext.

  20. Application of a lumped-process mathematical model to dissolution of non-uniformly distributed immiscible liquid in heterogeneous porous media. (United States)

    Marble, J C; DiFilippo, E L; Zhang, Z; Tick, G R; Brusseau, M L


    The use of a lumped-process mathematical model to simulate the complete dissolution of immiscible liquid non-uniformly distributed in physically heterogeneous porous-media systems was investigated. The study focused specifically on systems wherein immiscible liquid was poorly accessible to flowing water. Two representative, idealized scenarios were examined, one wherein immiscible liquid at residual saturation exists within a lower-permeability unit residing in a higher-permeability matrix, and one wherein immiscible liquid at higher saturation (a pool) exists within a higher-permeability unit adjacent to a lower-permeability unit. As expected, effluent concentrations were significantly less than aqueous solubility due to dilution and by-pass flow effects. The measured data were simulated with two mathematical models, one based on a simple description of the system and one based on a more complex description. The permeability field and the distribution of the immiscible-liquid zones were represented explicitly in the more complex, distributed-process model. The dissolution rate coefficient in this case represents only the impact of local-scale (and smaller) processes on dissolution, and the parameter values were accordingly obtained from the results of experiments conducted with one-dimensional, homogeneously-packed columns. In contrast, the system was conceptualized as a pseudo-homogeneous medium with immiscible liquid uniformly distributed throughout the system for the simpler, lumped-process model. With this approach, all factors that influence immiscible-liquid dissolution are incorporated into the calibrated dissolution rate coefficient, which in such cases serves as a composite or lumped term. The calibrated dissolution rate coefficients obtained from the simulations conducted with the lumped-process model were approximately two to three orders-of-magnitude smaller than the independently-determined values used for the simulations conducted with the

  1. Stereodirection of an α-ketoester at sub-molecular sites on chirally modified Pt(111): Heterogeneous asymmetric catalysis

    DEFF Research Database (Denmark)

    Demers-Carpentier, V.; Rasmussen, A.M.H.; Goubert, G.


    Chirally modified Pt catalysts are used in the heterogeneous asymmetric hydrogenation of α-ketoesters. Stereoinduction is believed to occur through the formation of chemisorbed modifier–substrate complexes. In this study, the formation of diastereomeric complexes by coadsorbed methyl 3,3,3-triflu......Chirally modified Pt catalysts are used in the heterogeneous asymmetric hydrogenation of α-ketoesters. Stereoinduction is believed to occur through the formation of chemisorbed modifier–substrate complexes. In this study, the formation of diastereomeric complexes by coadsorbed methyl 3...

  2. Prediction of molecular separation of polar-apolar mixtures on heterogeneous metal-organic frameworks: HKUST-1. (United States)

    Van Assche, Tom R C; Duerinck, Tim; Van der Perre, Stijn; Baron, Gino V; Denayer, Joeri F M


    Due to the combination of metal ions and organic linkers and the presence of different types of cages and channels, metal-organic frameworks often possess a large structural and chemical heterogeneity, complicating their adsorption behavior, especially for polar-apolar adsorbate mixtures. By allocating isotherms to individual subunits in the structure, the ideal adsorbed solution theory (IAST) can be adjusted to cope with this heterogeneity. The binary adsorption of methanol and n-hexane on HKUST-1 is analyzed using this segregated IAST (SIAST) approach and offers a significant improvement over the standard IAST model predictions. It identifies the various HKUST-1 cages to have a pronounced polar or apolar adsorptive behavior.

  3. Multi-Scale Coupling Between Monte Carlo Molecular Simulation and Darcy-Scale Flow in Porous Media

    KAUST Repository

    Saad, Ahmed Mohamed


    In this work, an efficient coupling between Monte Carlo (MC) molecular simulation and Darcy-scale flow in porous media is presented. The cell centered finite difference method with non-uniform rectangular mesh were used to discretize the simulation domain and solve the governing equations. To speed up the MC simulations, we implemented a recently developed scheme that quickly generates MC Markov chains out of pre-computed ones, based on the reweighting and reconstruction algorithm. This method astonishingly reduces the required computational times by MC simulations from hours to seconds. To demonstrate the strength of the proposed coupling in terms of computational time efficiency and numerical accuracy in fluid properties, various numerical experiments covering different compressible single-phase flow scenarios were conducted. The novelty in the introduced scheme is in allowing an efficient coupling of the molecular scale and the Darcy\\'s one in reservoir simulators. This leads to an accurate description of thermodynamic behavior of the simulated reservoir fluids; consequently enhancing the confidence in the flow predictions in porous media.

  4. Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media (United States)

    Zhang, Liyun; Li, Yuzhi; Yuan, Yuan; Jiang, Yuanyuan; Guo, Yanzhi; Li, Menglong; Pu, Xuemei


    In the work, we mainly used molecular dynamics (MD) simulation and protein structure network (PSN) to study subtilisin Carlsberg (SC) immobilized onto carbon nanotube (CNT) in water, acetonitrile and heptane solvents, in order to explore activation mechanism of enzymes in non-aqueous media. The result indicates that the affinity of SC with CNT follows the decreasing order of water > acetonitrile > heptane. The overall structure of SC and the catalytic triad display strong robustness to the change of environments, responsible for the activity retaining. However, the distances between two β-strands of substrate-binding pocket are significantly expanded by the immobilization in the increasing order of water < acetonitrile < heptane, contributing to the highest substrate-binding energy in heptane media. PSN analysis further reveals that the immobilization enhances structural communication paths to the substrate-binding pocket, leading to its larger change than the free-enzymes. Interestingly, the increase in the number of the pathways upon immobilization is not dependent on the absorbed extent but the desorbed one, indicating significant role of shifting process of experimental operations in influencing the functional region. In addition, some conserved and important hot-residues in the paths are identified, providing molecular information for functional modification.

  5. Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study | Office of Cancer Genomics (United States)

    Motivation: Molecular pathways and networks play a key role in basic and disease biology. An emerging notion is that networks encoding patterns of molecular interplay may themselves differ between contexts, such as cell type, tissue or disease (sub)type. However, while statistical testing of differences in mean expression levels has been extensively studied, testing of network differences remains challenging.

  6. Validation of GEANT4 simulations for percentage depth dose calculations in heterogeneous media by using small photon beams from the 6-MV Cyberknife: Comparison with photon beam dosimetry with EBT2 film (United States)

    Lee, Chung Il; Yoon, Sei-Chul; Shin, Jae Won; Hong, Seung-Woo; Suh, Tae Suk; Min, Kyung Joo; Lee, Sang Deok; Chung, Su Mi; Jung, Jae-Yong


    Percentage depth dose (PDD) distributions in heterogeneous phantoms with lung and soft bone equivalent media are studied by using the GEANT4 Monte Carlo code. For lung equivalent media, Balsa wood is used, and for soft bone equivalent media, a compound material with epoxy resin, hardener and calcium carbonate is used. Polystyrene slabs put together with these materials are used as a heterogeneous phantom. Dose measurements are performed with Gafchromic EBT2 film by using photon beams from the 6-MV CyberKnife at the Seoul Uridul Hospital. The cone sizes of the photon beams are varied from 5 to 10 to 30 mm. When the Balsa wood is inserted in the phantom, the dose measured with EBT2 film is found to be significantly different from the dose without the EBT2 film in and the dose beyond the Balsa wood region, particularly for small field sizes. On the other hand, when the soft bone equivalent material is inserted in the phantom, the discrepancy between the dose measured with EBT2 film and the dose without EBT2 film can be seen only in the region of the soft bone equivalent material. GEANT4 simulations are done with and without the EBT2 film to compare the simulation results with measurements. The GEANT4 simulations including EBT2 film are found to agree well with the measurements for all the cases within an error of 2.2%. The results of the present study show that GEANT4 gives reasonable results for the PDD calculations in heterogeneous media when using photon beams produced by the 6-MV CyberKnife

  7. Analysis and improvement of Brinkman lattice Boltzmann schemes: bulk, boundary, interface. Similarity and distinctness with finite elements in heterogeneous porous media. (United States)

    Ginzburg, Irina; Silva, Goncalo; Talon, Laurent


    This work focuses on the numerical solution of the Stokes-Brinkman equation for a voxel-type porous-media grid, resolved by one to eight spacings per permeability contrast of 1 to 10 orders in magnitude. It is first analytically demonstrated that the lattice Boltzmann method (LBM) and the linear-finite-element method (FEM) both suffer from the viscosity correction induced by the linear variation of the resistance with the velocity. This numerical artefact may lead to an apparent negative viscosity in low-permeable blocks, inducing spurious velocity oscillations. The two-relaxation-times (TRT) LBM may control this effect thanks to free-tunable two-rates combination Λ. Moreover, the Brinkman-force-based BF-TRT schemes may maintain the nondimensional Darcy group and produce viscosity-independent permeability provided that the spatial distribution of Λ is fixed independently of the kinematic viscosity. Such a property is lost not only in the BF-BGK scheme but also by "partial bounce-back" TRT gray models, as shown in this work. Further, we propose a consistent and improved IBF-TRT model which vanishes viscosity correction via simple specific adjusting of the viscous-mode relaxation rate to local permeability value. This prevents the model from velocity fluctuations and, in parallel, improves for effective permeability measurements, from porous channel to multidimensions. The framework of our exact analysis employs a symbolic approach developed for both LBM and FEM in single and stratified, unconfined, and bounded channels. It shows that even with similar bulk discretization, BF, IBF, and FEM may manifest quite different velocity profiles on the coarse grids due to their intrinsic contrasts in the setting of interface continuity and no-slip conditions. While FEM enforces them on the grid vertexes, the LBM prescribes them implicitly. We derive effective LBM continuity conditions and show that the heterogeneous viscosity correction impacts them, a property also shared

  8. The synthesis of 2-iminochromenes using mesoporous molecular sieve MCM-41 as a heterogeneous and recyclable catalyst

    Directory of Open Access Journals (Sweden)

    Majid M. Heravi


    Full Text Available A highly efficient procedure for the synthesis of 2-iminochromenes via condensation of o-hydroxybenzaldehydes and malononitrile using a catalytic amount of mesoporous molecular sieve MCM-41 in good yields is achieved.

  9. Molecular heterogeneity of Malassezia pachydermatis through RAPD-PCR - doi: 10.4025/actascibiolsci.v32i2.4788 Molecular heterogeneity of Malassezia pachydermatis through RAPD-PCR - doi: 10.4025/actascibiolsci.v32i2.4788

    Directory of Open Access Journals (Sweden)

    João Roberto Braga Mello


    Full Text Available Several methodologies in molecular biology have been used in the investigation of Malassezia pachydermatis and its differentiation into subtypes. Recent molecular research of this species includes the use of samples isolated from canine otitis externa and dermatitis, as well as from healthy animals, having in view an epidemiological study of the yeast. The aim of this study was to identify molecular differences in M. pachydermatis samples isolated from dogs with otitis externa. The M. pachydermatis strains were analyzed by means of the Random Amplification Primer DNA - Polimerase Chain Reaction (RAPD–PCR for molecular heterogeneity research. DNA extraction was carried out with phenol-chloroform and the RAPD technique using the AGAATCCGCC primer. A variation was observed in the number and arrangement of the bands among the 49 studied isolates, grouped into nine patterns. Isolate groupings were not found to be related to animal breed, age or sex. It was concluded that M. pachydermatis has differences in its molecular profile, as shown by the molecular technique (RAPD – PCR, which allows isolates to be classified into nine subtypes.Several methodologies in molecular biology have been used in the investigation of Malassezia pachydermatis and its differentiation into subtypes. Recent molecular research of this species includes the use of samples isolated from canine otitis externa and dermatitis, as well as from healthy animals, having in view an epidemiological study of the yeast. The aim of this study was to identify molecular differences in M. pachydermatis samples isolated from dogs with otitis externa. The M. pachydermatis strains were analyzed by means of the Random Amplification Primer DNA - Polimerase Chain Reaction (RAPD–PCR for molecular heterogeneity research. DNA extraction was carried out with phenol-chloroform and the RAPD technique using the AGAATCCGCC primer. A variation was observed in the number and arrangement of the bands

  10. Enhanced adsorption and regeneration with lignocellulose-based phosphorus removal media using molecular coating nanotechnology. (United States)

    Kim, Juyoung; Mann, Justin D; Kwon, Soonjo


    The removal of phosphorus in point and non-point-source pollution has become one of the leading problems in water quality since the beginning of the 21st century. Several natural, domestic, and industrial treatment systems already exist, but with very limited efficiencies and serious procedural defects. Lignocellulose-based Anion Removal Media (LAM) was developed in association with iron nanocoating technology as means of phosphorus adsorption from various concentrations of contaminated water. Results revealed that trivalent iron coated lignocellulose pellets can be used to effectively remove phosphorus contaminants from point and non-point-source polluted water. Removal capacities of pelletized cotton media surpass existing materials for phosphorus removal by at least 22 times, while remaining both efficient and cost effective. The materials were also investigated for regeneration, yielding high removal capacities even after the fifth regeneration. Treatment methodology and outlines are proposed, and procedural mechanisms are explored in this study. An economic evaluation of this technology is also assessed for a practical application of LAM to point/non-point-source polluted water.

  11. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.


    relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

  12. Temperature Dependence in Heterogeneous Nucleation with Application to the Direct Determination of Cluster Energy on Nearly Molecular Scale. (United States)

    McGraw, Robert L; Winkler, Paul M; Wagner, Paul E


    A re-examination of measurements of heterogeneous nucleation of water vapor on silver nanoparticles is presented here using a model-free framework that derives the energy of critical cluster formation directly from measurements of nucleation probability. Temperature dependence is correlated with cluster stabilization by the nanoparticle seed and previously found cases of unusual increasing nucleation onset saturation ratio with increasing temperature are explained. A necessary condition for the unusual positive temperature dependence is identified, namely that the critical cluster be more stable, on a per molecule basis, than the bulk liquid to exhibit the effect. Temperature dependence is next examined in the classical Fletcher model, modified here to make the energy of cluster formation explicit in the model.  The contact angle used in the Fletcher model is identified as the microscopic contact angle, which can be directly obtained from heterogeneous nucleation experimental data by a recently developed analysis method. Here an equivalent condition, increasing contact angle with temperature, is found necessary for occurrence of unusual temperature dependence. Our findings have immediate applications to atmospheric particle formation and nanoparticle detection in condensation particle counters (CPCs).

  13. A novel double-layer molecularly imprinted polymer film based surface plasmon resonance for determination of testosterone in aqueous media (United States)

    Tan, Yuan; Jing, Lijing; Ding, Yonghong; Wei, Tianxin


    This work aimed to prepare a novel double-layer structure molecularly imprinted polymer film (MIF) on the surface plasmon resonance (SPR) sensor chips for detection of testosterone in aqueous media. The film was synthesized by in-situ UV photo polymerization. Firstly, the modification of gold surface of SPR chip was performed by 1-dodecanethiol. Then double-layer MIF was generated on the 1-dodecanethiol modified gold surface. The non-modified and imprinted surfaces were characterized by atomic force microscopy (AFM), fourier transform infrared (FTIR) spectroscopy and contact angle measurements. Analysis of SPR spectroscopy showed that the imprinted sensing film displayed good selectivity for testosterone compared to other analogues and the non-imprinted polymer film (NIF). Within the concentrations range of 1 × 10-12-1 × 10-8 mol/L, the coupling angle changes of SPR were linear with the negative logarithm of testosterone concentrations (R2 = 0.993). Based on a signal/noise ratio of three, the detection limit was estimated to be 10-12 mol/L. Finally, the developed MIF was successfully applied to the seawater detection of testosterone. The results in the experiments suggested that a combination of SPR sensing with MIF was a promising alternative method for detection of testosterone in aqueous media.

  14. Hydrophilic Hollow Molecularly Imprinted Polymer Microparticles with Photo- and Thermoresponsive Template Binding and Release Properties in Aqueous Media. (United States)

    Li, Chenxi; Ma, Yue; Niu, Hui; Zhang, Huiqi


    A facile, general, and efficient approach to prepare hydrophilic hollow molecularly imprinted polymer (MIP) microparticles with photo- and thermoresponsive template binding and release behaviors in aqueous media is described, which includes the preparation of uniform "living" silica submicrospheres bearing surface atom transfer radical polymerization (ATRP)-initiating groups (i.e., alkyl halide groups) via a one-pot sol-gel method, their subsequent grafting of azobenzene (azo)-containing MIP shell and poly(N-isopropylacrylamide)-block-poly(2-hydroxyethyl methacrylate) (PNIPAAm-b-PHEMA) brushes via successive surface-initiated ATRP, and final removal of the silica core. The successful synthesis of such hydrophilic hollow MIP microparticles was confirmed with SEM, FT-IR, water dispersion stability, and static contact angle studies. They proved to show apparently higher template binding capacities than the corresponding solid ones and obvious photo- and thermoresponsive template binding properties in aqueous solutions. Moreover, their pronounced light- and temperature-controlled template release in aqueous media was also demonstrated. In particular, the introduction of PNIPAAm-b-PHEMA brushes onto hollow MIP microparticles imparted them with high surface hydrophilicity both below and above the lower critical solution temperature of PNIPAAm, which paves the way for their applications in such areas as controlled drug/chemical delivery and smart bioanalysis.

  15. Tumor Heterogeneity in Breast Cancer (United States)

    Turashvili, Gulisa; Brogi, Edi


    Breast cancer is a heterogeneous disease and differs greatly among different patients (intertumor heterogeneity) and even within each individual tumor (intratumor heterogeneity). Clinical and morphologic intertumor heterogeneity is reflected by staging systems and histopathologic classification of breast cancer. Heterogeneity in the expression of established prognostic and predictive biomarkers, hormone receptors, and human epidermal growth factor receptor 2 oncoprotein is the basis for targeted treatment. Molecular classifications are indicators of genetic tumor heterogeneity, which is probed with multigene assays and can lead to improved stratification into low- and high-risk groups for personalized therapy. Intratumor heterogeneity occurs at the morphologic, genomic, transcriptomic, and proteomic levels, creating diagnostic and therapeutic challenges. Understanding the molecular and cellular mechanisms of tumor heterogeneity that are relevant to the development of treatment resistance is a major area of research. Despite the improved knowledge of the complex genetic and phenotypic features underpinning tumor heterogeneity, there has been only limited advancement in diagnostic, prognostic, or predictive strategies for breast cancer. The current guidelines for reporting of biomarkers aim to maximize patient eligibility for targeted therapy, but do not take into account intratumor heterogeneity. The molecular classification of breast cancer is not implemented in routine clinical practice. Additional studies and in-depth analysis are required to understand the clinical significance of rapidly accumulating data. This review highlights inter- and intratumor heterogeneity of breast carcinoma with special emphasis on pathologic findings, and provides insights into the clinical significance of molecular and cellular mechanisms of heterogeneity. PMID:29276709

  16. Percentage depth dose calculation accuracy of model based algorithms in high energy photon small fields through heterogeneous media and comparison with plastic scintillator dosimetry. (United States)

    Alagar, Ananda Giri Babu; Mani, Ganesh Kadirampatti; Karunakaran, Kaviarasu


    Small fields smaller than 4 × 4 cm2 are used in stereotactic and conformal treatments where heterogeneity is normally present. Since dose calculation accuracy in both small fields and heterogeneity often involves more discrepancy, algorithms used by treatment planning systems (TPS) should be evaluated for achieving better treatment results. This report aims at evaluating accuracy of four model-based algorithms, X-ray Voxel Monte Carlo (XVMC) from Monaco, Superposition (SP) from CMS-Xio, AcurosXB (AXB) and analytical anisotropic algorithm (AAA) from Eclipse are tested against the measurement. Measurements are done using Exradin W1 plastic scintillator in Solid Water phantom with heterogeneities like air, lung, bone, and aluminum, irradiated with 6 and 15 MV photons of square field size ranging from 1 to 4 cm2. Each heterogeneity is introduced individually at two different depths from depth-of-dose maximum (Dmax), one setup being nearer and another farther from the Dmax. The central axis percentage depth-dose (CADD) curve for each setup is measured separately and compared with the TPS algorithm calculated for the same setup. The percentage normalized root mean squared deviation (%NRMSD) is calculated, which represents the whole CADD curve's deviation against the measured. It is found that for air and lung heterogeneity, for both 6 and 15 MV, all algorithms show maximum deviation for field size 1 × 1 cm2 and gradually reduce when field size increases, except for AAA. For aluminum and bone, all algorithms' deviations are less for 15 MV irrespective of setup. In all heterogeneity setups, 1 × 1 cm2 field showed maximum deviation, except in 6MV bone setup. All algorithms in the study, irrespective of energy and field size, when any heterogeneity is nearer to Dmax, the dose deviation is higher compared to the same heterogeneity far from the Dmax. Also, all algorithms show maximum deviation in lower-density materials compared to high-density materials.

  17. Molecular and stimulus-response profiles illustrate heterogeneity between peripheral and cord blood-derived human mast cells

    DEFF Research Database (Denmark)

    Jensen, Bettina M; Frandsen, Pernille; Raaby, Ellen Margrethe Nedergaard


    functionality. Mast cells were obtained from three culture protocols using two types of PBdMCs (CD34(+) PBdMC or CD133(+) PBdMC) and one type of CBdMC (CD133(+) CBdMC). We analyzed resting cells for specific mast cell markers at protein and mRNA levels, thereby creating a molecular profile. To characterize...... the SR profile, we stimulated cells with anti-IgE, C3a, C5a, Substance P, or Compound 48/80 and measured the release of histamine and cytokines (IL-10, IL-13, GM-CSF, TNF-α). Molecular profiling revealed that CD133(+) CBdMC expressed less chymase, FcεRIα, and CD203c but more CD117 compared with CD34...

  18. Heterogeneity of molecular resistance patterns in antimony-resistant field isolates of Leishmania species from the western Mediterranean area. (United States)

    Jeddi, Fakhri; Mary, Charles; Aoun, Karim; Harrat, Zoubir; Bouratbine, Aïda; Faraut, Françoise; Benikhlef, Rezika; Pomares, Christelle; Pratlong, Francine; Marty, Pierre; Piarroux, Renaud


    Antimonials remain the first-line treatment for the various manifestations of leishmaniasis in most areas where the disease is endemic, and increasing cases of therapeutic failure associated with parasite resistance have been reported. In this study, we assessed the molecular status of 47 clinical isolates of Leishmania causing visceral and cutaneous leishmaniasis from Algeria, Tunisia, and southern France. In total, we examined 14 genes that have been shown to exhibit significant variations in DNA amplification, mRNA levels, or protein expression with respect to resistance to antimonials. The gene status of each clinical isolate was assessed via qPCR and qRT-PCR. We then compared the molecular pattern against the phenotype determined via an in vitro sensitivity test of the clinical isolates against meglumine antimoniate, which is considered the reference technique. Our results demonstrate significant DNA amplification and/or RNA overexpression in 56% of the clinical isolates with the resistant phenotype. All clinical isolates that exhibited significant overexpression of at least 2 genes displayed a resistant phenotype. Among the 14 genes investigated, 10 genes displayed either significant amplification or overexpression in at least 1 clinical isolate; these genes are involved in several metabolic pathways. Moreover, various gene associations were observed depending on the clinical isolates, supporting the multifactorial nature of Leishmania resistance. Molecular resistance features were found in the 3 Leishmania species investigated (Leishmania infantum, Leishmania major, and Leishmania killicki). To our knowledge, this is the first report of the involvement of molecular resistance genes in field isolates of Leishmania major and Leishmania killicki with the resistance phenotype. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  19. Sea spray aerosol chemical composition: elemental and molecular mimics for laboratory studies of heterogeneous and multiphase reactions. (United States)

    Bertram, Timothy H; Cochran, Richard E; Grassian, Vicki H; Stone, Elizabeth A


    Sea spray aerosol particles (SSA), formed through wave breaking at the ocean surface, contribute to natural aerosol particle concentrations in remote regions of Earth's atmosphere, and alter the direct and indirect effects of aerosol particles on Earth's radiation budget. In addition, sea spray aerosol serves as suspended surface area that can catalyze trace gas reactions. It has been shown repeatedly that sea spray aerosol is heavily enriched in organic material compared to the surface ocean. The selective enrichment of organic material complicates the selection of representative molecular mimics of SSA for laboratory or computational studies. In this review, we first provide a short introduction to SSA formation processes and discuss chemical transformations of SSA that occur in polluted coastal regions and remote pristine air. We then focus on existing literature of the chemical composition of nascent SSA generated in controlled laboratory experiments and field investigations. We combine the evidence on the chemical properties of nascent SSA with literature measurements of SSA water uptake to assess SSA molecular composition and liquid water content. Efforts to speciate SSA organic material into molecular classes and specific molecules have led to the identification of saccharides, alkanes, free fatty acids, anionic surfactants, dicarboxylic acids, amino acids, proteinaceous matter, and other large macromolecules. However to date, less than 25% of the organic mass of nascent SSA has been quantified at a molecular level. As discussed here, quantitative measurements of size resolved elemental ratios, combined with determinations of water uptake properties, provides unique insight on the concentration of ions within SSA as a function of particle size, pointing to a controlling role for relative humidity and the hygroscopicity of SSA organic material at small particle diameters.

  20. Water oxidation catalysis upon evolution of molecular Co(III) cubanes in aqueous media. (United States)

    Genoni, Andrea; La Ganga, Giuseppina; Volpe, Andrea; Puntoriero, Fausto; Di Valentin, Marilena; Bonchio, Marcella; Natali, Mirco; Sartorel, Andrea


    The increasing global energy demand has stimulated great recent efforts in investigating new solutions for artificial photosynthesis, a potential source of clean and renewable solar fuel. In particular, according to the generally accepted modular approach aimed at optimising separately the different compartments of the entire process, many studies have focused on the development of catalytic systems for water oxidation to oxygen. While in recent years there have been many reports on new catalytic systems, the mechanism and the active intermediates operating the catalysis have been less investigated. Well-defined, molecular catalysts, constituted by transition metals stabilised by a suitable ligand pool, could help in solving this aspect. However, in some cases molecular species have been shown to evolve to active metal oxides that constitute the other side of this catalysis dichotomy. In this paper, we address the evolution of tetracobalt(III) cubanes, stabilised by a pyridine/acetate ligand pool, to active species that perform water oxidation to oxygen. Primary evolution of the cubane in aqueous solution is likely initiated by removal of an acetate bridge, opening the coordination sphere of the cobalt centres. This cobalt derivative, where the pristine ligands still impact on the reactivity, shows enhanced electron transfer rates to Ru(bpy)3(3+) (hole scavenging) within a photocatalytic cycle with Ru(bpy)3(2+) as the photosensitiser and S2O8(2-) as the electron sink. A more accentuated evolution occurs under continuous irradiation, where Electron Paramagnetic Resonance (EPR) spectroscopy reveals the formation of Co(ii) intermediates, likely contributing to the catalytic process that evolves oxygen. All together, these results confirm the relevant effect of molecular species, in particular in fostering the rate of the electron transfer processes involved in light activated cycles, pivotal in the design of a photoactive device.

  1. Heterogeneity of BRAF, NRAS, and TERT Promoter Mutational Status in Multiple Melanomas and Association with MC1R Genotype: Findings from Molecular and Immunohistochemical Analysis. (United States)

    Pellegrini, Cristina; Di Nardo, Lucia; Cipolloni, Gianluca; Martorelli, Claudia; De Padova, Marina; Antonini, Ambra; Maturo, Maria Giovanna; Del Regno, Laura; Strafella, Sara; Micantonio, Tamara; Leocata, Pietro; Peris, Ketty; Fargnoli, Maria Concetta


    Data on somatic heterogeneity and germline-somatic interaction in multiple primary melanoma (MPM) patients are limited. We investigated the mutational status of BRAF, NRAS, and TERT promoter genes in 97 melanomas of 44 MPM patients and compared molecular and immunohistochemical findings. We further evaluated the association of somatic alterations with the germline MC1R genotype. Mutations in BRAF gene were identified in 41.2% (40/97) of melanomas, in NRAS in 2.1% (2/97), and in TERT promoter in 19.6% (19/97). Distribution of BRAF mutations did not differ across multiple melanomas (P = 0.85), whereas TERT promoter changes decreased from first to subsequent melanomas (P = 0.04). Intrapatient discrepancy of BRAF mutations among multiple tumors was detected in 14 of 44 MPM patients (32%) and of BRAF/NRAS/TERT promoter genes in 20 of 44 (45%). We observed a high rate of agreement between allele-specific TaqMan assay and immunohistochemistry in BRAFV600E detection (κ = 0.83, P MC1R variants were identified in 81.4% (35/43) of MPM patients with no association of MC1R genotype with somatic mutations or with intrapatient concordance of somatic mutational profile. Our results support the genetic diversity of multiple melanomas and show that somatic heterogeneity is not influenced by inherited MC1R variants. Immunohistochemistry may be useful as an initial screening test. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  2. Molecular genetics of cystinuria: Identification of four new mutations and seven polymorphisms, and evidence for genetic heterogeneity

    Energy Technology Data Exchange (ETDEWEB)

    Gasparini, P.; Bisceglia, L.; Notarangelo, A. [Servizio di Genetica Medica, San Giovanni Rotondo (Italy)] [and others


    A cystinuria disease gene (rBAT) has been recently identified, and some mutations causing the disease have been described. The frequency of these mutations has been investigated in a large sample of 51 Italian and Spanish cystinuric patients. In addition, to identify new mutated alleles, genomic DNA has been analyzed by an accurate and sensitive method able to detect nucleotide changes. Because of the lack of information available on the genomic structure of rBAT gene, the study was carried out using the sequence data so far obtained by us. More than 70% of the entire coding sequence and 8 intron-exon boundaries have been analyzed. Four new mutations and seven intragenic polymorphisms have been detected. All mutations so far identified in rBAT belong only to cystinuria type I alleles, accounting for {approximately} 44% of all type I cystinuric chromosomes. Mutation M467T is the most common mutated allele in the Italian and Spanish populations. After analysis of 70% of the rBAT coding region, we have detected normal sequences in cystinuria type II and type III chromosomes. The presence of rBAT mutated alleles only in type I chromosomes of homozygous (type I/I) and heterozygous (type I/III) patients provides evidence for genetic heterogeneity where rBAT would be responsible only for type I cystinuria and suggests a complementation mechanism to explain the intermediate type I/type III phenotype. 25 refs., 1 fig., 3 tabs.

  3. Contribution of auxiliary information for the estimation of grades in heterogeneous media: example in soil pollution; Apport d'informations qualitatives pour l'estimation des teneurs en milieux heterogenes: cas d'une pollution de sols par des hydrocarbures aromatique polycycliques (HAP)

    Energy Technology Data Exchange (ETDEWEB)

    Jeannee, N.; Fouquet, Ch. de [Ecole des Mines de Paris, Centre de Geostatistique, 77 - Fontainebleau (France); Jeannee, N. [Centre National de Recherche sur les Sites et Sols Pollues - CNRSSP, 59 - Douai (France)


    Grade estimates are often of weak precision in the case of heterogeneous media, due to their high variability, even at small scale. Qualitative information is then useful to improve the quality of the estimates, without prohibitive additional costs. How can we sample such variables, and detect the ones that are of interest for the estimation of grades? The general methodology is presented and then illustrated for the estimation of the benzo(a)pyrene (a polycyclic aromatic hydrocarbon, PAH) concentration in soils, sampled on a former coking plant. (authors)

  4. Wave propagation simulation in the upper core of sodium-cooled fast reactors using a spectral-element method for heterogeneous media (United States)

    Nagaso, Masaru; Komatitsch, Dimitri; Moysan, Joseph; Lhuillier, Christian


    ASTRID project, French sodium cooled nuclear reactor of 4th generation, is under development at the moment by Alternative Energies and Atomic Energy Commission (CEA). In this project, development of monitoring techniques for a nuclear reactor during operation are identified as a measure issue for enlarging the plant safety. Use of ultrasonic measurement techniques (e.g. thermometry, visualization of internal objects) are regarded as powerful inspection tools of sodium cooled fast reactors (SFR) including ASTRID due to opacity of liquid sodium. In side of a sodium cooling circuit, heterogeneity of medium occurs because of complex flow state especially in its operation and then the effects of this heterogeneity on an acoustic propagation is not negligible. Thus, it is necessary to carry out verification experiments for developments of component technologies, while such kind of experiments using liquid sodium may be relatively large-scale experiments. This is why numerical simulation methods are essential for preceding real experiments or filling up the limited number of experimental results. Though various numerical methods have been applied for a wave propagation in liquid sodium, we still do not have a method for verifying on three-dimensional heterogeneity. Moreover, in side of a reactor core being a complex acousto-elastic coupled region, it has also been difficult to simulate such problems with conventional methods. The objective of this study is to solve these 2 points by applying three-dimensional spectral element method. In this paper, our initial results on three-dimensional simulation study on heterogeneous medium (the first point) are shown. For heterogeneity of liquid sodium to be considered, four-dimensional temperature field (three spatial and one temporal dimension) calculated by computational fluid dynamics (CFD) with Large-Eddy Simulation was applied instead of using conventional method (i.e. Gaussian Random field). This three-dimensional numerical

  5. A novel double-layer molecularly imprinted polymer film based surface plasmon resonance for determination of testosterone in aqueous media

    Energy Technology Data Exchange (ETDEWEB)

    Tan, Yuan; Jing, Lijing; Ding, Yonghong; Wei, Tianxin, E-mail:


    Highlights: • The in-situ photo-grafting polymerization method was used to prepare the polymer film. • The synthesized MIF was layer stucture film. • The MIF exhibited good imprinting effect and highly selectivity. - Abstract: This work aimed to prepare a novel double-layer structure molecularly imprinted polymer film (MIF) on the surface plasmon resonance (SPR) sensor chips for detection of testosterone in aqueous media. The film was synthesized by in-situ UV photo polymerization. Firstly, the modification of gold surface of SPR chip was performed by 1-dodecanethiol. Then double-layer MIF was generated on the 1-dodecanethiol modified gold surface. The non-modified and imprinted surfaces were characterized by atomic force microscopy (AFM), fourier transform infrared (FTIR) spectroscopy and contact angle measurements. Analysis of SPR spectroscopy showed that the imprinted sensing film displayed good selectivity for testosterone compared to other analogues and the non-imprinted polymer film (NIF). Within the concentrations range of 1 × 10{sup −12}–1 × 10{sup −8} mol/L, the coupling angle changes of SPR were linear with the negative logarithm of testosterone concentrations (R{sup 2} = 0.993). Based on a signal/noise ratio of three, the detection limit was estimated to be 10{sup −12} mol/L. Finally, the developed MIF was successfully applied to the seawater detection of testosterone. The results in the experiments suggested that a combination of SPR sensing with MIF was a promising alternative method for detection of testosterone in aqueous media.

  6. [Tumor genetic heterogeneity]. (United States)

    Yang, Yi-Ling; Chu, Jia-You; Wang, Ming-Rong


    Although the majority of spontaneous tumors derive from a single cell, people have come to realize intra-tumor heterogeneity of individual tumors. Human cancers frequently display substantial difference in phenotypic features, such as the degree of differentiation, cell proliferation rate, invasion and metastatic potential, response to therapy and many other aspects. Molecular biology studies have confirmed the occurrence of new mutations during the process of tumor progression, which provide more powerful evidences to show the existence of intra-tumor genetic heterogeneity. This re-view will focus on recent major advances in the study of tumor genetic heterogeneity. Considering that genetic heterogene-ity analysis can provide important information to indicate how long normal cells transform into tumor cells and how to spread and migrate, we firstly describe experimental evidences of intra-tumor genetic heterogeneity. Then we discuss the research value of genetic diversity in the evolutionary history of human individual tumor, introduce the two modes of the genetic heterogeneity - cancer stem cell model and the clonal evolution model, and summarize the implications of in-tra-tumor heterogeneity studies in metastasis and therapy. In addition, the article presents the research methods of genetic heterogeneity, including specific gene and genome-wide level, pointing out their strengths and limitations.

  7. Systematic molecular genetic analysis of congenital sideroblastic anemia: evidence for genetic heterogeneity and identification of novel mutations. (United States)

    Bergmann, Anke K; Campagna, Dean R; McLoughlin, Erin M; Agarwal, Suneet; Fleming, Mark D; Bottomley, Sylvia S; Neufeld, Ellis J


    Sideroblastic anemias are heterogeneous congenital and acquired bone marrow disorders characterized by pathologic iron deposits in mitochondria of erythroid precursors. Among the congenital sideroblastic anemias (CSAs), the most common form is X-linked sideroblastic anemia, due to mutations in 5-aminolevulinate synthase (ALAS2). A novel autosomal recessive CSA, caused by mutations in the erythroid specific mitochondrial transporter SLC25A38, was recently defined. Other known etiologies include mutations in genes encoding the thiamine transporter SLC19A2, the RNA-modifying enzyme pseudouridine synthase 1 (PUS1), a mitochondrial ATP-binding cassette transporter (ABCB7), glutaredoxin 5 (GLRX5), as well as mitochondrial DNA deletions. Despite these known diverse causes, in a substantial portion of CSA cases a presumed genetic defect remains unknown. In the context of the recent discovery of SLC25A38 as a major novel cause, we systematically analyzed a large cohort of previously unreported CSA patients. Sixty CSA probands (28 females, 32 males) were examined for ALAS2, SLC25A38, PUS1, GLRX5, and ABCB7 mutations. SLC19A2 and mitochondrial DNA were only analyzed if characteristic syndromic features were apparent. Twelve probands had biallelic mutations in SLC25A38. Seven ALAS2 mutations were detected in eight sporadic CSA cases, two being novel. We also identified a novel homozygous null PUS1 mutation and novel mitochondrial DNA deletions in two patients with Pearson syndrome. No mutations were encountered in GLRX5, ABCB7, or SLC19A2. The remaining undefined probands (43%) can be grouped according to gender, family, and clinical characteristics, suggesting novel X-linked and autosomal recessive forms of CSA. (c) 2009 Wiley-Liss, Inc.

  8. Systematic Molecular Genetic Analysis of Congenital Sideroblastic Anemia: Evidence for Genetic Heterogeneity and Identification of Novel Mutations (United States)

    Bergmann, Anke K.; Campagna, Dean R.; McLoughlin, Erin M.; Agarwal, Suneet; Fleming, Mark D.; Bottomley, Sylvia S.; Neufeld, Ellis J.


    Background Sideroblastic anemias are heterogeneous congenital and acquired bone marrow disorders characterized by pathologic iron deposits in mitochondria of erythroid precursors. Among the congenital sideroblastic anemias (CSAs), the most common form is X-linked sideroblastic anemia, due to mutations in 5-aminolevulinate synthase (ALAS2). A novel autosomal recessive CSA, caused by mutations in the erythroid specific mitochondrial transporter SLC25A38, was recently defined. Other known etiologies include mutations in genes encoding the thiamine transporter (SLC19A2), the RNA-modifying enzyme pseudouridine synthase 1 (PUS1), a mitochondrial ATP-binding cassette transporter (ABCB7), glutaredoxin 5 (GLRX5), as well as mitochondrial DNA deletions. Despite these known diverse causes, in a substantial portion of CSA cases a presumed genetic defect remains unknown. Procedure In the context of the recent discovery of SLC25A38 as a major novel cause, we systematically analyzed a large cohort of previously unreported CSA patients. Sixty CSA probands (28 females, 32 males) were examined for ALAS2, SLC25A38, PUS1, GLRX5, and ABCB7 mutations. SLC19A2 and mitochondrial DNA were only analyzed if characteristic syndromic features were apparent. Results Twelve probands had biallelic mutations in SLC25A38. Seven ALAS2 mutations were detected in eight sporadic CSA cases, two being novel. We also identified a novel homozygous null PUS1 mutation and novel mitochondrial DNA deletions in two patients with Pearson syndrome. No mutationswere encountered in GLRX5, ABCB7, or SLC19A2. Conclusions The remaining undefined probands (43%) can be grouped according to gender, family and clinical characteristics, suggesting novel X-linked and autosomal recessive forms of CSA. PMID:19731322

  9. Proteomic profiling of human retinal and choroidal endothelial cells reveals molecular heterogeneity related to tissue of origin. (United States)

    Zamora, David O; Riviere, Michael; Choi, Dongseok; Pan, Yuzhen; Planck, Stephen R; Rosenbaum, James T; David, Larry L; Smith, Justine R


    The ocular vascular endothelium plays a key role in the development of several leading retinal causes of blindness in Western nations. Choroidal endothelial cells are integral to the subretinal neovascular lesions that characterize the exudative form of late age-related macular degeneration (AMD), and retinal endothelial cells participate in the initiation of diabetic retinopathy and posterior uveitis. Vascular endothelial cells at different sites exhibit considerable molecular diversity. This diversity has implications for understanding the pathogenesis of tissue-specific diseases and for the development of targeted therapies to treat these conditions. Previous work from our group has identified significant differences in the gene transcript profiles of human retinal and choroidal endothelial cells. Because the proteome ultimately determines the behavior of any given cell, however, it is critical to determine whether molecular differences exist at the level of protein expression. Retinal and choroidal endothelial cells were separately isolated from five sets of human eyes by enzymatic digestion with type II collagenase followed by anti-CD31 antibody-conjugated magnetic bead separation. Cells were washed to remove serum peptides in the culture medium, and lysed by sonication in buffer containing 2% sodium dodecyl sulfate. Protein was then precipitated with acetone. Retinal and choroidal endothelial samples from each donor were labeled with Cy3 and Cy5, respectively, mixed with a Cy2-labeled pooled protein sample to facilitate spot matching across gels, and separated by two-dimensional difference gel electrophoresis (2D-DIGE). Following a global normalization, differentially abundant protein spots that were visible in at least four of five donor gels were detected by the significance analysis of microarrays method, with false discovery rate set at 5%. Corresponding spots were excised from additional DIGE-labeled or Coomassie-stained 2D electrophoretic gels. Protein

  10. Hydromagnetic waves in weakly-ionized media - I. Basic theory, and application to interstellar molecular clouds (United States)

    Mouschovias, Telemachos Ch.; Ciolek, Glenn E.; Morton, Scott A.


    We present a comprehensive study of magnetohydrodynamic (MHD) waves and instabilities in a weakly-ionized system, such as an interstellar molecular cloud. We determine all the critical wavelengths of perturbations across which the sustainable wave modes can change radically (and so can their decay rates), and various instabilities are present or absent. Hence, these critical wavelengths are essential for understanding the effects of MHD waves (or turbulence) on the structure and evolution of molecular clouds. Depending on the angle of propagation relative to the zeroth-order magnetic field and the physical parameters of a model cloud, there are wavelength ranges in which no wave can be sustained as such. Yet, for other directions of propagation or different properties of a model cloud, there may always exist some wave mode(s) at all wavelengths (smaller than the size of the model cloud). For a typical model cloud, magnetically-driven ambipolar diffusion leads to removal of any support against gravity that most short-wavelength waves (or turbulence) may have had, and gravitationally-driven ambipolar diffusion sets in and leads to cloud fragmentation into stellar-size masses, as first suggested by Mouschovias more than three decades ago - a single-stage fragmentation theory of star formation, distinct from the then prevailing hierarchical fragmentation picture. The phase velocities, decay times and eigenvectors (e.g. the densities and velocities of neutral particles and the plasma, and the three components of the magnetic field) are determined as functions of the wavelength of the disturbances in a mathematically transparent way and are explained physically. Comparison of the results with those of nonlinear analytical or numerical calculations is also presented where appropriate, excellent agreement is found, and confidence in the analytical, linear approach is gained to explore phenomena difficult to study through numerical simulations. Mode splitting (or

  11. Polyionic polymers – heterogeneous media for metal nanoparticles as catalyst in Suzuki–Miyaura and Heck–Mizoroki reactions under flow conditions

    Directory of Open Access Journals (Sweden)

    Klaas Mennecke


    Full Text Available The preparation of monolithic polyionic supports which serve as efficient heterogeneous supports for palladium(0 nanoparticles is described. These functionalized polymers were incorporated inside a flow reactor and employed in Suzuki–Miyaura and Heck cross couplings under continuous flow conditions.

  12. The Migration and Entrapment of DNAPLs in Physically and Chemically Heterogeneous Porous Media - Final Report - 09/15/1996 - 09/15/2000

    Energy Technology Data Exchange (ETDEWEB)

    Abriola, L. M.; Demond, A. H.


    Hazardous dense nonaqueous phase liquids (DNAPLs), such as chlorinated solvents, are slightly water soluble and pose a serious threat to soil and groundwater supplies in many portions of the United States. The migration and entrapment of DNAPLs in the subsurface environment is typically believed to be controlled by physical heterogeneities; i.e, layers and lenses of contrasting soil texture. The rationale for this assumption is that capillarity, as determined by the soil texture, is the dominant transport mechanism. Capillarity also depends on interfacial tension and medium wettability. Interfacial tension and medium wettability may be spatially and temporally dependent due to variations in aqueous phase chemistry, contaminant aging, and/or variations in mineralogy and organic matter distributions. Such chemical heterogeneities have largely been ignored to date, even though they are known to have dramatic effects on the hydraulic property relations. Numerical multiphase flow and transport models typically assume that solids are water-wet and that interfacial tension is constant. The primary objective of this research is to investigate the influence of coupled physical and chemical heterogeneities on the migration and entrapment of DNAPLs. This objective will be accomplished through a combination of laboratory and numerical experiments. Laboratory experiments will be conducted to examine: (i) aqueous phase chemistry effects on medium wettability and interfacial tension; and (ii) relative permeability-saturation-capillary pressure relations for chemically heterogeneous systems. An important objective of this research is to modify a two-dimensional multiphase flow and transport model to account for chemically and physically heterogeneous systems. This numerical simulator will be used in conjunction with independently measured parameters to simulate two-dimensional DNAPL infiltration experiments. Comparisons of simulated and laboratory data will provide a means to

  13. Enhanced anion electroadsorption into carbon molecular sieve electrodes in acidic media. (United States)

    Eliad, Linoam; Salitra, Gregory; Pollak, Elad; Soffer, Abraham; Aurbach, Doron


    We previously showed that, for neutral electrolytes of small cations and relatively larger anions, it is possible to design certain pore sizes in active carbons that are large enough to electroadsorb cations but too small to allow anion electroadsorption. This situation leads to an electrical double-layer (EDL) capacitance that is significant only at potentials that are negative to the potential of zero charge (PZC); hence, much smaller capacitance is measured at potentials positive to the PZC. It was found that when the electrolyte is a strong acid (e.g., H(2)SO(4), HCl), a considerable capacitance is observed at positive potentials, even when the average pore size is too small to allow the insertion of large anions in neutral electrolyte solutions. This effect disappears when the pore size becomes considerably larger than the size of the ions. In this case, the EDL capacitance at positive potentials for both neutral and acidic solutions is comparable. The following four-step mechanism was found to comply best with the experimental data: (1) By acid catalysis, the protons form carbonium species within the conjugated carbon network. (2) The anions react with the carbonium ions, providing uncharged species in an activated state, which are chemibound as surface groups to the walls of the pores. (3) Because these surface groups are effectively much smaller in size than are the charged ions, they can migrate by chemical bond exchange within the carbon skeleton via constrictions (known to exist in microporous and molecular sieving carbons), which are too narrow to accommodate hydrated charged species. (4) Upon reaching wider spaces, the uncharged species are reionized and solvated by water molecules, which can fill small pores. The justification for the above mechanism is thoroughly discussed and demonstrated by the experimental results.

  14. Energy transfer at heterogeneous protein-protein interfaces to investigate the molecular behaviour in the crowding environment. (United States)

    Ota, Chikashi


    Investigation of the behaviour of proteins in crowded environments is crucial for understanding the role of proteins in biological environments. In this study, the behaviour of bovine serum albumin (BSA) in crowded (highly concentrated) environments was investigated using time-resolved fluorescence spectroscopy as a model system. By using energy transfer as a molecular ruler, the crowding effect was clearly observed in the time resolved spectra. In addition, by using both time resolved anisotropy measurement and Raman spectroscopy, more detail insights from conformational and dynamic points of view were described. Consequently, it was revealed that in the highly concentrated solution, most of the BSA molecules are in the fast-reversible oligomeric state and the association at the "hard" and "soft" interfaces between protein surfaces occurred in a highly crowded environment with the aid of a charge-charge and short-range attractive interface. From both the conformational and dynamic aspects, the detail spectroscopic understanding of the behaviour of BSA in the crowding environment was obtained. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Investigating the composition of organic aerosol resulting from cyclohexene ozonolysis: low molecular weight and heterogeneous reaction products

    Directory of Open Access Journals (Sweden)

    J. F. Hamilton


    Full Text Available The composition of organic aerosol formed from the gas phase ozonolysis of cyclohexene has been investigated in a smog chamber experiment. Comprehensive gas chromatography with time of flight mass spectrometric detection was used to determine that dicarboxylic acids and corresponding cyclic anhydrides dominated the small gas phase reaction products found in aerosol sampled during the first hour after initial aerosol formation. Structural analysis of larger more polar molecules was performed using liquid chromatography with ion trap tandem mass spectrometry. This indicated that the majority of identified organic mass was in dimer form, built up from combinations of the most abundant small acid molecules, with frequent indication of the inclusion of adipic acid. Trimers and tetramers potentially formed via similar acid combinations were also observed in lower abundances. Tandem mass spectral data indicated dimers with either acid anhydride or ester functionalities as the linkage between monomers. High-resolution mass spectrometry identified the molecular formulae of the most abundant dimer species to be C10H16O6, C11H18O6, C10H14O8 and C11H16O8 and could be used in some cases to reduce uncertainty in exact chemical structure determination by tandem MS.

  16. Osteogenesis imperfecta type I: Molecular heterogeneity for COL1A1 null alleles of type I collagen

    Energy Technology Data Exchange (ETDEWEB)

    Willing, M.C.; Deschenes, S.P.; Pitts, S.H.; Arikat, H.; Roberts, E.J.; Scott, D.A.; Slayton, R.L. [Univ. of Iowa, Iowa City, IA (United States); Byers, P.H. [Univ. of Washington, Seattle, WA (United States)


    Osteogenesis imperfecta (OI) type I is the mildest form of inherited brittle-bone disease. Dermal fibroblasts from most affected individuals produce about half the usual amount of type I procollagen, as a result of a COL1A1 {open_quotes}null{close_quotes} allele. Using PCR amplification of genomic DNA from affected individuals, followed by denaturing gradient gel electrophoresis (DGGE) and SSCP, we identified seven different COL1A1 gene mutations in eight unrelated families with OI type I. Three families have single nucleotide substitutions that alter 5{prime} donor splice sites; two of these unrelated families have the same mutation. One family has a point mutation, in an exon, that creates a premature termination codon, and four have small deletions or insertions, within exons, that create translational frameshifts and new termination codons downstream of the mutation sites. Each mutation leads to both marked reduction in steady-state levels of mRNA from the mutant allele and a quantitative decrease in type I procollagen production. Our data demonstrate that different molecular mechanisms that have the same effect on type I collagen production result in the same clinical phenotype. 58 refs., 4 figs., 1 tab.

  17. A purification method for a molecular complex in which a scaffold molecule is fully loaded with heterogeneous molecules.

    Directory of Open Access Journals (Sweden)

    Shoji J Ohuchi

    Full Text Available An affinity resin-based pull-down method is convenient for the purification of biochemical materials. However, its use is difficult for the isolation of a molecular complex fully loaded with multiple components from a reaction mixture containing the starting materials and intermediate products. To overcome this problem, we have developed a new purification procedure that depends on sequential elimination of the residues. In practice, two affinity resins were used for purifying a triangular-shaped RNP (RNA-protein complex consisting of three ribosomal proteins (L7Ae bound to an RNA scaffold. First, a resin with immobilized L7Ae protein captured the incomplete RNP complexes and the free RNA scaffold. Next, another resin with an immobilized chemically modified RNA of a derivative of Box C/D motif, the binding partner of L7Ae, was used to capture free protein. The complete triangular RNP was successfully purified from the mixture by these two steps. Obviously, the purified triangular RNP displaying three protein-binding peptides exhibited an improved performance when compared with the unrefined product. Conceptually, this purification procedure should be applicable for the purification of a variety of complexes consisting of multiple components other than RNP.

  18. Structure of solvates of o-hydroxybenzoic acid in supercritical CO2-cosolvent media, according to molecular dynamics data (United States)

    Petrenko, V. E.; Antipova, M. L.; Gurina, D. L.


    Three-component supercritical carbon dioxide-cosolvent (methanol, ethanol, water)- o-hydroxybenzoic acid ( o-HBA) mixtures at a density of 0.7 g/cm3 and temperatures of 318 and 348 K are simulated by means of molecular dynamics. The solvate structures are investigated. It is shown that the solvation mechanism of o-HBA (particularly the o-HBA molecule forming a stable solvate complex with one molecule of a cosolvent via a hydrogen bond through the carboxyl group) does not depend on the temperature or the cosolvent. It is noted that the form of the cosolvent in a supercritical fluid varies: alcohols are distributed in the bulk in the form of monomers and hydrogen-bonded dimers, and water molecules tend to form microclusters along with chained and spatially branched structures by means of hydrogen bonds. It is established that the local molar fraction of cosolvent around the solvate complexes grows. It is concluded that the solvation of o-HBA is determined by the behavior of cosolvent in media of supercritical CO2.

  19. Molecular imaging as a tool to investigate heterogeneity of advanced HER2-positive breast cancer and to predict patient outcome under trastuzumab emtansine (T-DM1) : the ZEPHIR trial

    NARCIS (Netherlands)

    Gebhart, G.; Lamberts, L. E.; Wimana, Z.; Garcia, C.; Emonts, P.; Ameye, L.; Stroobants, S.; Huizing, M.; Aftimos, P.; Tol, J.; Oyen, W. J. G.; Vugts, D. J.; Hoekstra, O. S.; Schroder, C. P.; van Oordt, C. W. Menke-van der Houven; Guiot, T.; Brouwers, A. H.; Awada, A.; de Vries, E. G. E.; Flamen, P.

    Molecular imaging of metastatic human epidermal growth factor receptor 2 (HER2)-positive breast cancer reveals marked intra- and interpatient heterogeneity in HER2 mapping, which correlates with clinical outcome under T-DM1 therapy.Only human epidermal growth factor receptor (HER)2 status determined

  20. Congenital abnormalities of cranial nerve development: overview, molecular mechanisms, and further evidence of heterogeneity and complexity of syndromes with congenital limitation of eye movements. (United States)

    Traboulsi, Elias I


    The clinical and molecular genetic classification of syndromes with congenital limitation of eye movements and evidence of cranial nerve dysgenesis continues to evolve. This monograph details clinical and molecular genetic data on a number of families and isolated patients with congenital fibrosis of the extraocular muscles (CFEOM) and related disorders, and presents an overview of the mechanisms of abnormal patterns of motor and sensory cranial nerve development in these rare syndromes. Clinical examination of one patient with CFEOM1, one family with clinical features of CFEOM2, one family with recessive CFEOM3, one family with horizontal gaze palsy and progressive scoliosis (HGPPS), and four patients with various combinations of congenital cranial nerve abnormalities. Genotyping of families with CFEOM and HGPPS for polymorphic markers in the regions of the three known CFEOM loci and in the HGPPS region, and mutation analysis of the ARIX and KIF21A genes in patients with CFEOM were performed according to standard published protocols. The patient with CFEOM1 had the second most common mutation in KIF21A, a 2861 G>A mutation that resulted in an R954Q substitution. The family with CFEOM2 phenotype did not map to the CFEOM2 locus. The family with recessive CFEOM3 did not map to any of the known loci. The HGPPS family mapped to 11q23-q25. One patient had optic nerve hypoplasia and fifth nerve dysfunction. Two patients had the rare combination of Möbius syndrome and CFEOM. One patient had Möbius syndrome and fifth nerve dysfunction. There is genetic heterogeneity in CFEOM2 and CFEOM3. Abnormalities in sensory nerves can also accompany abnormalities of motor nerves, further substantiating the effect of individual mutations on developing motor as well as sensory cranial nerve nuclei.

  1. Micromechanics of heterogeneous materials

    CERN Document Server

    Buryachenko, Valeriy


    Here is an accurate and timely account of micromechanics, which spans materials science, mechanical engineering, applied mathematics, technical physics, geophysics, and biology. The book features rigorous and unified theoretical methods of applied mathematics and statistical physics in the material science of microheterogeneous media. Uniquely, it offers a useful demonstration of the systematic and fundamental research of the microstructure of the wide class of heterogeneous materials of natural and synthetic nature.

  2. Ceria-Based Mixed Oxide Supported Nano-Gold as an Efficient and Durable Heterogeneous Catalyst for Oxidative Dehydrogenation of Amines to Imines Using Molecular Oxygen

    Directory of Open Access Journals (Sweden)

    Bashir Ahmad Dar


    Full Text Available The present work is intended to determine the catalytic activity of Mixed Oxide supported gold for aerobic oxidative dehydrogenation of amines to imines using Ceria as a main constituent of the each support. The model catalysts Au/CeO2:TiO2 Au/CeO2:SiO2, Au/CeO2:ZrO2 and Au/CeO2:Al2Os were prepared by deposition co-precipitation method and deposition of gold was determined by EDEX analysis. The supported nano-gold catalyzes the dehydrogenation of secondary amines to imines without loss of activity. On recycling good amount of product yield is obtained. Oxidation of secondary amines to imines is carried at 100˚C and almost 90 % conversion was obtained with >99% selectivity. © 2012 BCREC UNDIP. All rights reservedReceived: 26th December 2011; Revised: 7th June 2012; Accepted: 13rd June 2012[How to Cite: B.A. Dar, M. Sharma, B. Singh. (2012. Ceria-Based Mixed Oxide Supported Nano-Gold as an Efficient and Durable Heterogeneous Catalyst for Oxidative Dehydrogenation of Amines to Imines Using Molecular Oxygen. Bulletin of Chemical Reaction Engineering & Catalysis, 7(1: 79-84.  doi:10.9767/bcrec.7.1.1257.79-84][How to Link / DOI: ] | View in 

  3. Molecular characteristics and virulence factors in methicillin-susceptible, resistant, and heterogeneous vancomycin-intermediate Staphylococcus aureus from central-southern China. (United States)

    Liu, Cailin; Chen, Zhong-ju; Sun, Ziyong; Feng, Xianju; Zou, Mingxiang; Cao, Wei; Wang, Shanmei; Zeng, Ji; Wang, Yue; Sun, Mingyue


    Staphylococcus aureus is a leading cause of nosocomial infections. The purpose of this study was to evaluate the prevalence of methicillin-resistant S. aureus (MRSA) and heterogeneous vancomycin-intermediate S. aureus (hVISA), and compare the antimicrobial susceptibility, molecular characteristic, and virulence factors in methicillin-susceptible S. aureus (MSSA), MRSA, and hVISA from central-southern China. A total of 184 S. aureus were isolated from sterile body fluids. All isolates were subjected to population analysis profiling for the identification of hVISA phenotype and polymerase chain reaction analysis for genotyping and 31 virulence genes. The prevalence of MRSA isolates was 41.8% in central-southern China. Of 77 MRSA isolates, 17 (22.1%) were identified as hVISA. The most common MRSA and MSSA clones were ST239-MRSA-SCCmecIII-t030-agr-I (55.8%) and ST188-MSSA-t189-agr-I (20.6%), respectively. The frequency of carriage of pvl, hemolysins, tst, and staphylococcal enterotoxin genes among MSSA isolates was significantly higher than that for MRSA isolates (p aureus isolates; the virulence genes were more diverse and frequent among MSSA isolates than among MRSA isolates. Furthermore, the distribution of some virulence genes was correlated with the different S. aureus CCs. Copyright © 2014. Published by Elsevier B.V.

  4. Effect of lipase immobilization on resolution of (R, S)-2-octanol in nonaqueous media using modified ultrastable-Y molecular sieve as support. (United States)

    Dai, Dazhang; Xia, Liming


    The lipase from Penicillium expansum PED-03 (PEL) was immobilized onto modified ultrastable-Y (USY) molecular sieve and the resolution of (R, S)- 2-octanol was carried out in a bioreactor in nonaqueous media by the immobilized lipase. It was found that the conversion rate, enantiomeric excess (ee) value, and enantioselectivity (E) value of the resolution catalyzed by PEL immobilized on modified USY molecular sieve were much higher than those of the reaction catalyzed by free PEL and PEL immobilized on other supports. Immobilized on modified USY molecular sieve, the PEL exhibited obvious activity within a wider pH range and at a much higher temperature and showed a markedly enhanced stability against thermal inactivation, by which the suitable pH of the buffer used for immobilization could be "memorized." The conversion rate of the reaction catalyzed by PEL immobilized on modified USY molecular sieve reached 48.84%, with excellent enantioselectivity (average E value of eight batches >460) in nonaqueous media at "memorial" pH 9.5, 50 degrees C for 24 h, demonstrating a good application potential in the production of optically pure (R, S)-2-octanol.

  5. Recapitulation of tumor heterogeneity and molecular signatures in a 3D brain cancer model with decreased sensitivity to histone deacetylase inhibition.

    Directory of Open Access Journals (Sweden)

    Stuart J Smith

    Full Text Available INTRODUCTION: Physiologically relevant pre-clinical ex vivo models recapitulating CNS tumor micro-environmental complexity will aid development of biologically-targeted agents. We present comprehensive characterization of tumor aggregates generated using the 3D Rotary Cell Culture System (RCCS. METHODS: CNS cancer cell lines were grown in conventional 2D cultures and the RCCS and comparison with a cohort of 53 pediatric high grade gliomas conducted by genome wide gene expression and microRNA arrays, coupled with immunohistochemistry, ex vivo magnetic resonance spectroscopy and drug sensitivity evaluation using the histone deacetylase inhibitor, Vorinostat. RESULTS: Macroscopic RCCS aggregates recapitulated the heterogeneous morphology of brain tumors with a distinct proliferating rim, necrotic core and oxygen tension gradient. Gene expression and microRNA analyses revealed significant differences with 3D expression intermediate to 2D cultures and primary brain tumors. Metabolic profiling revealed differential profiles, with an increase in tumor specific metabolites in 3D. To evaluate the potential of the RCCS as a drug testing tool, we determined the efficacy of Vorinostat against aggregates of U87 and KNS42 glioblastoma cells. Both lines demonstrated markedly reduced sensitivity when assaying in 3D culture conditions compared to classical 2D drug screen approaches. CONCLUSIONS: Our comprehensive characterization demonstrates that 3D RCCS culture of high grade brain tumor cells has profound effects on the genetic, epigenetic and metabolic profiles of cultured cells, with these cells residing as an intermediate phenotype between that of 2D cultures and primary tumors. There is a discrepancy between 2D culture and tumor molecular profiles, and RCCS partially re-capitulates tissue specific features, allowing drug testing in a more relevant ex vivo system.

  6. Heterogeneous Catalysis. (United States)

    Miranda, R.


    Described is a heterogeneous catalysis course which has elements of materials processing embedded in the classical format of catalytic mechanisms and surface chemistry. A course outline and list of examples of recent review papers written by students are provided. (MVL)


    Directory of Open Access Journals (Sweden)

    Bruno H. Vilsinski


    Full Text Available Aluminum phthalocyanine chloride (AlPcCl is a photoactive compound which has been used as a photosensitizer (PS in photodynamic therapy (PDT. Its spectroscopic properties have been studied in solvents of different polarities (ethanol, acetone, dimethylsulfoxide and chloroform. Its solubility has been found to decrease with increasing solvent polarity, together with full self-aggregation in aqueous solution. The binding of AlPcCl to the copolymer PluronicTM micellar class P-123 and F-127 used as solubilizer/carriers was studied. Greater interaction between the more hydrophobic copolymer P-123 and AlPcCl was observed, besides a complex interaction profile involving different AlPcCl forms (self-aggregate/monomeric form in the copolymers. Time- and temperature-dependent structural organization of AlPcCl in the copolymers was also observed. Thus, AlPcCl has a strong tendency to self-aggregate with increasing solvent polarity, an effect also observed in micellar media.

  8. Reservoir simulation with imposed flux continuity conditions on heterogeneous and anisotropic media for general geometries, and the inclusion of hysteresis in forward modeling

    Energy Technology Data Exchange (ETDEWEB)

    Eigestad, Geir Terje


    The thesis is divided into two main parts. Part I gives an overview and summary of the theory that lies behind the flow equations and the discretization principles used in the work. Part II is a collection of research papers that have been written by the candidate (in collaboration with others). The main objective of this thesis is the discretization of an elliptic PDE which describes the pressure in a porous medium. The porous medium will in general be described by permeability tensors which are heterogeneous and anisotropic. In addition, the geometry is often complex for practical applications. This requires discretization approaches that are suited for the problems in mind. The discretization approaches used here are based on imposed flux and potential continuity, and will be discussed in detail in Chapter 3 of Part I. These methods are called Multi Point Flux Approximation Methods, and the acronym MPFA will be used for them. Issues related to these methods will be the main issue of this thesis. The rest of this thesis is organised as follows: Part I: Chapter 1 gives a brief overview of the physics and mathematics behind reservoir simulation. The standard mass balance equations are presented, and we try to explain what reservoir simulation is. Some standard discretization s methods are briefly discussed in Chapter 2. The main focus in Part I is on the MPFA discretization approach for various geometries, and is given in Chapter 3. Some details may have been left out in the papers of Part II, and the section serves both as a summary of the discretization method(s), as well as a more detailed description than what is found in the papers. In Chapter 4, extensions to handle time dependent and nonlinear problems are discussed. Some of the numerical examples presented in Part II deal with two phase flow, and are based on the extension given in this chapter. Chapter 5 discusses numerical results that have been obtained for the MPFA methods for elliptic problems, and

  9. Resolving Heterogeneity

    DEFF Research Database (Denmark)

    Hölzenspies, Jurriaan; Dela Cruz, Gelo Victoriano; M Brickman, Joshua


    sets of pluripotency and differentiation markers. It has become increasingly apparent that this transcriptional heterogeneity is an important characteristic of ESC culture. By sorting for specific populations of ESCs it is possible to enrich for cells with a capacity to colonize the embryo proper...

  10. Effects of organic solvent and crystal water on γ-chymotrypsin in acetonitrile media: observations from molecular dynamics simulation and DFT calculation. (United States)

    Zhu, Lijuan; Yang, Wei; Meng, Yan Yan; Xiao, Xiuchan; Guo, Yanzhi; Pu, Xuemei; Li, Menglong


    The use of enzymes in nonaqueous solvent has been one of the most exciting facets of enzymology in recent times; however, the mechanism of how organic solvent and essential water influence on structure and function of enzyme has been not satisfactorily explained in experiments, which limit its further application. Herein, we used molecular dynamics (MD) simulation to study γ-chymotrypsin in two types of media (viz., acetonitrile media with inclusion of 151 crystal water molecules and aqueous solution). On the basis of the MD result, the truncated active site modes containing two specific solvent molecules are furthered studied at the B3LYP/6-31+G(d,p) level of theory within the framework of PCM model. The results show that the acetontrile solvent gives rise to an extent deviation of enzyme structure from the native one, a drop in the flexibility and the total SASA of enzyme. The QM study further reveals that the structure variation of the active pocket caused by acetonitrile would lead to a weakened strength in the catalytic H-bond network, a drop in the pK(a) value of His57, and an increase in the proton transfer barriers from the Ser195 to the His57 residue, which may contribute to the drop in the enzymatic activity in acetontrile media. In addition, the crystal waters play an importance role in retaining the catalytic H-bond network and weakening the acetonitrile-induced variations above, which may be associated with the fact that the enzyme could retain catalytic activity in microhydration acetonitrile media. © 2012 American Chemical Society

  11. Porous polymer adsorbent media constructed by molecular dynamics modeling and simulations: the immobilization of charged ligands and their effect on pore structure and local nonelectroneutrality. (United States)

    Riccardi, E; Wang, J-C; Liapis, A I


    A molecular dynamics modeling and simulation approach is presented and employed to construct porous dextran polymer ion-exchange adsorbent media. Both the activation step of the surface of the pores of the dextran polymer layer grafted on an agarose surface and the immobilization of charged ligands on the activated surface of the porous dextran polymer layer are considered. For the systems studied in this work, the activation step modifies slightly the pore structure of the base, nonactivated porous dextran polymer, while the immobilization of the ligands on the activated pore surface of the dextran layer changes significantly the pore structure of the activated dextran layer. The density distributions of the counterions and immobilized charged ligands along the direction of net transport in the adsorbent media constructed in this study are found to be nonuniform. The variables that affect the shape and magnitude of the density distributions of the counterions and immobilized charged ligands as well as the total number of charged ligands that can be immobilized on the activated porous dextran layer are identified and presented in this work. Furthermore, the data clearly show that there is local nonelectroneutrality in the porous dextran polymer ion-exchange adsorbent media, and this result has very important practical implications for the operation and performance of separation systems involving ion-exchange adsorbent media (e.g., ion-exchange chromatography systems). Also, the results of this work suggest approaches for (1) controlling the immobilization process of charged ligands and (2) constructing and studying the behavior of chromatographic polymeric monoliths and packed bed columns having a gradient of density of functionalities along the axis of the chromatographic polymeric monolith or packed bed column.

  12. Identification and molecular characterization of the homogentisate pathway responsible for pyomelanin production, the major melanin constituents in Aeromonas media WS. (United States)

    Wang, He; Qiao, Yunqian; Chai, Baozhong; Qiu, Chenxi; Chen, Xiangdong


    The pigmentation of many Aeromonas species has been thought to be due to the production of a L-DOPA (L-3,4-dihydroxyphenylalanine) based melanin. However, in this study we found that although L-DOPA synthesis occurs in the high-melanin-yielding Aeromonas media strain WS, it plays a minor, if any, role in pigmentation. Instead, the pigmentation of A. media strain WS is due to the production of pyomelanin through HGA (homogentisate). Gene products of phhA (encodes phenylalanine hydroxylase), tyrB and aspC (both encode aromatic amino acid aminotransferase), and hppD (encodes 4-hydroxyphenylpyruvate dioxygenase) constitute a linear pathway of converting phenylalanine to HGA and disruption of any one of these genes impairs or blocks pigmentation of A. media strain WS. This HGA biosynthesis pathway is widely distributed in Aeromonas, but HGA is only detectable in the cultures of pigmented Aeromonas species. Heterologous expression of HppD from both pigmented and non-pigmented Aeromonas species in E. coli leads to the production of pyomelanin and thus pigmentation, suggesting that most Aeromonas species have the critical enzymes to produce pyomelanin through HGA. Taken together, we have identified a widely conserved biosynthesis pathway of HGA based pyomelanin in Aeromonas that may be responsible for pigmentation of many Aeromonas species.

  13. Identification and molecular characterization of the homogentisate pathway responsible for pyomelanin production, the major melanin constituents in Aeromonas media WS.

    Directory of Open Access Journals (Sweden)

    He Wang

    Full Text Available The pigmentation of many Aeromonas species has been thought to be due to the production of a L-DOPA (L-3,4-dihydroxyphenylalanine based melanin. However, in this study we found that although L-DOPA synthesis occurs in the high-melanin-yielding Aeromonas media strain WS, it plays a minor, if any, role in pigmentation. Instead, the pigmentation of A. media strain WS is due to the production of pyomelanin through HGA (homogentisate. Gene products of phhA (encodes phenylalanine hydroxylase, tyrB and aspC (both encode aromatic amino acid aminotransferase, and hppD (encodes 4-hydroxyphenylpyruvate dioxygenase constitute a linear pathway of converting phenylalanine to HGA and disruption of any one of these genes impairs or blocks pigmentation of A. media strain WS. This HGA biosynthesis pathway is widely distributed in Aeromonas, but HGA is only detectable in the cultures of pigmented Aeromonas species. Heterologous expression of HppD from both pigmented and non-pigmented Aeromonas species in E. coli leads to the production of pyomelanin and thus pigmentation, suggesting that most Aeromonas species have the critical enzymes to produce pyomelanin through HGA. Taken together, we have identified a widely conserved biosynthesis pathway of HGA based pyomelanin in Aeromonas that may be responsible for pigmentation of many Aeromonas species.

  14. Heterogeneous Gossip (United States)

    Frey, Davide; Guerraoui, Rachid; Kermarrec, Anne-Marie; Koldehofe, Boris; Mogensen, Martin; Monod, Maxime; Quéma, Vivien

    Gossip-based information dissemination protocols are considered easy to deploy, scalable and resilient to network dynamics. Load-balancing is inherent in these protocols as the dissemination work is evenly spread among all nodes. Yet, large-scale distributed systems are usually heterogeneous with respect to network capabilities such as bandwidth. In practice, a blind load-balancing strategy might significantly hamper the performance of the gossip dissemination.

  15. A computer model for one-dimensional mass and energy transport in and around chemically reacting particles, including complex gas-phase chemistry, multicomponent molecular diffusion, surface evaporation, and heterogeneous reaction (United States)

    Cho, S. Y.; Yetter, R. A.; Dryer, F. L.


    Various chemically reacting flow problems highlighting chemical and physical fundamentals rather than flow geometry are presently investigated by means of a comprehensive mathematical model that incorporates multicomponent molecular diffusion, complex chemistry, and heterogeneous processes, in the interest of obtaining sensitivity-related information. The sensitivity equations were decoupled from those of the model, and then integrated one time-step behind the integration of the model equations, and analytical Jacobian matrices were applied to improve the accuracy of sensitivity coefficients that are calculated together with model solutions.

  16. Heterogeneous catalysis in complex, condensed reaction media

    Energy Technology Data Exchange (ETDEWEB)

    Cantu, David C.; Wang, Yang-Gang; Yoon, Yeohoon; Glezakou, Vassiliki-Alexandra; Rousseau, Roger; Weber, Robert S.


    Many reactions required for the upgrading of biomass into fuels and chemicals—hydrogenation, hydrodeoxygenation, hydrocracking—are ostensibly similar to those practiced in the upgrading of petroleum into fuels. But, repurposing hydroprocessing catalysts from refinery operations to treat bio-oil has proved to be unsatisfactory. New catalysts are needed because the composition of the biogenic reactants differs from that of petroleum-derived feedstocks (e.g. the low concentration of sulfur in cellulose-derived biomass precludes use of metal sulfide catalysts unless sulfur is added to the reaction stream). New processes are needed because bio-oils oligomerize rapidly, forming intractable coke and “gunk”, at temperatures so low that the desired upgrading reactions are impractically slow, and so low that the bio-oil upgrading must be handled as a condensed fluid. Ideally, the new catalysts and processes would exploit the properties of the multiple phases present in condensed bio-oil, notably the polarizability and structure of the fluid near a catalyst’s surface in the cybotactic region. The results of preliminary modeling of the cybotactic region of different catalyst surfaces in the hydrogenation of phenol suggest that Pd catalysts supported on hydrophilic surfaces are more active than catalysts based on lipophilic supports because the former serve to enhance the concentration of the phenol in the vicinity of the Pd. The effect stems from thermodynamics, not the rate of mass transport. This work was supported by the US Department of Energy, Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.

  17. Stress Wave Propagation Through Heterogeneous Media

    National Research Council Canada - National Science Library


    .... In this work the influence of interface scattering on finite-amplitude shock waves was experimentally investigated by impacting flyer plates onto periodically layered polycarbonate/6061 aluminum...

  18. Wave Velocity Estimation in Heterogeneous Media

    KAUST Repository

    Asiri, Sharefa M.


    In this paper, modulating functions-based method is proposed for estimating space-time dependent unknown velocity in the wave equation. The proposed method simplifies the identification problem into a system of linear algebraic equations. Numerical simulations on noise-free and noisy cases are provided in order to show the effectiveness of the proposed method.

  19. Superhydrophilic molecularly imprinted polymers based on a water-soluble functional monomer for the recognition of gastrodin in water media. (United States)

    Ji, Wenhua; Zhang, Mingming; Wang, Daijie; Wang, Xiao; Liu, Jianhua; Huang, Luqi


    In this study, the first successfully developed superhydrophilic molecularly imprinted polymers (MIPs) for gastrodin recognition have been described. MIPs were prepared via the bulk polymerization process in an aqueous solution using alkenyl glycosides glucose (AGG) as the water-soluble functional monomer. The non-imprinted polymers (NIPs) were also synthesized using the same method without the use of the template. The dynamic water contact angles and photographs of the dispersion properties confirmed that the molecularly imprinted polymers displayed excellent superhydrophilicity. The results demonstrated that the MIPs exhibited high selectivity and an excellent imprinting effect. A molecularly imprinted solid phase extraction (MISPE) method was established. Optimization of various parameters affecting MISPE was investigated. Under the optimized conditions, a wide linear range (0.001-100.0μgmL(-1)) and low limits of detection (LOD) and quantification (LOQ) (0.03 and 0.09ngmL(-1), respectively) were achieved. When compared with the NIPs, higher recoveries (90.5% to 97.6%) of gastrodin with lower relative standard deviations values (below 6.4%) using high performance liquid chromatography were obtained at three spiked levels in three blank samples. These results demonstrated one efficient, highly selective and environmentally-friendly MISPE technique with excellent reproducibility for the purification and pre-concentration of gastrodin from an aqueous extract of Gastrodia elata roots. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Modelling Digital Media Objects

    DEFF Research Database (Denmark)

    Troelsgaard, Rasmus

    The goal of this thesis is to investigate two relevant issues regarding computational representation and classification of digital multi-media objects. With a special focus on music, a model for representation of objects comprising multiple heterogeneous data types is investigated. Necessary...

  1. Cardio-chemical exchange saturation transfer magnetic resonance imaging reveals molecular signatures of endogenous fibrosis and exogenous contrast media. (United States)

    Vandsburger, Moriel; Vandoorne, Katrien; Oren, Roni; Leftin, Avigdor; Mpofu, Senzeni; Delli Castelli, Daniela; Aime, Silvio; Neeman, Michal


    Application of emerging molecular MRI techniques, including chemical exchange saturation transfer (CEST)-MRI, to cardiac imaging is desirable; however, conventional methods are poorly suited for cardiac imaging, particularly in small animals with rapid heart rates. We developed a CEST-encoded steady state and retrospectively gated cardiac cine imaging sequence in which the presence of fibrosis or paraCEST contrast agents was directly encoded into the steady-state myocardial signal intensity (cardioCEST). Development of cardioCEST: A CEST-encoded cardiac cine MRI sequence was implemented on a 9.4T small animal scanner. CardioCEST of fibrosis was serially performed by acquisition of a series of CEST-encoded cine images at multiple offset frequencies in mice (n=7) after surgically induced myocardial infarction. Scar formation was quantified using a spectral modeling approach and confirmed with histological staining. Separately, circulatory redistribution kinetics of the paramagnetic CEST agent Eu-HPDO3A were probed in mice using cardioCEST imaging, revealing rapid myocardial redistribution, and washout within 30 minutes (n=6). Manipulation of vascular tone resulted in heightened peak CEST contrast in the heart, but did not alter redistribution kinetics (n=6). At 28 days after myocardial infarction (n=3), CEST contrast kinetics in infarct zone tissue were altered, demonstrating gradual accumulation of Eu-HPDO3A in the increased extracellular space. cardioCEST MRI enables in vivo imaging of myocardial fibrosis using endogenous contrast mechanisms, and of exogenously delivered paraCEST agents, and can enable multiplexed imaging of multiple molecular targets at high-resolution coupled with conventional cardiac MRI scans. © 2013 American Heart Association, Inc.

  2. Media life of the young

    DEFF Research Database (Denmark)

    Westlund, Oscar; Bjur, Jakob


    This is a thorough investigation into contemporary young people and their media life. The article conceptualizes a typology of media life, drawing on a theoretical body involving the sociology of generations, life course research, media life and individualization. This empirically derived typology...... makes a strong instrument for an understanding of the media life of the young, furnishing insights into how they have constructed their use of media. The investigation is based on a robust national survey with Swedes born 1994–2001, conducted in 2010, and focusing on four media: television, gaming......, the Internet and mobile devices. Two of the findings are particularly surprising. Firstly, the results reveal that the young generally lead heterogeneous media lives, varying with age and sex. Secondly, although some young people literarily live their life in media, there are also de facto young who live...

  3. Phenotypic heterogeneity in fungi: importance and methodology


    Hewitt, Sarah K.; Foster, David S.; Dyer, Paul S.; Avery, Simon V.


    Phenotypic heterogeneity describes the variation that exists between individual cells, spores or other biological entities within genetically-uniform populations of fungi or other organisms. Studies over the last 10–-15 years have successfully used laboratory- and modelling-based approaches to demonstrate the prevalence of phenotypic heterogeneity and characterise the molecular bases of the phenomenon (primarily centred around heterogeneous gene expression). In contrast to progress in these a...

  4. Polygenic dissection of major depression clinical heterogeneity

    NARCIS (Netherlands)

    Milaneschi, Y.; Winkelman, F.; Peyrot, W.; Abdellaoui, A.; Willemsen, G.; Hottenga, J.J.; Jansen, R.; Mbarek, H.; Dehghan, A.; Lu, C.; Boomsma, D.I.; Penninx, B.W.J.H.


    The molecular mechanisms underlying major depressive disorder (MDD) are largely unknown. Limited success of previous genetics studies may be attributable to heterogeneity of MDD, aggregating biologically different subtypes. We examined the polygenic features of MDD and two common clinical subtypes

  5. Influence of HIV-associated degree of immune suppression on molecular heterogeneity of hepatitis B virus among HIV co-infected patients. (United States)

    Pal, Ananya; Panigrahi, Rajesh; Biswas, Avik; Datta, Sibnarayan; Sarkar, Neelakshi; Guha, Subhashish Kamal; Saha, Bibhuti; Banerjee, Arup; Chakrabarti, Sekhar; Chakravarty, Runu


    We have investigated the molecular diversity of Hepatitis B virus (HBV) among the HIV co-infected patients from eastern-India. HBsAg/HBV-DNA positive subjects (n=73) from 874 HIV-infected patients were analyzed by sequencing followed by genetic diversity quantification. HBV/genotype-D and HBV/sugenotype-D2 were predominant. HBV/D2 isolates from patients with low CD4 count manifested significantly lower non-synonymous substitutions (ptype characteristics in the low CD4 count, leading to its increased prevalence in this group. Interestingly, genetic diversity in HBV/A1, the next common subgenotype, was modified in the opposite manner. Together our results underscore the need for proper HBV molecular monitoring in HIV co-infection. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Methods and Tools to allow molecular flow simulations to be coupled to higher level continuum descriptions of flows in porous/fractured media and aerosol/dust dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Loyalka, Sudarshan [Univ. of Missouri, Columbia, MO (United States)


    The purpose of this project was to develop methods and tools that will aid in safety evaluation of nuclear fuels and licensing of nuclear reactors relating to accidents.The objectives were to develop more detailed and faster computations of fission product transport and aerosol evolution as they generally relate to nuclear fuel and/or nuclear reactor accidents. The two tasks in the project related to molecular transport in nuclear fuel and aerosol transport in reactor vessel and containment. For both the tasks, explorations of coupling of Direct Simulation Monte Carlo with Navier-Stokes solvers or the Sectional method were not successful. However, Mesh free methods for the Direct Simulation Monte Carlo method were successfully explored.These explorations permit applications to porous and fractured media, and arbitrary geometries.The computations were carried out in Mathematica and are fully parallelized. The project has resulted in new computational tools (algorithms and programs) that will improve the fidelity of computations to actual physics, chemistry and transport of fission products in the nuclear fuel and aerosol in reactor primary and secondary containments.

  7. The association of carotid intima media thickness with retinol binding protein-4 and total and high molecular weight adiponectin in type 2 diabetic patients

    Directory of Open Access Journals (Sweden)

    Mansouri Masoumeh


    Full Text Available Abstract Background The aim of this study was to investigate whether carotid intima media thickness (CIMT is associated with serum level of retinol- binding protein-4 (RBP4 and total and high molecular weight (HMW adiponectin in type 2 diabetes (T2DM without clinical symptom of atherosclerotic disease. Method 101 type 2 diabetic patients (mean age, 53.63 ± 8.42 years and 42 body mass index (BMI matched control (mean age 50.1 ± 8.4 were recruited. The CIMT was assessed by using B-mode ultrasonography, while serum levels of RBP4 and total and HMW adiponectin were measured by using enzyme linked immunosorbant assay (ELISA. Linear regression analysis was performed with CIMT as dependent variable and adipokines and cardio metabolic risk factors as independent variables. Result The CIMT was higher in diabetic group compared to control group (p Age (B = 0.44 P Conclusion In conclusion, the present study showed that serum levels of RBP4 or total and HMW adiponectin were not potential predictors of CIMT in type 2 diabetic patients who exposed to this risk factor at least for nine years.

  8. Massively parallel molecular dynamics simulation of formation of clathrate-hydrate precursors at planar water-methane interfaces: insights into heterogeneous nucleation. (United States)

    English, Niall J; Lauricella, Marco; Meloni, Simone


    The formation of methane-hydrate precursors at large planar water-methane interfaces has been studied using massively parallel molecular dynamics in systems of varying size from around 10 000 to almost 7 × 10(6) molecules. This process took two distinct steps. First, the concentration of solvated methane clusters increases just inside the aqueous domain via slow diffusion from the methane-water interface, forming "clusters" of solvated methane molecules. Second, the re-ordering process of solvated methane and water molecules takes place in a manner very roughly consistent with the "blob" hypothesis, although with important differences, to form hydrate precursors, necessary for subsequent hydrate nucleation and crystallisation. It was found that larger system sizes serve to promote the formation rate of precursors.

  9. Molecular analysis of echinostome metacercariae from their second intermediate host found in a localised geographic region reveals genetic heterogeneity and possible cryptic speciation.

    Directory of Open Access Journals (Sweden)

    Waraporn Noikong


    Full Text Available Echinostome metacercariae are the infective stage for humans and animals. The identification of echinostomes has been based until recently on morphology but molecular techniques using sequences of ribosomal RNA and mitochondrial DNA have indicated major clades within the group. In this study we have used the ITS2 region of ribosomal RNA and the ND1 region of mitochondrial DNA to identify metacercariae from snails collected from eight well-separated sites from an area of 4000 km2 in Lamphun Province, Thailand. The derived sequences have been compared to those collected from elsewhere and have been deposited in the nucleotide databases. There were two aims of this study; firstly, to determine the species of echinostome present in an endemic area, and secondly, to assess the intra-specific genetic diversity, as this may be informative with regard to the potential for the development of anthelmintic resistance and with regard to the spread of infection by the definitive hosts. Our results indicate that the most prevalent species are most closely related to E. revolutum, E. trivolvis, E. robustum, E. malayanum and Euparyphium albuferensis. Some sites harbour several species and within a site there could be considerable intra-species genetic diversity. There is no significant geographical structuring within this area. Although the molecular techniques used in this study allowed the assignment of the samples to clades within defined species, however, within these groupings there were significant differences indicating that cryptic speciation may have occurred. The degree of genetic diversity present would suggest the use of targeted regimes designed to minimise the selection of anthelmintic resistance. The apparent lack of geographic structuring is consistent with the transmission of the parasites by the avian hosts.

  10. Effectively designed molecularly imprinted polymers for selective isolation of the antidiabetic drug metformin and its transformation product guanylurea from aqueous media

    Energy Technology Data Exchange (ETDEWEB)

    Kyzas, George Z.; Nanaki, Stavroula G. [Laboratory of Polymer Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24 Thessaloniki (Greece); Koltsakidou, Anastasia; Papageorgiou, Myrsini; Kechagia, Maria [Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24 Thessaloniki (Greece); Bikiaris, Dimitrios N. [Laboratory of Polymer Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24 Thessaloniki (Greece); Lambropoulou, Dimitra A., E-mail: [Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24 Thessaloniki (Greece)


    Highlights: • Preparation of novel MIPs with remarkable recognition properties. • Selective isolation and removal of metformin and guanylurea from aqueous media. • Detailed adsorbent characterization and adsorption studies. • Successful application of synthesized MIPs as dispersive SPE sorbents. • Estimation of expanded uncertainty following a bottom-up approach. - Abstract: In the present study, two novel molecularly imprinted polymers (MIPs) with remarkable recognition properties for metformin and its transformation product, guanylurea, have been prepared for their selective, enrichment, isolation and removal from aqueous media. The prepared adsorbents were characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and swelling experiments. The performance of the prepared MIPs was evaluated by various parameters including the influence of pH, contact time, temperature and initial compound concentration. The effects on the adsorption behavior of the removal process parameters were studied and the equilibrium data were fitted by the Langmuir and Freundlich models. Due to the imprinting effect, adsorption performance of MIPs was always superior to its corresponding NIP (non-imprinted polymer), with maximum adsorption capacity ∼80 mg g{sup −1} for both MIPs. Stability and reusability of the MIPs up to the 5th cycle meant that they could be applied repeatedly without losing substantial removal ability. In the next step, the prepared MIP nanoparticles were evaluated as sorbents in a dispersive solid phase extraction (D-SPE) configuration for selective enrichment and determination of metformin and guanylurea in different aqueous matrices. Under the working extraction conditions, the D-SPE method showed good linearity in the range of 50–1000 ng L{sup −1}, repeatability of the extractions (RSD 2.1–5.1%, n = 3), and low limits of detection (1.5–3.4 ng L{sup −1}). The expanded uncertainty of the data obtained

  11. Molecular analysis of clonal trichomonad isolates indicate the existence of heterogenic species present in different birds and within the same host. (United States)

    Grabensteiner, Elvira; Bilic, Ivana; Kolbe, Thomas; Hess, Michael


    Trichomonas gallinae is a flagellated protozoon and the etiological agent of avian trichomoniasis. Despite its importance, especially in columbiformes and falconiformes, only a few molecular studies have yet been performed in order to investigate the degree of genetic diversity and cross-transmissibility between different isolates of this parasite. To address these questions 63 clonal cultures of Trichomonas spp. isolates were established by successful isolation of single trichomonads from a mixture of micro-organisms obtained from 17 birds belonging to five different species. All birds were from Austria with the exception of one bird which originated from the Czech Republic. The sequence of the complete genomic region spanning the two ribosomal RNA internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene was determined for all 63 isolates. In addition, in order to compare the results obtained with the ITS1-5.8S-ITS2 region the sequence of the 18S rRNA gene was determined from a subset of isolates. Unrooted phylogenetic trees inferred by distance, parsimony, and likelihood methods suggest the existence of at least three clusters within the T. gallinae species complex, two groups being closely related to the human pathogens, Trichomonas vaginalis and Trichomonas tenax. Furthermore, for the first time two different trichomonad sequence types isolated at the same time from a single bird could be detected in the crops of two pigeons. (c) 2010 Elsevier B.V. All rights reserved.

  12. Genome-Wide Analysis Identifies MEN1 and MAX Mutations and a Neuroendocrine-Like Molecular Heterogeneity in Quadruple WT GIST. (United States)

    Pantaleo, Maria A; Urbini, Milena; Indio, Valentina; Ravegnini, Gloria; Nannini, Margherita; De Luca, Matilde; Tarantino, Giuseppe; Angelini, Sabrina; Gronchi, Alessandro; Vincenzi, Bruno; Grignani, Giovanni; Colombo, Chiara; Fumagalli, Elena; Gatto, Lidia; Saponara, Maristella; Ianni, Manuela; Paterini, Paola; Santini, Donatella; Pirini, M Giulia; Ceccarelli, Claudio; Altimari, Annalisa; Gruppioni, Elisa; Renne, Salvatore L; Collini, Paola; Stacchiotti, Silvia; Brandi, Giovanni; Casali, Paolo G; Pinna, Antonio D; Astolfi, Annalisa; Biasco, Guido


    Quadruple wild-type (WT) gastrointestinal stromal tumor (GIST) is a genomic subgroup lacking KIT/PDGFRA/RAS pathway mutations, with an intact succinate dehydrogenase (SDH) complex. The aim of this work is to perform a wide comprehensive genomic study on quadruple WT GIST to improve the characterization of these patients. We selected 14 clinical cases of quadruple WT GIST, of which nine cases showed sufficient DNA quality for whole exome sequencing (WES). NF1 alterations were identified directly by WES. Gene expression from whole transcriptome sequencing (WTS) and miRNA profiling were performed using fresh-frozen, quadruple WT GIST tissue specimens and compared with SDH and KIT/PDGFRA-mutant GIST. WES identified an average of 18 somatic mutations per sample. The most relevant somatic oncogenic mutations identified were in TP53, MEN1, MAX, FGF1R, CHD4, and CTDNN2. No somatic alterations in NF1 were identified in the analyzed cohort. A total of 247 mRNA transcripts and 66 miRNAs were differentially expressed specifically in quadruple WT GIST. Overexpression of specific molecular markers (COL22A1 and CALCRL) and genes involved in neural and neuroendocrine lineage (ASCL1, Family B GPCRs) were detected and further supported by predicted miRNA target analysis. Quadruple WT GIST show a specific genetic signature that deviates significantly from that of KIT/PDGFRA-mutant and SDH-mutant GIST. Mutations in MEN1 and MAX genes, a neural-committed phenotype and upregulation of the master neuroendocrine regulator ASCL1, support a genetic similarity with neuroendocrine tumors, with whom they also share the great variability in oncogenic driver genes. Implications: This study provides novel insights into the biology of quadruple WT GIST that potentially resembles neuroendocrine tumors and should promote the development of specific therapeutic approaches. Mol Cancer Res; 15(5); 553-62. ©2017 AACR . ©2017 American Association for Cancer Research.

  13. Heterogeneous nucleation of solid Al from the melt by TiB2 and Al3Ti: An ab initio molecular dynamics study

    KAUST Repository

    Wang, Junsheng


    The nucleation of solid Al from the melt by TiB2 is well established and is believed to involve the formation of Al3Ti. Since the atomic-scale mechanisms involved are not fully understood, we look to computer simulation to provide insight. As there is an absence of suitable potentials for all of this complex system we have performed large-scale density-functional-theory molecular dynamics simulations of the nucleation of solid Al from the melt on TiB2 and Al3Ti substrates at undercoolings of around 2 K. Using periodic boundary conditions, we find limited ordering and no signs of incipient growth in the liquid Al close to the B-terminated surface of TiB2. By contrast, we see fcc-like ordering near the Ti-terminated surface, with growth being frustrated by the lattice mismatch between bulk Al and the TiB2 substrate. The Al interatomic distances at the Ti-terminated surface are similar to distances found in Al3Ti; we suggest that the layer encasing TiB2 observed experimentally may be strained Al on a Ti-terminated surface rather than Al3Ti. For the Al3Ti substrate, fcc-like structures are observed on both sides which extend rapidly into the melt. Periodic boundaries introduce unphysical stresses which we removed by introducing a vacuum region to separate the liquid from the solid at one of the interfaces. We see ordering in the Al on both the B-terminated (0001) surface of TiB2, and on Al3Ti(112), with the ordering able to be stronger on the Al3Ti substrate. However, we cannot draw strong conclusions as these simulations need more time to allow long-ranged fluctuations in the liquid Al to dampen out. The huge computational cost restricted the range and duration of simulations that was possible.

  14. Miscible, Porous Media Displacements with Density Stratification

    National Research Council Canada - National Science Library



    A bstract : High accuracy, three‐dimensional numerical simulations of miscible displacements with gravity override, in both homogeneous and heterogeneous porous media, are discussed for the quarter five‐spot configuration...

  15. Differentiating homogeneous and heterogeneous water oxidation catalysis: confirmation that [Co4(H2O)2(α-PW9O34)2]10- is a molecular water oxidation catalyst. (United States)

    Vickers, James W; Lv, Hongjin; Sumliner, Jordan M; Zhu, Guibo; Luo, Zhen; Musaev, Djamaladdin G; Geletii, Yurii V; Hill, Craig L


    Distinguishing between homogeneous and heterogeneous catalysis is not straightforward. In the case of the water oxidation catalyst (WOC) [Co4(H2O)2(PW9O34)2](10-) (Co4POM), initial reports of an efficient, molecular catalyst have been challenged by studies suggesting that formation of cobalt oxide (CoOx) or other byproducts are responsible for the catalytic activity. Thus, we describe a series of experiments for thorough examination of active species under catalytic conditions and apply them to Co4POM. These provide strong evidence that under the conditions initially reported for water oxidation using Co4POM (Yin et al. Science, 2010, 328, 342), this POM anion functions as a molecular catalyst, not a precursor for CoOx. Specifically, we quantify the amount of Co(2+)(aq) released from Co4POM by two methods (cathodic adsorptive stripping voltammetry and inductively coupled plasma mass spectrometry) and show that this amount of cobalt, whatever speciation state it may exist in, cannot account for the observed water oxidation. We document that catalytic O2 evolution by Co4POM, Co(2+)(aq), and CoOx have different dependences on buffers, pH, and WOC concentration. Extraction of Co4POM, but not Co(2+)(aq) or CoOx into toluene from water, and other experiments further confirm that Co4POM is the dominant WOC. Recent studies showing that Co4POM decomposes to a CoOx WOC under electrochemical bias (Stracke and Finke, J. Am. Chem. Soc., 2011, 133, 14872), or displays an increased ability to reduce [Ru(bpy)3](3+) upon aging (Scandola, et al., Chem. Commun., 2012, 48, 8808) help complete the picture of Co4POM behavior under various conditions but do not affect our central conclusions.

  16. The permeability of heterogeneous rocks (United States)

    Selvadurai, Patrick


    Darcy's original concept of permeability is largely associated with estimation of the hydraulic conductivity characteristics of isotropic and homogeneous porous media where the fluid flow characteristics can be estimated by appeal to a single scalar measure. Naturally occurring geomaterials are heterogeneous and the estimation of the effective permeability characteristics of such geomaterials presents a challenge not only in terms of the experimental procedures that should be used to ensure flow through the porous medium but also in the correct use of the theoretical concepts needed to accurately interpret the data. Relatively widely referred to rocks such as Indiana Limestone can exhibit spatial heterogeneity in the permeability characteristics even though the visual appearance can suggest the absence of such spatial and directional attributes (Selvadurai and Selvadurai, 2010). Argillaceous rocks such as the Cobourg Limestone found in southern Ontario, Canada can display hydraulic heterogeneity that is attributed to the presence of dolomitic and calcite nodular regions separated by calcite rock partings that contain an argillaceous component (Figure 1). Also, these rocks have extremely low permeability that requires the use of transient hydraulic pulse tests for the estimation of permeability. The performance of such pulse tests will be influenced by the bulk compressibility and bulk porosity of the porous skeleton consisting of the identifiable phases and their spatial distributions. The concepts of effective compressibilities and porosities therefore needs to be introduced if convenient procedures are to be developed for the accurate interpretation of even bench scale experiments (Selvadurai and Gɫowacki, 2017). The paper will describe both experimental and theoretical approaches for interpreting the effective Darcy permeability of the heterogeneous rocks using both experimental and computational approaches. In particular, the applicability of the "Geometric

  17. Media education. (United States)

    Strasburger, Victor C


    The American Academy of Pediatrics recognizes that exposure to mass media (eg, television, movies, video and computer games, the Internet, music lyrics and videos, newspapers, magazines, books, advertising) presents health risks for children and adolescents but can provide benefits as well. Media education has the potential to reduce the harmful effects of media and accentuate the positive effects. By understanding and supporting media education, pediatricians can play an important role in reducing harmful effects of media on children and adolescents.

  18. Les systèmes hétérogènes « eau zéolithe hydrophobe »: de nouveaux ressorts moléculairesThe heterogeneous systems 'water hydrophobic zeolites': new molecular springs (United States)

    Eroshenko, Valentin; Regis, Robert-Charles; Soulard, Michel; Patarin, Joël

    Pressure-volume isotherms have been determined for three heterogeneous 'water-zeolite' systems. The first two concern hydrophobic purely siliceous zeolites: silicalite-1 (F -) and zeolite β (F -); the third comprises a more hydrophilic commercial zeolite of the type ZSM-5. The P- V diagram for the water-silicalite-1 (F -) system is characterized by a plateau corresponding to the intrusion of water inside the pores of the solid. During the release the phenomenon is reversible. This system, which is able to accumulate and restore superficial energy, constitutes a molecular spring. For zeolite β, the P- V curve displays a plateau during the compression, but during the release, the phenomenon is not reversible. In that case, the system absorbs mechanical energy and acts as a bumper. The third system, based on the more hydrophilic ZSM-5 zeolite shows a linear isotherm without any plateau. These results open new applications perspectives in the field of the energetics for hydrophobic zeolites in contact with water. To cite this article: V. Eroshenko et al., C. R. Physique 3 (2002) 111-119

  19. [Review on landscape heterogeneity]. (United States)

    Zhao, Yutao; Yu, Xinxiao; Guang, Wenbin


    On the base of precedent studies, the occurring mechanism, classification, measurement methods, and the important role of landscape heterogeneity in landscape ecology were reviewed. The inner and outer uncertain factors result in landscape heterogeneity. Landscape heterogeneity has close relations with landscape stability, landscape design, architecture, management and disturbance, scale and ecological diversity in ecology. Complexity of landscape heterogeneity research, non-system of measurement indices and methods, difficulties and limitations of landscape heterogeneity modelling were all discussed respectively. In addition, it is suggested that the theory and methods of ecological complexity should be used to improve landscape heterogeneity research.

  20. Heterogeneous continuous-time random walks (United States)

    Grebenkov, Denis S.; Tupikina, Liubov


    We introduce a heterogeneous continuous-time random walk (HCTRW) model as a versatile analytical formalism for studying and modeling diffusion processes in heterogeneous structures, such as porous or disordered media, multiscale or crowded environments, weighted graphs or networks. We derive the exact form of the propagator and investigate the effects of spatiotemporal heterogeneities onto the diffusive dynamics via the spectral properties of the generalized transition matrix. In particular, we show how the distribution of first-passage times changes due to local and global heterogeneities of the medium. The HCTRW formalism offers a unified mathematical language to address various diffusion-reaction problems, with numerous applications in material sciences, physics, chemistry, biology, and social sciences.

  1. Link-Heterogeneity vs. Node-Heterogeneity in Clusters


    Beaumont, Olivier; Rosenberg, Arnold


    International audience; Heterogeneity in resources pervades all modern computing platforms. How do the effects of heterogeneity depend on which resources differ among computers in a platform? Some answers are derived within a formal framework, by comparing heterogeneity in computing power (node-heterogeneity) with heterogeneity in communication speed (link-heterogeneity). The former genre of heterogeneity seems much easier to understand than the latter.

  2. Heterogeneous network architectures

    DEFF Research Database (Denmark)

    Christiansen, Henrik Lehrmann


    Future networks will be heterogeneous! Due to the sheer size of networks (e.g., the Internet) upgrades cannot be instantaneous and thus heterogeneity appears. This means that instead of trying to find the olution, networks hould be designed as being heterogeneous. One of the key equirements here...

  3. Media Komunitas dan Media Literacy

    Directory of Open Access Journals (Sweden)

    Pawito .


    Full Text Available Abstract:This essay deals with community media in relation to media literacy. After a short discussion on a number of community media characters is made the essay goes further with somewhat detail theoretical presumptions of the roles of media community with respect primarily to the development as Amartya Sen mentioned about. The author suggests that community media may play some significant roles in the development including (a disseminating information (from varieties of perspective, (b facilitating public discussion, (c helping to reach solutions of problems, (d encouraging participations, and (e encouraging the development of media literacy. Regarding the last point the author remarks that media community may have a dual-roles i.e facilitating community’s member in media participation and facilitating community’s member in media education.

  4. Molecular cloning, heterogenous expression and the induction ...

    African Journals Online (AJOL)



    May 24, 2012 ... 2The Key Sericultural Laboratory of the Agricultural Ministry of China, Southwest University, Chongqing, 400716, China. ... RT-PCR analysis showed that .... expression level of Bmae33 after exposure experiment through. qRT-PCR. The products of reverse-transcription was diluted then used as template.

  5. Media, Gadgets. (United States)

    Journal of Chemical Education, 1981


    Summarizes papers presented at the Sixth Biennial Conference on Chemical Education describing new media and gadgets, particularly models, computers, and other media. A bibliography of 15 presented papers on these topics is attached. (CS)

  6. Flows and chemical reactions in heterogeneous mixtures

    CERN Document Server

    Prud'homme, Roger


    This book - a sequel of previous publications 'Flows and Chemical Reactions' and 'Chemical Reactions in Flows and Homogeneous Mixtures' - is devoted to flows with chemical reactions in heterogeneous environments.  Heterogeneous media in this volume include interfaces and lines. They may be the site of radiation. Each type of flow is the subject of a chapter in this volume. We consider first, in Chapter 1, the question of the generation of environments biphasic individuals: dusty gas, mist, bubble flow.  Chapter 2 is devoted to the study at the mesoscopic scale: particle-fluid exchange of mom

  7. Heterogeneity and Microeconometrics Modelling

    DEFF Research Database (Denmark)

    Browning, Martin; Carro, Jesus

    Presented at the 2005 Econometric Society World Congress Plenary Session on "Modelling Heterogeneity". We survey the treatment of heterogeneity in applied microeconometrics analyses. There are three themes. First, there is usually much more heterogeneity than empirical researchers allow for. Second......, the inappropriate treatment of heterogeneity can lead to serious error when estimating outcomes of interest. Finally, once we move away from the traditional linear model with a single 'fixed effect', it is very difficult to account for heterogeneity and fit the data and maintain coherence with theory structures....... The latter task is one for economists: "heterogeneity is too important to be left to the statisticians". The paper concludes with a report of our own research on dynamic discrete choice models that allow for maximal heterogeneity...

  8. Media Entrepreneurship

    DEFF Research Database (Denmark)

    Khajeheian, Datis


    Media Entrepreneurship has been an ambiguous, unclear and controversial concept and despite of growing academic efforts in the last decade, it is still a poorly defined subject. This paper is an effort to fill this gap by providing a comprehensive definition of media entrepreneurship. Firstly......, a literature review conducted and entrepreneurship, media, opportunity and innovation as building blocks of media entrepreneurship explained. Then by using of a mixed of bibliographic method and a Delphi method with multi-stage analysis process, a consensual definition of media entrepreneurship proposed...... entrepreneurship....

  9. Media Technology

    Directory of Open Access Journals (Sweden)

    Zhou Gang


    Full Text Available Modern colleges are faced with the dual pressures of university reform and international competition, how to overcome difficulties, to play the role of modern English teaching in colleges and colleges to enhance the core competitiveness of colleges, colleges and colleges modern English teaching problems to be solved. Based on the current situation of modern colleges in the premise of the Modern media platform fully demonstrated the characteristics and viability of the Modern media English teaching, the necessity of modern English teaching of college Modern media. Discusses the Modern media targeting English teaching and important role is in the English teaching to guide the development of modern colleges modern media.

  10. Media Framing

    DEFF Research Database (Denmark)

    Pedersen, Rasmus T.


    The concept of media framing refers to the way in which the news media organize and provide meaning to a news story by emphasizing some parts of reality and disregarding other parts. These patterns of emphasis and exclusion in news coverage create frames that can have considerable effects on news...... consumers’ perceptions and attitudes regarding the given issue or event. This entry briefly elaborates on the concept of media framing, presents key types of media frames, and introduces the research on media framing effects....

  11. Social media and the transformation of activist communication: exploring the social media ecology of the 2010 Toronto G20 protests

    NARCIS (Netherlands)

    Poell, T.


    How does the massive use of social media in contemporary protests affect the character of activist communication? Moving away from the conceptualization of social media as tools, this research explores how activist social media communication is entangled with and shaped by heterogeneous

  12. Voice over IP in Wireless Heterogeneous Networks

    DEFF Research Database (Denmark)

    Fathi, Hanane; Chakraborty, Shyam; Prasad, Ramjee

    with the deployment of wireless heterogeneous systems, both speech and data traffic are carrried over wireless links by the same IP-based packet-switched infrastructure. However, this combination faces some challenges due to the inherent properties of the wireless network. The requirements for good quality VoIP...... communications are difficult to achieve in a time-varying environment due to channel errors and traffic congestion and across different systems. The provision of VoIP in wireless heterogeneous networks requires a set of time-efficient control mechanisms to support a VoIP session with acceptable quality....... The focus of Voice over IP in Wierless Heterogeneous Networks is on mechanisms that affect the VoIP user satisfaction  while not explicitly involved in the media session. This relates to the extra delays introduced by the security and the signaling protocols used to set up an authorized VoIP session...

  13. Media stylistics


    Lambrou, Marina; Durant, Alan


    In this chapter we review the concept of ‘media stylistics’. In particular, we disentangle the polysemy of these two terms which, when combined, describe but can also obscure work in this area; and we discuss key themes and concerns which emerge. Through analysis of two short extracts of media discourse in English, we elaborate a distinction between two alternative emphases: study of media language as concerned with the capabilities associated with changing technologies for conveying linguist...

  14. Media Flow

    DEFF Research Database (Denmark)

    Kabel, Lars


    News and other kinds of journalistic stories, 16-17 hours a day, all year round, on all platforms, also the moderated social media. The key research thesis behind this article is that the continuous and speedy stream of news stories and media content now is becoming the centre of the production...... processes and the value creation in converged multimedia newsrooms. The article identify new methods and discuss editorial challenges in handling media flow....

  15. Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation. (United States)

    Tian, Xue; Jiang, Lin; Yuan, Yuan; Wang, Minqi; Guo, Yanzhi; Zeng, Xiaojun; Li, Menglong; Pu, Xuemei


    The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 % v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution and H-bonding are analyzed in the two organic media. Our results show that the changes in overall structure of the protein almost display a clear correlation with the water content in hexane media while to some extent U-shaped/bell-shaped dependence on the water content is observed in acetonitrile media with a minimum/maximum at 10-20 % water content. In contrast, the water content change in the two organic solvents does not play an observable role in the stability of catalytic hydrogen-bond network, which still exhibits high stability in all hydration levels, different from observations on the free enzyme system [Zhu L, Yang W, Meng YY, Xiao X, Guo Y, Pu X, Li M (2012) J Phys Chem B 116(10):3292-3304]. In low hydration levels, most water molecules mainly distribute near the protein surface and an increase in the water content could not fully exclude the organic solvent from the protein surface. However, the acetonitrile solvent displays a stronger ability to strip off water molecules from the protein than the hexane. In a summary, the difference in the calculated properties between the two organic solvents is almost significant in low water content (water content. In addition, some structural properties at 10 ~ 20 % v/v hydration zone, to large extent, approach to those in aqueous solution.

  16. Exploring tumor heterogeneity

    NARCIS (Netherlands)

    Fessler, E.


    Cancer is a heterogeneous disease, which is reflected both on the cellular and the population level. Advances in detection, diagnosis, and treatment of malignancies have increased survival time of cancer patients; yet, the heterogeneity observed within and between tumors complicates accurate

  17. Unscrewing social media networks, twice

    DEFF Research Database (Denmark)

    Birkbak, Andreas


    Social media are often claimed to be an important new force in politics. One way to investigate such a claim is to follow an early call made in actor-network theory (ANT) to “unscrew” those entities that are assumed to be important and show how they are made up of heterogeneous networks of many...... different actors (Callon and Latour 1981). In this article I take steps towards unscrewing seven Facebook pages that were used to mobilize citizens for and against road pricing in Copenhagen in 2011-2012. But I encounter the difficulty that social media are already explicitly understood in Internet Studies...... that it can be combined with liberal notions of a singular public sphere (Somers 1995b; 1995a). In order to unscrew social media as a political force, I suggest that we need to work through both the assembling of social media networks and attend to corresponding reconstructions of liberal political narratives...

  18. Simulation of Tracer Transport in Porous Media: Application to Bentonites; Simulacion del Transporte de Trazadores en Medios Porosos: Aplicacion al Caso de Arcillas

    Energy Technology Data Exchange (ETDEWEB)

    Bru, A.; Casero, D. [CIEMAT, Madrid (Spain)


    We present a formal framework to describe tracer transport in heterogeneous media, such as porous media like bentonites. In these media, mean field approximation is not valid because there exist some geometrical constraints and the transport is anomalous. (Author)

  19. Print media vs internet media


    Koganuramath, M. M.; Angadi, Mallikarjun


    The Information Technology has revolutionised the communication media with the emergence of Internet. This paper describes the pace of change in print media to On-line journalism. The process has began with On-line journalism utilising Internet wherein websites are replacing the print media. Most of the On-line newspapers are free, interactive and archival in nature and it provides users to search the information on newspapers through various access points i.e. by contributors, title, and dat...

  20. Media darling

    CERN Multimedia

    Chalmers, Matthew


    He is the media-friendly face of particle physics, appearing on countless TV and radio shows in the run-up to the opening of CERN's Large Hadron Collider. Matthew Chalmers discovers how Brian Cox finds the time to be both a physicist and a media personality. (2 pages)

  1. Travelling wave phenomena in non-heterogeneous tissues

    DEFF Research Database (Denmark)

    Pedersen, Michael


    Disturbances (or information) propagating in heterogeneous biological tissues (or other media) are often modeled by a partial differential equation of the form $$ u''(t,x) +D(x)u'(t,x) +A(x)u(t,x)=f(t,x), $$ for $ 0......Disturbances (or information) propagating in heterogeneous biological tissues (or other media) are often modeled by a partial differential equation of the form $$ u''(t,x) +D(x)u'(t,x) +A(x)u(t,x)=f(t,x), $$ for $ 0...

  2. Heterogeneous cellular networks

    CERN Document Server

    Hu, Rose Qingyang


    A timely publication providing coverage of radio resource management, mobility management and standardization in heterogeneous cellular networks The topic of heterogeneous cellular networks has gained momentum in industry and the research community, attracting the attention of standardization bodies such as 3GPP LTE and IEEE 802.16j, whose objectives are looking into increasing the capacity and coverage of the cellular networks. This book focuses on recent progresses,  covering the related topics including scenarios of heterogeneous network deployment, interference management i

  3. Unexpected heterogeneity derived from Cas9 ribonucleoprotein-introduced clonal cells at the HPRT1 locus. (United States)

    Sakuma, Tetsushi; Mochida, Keiji; Nakade, Shota; Ezure, Toru; Minagawa, Sachi; Yamamoto, Takashi


    Single-cell cloning is an essential technique for establishing genome-edited cell clones mediated by programmable nucleases such as CRISPR-Cas9. However, residual genome-editing activity after single-cell cloning may cause heterogeneity in the clonal cells. Previous studies showed efficient mutagenesis and rapid degradation of CRISPR-Cas9 components in cultured cells by introducing Cas9 ribonucleoproteins (RNPs). In this study, we investigated how the timing for single-cell cloning of Cas9 RNP-transfected cells affected the heterogeneity of the resultant clones. We carried out transfection of Cas9 RNPs targeting several loci in the HPRT1 gene in HCT116 cells, followed by single-cell cloning at 24, 48, 72 hr and 1 week post-transfection. After approximately 3 weeks of incubation, the clonal cells were collected and genotyped by high-resolution microchip electrophoresis and Sanger sequencing. Unexpectedly, long-term incubation before single-cell cloning resulted in highly heterogeneous clones. We used a lipofection method for transfection, and the media containing transfectable RNPs were not removed before single-cell cloning. Therefore, the active Cas9 RNPs were considered to be continuously incorporated into cells during the precloning incubation. Our findings provide a warning that lipofection of Cas9 RNPs may cause continuous introduction of gene mutations depending on the experimental procedures. © 2018 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

  4. Self-diffusion studies by intra- and inter-molecular spin-lattice relaxometry using field-cycling: Liquids, plastic crystals, porous media, and polymer segments. (United States)

    Kimmich, Rainer; Fatkullin, Nail


    Field-cycling NMR relaxometry is a well-established technique for probing molecular dynamics in a frequency range from typically a few kHz up to several tens of MHz. For the interpretation of relaxometry data, it is quite often assumed that the spin-lattice relaxation process is of an intra-molecular nature so that rotational fluctuations dominate. However, dipolar interactions as the main type of couplings between protons and other dipolar species without quadrupole moments can imply appreciable inter-molecular contributions. These fluctuate due to translational displacements and to a lesser degree also by rotational reorientations in the short-range limit. The analysis of the inter-molecular proton spin-lattice relaxation rate thus permits one to evaluate self-diffusion variables such as the diffusion coefficient or the mean square displacement on a time scale from nanoseconds to several hundreds of microseconds. Numerous applications to solvents, plastic crystals and polymers will be reviewed. The technique is of particular interest for polymer dynamics since inter-molecular spin-lattice relaxation diffusometry bridges the time scales of quasi-elastic neutron scattering and field-gradient NMR diffusometry. This is just the range where model-specific intra-coil mechanisms are assumed to occur. They are expected to reveal themselves by characteristic power laws for the time-dependence of the mean-square segment displacement. These can be favorably tested on this basis. Results reported in the literature will be compared with theoretical predictions. On the other hand, there is a second way for translational diffusion phenomena to affect the spin-lattice relaxation dispersion. If rotational diffusion of molecules is restricted, translational diffusion properties can be deduced even from molecular reorientation dynamics detected by intra-molecular spin-lattice relaxation. This sort of scenario will be relevant for adsorbates on surfaces or polymer segments under

  5. Media violence. (United States)

    Cantor, J


    Research on the effects of media violence is not well understood by the general public. Despite this fact, there is an overwhelming consensus in the scientific literature about the unhealthy effects of media violence. Meta-analyses show that media-violence viewing consistently is associated with higher levels of antisocial behavior, ranging from the trivial (imitative violence directed against toys) to the serious (criminal violence), with many consequential outcomes in between (acceptance of violence as a solution to problems, increased feelings of hostility, and the apparent delivery of painful stimulation to another person). Desensitization is another well-documented effect of viewing violence, which is observable in reduced arousal and emotional disturbance while witnessing violence, the reduced tendency to intervene in a fight, and less sympathy for the victims of violence. Although there is evidence that youth who are already violent are more likely to seek out violent entertainment, there is strong evidence that the relationship between violence viewing and antisocial behavior is bidirectional. There is growing evidence that media violence also engenders intense fear in children which often lasts days, months, and even years. The media's potential role in solutions to these problems is only beginning to be explored, in investigations examining the uses and effects of movie ratings, television ratings, and the V-chip, and the effects of media literacy programs and public education efforts. Future research should explore important individual differences in responses to media violence and effective ways to intervene in the negative effects.

  6. Multiphase, Multicomponent Fluid Flow in Homogeneous and Heterogeneous Porous Media Écoulement de fluides multiconstituants polyphasiques dans des milieux poreux homogènes et hétérogènes

    Directory of Open Access Journals (Sweden)

    Chella R.


    Full Text Available The flow of several components and several phases through a porous medium is generally described by introducing macroscopic mass-balance equations under the form of generalized dispersion equations. This model raises several questions that are discussed in this paper on the basis of results obtained from the volume averaging method, coupled with pore-scale simulations of the multiphase flow. The study is limited to a binary, two-phase system, and we assume that the momentum equations can be solved independently from the diffusion/advection equations. The assumption of local-equilibrium is discussed and several length-scale and time-scale constraints are provided. A key issue concerns the impact on the dispersion tensors of the pore-scale equilibrium condition at the interface between the different phases. Our results show that this phenomenon may lead to significant variations of the dispersion coefficients with respect to passive dispersion, i. e. , dispersion without interfacial mass fluxes. Macroscopic equations are then obtained in the general case, and several local closure problems are provided that allow one to calculate the dispersion tensors and others properties, from the pore-scale geometry, velocities, and fluid characteristics. Examples of solutions of these closure problems are given in the case of two-dimensional representative unit cells. The two-phase flow equations are solved in two different ways : a boundary element technique, or a modified lattice Boltzmann approach. Solutions of the closure problems associated with the dispersion equations are then given using a finite volume element formulation of the partial differential equations. The results show the influence of velocity and saturation on the effective parameters. They emphasize the importance of geometry on the behavior of the dispersion tensor. Extension of these results to a larger-scale including the effect of heterogeneities is proposed in a limited case

  7. Aplicación de la metodología Molecular de Orbitales de Defecto Cuántico (MQDO) al cálculo de intensidades vibrónicas y vidas medias de niveles vibracionales (United States)

    María Velasco Sanz, Ana

    Desde que se formuló, en 1996, la metodología Molecular de Orbitales de Defecto Cuántico (MQDO) [1], se han obtenido datos de calidad relativos a intensidades de bandas electrónicas que implican estados Rydberg para una gran variedad de sistemas moleculares [2]. Animados por los buenos resultados obtenidos, recientemente hemos abordado el estudio de transiciones vibrónicas, es decir aquellas que ocurren entre estados vibracionales que pertenecen a distintos estados Rydberg electrónicos. Como prototipo adecuado para nuestros propósitos hemos elegido la molécula de NO, importante en la química de la atmósfera, y para la cual existen en la bibliografía datos experimentales de calidad suficiente para contrastar la validez de nuestros resultados. En concreto, hemos calculado las fuerzas de oscilador y coeficientes de Einstein para transiciones electrónicas y vibrónicas de las principales bandas del NO, al igual que vidas medias radiativas de niveles vibracionales de dicha molécula. Las propiedades estudiadas son esenciales para la comprensión de los aspectos teóricos de los procesos físicos básicos relativos a la dispersión electrónica en moléculas heteronucleares con capas abiertas. Además, valores fiables de probabilidades de transición moleculares tienen importantes aplicaciones en Astrofísica, en la modelización de procesos fotodinámicos moleculares, etc., al igual que para evaluar más profundamente la validez de nuestra metodología teórica.

  8. Improved Heterogeneous Distance Functions


    Wilson, D. R.; Martinez, T. R.


    Instance-based learning techniques typically handle continuous and linear input values well, but often do not handle nominal input attributes appropriately. The Value Difference Metric (VDM) was designed to find reasonable distance values between nominal attribute values, but it largely ignores continuous attributes, requiring discretization to map continuous values into nominal values. This paper proposes three new heterogeneous distance functions, called the Heterogeneous Value Difference M...


    National Research Council Canada - National Science Library

    Christine Weiser


      For the leaders assembled in the SchoolCIO working group, it seems the most successful implementations of social media use are found in those schools that recognize the importance of guiding students in their journey...

  10. From Augmentation Media to Meme Media. (United States)

    Tanaka, Yuzuru

    Computers as meta media are now evolving from augmentation media vehicles to meme media vehicles. While an augmentation media system provides a seamlessly integrated environment of various tools and documents, meme media system provides further functions to edit and distribute tools and documents. Documents and tools on meme media can easily…

  11. Community Media: Muting the Democratic Media Discourse?

    NARCIS (Netherlands)

    Carpentier, N.; Lie, R.; Servaes, J.


    Focuses on the concept of community media. Components that construct the identity of community media; Multi-theoretical approaches for analysis of community media; Definition of community media based on the concept of alternative media; Link between community media and civil society; Problems faced

  12. Media Bias


    Sendhil Mullainathan; Andrei Shleifer


    There are two different types of media bias. One bias, which we refer to as ideology, reflects a news outlet's desire to affect reader opinions in a particular direction. The second bias, which we refer to as spin, reflects the outlet's attempt to simply create a memorable story. We examine competition among media outlets in the presence of these biases. Whereas competition can eliminate the effect of ideological bias, it actually exaggerates the incentive to spin stories.

  13. Intertumoral Heterogeneity within Medulloblastoma Subgroups. (United States)

    Cavalli, Florence M G; Remke, Marc; Rampasek, Ladislav; Peacock, John; Shih, David J H; Luu, Betty; Garzia, Livia; Torchia, Jonathon; Nor, Carolina; Morrissy, A Sorana; Agnihotri, Sameer; Thompson, Yuan Yao; Kuzan-Fischer, Claudia M; Farooq, Hamza; Isaev, Keren; Daniels, Craig; Cho, Byung-Kyu; Kim, Seung-Ki; Wang, Kyu-Chang; Lee, Ji Yeoun; Grajkowska, Wieslawa A; Perek-Polnik, Marta; Vasiljevic, Alexandre; Faure-Conter, Cecile; Jouvet, Anne; Giannini, Caterina; Nageswara Rao, Amulya A; Li, Kay Ka Wai; Ng, Ho-Keung; Eberhart, Charles G; Pollack, Ian F; Hamilton, Ronald L; Gillespie, G Yancey; Olson, James M; Leary, Sarah; Weiss, William A; Lach, Boleslaw; Chambless, Lola B; Thompson, Reid C; Cooper, Michael K; Vibhakar, Rajeev; Hauser, Peter; van Veelen, Marie-Lise C; Kros, Johan M; French, Pim J; Ra, Young Shin; Kumabe, Toshihiro; López-Aguilar, Enrique; Zitterbart, Karel; Sterba, Jaroslav; Finocchiaro, Gaetano; Massimino, Maura; Van Meir, Erwin G; Osuka, Satoru; Shofuda, Tomoko; Klekner, Almos; Zollo, Massimo; Leonard, Jeffrey R; Rubin, Joshua B; Jabado, Nada; Albrecht, Steffen; Mora, Jaume; Van Meter, Timothy E; Jung, Shin; Moore, Andrew S; Hallahan, Andrew R; Chan, Jennifer A; Tirapelli, Daniela P C; Carlotti, Carlos G; Fouladi, Maryam; Pimentel, José; Faria, Claudia C; Saad, Ali G; Massimi, Luca; Liau, Linda M; Wheeler, Helen; Nakamura, Hideo; Elbabaa, Samer K; Perezpeña-Diazconti, Mario; Chico Ponce de León, Fernando; Robinson, Shenandoah; Zapotocky, Michal; Lassaletta, Alvaro; Huang, Annie; Hawkins, Cynthia E; Tabori, Uri; Bouffet, Eric; Bartels, Ute; Dirks, Peter B; Rutka, James T; Bader, Gary D; Reimand, Jüri; Goldenberg, Anna; Ramaswamy, Vijay; Taylor, Michael D


    While molecular subgrouping has revolutionized medulloblastoma classification, the extent of heterogeneity within subgroups is unknown. Similarity network fusion (SNF) applied to genome-wide DNA methylation and gene expression data across 763 primary samples identifies very homogeneous clusters of patients, supporting the presence of medulloblastoma subtypes. After integration of somatic copy-number alterations, and clinical features specific to each cluster, we identify 12 different subtypes of medulloblastoma. Integrative analysis using SNF further delineates group 3 from group 4 medulloblastoma, which is not as readily apparent through analyses of individual data types. Two clear subtypes of infants with Sonic Hedgehog medulloblastoma with disparate outcomes and biology are identified. Medulloblastoma subtypes identified through integrative clustering have important implications for stratification of future clinical trials. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. A stochastic model for tumor heterogeneity

    CERN Document Server

    Simone, Giuseppina


    Phenotype variations define heterogeneity of biological and molecular systems, which play a crucial role in several mechanisms. Heterogeneity has been demonstrated in tumor cells. Here, samples from blood of patients affected from colon tumor were analyzed and fished with a microfluidic assay based on galactose active moieties, and incubated, for culturing, in SCID mice. Following the experimental investigation, a model based on Markov theory was implemented and discussed to explain the equilibrium existing between phenotypes of subpopulations of cells sorted using the microfluidic assay. The model in combination with the experimental results had many implications for tumor heterogeneity. It displayed interconversion of phenotypes, as observed after experiments. The interconversion generates of metastatic cells and implies that targeting the CTCs will be not an efficient method to prevent tumor recurrence. Most importantly, understanding the transitions between cell phenotypes in cell population can boost the...

  15. Temporal disorder as a mechanism for spatially heterogeneous diffusion (United States)

    Bressloff, Paul C.; Lawley, Sean D.


    A fundamental issue in analyzing diffusion in heterogeneous media is interpreting the space dependence of the associated diffusion coefficient. This reflects the well-known Ito-Stratonovich dilemma for continuous stochastic processes with multiplicative noise. In order to resolve this dilemma it is necessary to introduce additional constraints regarding the underlying physical system. Here we introduce a mechanism for generating nonlinear Brownian motion based on a form of temporal disorder. Motivated by switching processes in molecular biology, we consider a Brownian particle that randomly switches between two distinct conformational states with different diffusivities. In each state the particle undergoes normal diffusion (additive noise) so there is no ambiguity in the interpretation of the noise. However, if the switching rates depend on position, then in the fast-switching limit one obtains Brownian motion with a space-dependent diffusivity. We show that the resulting multiplicative noise process is of the Ito form. In particular, we solve a first-passage time problem for finite switching rates and show that the mean first-passage time reduces to the Ito version in the fast-switching limit.

  16. Annotation of Heterogeneous Multimedia Content Using Automatic Speech Recognition

    NARCIS (Netherlands)

    Huijbregts, M.A.H.; Ordelman, Roeland J.F.; de Jong, Franciska M.G.


    This paper reports on the setup and evaluation of robust speech recognition system parts, geared towards transcript generation for heterogeneous, real-life media collections. The system is deployed for generating speech transcripts for the NIST/TRECVID-2007 test collection, part of a Dutch real-life

  17. Dynamical heterogeneity of star-polymers (United States)

    Emamy, Hamed; Chremos, Alexandros; Douglas, Jack; Starr, Francis

    The formation of a glass is one of the most vital features of amorphous polymers. While this subject has been exhaustively studied for linear chain polymers, comparatively little is known about the glass formation of star polymers, one of the most important classes of branched polymers. Using molecular dynamics simulation methods, we study the dynamical heterogeneity of star-polymers. We characterize the cooperative nature of the dynamic properties melts via the non-Gaussian nature of displacements, four-point correlations, clusters of highly mobile monomers, and subsets of string-like monomer motion. We contrast the behavior to that of ordinary linear chains, considering the role of both number of arms and molecular weight. In doing so, we quantify the degree to which the topology of star polymer plays a role in dynamical heterogeneity.

  18. Green heterogeneous wireless networks

    CERN Document Server

    Ismail, Muhammad; Nee, Hans-Peter; Qaraqe, Khalid A; Serpedin, Erchin


    This book focuses on the emerging research topic "green (energy efficient) wireless networks" which has drawn huge attention recently from both academia and industry. This topic is highly motivated due to important environmental, financial, and quality-of-experience (QoE) considerations. Specifically, the high energy consumption of the wireless networks manifests in approximately 2% of all CO2 emissions worldwide. This book presents the authors’ visions and solutions for deployment of energy efficient (green) heterogeneous wireless communication networks. The book consists of three major parts. The first part provides an introduction to the "green networks" concept, the second part targets the green multi-homing resource allocation problem, and the third chapter presents a novel deployment of device-to-device (D2D) communications and its successful integration in Heterogeneous Networks (HetNets). The book is novel in that it specifically targets green networking in a heterogeneous wireless medium, which re...

  19. Isotopes in heterogeneous catalysis

    CERN Document Server

    Hargreaves, Justin SJ


    The purpose of this book is to review the current, state-of-the-art application of isotopic methods to the field of heterogeneous catalysis. Isotopic studies are arguably the ultimate technique in in situ methods for heterogeneous catalysis. In this review volume, chapters have been contributed by experts in the field and the coverage includes both the application of specific isotopes - Deuterium, Tritium, Carbon-14, Sulfur-35 and Oxygen-18 - as well as isotopic techniques - determination of surface mobility, steady state transient isotope kinetic analysis, and positron emission profiling.

  20. Social media management and media environment


    Šiđanin Iva


    The paper deals with the system of services that social media management can offer to a variety of users. As social media systems are emerging, social media management can strengthen teams in social media and help to manage numerous social channels and distribution of social information from one place. Social media management is a system of procedures that are used to manage the flow of information in the environment of social media. This involves connecting with social media like Facebook, T...

  1. Glioblastoma Multiforme: A Look Inside Its Heterogeneous Nature

    Energy Technology Data Exchange (ETDEWEB)

    Inda, Maria-del-Mar, E-mail:; Bonavia, Rudy [Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron University Hospital, 119-129 Passeig Vall d’Hebron, Barcelona 08035 (Spain); Seoane, Joan [Translational Research Program, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron University Hospital, 119-129 Passeig Vall d’Hebron, Barcelona 08035 (Spain); Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08035 (Spain)


    Heterogeneity is a hallmark of tumors and has a crucial role in the outcome of the malignancy, because it not only confounds diagnosis, but also challenges the design of effective therapies. There are two types of heterogeneity: inter-tumor and intra-tumor heterogeneity. While inter-tumor heterogeneity has been studied widely, intra-tumor heterogeneity has been neglected even though numerous studies support this aspect of tumor pathobiology. The main reason has been the technical difficulties, but with new advances in single-cell technology, intra-tumor heterogeneity is becoming a key area in the study of cancer. Several models try to explain the origin and maintenance of intra-tumor heterogeneity, however, one prominent model compares cancer with a tree where the ubiquitous mutations compose the trunk and mutations present in subpopulations of cells are represented by the branches. In this review we will focus on the intra-tumor heterogeneity of glioblastoma multiforme (GBM), the most common brain tumor in adults that is characterized by a marked heterogeneity at the cellular and molecular levels. Better understanding of this heterogeneity will be essential to design effective therapies against this devastating disease to avoid tumor escape.

  2. Heterogeneous and Homogeneous Routes in Water Oxidation Catalysis Starting from Cu(II) Complexes with Tetraaza Macrocyclic Ligands. (United States)

    Prevedello, Andrea; Bazzan, Irene; Dalle Carbonare, Nicola; Giuliani, Angela; Bhardwaj, Sunil; Africh, Cristina; Cepek, Cinzia; Argazzi, Roberto; Bonchio, Marcella; Caramori, Stefano; Robert, Marc; Sartorel, Andrea


    Since the first report in 2012, molecular copper complexes have been proposed as efficient electrocatalysts for water oxidation reactions, carried out in alkaline/neutral aqueous media. However, in some cases the copper species have been recognized as precursors of an active copper oxide layer, electrodeposited onto the working electrode. Therefore, the question whether copper catalysis is molecular or not is particularly relevant in the field of water oxidation. In this study, we investigate the electrochemical activity of copper(II) complexes with two tetraaza macrocyclic ligands, distinguishing heterogeneous or homogeneous processes depending on the reaction media. In an alkaline aqueous solution, and upon application of an anodic bias to working electrodes, an active copper oxide layer is observed to electrodeposit at the electrode surface. Conversely, water oxidation in neutral aqueous buffers is not associated to formation of the copper oxide layer, and could be exploited to evaluate and optimize a molecular, homogeneous catalysis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Media Training

    CERN Multimedia

    CERN. Geneva


    With the LHC starting up soon, the world's media are again turning their attention to CERN. We're all likely to be called upon to explain what is happening at CERN to media, friends and neighbours. The seminar will be given by BBC television news journalists Liz Pike and Nadia Marchant, and will deal with the kind of questions we're likely to be confronted with through the restart period. The training is open for everybody. Make sure you arrive early enough to get a seat - there are only 200 seats in the Globe. The session will also be webcast:

  4. On the relationship between corrosion inhibiting effect and molecular structure of 2,5-bis(n-pyridyl)-1,3,4-thiadiazole derivatives in acidic media: Ac impedance and DFT studies

    Energy Technology Data Exchange (ETDEWEB)

    Bentiss, F., E-mail: fbentiss@enscl.f [Laboratoire de Chimie de Coordination et d' Analytique (LCCA), Faculte des Sciences, Universite Chouaib Doukkali, B.P. 20, M-24000 El Jadida (Morocco); Mernari, B. [Laboratoire de Chimie de Coordination et d' Analytique (LCCA), Faculte des Sciences, Universite Chouaib Doukkali, B.P. 20, M-24000 El Jadida (Morocco); Traisnel, M. [Unite Materiaux et Transformations (UMET), Ingenierie des Systemes Polymeres, CNRS UMR 8207, ENSCL, B.P. 90108, F-59652 Villeneuve d' Ascq Cedex (France); Vezin, H. [Laboratoire de Spectrochimie Infrarouge et Raman (LASIR), UMR-CNRS 8516, Universite des Sciences et Technologies de Lille, Batiment C5, F-59655 Villeneuve d' Ascq Cedex (France); Lagrenee, M., E-mail: michel.lagrenee@ensc-lille.f [Unite de Catalyse et de Chimie du Solide (UCCS), UMR-CNRS 8181, ENSCL, B.P. 90108, F-59652 Villeneuve d' Ascq Cedex (France)


    Research highlights: {yields}2,5-Bis(n-pyridyl)-1,3,4-thiadiazoles (n-PTH) act as good inhibitors for the mild steel in acidic media. {yields}The inhibiting protection depends on the position of the nitrogen on the pyridinium substituent according to order 3-PTH > 2-PTH > 4-PTH. {yields}The adsorption of n-PTH is found to follow the Langmuir's adsorption isotherm. {yields}Data obtained from quantum chemical calculations using DFT method were correlated to the experimentally obtained inhibition efficiencies. - Abstract: The inhibition properties of 2,5-bis(n-pyridyl)-1,3,4-thiadiazoles (n-PTH) on corrosion of mild steel in different acidic media (1 M HCl, 0.5 M H{sub 2}SO{sub 4} and 1 M HClO{sub 4}) were analyzed by electrochemical impedance spectroscopy (EIS). The n-PTH derivatives exhibit good inhibition properties in different acidic solutions and the calculated values of {Delta}G{sub ads}{sup 0} revealed that the adsorption mechanism of n-PTH on steel surface is mainly due to chemisorption. While in 1 M HClO{sub 4}, both 2-PTH and 4-PTH isomers stimulate the corrosion process especially at low concentrations. Quantum chemical calculations using the density functional theory (DFT) were performed on n-PTH derivatives to determine the relationship between molecular structure and their inhibition efficiencies. The results of the quantum chemical calculations and experimental inhibition efficiency were subjected to correlation analysis and indicate that the inhibition effects of n-PTH may be explained in terms of electronic properties.

  5. Heterogeneity and option pricing

    NARCIS (Netherlands)

    Benninga, Simon; Mayshar, Joram


    An economy with agents having constant yet heterogeneous degrees of relative risk aversion prices assets as though there were a single decreasing relative risk aversion pricing representative agent. The pricing kernel has fat tails and option prices do not conform to the Black-Scholes formula.

  6. Why does heterogeneity matter? (United States)

    K.B. Pierce


    This is a review of the book "Ecosystem function in heterogeneous landscapes" published in 2005. The authors are G. Lovett, C. Jones, M.G. Turner, and K.C. Weathers. It was published by Springer, New York. The book is a synthesis of the 10th Gary conference held at the Institute of Ecosystem Studies in Millbrook, New York, in 2003.

  7. Heterogeneous chromium catalysts

    NARCIS (Netherlands)


    The present invention relates to a heterogeneous chromium catalyst system for the polymerisation of ethylene and/or alpha olefins prepared by the steps of: (a) providing a silica-containing support, (b) treating the silica-containing support with a chromium compound to form a chromium-based

  8. Receiver Heterogeneity Helps

    DEFF Research Database (Denmark)

    Kovács, Erika R.; Pedersen, Morten Videbæk; Roetter, Daniel Enrique Lucani


    Heterogeneity amongst devices and desired service are commonly seen as a source of additional challenges for setting up an efficient multi-layer multicast service. In particular, devices requiring only the base layer can become a key bottleneck to the performance for other devices. This paper...

  9. Heterogeneity of Intellectual Assets

    DEFF Research Database (Denmark)

    Dahlgren, Johan Henrich; Lund Jensen, Rasmus; Valentin, Finn


    This paper deals with methodological issues of assessing the composition and level ofheterogeneity of firms' intellectual assets. It develops an original metric - referred to asthe H-index - for measuring heterogeneity using data extracted from patent documents.The main purpose is to improve...

  10. Quantifying hidden individual heterogeneity

    DEFF Research Database (Denmark)

    Steiner, Ulrich; Lenart, Adam; Vaupel, James W.

    Aging is assumed to be driven by the accumulation of damage or some other aging factor which shapes demographic patterns, including the classical late age mortality plateaus. However to date, heterogeneity in these damage stages is not observed. Here, we estimate underlying stage distributions...

  11. Heterogeneity of Dutch rainfall

    NARCIS (Netherlands)

    Witter, J.V.


    Rainfall data for the Netherlands have been used in this study to investigate aspects of heterogeneity of rainfall, in particular local differences in rainfall levels, time trends in rainfall, and local differences in rainfall trend. The possible effect of urbanization and industrialization on the

  12. Heterogeneous computing in economics

    DEFF Research Database (Denmark)

    Dziubinski, Matt P.; Grassi, Stefano


    This paper shows the potential of heterogeneous computing in solving dynamic equilibrium models in economics. We illustrate the power and simplicity of C++ Accelerated Massive Parallelism (C++ AMP) recently introduced by Microsoft. Starting from the same exercise as Aldrich et al. (J Econ Dyn...

  13. Scales of mantle heterogeneity (United States)

    Moore, J. C.; Akber-Knutson, S.; Konter, J.; Kellogg, J.; Hart, S.; Kellogg, L. H.; Romanowicz, B.


    A long-standing question in mantle dynamics concerns the scale of heterogeneity in the mantle. Mantle convection tends to both destroy (through stirring) and create (through melt extraction and subduction) heterogeneity in bulk and trace element composition. Over time, these competing processes create variations in geochemical composition along mid-oceanic ridges and among oceanic islands, spanning a range of scales from extremely long wavelength (for example, the DUPAL anomaly) to very small scale (for example, variations amongst melt inclusions). While geochemical data and seismic observations can be used to constrain the length scales of mantle heterogeneity, dynamical mixing calculations can illustrate the processes and timescales involved in stirring and mixing. At the Summer 2004 CIDER workshop on Relating Geochemical and Seismological Heterogeneity in the Earth's Mantle, an interdisciplinary group evaluated scales of heterogeneity in the Earth's mantle using a combined analysis of geochemical data, seismological data and results of numerical models of mixing. We mined the PetDB database for isotopic data from glass and whole rock analyses for the Mid-Atlantic Ridge (MAR) and the East Pacific Rise (EPR), projecting them along the ridge length. We examined Sr isotope variability along the East Pacific rise by looking at the difference in Sr ratio between adjacent samples as a function of distance between the samples. The East Pacific Rise exhibits an overall bowl shape of normal MORB characteristics, with higher values in the higher latitudes (there is, however, an unfortunate gap in sampling, roughly 2000 km long). These background characteristics are punctuated with spikes in values at various locations, some, but not all of which are associated with off-axis volcanism. A Lomb-Scargle periodogram for unevenly spaced data was utilized to construct a power spectrum of the scale lengths of heterogeneity along both ridges. Using the same isotopic systems (Sr, Nd

  14. Digital Humanities and networked digital media

    DEFF Research Database (Denmark)

    Finnemann, Niels Ole


    This article discusses digital humanities and the growing diversity of digital media, digital materials and digital methods. The first section describes the humanities computing tradition formed around the interpretation of computation as a rule-based process connected to a concept of digital...... of software-supported methods. This is so, in part, because of the complexity of the world and, in part, because digital media remain open to the projection of new epistemologies onto the functional architecture of these media. The third section discusses the heterogeneous character of digital materials...

  15. Convection in Porous Media

    CERN Document Server

    Nield, Donald A


    Convection in Porous Media, 4th Edition, provides a user-friendly introduction to the subject, covering a wide range of topics, such as fibrous insulation, geological strata, and catalytic reactors. The presentation is self-contained, requiring only routine mathematics and the basic elements of fluid mechanics and heat transfer. The book will be of use not only to researchers and practicing engineers as a review and reference, but also to graduate students and others entering the field. The new edition features approximately 1,750 new references and covers current research in nanofluids, cellular porous materials, strong heterogeneity, pulsating flow, and more. Recognized as the standard reference in the field Includes a comprehensive, 250-page reference list Cited over 2300 times to date in its various editions Serves as an introduction for those entering the field and as a comprehensive reference for experienced researchers Features new sections on nanofluids, carbon dioxide sequestration, and applications...

  16. Otitis media

    NARCIS (Netherlands)

    Rovers, MM; Schilder, AGM; Zielhuis, GA; Rosenfeld, RM


    Otitis media (OM) continues to be one of the most common childhood infections and is a major cause of morbidity in children. The pathogenesis of OM is multifactorial, involving the adaptive and native immune system, Eustachian-tube dysfunction, viral and bacterial load, and genetic and environmental

  17. Social Media (United States)


    Digital Marketing and Ecommerce Professionals. 29 January 2010. 20 May 2010. < media...Statistics Revisited.” Econsultancy | Community of Digital Marketing and Ecommerce Professionals. 29 Jan. 2010. 20 May 2010. <

  18. Streaming Media (United States)

    Pulley, John


    At a time when the evolutionary pace of new media resembles the real-time mutation of certain microorganisms, the age-old question of how best to connect with constituents can seem impossibly complex--even for an elite institution plugged into the motherboard of Silicon Valley. Identifying the most effective vehicle for reaching a particular…

  19. Defining, distinguishing and detecting the contribution of heterogeneous methylation to cancer heterogeneity. (United States)

    Pisanic, Thomas R; Athamanolap, Pornpat; Wang, Tza-Huei


    DNA methylation is a fundamental means of epigenetic gene regulation that occurs in virtually all cell types. In many higher organisms, including humans, it plays vital roles in cell differentiation and homeostatic maintenance of cell phenotype. The control of DNA methylation has traditionally been attributed to a highly coordinated, linear process, whose dysregulation has been associated with numerous pathologies including cancer, where it occurs early in, and even prior to, the development of neoplastic tissues. Recent experimental evidence has demonstrated that, contrary to prevailing paradigms, methylation patterns are actually maintained through inexact, dynamic processes. These processes normally result in minor stochastic differences between cells that accumulate with age. However, various factors, including cancer itself, can lead to substantial differences in intercellular methylation patterns, viz. methylation heterogeneity. Advancements in molecular biology techniques are just now beginning to allow insight into how this heterogeneity contributes to clonal evolution and overall cancer heterogeneity. In the current review, we begin by presenting a didactic overview of how the basal bimodal methylome is established and maintained. We then provide a synopsis of some of the factors that lead to the accrual of heterogeneous methylation and how this heterogeneity may lead to gene silencing and impact the development of cancerous phenotypes. Lastly, we highlight currently available methylation assessment techniques and discuss their suitability to the study of heterogeneous methylation. Copyright © 2016. Published by Elsevier Ltd.

  20. Panel 7: Otitis Media: Treatment and Complications. (United States)

    Schilder, Anne G M; Marom, Tal; Bhutta, Mahmood F; Casselbrant, Margaretha L; Coates, Harvey; Gisselsson-Solén, Marie; Hall, Amanda J; Marchisio, Paola; Ruohola, Aino; Venekamp, Roderick P; Mandel, Ellen M


    Objective We aimed to summarize key articles published between 2011 and 2015 on the treatment of (recurrent) acute otitis media, otitis media with effusion, tympanostomy tube otorrhea, chronic suppurative otitis media and complications of otitis media, and their implications for clinical practice. Data Sources PubMed, Ovid Medline, the Cochrane Library, and Clinical Evidence (BMJ Publishing). Review Methods All types of articles related to otitis media treatment and complications between June 2011 and March 2015 were identified. A total of 1122 potential related articles were reviewed by the panel members; 118 relevant articles were ultimately included in this summary. Conclusions Recent literature and guidelines emphasize accurate diagnosis of acute otitis media and optimal management of ear pain. Watchful waiting is optional in mild to moderate acute otitis media; antibiotics do shorten symptoms and duration of middle ear effusion. The additive benefit of adenoidectomy to tympanostomy tubes in recurrent acute otitis media and otitis media with effusion is controversial and age dependent. Topical antibiotic is the treatment of choice in acute tube otorrhea. Symptomatic hearing loss due to persistent otitis media with effusion is best treated with tympanostomy tubes. Novel molecular and biomaterial treatments as adjuvants to surgical closure of eardrum perforations seem promising. There is insufficient evidence to support the use of complementary and alternative treatments. Implications for Practice Emphasis on accurate diagnosis of otitis media, in its various forms, is important to reduce overdiagnosis, overtreatment, and antibiotic resistance. Children at risk for otitis media and its complications deserve special attention.

  1. Dynamic deformation of heterogeneous media: A materials scientist's perspective (United States)

    Kumar, Mukul


    Traditionally, materials design assumes full density during the usage of materials, and rather explicitly excludes open spaces. However, with increasing usage in structural applications of cellular solids and the advent of additive manufacturing to make intricate shapes this assumption is flying out the window. But this raises the question of how we deal with the underlying physics associated with the void space, particularly when such materials architectures are dynamically loaded. This builds upon decades of work on granular systems, particularly powder composites and sand. Using as examples polymeric structured lattices and particle composite mixtures we will examine the influence of the void space on the overall response of the material mesostructure. This work was performed under the auspices of the US DOE by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  2. Dynamical heterogeneities in glasses colloids and granular media

    CERN Document Server


    Most everyday solid materials, from plastics to cosmetic gels, exist in a non-crystalline, amorphous form: they are glasses. Yet we are still seeking an explanation as to what glasses really are and to why they form. Here, leading experts present broad perspectives on one of the deepest mysteries of condensed matter physics.

  3. A mathematical framework for inverse wave problems in heterogeneous media

    NARCIS (Netherlands)

    Blazek, K.D.; Stolk, C.; Symes, W.W.


    This paper provides a theoretical foundation for some common formulations of inverse problems in wave propagation, based on hyperbolic systems of linear integro-differential equations with bounded and measurable coefficients. The coefficients of these time-dependent partial differential equations

  4. Multiscale gradient computation for flow in heterogeneous porous media (United States)

    Moraes, Rafael J. de; Rodrigues, José R. P.; Hajibeygi, Hadi; Jansen, Jan Dirk


    An efficient multiscale (MS) gradient computation method for subsurface flow management and optimization is introduced. The general, algebraic framework allows for the calculation of gradients using both the Direct and Adjoint derivative methods. The framework also allows for the utilization of any MS formulation that can be algebraically expressed in terms of a restriction and a prolongation operator. This is achieved via an implicit differentiation formulation. The approach favors algorithms for multiplying the sensitivity matrix and its transpose with arbitrary vectors. This provides a flexible way of computing gradients in a form suitable for any given gradient-based optimization algorithm. No assumption w.r.t. the nature of the problem or specific optimization parameters is made. Therefore, the framework can be applied to any gradient-based study. In the implementation, extra partial derivative information required by the gradient computation is computed via automatic differentiation. A detailed utilization of the framework using the MS Finite Volume (MSFV) simulation technique is presented. Numerical experiments are performed to demonstrate the accuracy of the method compared to a fine-scale simulator. In addition, an asymptotic analysis is presented to provide an estimate of its computational complexity. The investigations show that the presented method casts an accurate and efficient MS gradient computation strategy that can be successfully utilized in next-generation reservoir management studies.

  5. Multiscale stabilization for convection-dominated diffusion in heterogeneous media

    KAUST Repository

    Calo, Victor M.


    We develop a Petrov-Galerkin stabilization method for multiscale convection-diffusion transport systems. Existing stabilization techniques add a limited number of degrees of freedom in the form of bubble functions or a modified diffusion, which may not be sufficient to stabilize multiscale systems. We seek a local reduced-order model for this kind of multiscale transport problems and thus, develop a systematic approach for finding reduced-order approximations of the solution. We start from a Petrov-Galerkin framework using optimal weighting functions. We introduce an auxiliary variable to a mixed formulation of the problem. The auxiliary variable stands for the optimal weighting function. The problem reduces to finding a test space (a dimensionally reduced space for this auxiliary variable), which guarantees that the error in the primal variable (representing the solution) is close to the projection error of the full solution on the dimensionally reduced space that approximates the solution. To find the test space, we reformulate some recent mixed Generalized Multiscale Finite Element Methods. We introduce snapshots and local spectral problems that appropriately define local weight and trial spaces. In particular, we use energy minimizing snapshots and local spectral decompositions in the natural norm associated with the auxiliary variable. The resulting spectral decomposition adaptively identifies and builds the optimal multiscale space to stabilize the system. We discuss the stability and its relation to the approximation property of the test space. We design online basis functions, which accelerate convergence in the test space, and consequently, improve stability. We present several numerical examples and show that one needs a few test functions to achieve an error similar to the projection error in the primal variable irrespective of the Peclet number.

  6. Mass transfer in porous media with heterogeneous chemical reaction

    Directory of Open Access Journals (Sweden)

    Souza S.M.A.G.Ulson de


    Full Text Available In this paper, the modeling of the mass transfer process in packed-bed reactors is presented and takes into account dispersion in the main fluid phase, internal diffusion of the reactant in the pores of the catalyst, and surface reaction inside the catalyst. The method of volume averaging is applied to obtain the governing equation for use on a small scale. The local mass equilibrium is assumed for obtaining the one-equation model for use on a large scale. The closure problems are developed subject to the length-scale constraints and the model of a spatially periodic porous medium. The expressions for effective diffusivity, hydrodynamic dispersion, total dispersion and the Darcy's law permeability tensors are presented. Solution of the set of final equations permits the variations of velocity and concentration of the chemical species along the packed-bed reactors to be obtained.

  7. [Chronic otitis mediaChronic Otitis Media]. (United States)

    Kohles, N; Schulz, T; Eßer, D


    There are 2 different kinds of chronic otitis media: Otitis media chronica mesotympanalis and otitis media chronica epitympanalis (cholesteatoma). The incidence of chronic otitis media as reported in literature differs in a wide range. The incidence rates vary between 0.45 and 46%. Both, otitis media chronica mesotympanalis and cholesteatoma, lead to eardrum perforation due to lengthy and recurring inflammations. Furthermore, chronic otitis media is characterized by frequently recurring otorrhea and conductive hearing loss. Georg Thieme Verlag KG Stuttgart · New York.

  8. Praktik Internasionalisasi Media Beritasatu Media Holdings


    Endang SM, Anis


    This study aimed to determine the practice of Internationalization carried out by BeritaSatu Media Holdings in supporting global economic interests of Lippo Group Company. Internationalization is an implication of media industrialization which the media company owner sought to reduce the spatial distance to obtain greater profits. Theory of Political Economy Media used to see how media content represents the interests of certain political economy, especially from media owners. To view the pra...

  9. Tumour Heterogeneity: The Key Advantages of Single-Cell Analysis (United States)

    Tellez-Gabriel, Marta; Ory, Benjamin; Lamoureux, Francois; Heymann, Marie-Francoise; Heymann, Dominique


    Tumour heterogeneity refers to the fact that different tumour cells can show distinct morphological and phenotypic profiles, including cellular morphology, gene expression, metabolism, motility, proliferation and metastatic potential. This phenomenon occurs both between tumours (inter-tumour heterogeneity) and within tumours (intra-tumour heterogeneity), and it is caused by genetic and non-genetic factors. The heterogeneity of cancer cells introduces significant challenges in using molecular prognostic markers as well as for classifying patients that might benefit from specific therapies. Thus, research efforts for characterizing heterogeneity would be useful for a better understanding of the causes and progression of disease. It has been suggested that the study of heterogeneity within Circulating Tumour Cells (CTCs) could also reflect the full spectrum of mutations of the disease more accurately than a single biopsy of a primary or metastatic tumour. In previous years, many high throughput methodologies have raised for the study of heterogeneity at different levels (i.e., RNA, DNA, protein and epigenetic events). The aim of the current review is to stress clinical implications of tumour heterogeneity, as well as current available methodologies for their study, paying specific attention to those able to assess heterogeneity at the single cell level. PMID:27999407

  10. Information and Heterogeneous Beliefs

    DEFF Research Database (Denmark)

    Christensen, Peter Ove; Qin, Zhenjiang


    In an incomplete market with heterogeneous prior beliefs, we show public information can have a substantial impact on the ex ante cost of capital, trading volume, and investor welfare. The Pareto effcient public information system is the system enjoying the maximum ex ante cost of capital...... ante risk premium is unaffected by the informativeness of the public information system. Similar results are obtained in a production economy, but the impact on the ex ante cost of capital is dampened compared to the exchange economy due to welfare improving reductions in real investments to smooth...... and the maximum expected abnormal trading volume. Imperfect public information increases the gains-to-trade based on heterogeneously updated posterior beliefs. In an exchange economy, this leads to higher growth in the investors' certainty equivalents and, thus, a higher equilibrium interest rate, whereas the ex...



    the “product component” is a result of technology push only, it struggles to fit into a conservative system environment . If the “product component...makes the categorization difficult. In a technology push environment , the evolution of technology is easier to track since it starts evolving from a... environmental information. The role of the heterogeneous integration technology for reducing the size and the power consumption of small sensors was studied

  12. Heterogeneous chromium catalysts



    The present invention relates to a heterogeneous chromium catalyst system for the polymerisation of ethylene and/or alpha olefins prepared by the steps of: (a) providing a silica-containing support, (b) treating the silica-containing support with a chromium compound to form a chromium-based silica-containing support, (c) activating the chromium-based silica-containing support, (d) chemically reducing the activated chromium-based silica-containing support to produce a precursor catalyst, (e) r...

  13. Otitis media with effusion (United States)

    OME; Secretory otitis media; Serous otitis media; Silent otitis media; Silent ear infection; Glue ear ... Kerschner JE, Preciado D. Otitis media. In: Kliegman RM, Stanton BF, St. ... of Pediatrics . 20th ed. Philadelphia, PA: Elsevier; 2016: ...

  14. Genetic Characteristics of Glioblastoma: Clinical Implications of Heterogeneity

    Directory of Open Access Journals (Sweden)

    Qian Li


    Full Text Available Glioblastoma multiforme (GBM is a heterogeneous group of tumors, each with its own distinct molecular and genetic signatures. This heterogeneity is a major clinical hurdle for classifying tumors and for devising effective personalized therapies targeting the disease pathways. Herein, the primary genetic and epigenetic alterations in GBM that have been used as therapeutic targets in clinical settings nowadays, with or without clinical benefits for patients, as well as the future directions for developing novel strategies were discussed.

  15. Molecular sensing behavior of di-2-pyridyl ketone p-aminophenylhydrazone hydrate (dpkabh·H 2O) in non-aqueous media (United States)

    Bakir, Mohammed; Green, Orville; Gyles, Colin


    1H NMR studies on di-2-pyridyl ketone p-aminobenzoylhydrazone hydrate (dpkabh·H 2O) in non-aqueous solvents show high sensitivity to its surrounding. In protophilic solvents ( d6-dmso or d7-dmf), the amine protons are equivalent, while in CDCl 3 they are not. Variable temperature analysis in CDCL 3 show the NH proton to exhibit high temperature dependence due to strong intra-molecular hydrogen bonding of the type N-H⋯N between the amide (NH) and N atom of a pyridine ring. The temperature dependence for the same proton in d6-dmso and d7-dmf is due to hydrogen bonding of the type N-H⋯O between the amide proton and oxygen atom of the solvent. Optical measurements on dpkabh·H 2O show one intra-ligand charge transfer (ILCT) transition in CH 2Cl 2 and in protophilic solvents, two ILCT of the donor-acceptor type due to dpkabh·H 2O and its conjugate base appeared. Variable temperature studies on protophilic solution of dpkabh·H 2O confirm the sensitivity of dpkabh·H 2O to its surroundings and show facile reversible inter-conversion between dpkabh·H 2O and its conjugate base. Changes in enthalpy (Δ Hϕ) of -5.2 ± 0.4 and -24.2 ± 1.20 kJ mol -1, entropy (Δ Sϕ) of +9.6 ± 0.5 and -63.0 ± 2.0 JK -1 mol -1, and free energy (Δ Gϕ) of +2.3 ± 0.2 and +5.4 ± 0.2 kJ mol -1 were calculated for dpkabh·H 2O at 298 K in dmso and dmf, respectively. When stoichiometric amounts of NaBH 4 or MCl 2 (M = Zn, Cd or Hg) were added to protophilic solution of dpkanh·H 2O conversion from the high to low energy electronic transition was observed and show that substrates in low concentrations can be detected and determined using protophilic solution of dpkabh·H 2O.

  16. Media places

    DEFF Research Database (Denmark)

    Linde, Per; Messeter, Jörn

    are no longer neutral layers in urban living, but rather an integrated part of the materialities of architecture and urban planning, the social dimensions of city life and emerging new cultural frameworks. Arguably, we have reached a point at which digital designs may be regarded as elements of our everyday...... for the Media places project, give some brief insights into the themes of setting up temporary digital streams of media and mobile games. Considering the work-in-progress character of the research and the smaller format of text, no real in-depth analysis will be carried out. The goal is rather to position...... construction of place in the urban setting. The concept of Hertzian space, put forth by Anthony Dunne and others (Dunne, 1999) also carries a dimension of how spaces of wireless communication may be problematized, and how we can criticize cultural phenomena taken for granted through innovative technology. From...

  17. Deformation of Heterogeneous Nanocrystalline Lamella with a Preexisting Crack (United States)

    Huang, Sixie; Wang, Jian; Zhou, Caizhi


    Molecular dynamics simulations were performed on heterogeneous nanocrystalline Al lamellae composed of nanocrystalline (NC) and single-crystalline (SC) layers to study the effect of the heterogeneous microstructures on the propagation of preexisting cracks. Under tensile loading, the heterogeneous NC Al lamella exhibited higher crack growth resistance than the pure NC Al. In addition, a lower volume fraction of the NC layer provided better crack growth resistance in heterogeneous lamellae (HL) samples, which agrees well with previous experiment results. After analyzing the distribution of the atom-level virial stress and microstructure evolution during the deformation, we found that the average stress on grain boundary atoms was much lower in HL samples than that in pure NC sample. When the crack approaches the interface, the heterogeneous microstructure can reduce the stress concentration by emitting dislocations from the interface into the SC layer.

  18. Dynamic heterogeneity in life histories

    DEFF Research Database (Denmark)

    Tuljapurkar, Shripad; Steiner, Uli; Orzack, Steven Hecht


    generate dynamic heterogeneity: life-history differences produced by stochastic stratum dynamics. We characterize dynamic heterogeneity in a range of species across taxa by properties of the Markov chain: the entropy, which describes the extent of heterogeneity, and the subdominant eigenvalue, which...... distributions of lifetime reproductive success. Dynamic heterogeneity contrasts with fixed heterogeneity: unobserved differences that generate variation between life histories. We show by an example that observed distributions of lifetime reproductive success are often consistent with the claim that little...... or no fixed heterogeneity influences this trait. We propose that dynamic heterogeneity provides a 'neutral' model for assessing the possible role of unobserved 'quality' differences between individuals. We discuss fitness for dynamic life histories, and the implications of dynamic heterogeneity...

  19. Molecular imaging as a tool to investigate heterogeneity of advanced HER2-positive breast cancer and to predict patient outcome under trastuzumab emtansine (T-DM1): the ZEPHIR trial

    NARCIS (Netherlands)

    Gebhart, G.; Lamberts, L.E.; Wimana, Z.; Garcia, C.; Emonts, P.; Ameye, L.; Stroobants, S.; Huizing, M.; Aftimos, P.; Tol, J.; Oyen, W.J.G.; Vugts, D.J.; Hoekstra, O.S.; Schroder, C.P.; Oordt, C.W. Menke-van der H; Guiot, T.; Brouwers, A.H.; Awada, A.; Vries, E.G. de; Flamen, P.


    BACKGROUND: Only human epidermal growth factor receptor (HER)2 status determined by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) has been validated to predict efficacy of HER2-targeting antibody-drug-conjugate trastuzumab emtansine (T-DM1). We propose molecular imaging to

  20. Media matters. (United States)

    Martinez, L M


    The impact of the mass media on woman's status was addressed at two 1995 conferences: the Fourth World Conference on Women, held in Beijing, China, and the Congress of the World Association for Christian Communication, held in Puebla, Mexico. The globalization process facilitated by the mass media has served to increase the power of patriarchy, with no advantages to the cause of women's rights. Coverage of popular movements has been suppressed out of deference to male-controlled governments. Coverage of the Beijing Conference highlighted celebrities and personal stories, to the exclusion of the economic and political issues under debate. Television has commodified women, reinforcing their oppression. On the other hand, the alternative media, which tend to be decentralized, democratic, low-cost, and low in technology, are presenting women as subjects rather than objects and deconstructing gender stereotypes. Of concern, however, is the tendency of computer technology to widen the gap between social classes and developed and developing countries. Women must use information networks to disseminate information on women's rights and strengthen the links between women throughout the world.

  1. Genetic heterogeneity of retinitis pigmentosa


    Hartono, Hartono


    Genetic heterogeneity is a phenomenon in which a genetic disease can be transmitted by several modes of inheritance. The understanding of genetic heterogeneity is important in giving genetic counselling.The presence of genetic heterogeneity can be explained by the existence of:1.different mutant alleles at a single locus, and2.mutant alleles at different loci affecting the same enzyme or protein, or affecting different enzymes or proteins.To have an overall understanding of genetic heterogene...

  2. Media Education Initiatives by Media Organizations: The Uses of Media Literacy in Hong Kong Media (United States)

    Chu, Donna; Lee, Alice Y. L.


    As more media organizations have engaged in media education, this paper investigates the goals and practices of these activities. This article coins media education initiatives by media organizations with the term "media-organization media literac"y (MOML). Four MOML projects in Hong Kong were selected for examination. Built on critical…

  3. The coalescence of heterogeneous liquid metal on nano substrate (United States)

    Wang, Long; Li, Yifan; Zhou, Xuyan; Li, Tao; Li, Hui


    Molecular dynamics simulation has been performed to study the asymmetric coalescence of heterogeneous liquid metal on graphene. Simulation results show that the anomalies in the drop coalescence is mainly caused by the wettability of heterogeneous liquid metal. The silver atoms incline to distribute on the outer layer of the gold and copper droplets, revealing that the structure is determined by the interaction between different metal atoms. The coalescence and fusion of heterogeneous liquid metal drop can be predicted by comparing the wettability and the atomic mass of metallic liquid drops, which has important implications in the industrial application such as ink-jet printing and metallurgy.

  4. Dialysis and contrast media

    Energy Technology Data Exchange (ETDEWEB)

    Morcos, Sameh K. [Department of Diagnostic Imaging, Northern General Hospital, Sheffield Teaching Hospitals NHS Trust, Sheffield S5 7AU (United Kingdom); Thomsen, Henrik S. [Department of Diagnostic Radiology 54E2, Copenhagen University Hospital at Herlev, Herlev Ringvej 75, 2730 Herlev (Denmark); Webb, Judith A.W. [Department of Diagnostic Imaging, St Bartholomew' s Hospital, London EC1A 7BE (United Kingdom)


    In a previous survey we revealed uncertainty among responders about (a) whether or not to perform hemodialysis in patients with severely reduced renal function who had received contrast medium; and (b) when to perform hemodialysis in patients on regular treatment with hemodialysis or continuous ambulatory dialysis who received contrast medium. Therefore, the Contrast Media Safety Committee of The European Society of Urogenital Radiology decided to review the literature and to issue guidelines. The committee performed a Medline search. Based on this, a report and guidelines were prepared. The report was discussed at the Ninth European Symposium on Urogenital Radiology in Genoa, Italy. Hemodialysis and peritoneal dialysis safely remove both iodinated and gadolinium-based contrast media. The effectiveness of hemodialysis depends on many factors including blood and dialysate flow rate, permeability of dialysis membrane, duration of hemodialysis and molecular size, protein binding, hydrophilicity, and electrical charge of the contrast medium. Generally, several hemodialysis sessions are needed to removal all contrast medium, whereas it takes 3 weeks for continuous ambulatory dialysis to remove the agent completely. There is no need to schedule the dialysis in relation to the injection of iodinated or MR contrast media or the injection of contrast agent in relation to the dialysis program. Hemodialysis does not protect poorly functioning kidneys against contrast-medium-induced nephrotoxicity. Simple guidelines are given. (orig.)

  5. Critical media pedagogy - theoretical underpinning and contribution to media education


    Valenta, Petr


    Critical media pedagogy - theoretical underpinnigs and contribution to media education Dissertation Mgr. Petr Valenta Keywords critical theory, critical media pedagogy, media literacy, critical pedagogy, media, ideology, discourse, power, symbolic power, knowledge Abstract The theoretical dissertation analyzes the traditional media education model issues, which derives from the orientation of media literacy on the dominant paradigm of media effects research in media studies. Media education t...

  6. Poromechanics of microporous media (United States)

    Brochard, L.; Vandamme, M.; Pellenq, R. J.-M.


    Microporous media, i.e., porous media made of pores with a nanometer size, are important for a variety of applications, for instance for sequestration of carbon dioxide in coal, or for storage of hydrogen in metal-organic frameworks. In a pore of nanometer size, fluid molecules are not in their bulk state anymore since they interact with the atoms of the solid: they are said to be in an adsorbed state. For such microporous media, conventional poromechanics breaks down. In this work we derive poroelastic constitutive equations which are valid for a generic porous medium, i.e., even for a porous medium with pores of nanometer size. The complete determination of the poromechanical behavior of a microporous medium requires knowing how the amount of fluid adsorbed depends on both the fluid bulk pressure and the strain of the medium. The derived constitutive equations are validated with the help of molecular simulations on one-dimensional microporous media. Even when a microporous medium behaves linearly in the absence of any fluid (i.e., its bulk modulus does not depend on strain), we show that fluid adsorption can induce non-linear behavior (i.e., its drained bulk modulus can then depend significantly on strain). We also show that adsorption can lead to an apparent Biot coefficient of the microporous medium greater than unity or smaller than zero. The poromechanical response of a microporous medium to adsorption significantly depends on the pore size distribution. Indeed, the commensurability (i.e., the ratio of the size of the pores to that of the fluid molecules) proves to play a major role. For a one-dimensional model of micropores with a variety of pore sizes, molecular simulations show that the amount of adsorbed fluid depends linearly on the strain of the medium. We derive linearized constitutive equations which are valid when such a linear dependence of the adsorbed amount of fluid on the strain is observed. As an application, the case of methane and coal is

  7. Flow heterogeneity in reservoir rocks

    Energy Technology Data Exchange (ETDEWEB)

    Rosman, A.; Simon, R.


    A study by Chevron Oil Field Research Co. shows that microscopic flow heterogeneity values are essential for interpreting laboratory displacement data and properly evaluating field displacement projects. Chevron discusses microscopic flow heterogeneity in reservoir rocks: a measuring method, results of some measurements, and several applications to reservoir engineering problems. Heterogeneity is expressed in terms of both breakthrough recovery and the Dykstra-Parsons permeability variation. Microscopic flow heterogeneity in a reservoir rock is related to pore size, pore shape, and location of the different pore sizes that determine flow paths of various permeabilities. This flow heterogeneity affects secondary recovery displacement efficiency, residual oil and water saturations, and capillary pressure measurements.

  8. Modeling Approaches for Describing Microbial Population Heterogeneity

    DEFF Research Database (Denmark)

    Lencastre Fernandes, Rita

    population consists of cells in different states, and it implies a heterogeneous distribution of activities (e.g. respiration, product yield), including different responses to extracellular stimuli. The existence of a heterogeneous cell population may explain the lower productivities obtained......) to predict distributions of certain population properties including particle size, mass or volume, and molecular weight. Similarly, PBM allow for a mathematical description of distributed cell properties within microbial populations. Cell total protein content distributions (a measure of cell mass) have been...... population dynamics, in response to the substrate consumption observed during batch cultivation. Cell size and cell cycle position distributions were used to describe the cell population. A two-stage PBM was developed and coupled to an unstructured model describing the extracellular environment. The good...

  9. Heterogeneous data fusion for brain tumor classification. (United States)

    Metsis, Vangelis; Huang, Heng; Andronesi, Ovidiu C; Makedon, Fillia; Tzika, Aria


    Current research in biomedical informatics involves analysis of multiple heterogeneous data sets. This includes patient demographics, clinical and pathology data, treatment history, patient outcomes as well as gene expression, DNA sequences and other information sources such as gene ontology. Analysis of these data sets could lead to better disease diagnosis, prognosis, treatment and drug discovery. In this report, we present a novel machine learning framework for brain tumor classification based on heterogeneous data fusion of metabolic and molecular datasets, including state-of-the-art high-resolution magic angle spinning (HRMAS) proton (1H) magnetic resonance spectroscopy and gene transcriptome profiling, obtained from intact brain tumor biopsies. Our experimental results show that our novel framework outperforms any analysis using individual dataset.

  10. Fourier mode analysis of source iteration in spatially periodic media

    Energy Technology Data Exchange (ETDEWEB)

    Zika, M.R. [Lawrence Livermore National Lab., CA (United States); Larsen, E.W. [Univ. of Michigan, Ann Arbor, MI (United States)


    The standard Fourier mode analysis is an indispensable tool when designing acceleration techniques for transport iterations; however, it requires the assumption of a homogeneous infinite medium. For problems of practical interest, material heterogeneities may significantly impact iterative performance. Recent work has applied a Fourier analysis to the discretized two-dimensional transport operator with heterogeneous material properties. The results of these analyses may be difficult to interpret because the heterogeneity effects are inherently coupled to the discretization effects. Here, the authors describe a Fourier analysis of source iteration (SI) that allows the calculation of the eigenvalue spectrum for the one-dimensional continuous transport operator with spatially periodic heterogeneous media.

  11. Mass Spectrometry Imaging for the Investigation of Intratumor Heterogeneity. (United States)

    Balluff, B; Hanselmann, M; Heeren, R M A


    One of the big clinical challenges in the treatment of cancer is the different behavior of cancer patients under guideline therapy. An important determinant for this phenomenon has been identified as inter- and intratumor heterogeneity. While intertumor heterogeneity refers to the differences in cancer characteristics between patients, intratumor heterogeneity refers to the clonal and nongenetic molecular diversity within a patient. The deciphering of intratumor heterogeneity is recognized as key to the development of novel therapeutics or treatment regimens. The investigation of intratumor heterogeneity is challenging since it requires an untargeted molecular analysis technique that accounts for the spatial and temporal dynamics of the tumor. So far, next-generation sequencing has contributed most to the understanding of clonal evolution within a cancer patient. However, it falls short in accounting for the spatial dimension. Mass spectrometry imaging (MSI) is a powerful tool for the untargeted but spatially resolved molecular analysis of biological tissues such as solid tumors. As it provides multidimensional datasets by the parallel acquisition of hundreds of mass channels, multivariate data analysis methods can be applied for the automated annotation of tissues. Moreover, it integrates the histology of the sample, which enables studying the molecular information in a histopathological context. This chapter will illustrate how MSI in combination with statistical methods and histology has been used for the description and discovery of intratumor heterogeneity in different cancers. This will give evidence that MSI constitutes a unique tool for the investigation of intratumor heterogeneity, and could hence become a key technology in cancer research. © 2017 Elsevier Inc. All rights reserved.

  12. An application of fractional calculus to anomalous diffusion and imaging in inhomogeneous media (United States)

    Buonocore, Salvatore

    In recent years several studies have shown that field transport phenomena in media with non-homogeneous properties are characterized by unconventional behaviors. These processes, usually denoted as anomalous transport phenomena, are accurately described by fractional order mathematical models, whereas the classical integer order models fail to capture their properties. There are several examples of anomalous diffusion throughout the different fields of physics, such as wave propagation and diffusion processes in viscoelastic and heterogeneous media (e.g. soil, porous materials, etc.) fluid flow in porous media, non classical heat transfer. In particular, the diffusion processes in heterogeneous materials have shown to develop anomalous features characterized by non-local behavior due to the onset of long-range interactions. While integer order transport models are not able to explain these effects, fractional order models have shown to be able to capture these phenomena. The aim of this thesis is to investigate the occurrence of anomalous transport mechanisms associated to wave-like fields propagating in highly scattering media and to diffusive fields propagating in inhomogeneous media. Anomalous diffusion models are applicable to complex and inhomogeneous environments where classical diffusion theory ceases to be valid. Anomalous diffusion shows a nonlinear time dependence for the mean-squared displacement, and predicts stretched exponential decay for the temporal evolution of the system response. These unique characteristics of anomalous diffusion enable to probe complex media, with an approach that is not permitted by classical diffusion imaging. The behavior of the initial wave-like field turning into a diffused one will be governed by a classical or anomalous diffusive mechanism depending on the density of the medium. In this work this conversion phenomenon will be studied via a combination of stochastic molecular and fractional continuum models in order to

  13. Large epidemic thresholds emerge in heterogeneous networks of heterogeneous nodes


    Hui Yang; Ming Tang; Thilo Gross


    One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been shown that network heterogeneity, i.e. a broad degree distribution, can lower the epidemic threshold at which epidemics can invade the system. Network heterogeneity can thus allow diseases with lower transmission probabilities to persist and spread. Howeve...

  14. Managing Media: Segmenting Media Through Consumer Expectancies

    Directory of Open Access Journals (Sweden)

    Matt Eastin


    Full Text Available It has long been understood that consumers are motivated to media differently. However, given the lack of comparative model analysis, this assumption is without empirical validation, and thus, the orientation of segmentation from a media management perspective is without motivational grounds. Thus, evolving the literature on media consumption, the current study develops and compares models of media segmentation within the context of use. From this study, six models of media expectancies were constructed so that motivational differences between media (i.e., local and national newspapers, network and cable television, radio, and Internet could be observed. Utilizing higher order statistical analyses the data indicates differences across a model comparison approach for media motivations. Furthermore, these differences vary across numerous demographic factors. Results afford theoretical advancement within the literature of consumer media consumption as well as provide media planners’ insight into consumer choices.

  15. Direct molecular detection of pathogens in blood as specific rule-in diagnostic biomarker in patients with presumed sepsis: our experience on a heterogeneous cohort of patients with signs of infective systemic inflammatory response syndrome. (United States)

    Avolio, Manuela; Diamante, Paola; Modolo, Maria Luisa; De Rosa, Rita; Stano, Paola; Camporese, Alessandro


    The practical value of blood cultures in the diagnosis of sepsis is impaired by a delay in the turnaround time to result and by the fact that blood culture positive can be found for only about 30% of these patients. Conventional laboratory signs of sepsis and acute phase protein biomarkers are sensitive and easy to use, but often also very nonspecific. Molecular diagnostic reflects currently the most promising avenue to decrease time to result and to influence decision making for antibiotic therapy in the septic host. In this study, we wish to highlight the impact of the LightCycler SeptiFast, a multipathogen probe-based real-time polymerase chain reaction, in the rapid etiological diagnosis of sepsis in patients with clinical and laboratory signs of bloodstream infections. We have evaluated prospectively 830 adult patients with suspected bloodstream infection and at least two criteria of systemic inflammatory response syndrome. In more than 50% of critically ill patients strongly suspected of having sepsis, we arrived to an etiological diagnosis only by the molecular method in a median time of 15 h, with specificity and predictive positive values of 96% and 94%, respectively. We highlight the role of DNAemia as time-critical, high-specificity, etiological, non-culture-based rule-in diagnostic biomarker in patients with presumed sepsis.

  16. Large epidemic thresholds emerge in heterogeneous networks of heterogeneous nodes. (United States)

    Yang, Hui; Tang, Ming; Gross, Thilo


    One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been shown that network heterogeneity, i.e. a broad degree distribution, can lower the epidemic threshold at which epidemics can invade the system. Network heterogeneity can thus allow diseases with lower transmission probabilities to persist and spread. However, it has been pointed out that networks in which the properties of nodes are intrinsically heterogeneous can be very resilient to disease spreading. Heterogeneity in structure can enhance or diminish the resilience of networks with heterogeneous nodes, depending on the correlations between the topological and intrinsic properties. Here, we consider a plausible scenario where people have intrinsic differences in susceptibility and adapt their social network structure to the presence of the disease. We show that the resilience of networks with heterogeneous connectivity can surpass those of networks with homogeneous connectivity. For epidemiology, this implies that network heterogeneity should not be studied in isolation, it is instead the heterogeneity of infection risk that determines the likelihood of outbreaks.

  17. Geographic Media Literacy (United States)

    Lukinbeal, Chris


    While the use of media permeates geographic research and pedagogic practice, the underlying literacies that link geography and media remain uncharted. This article argues that geographic media literacy incorporates visual literacy, information technology literacy, information literacy, and media literacy. Geographic media literacy is the ability…

  18. Measuring News Media Literacy (United States)

    Maksl, Adam; Ashley, Seth; Craft, Stephanie


    News media literacy refers to the knowledge and motivations needed to identify and engage with journalism. This study measured levels of news media literacy among 500 teenagers using a new scale measure based on Potter's model of media literacy and adapted to news media specifically. The adapted model posits that news media literate individuals…

  19. The Mass Media Book. (United States)

    Holmgren, Rod, Ed.; Norton, William, Ed.

    This anthology consists of two major sections, "The News Media" and "The Entertainment Media." Both feature essays by critics, working professionals, and professional observers of the media. One aim of the anthology is to show the pervasive effect of the media on us. The section on news media comments on such topics as credibility gap, Vice…

  20. Heterogeneous logics of competition

    DEFF Research Database (Denmark)

    Mossin, Christiane


    The purpose of the article is to demonstrate that in order to understand competition as a socially organizing phenomenon, we should not examine competition in isolation, but as constellations of heterogeneous logics. More precisely, the article is based on two main theoretical points: (1) Logics...... of competition are only realized as particular forms of social organization by virtue of interplaying with other kinds of logics, like legal logics. (2) Competition logics enjoy a peculiar status in-between constructedness and givenness; although competition depends on laws and mechanisms of socialization, we...... still experience competition as an expression of spontaneous human activities. On the basis of these perspectives, a study of fundamental rights of EU law, springing from the principle of ‘free movement of people’, is conducted. The first part of the empirical analysis seeks to detect the presence...

  1. Heterogenous networks and services

    DEFF Research Database (Denmark)

    Tan, Su-En


    of the market. If mainstream technology firms do not address the disruption, it is likely they will fail and the new disruptive firm will grow in size and importance in the industry. As we move to 3G (3rd Generation Mobile Services) and beyond 3G, one of the biggest challenges is to bridge network heterogeneity...... representations of strategy, will then help to determine the success or failure of the technology. This is shown typically in the case of WiFi. WiFi is a wireless technology that addressed a new market, but was soon adopted as a complement by mobile operators into their suite of services. However, the future......This thesis considers the development of the mobile industry from a techno-economic perspective. Theory of disruptive technologies and related theories are examined and further developed. While much of technology change has been analysed on either a technical level or a market level, another plane...

  2. Combining Deterministic structures and stochastic heterogeneity for transport modeling (United States)

    Zech, Alraune; Attinger, Sabine; Dietrich, Peter; Teutsch, Georg


    Contaminant transport in highly heterogeneous aquifers is extremely challenging and subject of current scientific debate. Tracer plumes often show non-symmetric but highly skewed plume shapes. Predicting such transport behavior using the classical advection-dispersion-equation (ADE) in combination with a stochastic description of aquifer properties requires a dense measurement network. This is in contrast to the available information for most aquifers. A new conceptual aquifer structure model is presented which combines large-scale deterministic information and the stochastic approach for incorporating sub-scale heterogeneity. The conceptual model is designed to allow for a goal-oriented, site specific transport analysis making use of as few data as possible. Thereby the basic idea is to reproduce highly skewed tracer plumes in heterogeneous media by incorporating deterministic contrasts and effects of connectivity instead of using unimodal heterogeneous models with high variances. The conceptual model consists of deterministic blocks of mean hydraulic conductivity which might be measured by pumping tests indicating values differing in orders of magnitudes. A sub-scale heterogeneity is introduced within every block. This heterogeneity can be modeled as bimodal or log-normal distributed. The impact of input parameters, structure and conductivity contrasts is investigated in a systematic manor. Furthermore, some first successful implementation of the model was achieved for the well known MADE site.

  3. Porting Social Media Contributions with SIOC (United States)

    Bojars, Uldis; Breslin, John G.; Decker, Stefan

    Social media sites, including social networking sites, have captured the attention of millions of users as well as billions of dollars in investment and acquisition. To better enable a user's access to multiple sites, portability between social media sites is required in terms of both (1) the personal profiles and friend networks and (2) a user's content objects expressed on each site. This requires representation mechanisms to interconnect both people and objects on the Web in an interoperable, extensible way. The Semantic Web provides the required representation mechanisms for portability between social media sites: it links people and objects to record and represent the heterogeneous ties that bind each to the other. The FOAF (Friend-of-a-Friend) initiative provides a solution to the first requirement, and this paper discusses how the SIOC (Semantically-Interlinked Online Communities) project can address the latter. By using agreed-upon Semantic Web formats like FOAF and SIOC to describe people, content objects, and the connections that bind them together, social media sites can interoperate and provide portable data by appealing to some common semantics. In this paper, we will discuss the application of Semantic Web technology to enhance current social media sites with semantics and to address issues with portability between social media sites. It has been shown that social media sites can serve as rich data sources for SIOC-based applications such as the SIOC Browser, but in the other direction, we will now show how SIOC data can be used to represent and port the diverse social media contributions (SMCs) made by users on heterogeneous sites.

  4. Heterogeneity in recombinant protein production

    DEFF Research Database (Denmark)

    Schalén, Martin; Johanson, Ted; Lundin, Luisa


    contribute to make a population in a fermenter heterogeneous, resulting in cell-to-cell variation in physiological parameters of the microbial culture. Our study aims at investigating how population heterogeneity and recombinant protein production is affected by environmental gradients in bioreactors...... are simulated in small bioreactors and the population heterogeneity can be visualised by analysing single cells with flow cytometry. This can give new insights to cell physiology and recombinant protein production at the industrial scale....

  5. Space Qualified Heterogeneous Processing Project (United States)

    National Aeronautics and Space Administration — Space Micro proposes to develop a radiation hardened, monolithic, heterogeneous processor for space imaging and radar systems. High performance processors are needed...

  6. HCV genetic heterogeneity and its host genetics

    Directory of Open Access Journals (Sweden)

    NIE Yonghong


    Full Text Available Hepatitis C represents a major worldwide public health problem. Studies have shown that both genetic diversity of hepatitis C virus (HCV and genetic polymorphisms of IL-28B, ITPA, and IP-10 in the host are implicated in the progression of hepatitis C, treatment response, and adverse effects. The research advances in the molecular epidemiology and clinical and therapeutic interventions of HCV genetic heterogeneity and single nucleotide polymorphisms in its host are reviewed. It is suggested that there is a pressing need for reliable data on the molecular epidemiology of HCV and its host, which will assist in the decision making of public health issues and reduce the morbidity and mortality of hepatitis C worldwide.

  7. Quantifying seismic anisotropy induced by small-scale chemical heterogeneities (United States)

    Alder, C.; Bodin, T.; Ricard, Y.; Capdeville, Y.; Debayle, E.; Montagner, J. P.


    Observations of seismic anisotropy are usually used as a proxy for lattice-preferred orientation (LPO) of anisotropic minerals in the Earth's mantle. In this way, seismic anisotropy observed in tomographic models provides important constraints on the geometry of mantle deformation associated with thermal convection and plate tectonics. However, in addition to LPO, small-scale heterogeneities that cannot be resolved by long-period seismic waves may also produce anisotropy. The observed (i.e. apparent) anisotropy is then a combination of an intrinsic and an extrinsic component. Assuming the Earth's mantle exhibits petrological inhomogeneities at all scales, tomographic models built from long-period seismic waves may thus display extrinsic anisotropy. In this paper, we investigate the relation between the amplitude of seismic heterogeneities and the level of induced S-wave radial anisotropy as seen by long-period seismic waves. We generate some simple 1-D and 2-D isotropic models that exhibit a power spectrum of heterogeneities as what is expected for the Earth's mantle, that is, varying as 1/k, with k the wavenumber of these heterogeneities. The 1-D toy models correspond to simple layered media. In the 2-D case, our models depict marble-cake patterns in which an anomaly in shear wave velocity has been advected within convective cells. The long-wavelength equivalents of these models are computed using upscaling relations that link properties of a rapidly varying elastic medium to properties of the effective, that is, apparent, medium as seen by long-period waves. The resulting homogenized media exhibit extrinsic anisotropy and represent what would be observed in tomography. In the 1-D case, we analytically show that the level of anisotropy increases with the square of the amplitude of heterogeneities. This relation is numerically verified for both 1-D and 2-D media. In addition, we predict that 10 per cent of chemical heterogeneities in 2-D marble-cake models can

  8. Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. (United States)

    Zimmermann, Jörg; Oakman, Erin L; Thorpe, Ian F; Shi, Xinghua; Abbyad, Paul; Brooks, Charles L; Boxer, Steven G; Romesberg, Floyd E


    The evolution of proteins with novel function is thought to start from precursor proteins that are conformationally heterogeneous. The corresponding genes may be duplicated and then mutated to select and optimize a specific conformation. However, testing this idea has been difficult because of the challenge of quantifying protein flexibility and conformational heterogeneity as a function of evolution. Here, we report the characterization of protein heterogeneity and dynamics as a function of evolution for the antifluorescein antibody 4-4-20. Using nonlinear laser spectroscopy, surface plasmon resonance, and molecular dynamics simulations, we demonstrate that evolution localized the Ab-combining site from a heterogeneous ensemble of conformations to a single conformation by introducing mutations that act cooperatively and over significant distances to rigidify the protein. This study demonstrates how protein dynamics may be tailored by evolution and has important implications for our understanding of how novel protein functions are evolved.

  9. Numerical simulation of backward erosion piping in heterogeneous fields (United States)

    Liang, Yue; Yeh, Tian-Chyi Jim; Wang, Yu-Li; Liu, Mingwei; Wang, Junjie; Hao, Yonghong


    Backward erosion piping (BEP) is one of the major causes of seepage failures in levees. Seepage fields dictate the BEP behaviors and are influenced by the heterogeneity of soil properties. To investigate the effects of the heterogeneity on the seepage failures, we develop a numerical algorithm and conduct simulations to study BEP progressions in geologic media with spatially stochastic parameters. Specifically, the void ratio e, the hydraulic conductivity k, and the ratio of the particle contents r of the media are represented as the stochastic variables. They are characterized by means and variances, the spatial correlation structures, and the cross correlation between variables. Results of the simulations reveal that the heterogeneity accelerates the development of preferential flow paths, which profoundly increase the likelihood of seepage failures. To account for unknown heterogeneity, we define the probability of the seepage instability (PI) to evaluate the failure potential of a given site. Using Monte-Carlo simulation (MCS), we demonstrate that the PI value is significantly influenced by the mean and the variance of ln k and its spatial correlation scales. But the other parameters, such as means and variances of e and r, and their cross correlation, have minor impacts. Based on PI analyses, we introduce a risk rating system to classify the field into different regions according to risk levels. This rating system is useful for seepage failures prevention and assists decision making when BEP occurs.

  10. The nature of the active site in heterogeneous metal catalysis

    DEFF Research Database (Denmark)

    Nørskov, Jens Kehlet; Bligaard, Thomas; Larsen, Britt Hvolbæk


    This tutorial review, of relevance for the surface science and heterogeneous catalysis communities, provides a molecular-level discussion of the nature of the active sites in metal catalysis. Fundamental concepts such as "Bronsted-Evans-Polanyi relations'' and "volcano curves'' are introduced...

  11. Is dynamic heterogeneity of water in presence of a protein ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 12. Is dynamic heterogeneity of water in presence of a protein denaturing agent different from that in presence of a protein stabilizer? A molecular dynamics simulation study. SANDIPA INDRA RANJIT BISWAS BISWAS. Regular Article Volume 128 Issue 12 ...

  12. Asynchronous replica exchange software for grid and heterogeneous computing (United States)

    Gallicchio, Emilio; Xia, Junchao; Flynn, William F.; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M.


    Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.

  13. Media Pembelajaran Global Warming


    Tham, Fikri Jufri; Liliana, Liliana; Purba, Kristo Radion


    Computer based learning media is one of the media has an important role in learning. Learning media will be attractive when packaged through interactive media , such as interactive media created in paper manufacture " instructional media global warming" . The advantage gained is that it can increase knowledge, generally educate people to be more concerned about the environment , and also can be a means of entertainment. This application is focused to learn about global warming and packaged in...

  14. Social media metrics


    Balvín, Radek


    With growing amount of data produced by users on social media the need of extraction of relevant data for marketing, research and other uses grows as well. The bachelor thesis named "Social media metrics" presents the issues of monitoring, measurement and metrics of social media. In the research part it also maps and captures the present Czech practice in measurement and monitoring of social media. I also rate the use of social media monitoring tools and usual methods of social media measurem...

  15. Homologous series of low molecular weight (C1-C10) monocarboxylic acids, benzoic acid and hydroxyacids in fine-mode (PM2.5) aerosols over the Bay of Bengal: Influence of heterogeneity in air masses and formation pathways (United States)

    Boreddy, Suresh K. R.; Mochizuki, Tomoki; Kawamura, Kimitaka; Bikkina, Srinivas; Sarin, M. M.


    Low molecular weight monocarboxylic acids (LMW monoacids) are most abundant volatile organic compounds (VOCs) in the atmosphere and often act as important contributors to the acidity of precipitation in addition to inorganic acids. However, there is a large uncertainty in the sources and secondary formations of these acids in the atmosphere. This study reports homologous series of LMW monoacids, including normal (C1-C10), branched chain (iC4-iC6), aromatic (benzoic acid) and hydroxyacids (lactic and glycolic acids) in the fine-mode (PM2.5) aerosols collected over the Bay of Bengal (BoB) during a winter cruise (December 2008 to January 2009). The samples were associated with two distinct continental air masses arriving from the Indo-Gangetic Plain (IGP-outflow) and Southeast Asia (SEA-outflow). The molecular distributions of organic acids are characterized by the dominance of formic acid (C1) followed by acetic acid (C2) and nonanoic acid (C9) in the IGP-outflow, whereas dominance of C1 or C9 was observed in the SEA-outflow followed by C2. Formic-to-acetic acid (C1/C2) ratios were higher than unity (mean: 1.3 ± 0.3) in the IGP-outflow, whereas they were less than unity (0.9 ± 0.5) in the SEA-outflow. These results suggest that secondary formation of organic acids is largely important in the IGP-outflow whereas primary emission is a major source of organic acids in the SEA-outflow. Based on the correlation coefficient matrix analysis and C1/C2 and C4/C3 ratios, we consider that the sources of C1 are probably associated with the secondary formation via the oxidation of biogenic VOCs, while C2 has both primary and secondary formations associated with anthropogenic sources in the IGP-outflow. On the other hand, C1 and C2 have similar sources (both primary and secondary) originated from biomass burning and bacterial activities via long-range atmospheric transport in the SEA-outflow, as inferred from the MODIS fire spot data, significant concentrations of isovaleric

  16. Heterogeneity of an earth (United States)

    Litvinova, T.; Petrova, A.


    The study of magnetic anomaly field structure of the Barents Sea water area along seismic and extended profiles intersecting known fields is carried out. Geomagnetic and density sections down to 40 km depth are constructed. This allowed the estimation of heterogeneities of the Barents Sea water area deep structure. The analysis of geomagnetic and density sections along extended profiles showed the confinedness of oil-and-gas bearing provinces to deep permeable zones characterized by reduced magnetic and density features. Based on the analysis of permeable zones, regional diagnostic features similar to those obtained earlier in oil-and-gas bearing provinces in other regions, for example, in Timan-Pechora, Volga-Urals and Siberian, as well as in the Northern and Norwegian seas water areas, are revealed. The analysis of magnetic and gravity fields over the region area allowed the delineation of weakened zones as intersection areas of weakly magnetic areals with reduced density. Within the Barents Sea water area, permeable areas with lenticular-laminated structure of the upper and lower Earth's crust containing weakly magnetic areals with reduced rock density within the depth range of 8-12 and 15-20 km are revealed. Such ratio of magnetic and density heterogeneities in the Earth's crust is characteristic for zones with proved oil-and-gas content in the European part of the Atlantic Ocean water area. North Kildin field on 1 AR profile is confined to a trough with thick weakly magnetic stratum discontinuously traced to a depth of 6-10 km. At a depth of approximately 15 km, a lens of weakly magnetic and porous formations is observed. Ludlov field in the North Barents trough is confined to a zone of weakly magnetic rocks with reduced density traced to a depth of 8-9 km. Deeper, at Н=15 km, a lenticular areal of weakly magnetic formations with reduced density is observed. The profile transecting the Stockman field shows that it is located in the central part of a permeable

  17. Social media management and media environment

    Directory of Open Access Journals (Sweden)

    Šiđanin Iva


    Full Text Available The paper deals with the system of services that social media management can offer to a variety of users. As social media systems are emerging, social media management can strengthen teams in social media and help to manage numerous social channels and distribution of social information from one place. Social media management is a system of procedures that are used to manage the flow of information in the environment of social media. This involves connecting with social media like Facebook, Twitter, LinkedIn, Plaxo, Ecademy, YouTube and many others, then the aggregation and management of social data. Social media management services are analysed through various fields, such as managing multiple social media profiles, mail scheduling and filtering, reporting and analytics. Social media management enables managing personal business through social media, which contributes to a significant reduction in expenditures. The paper also discusses the importance of social media management in marketing activities and various forms of social promotion, which allow companies to easily reach their customers.

  18. Molecular heterogeneity of plpE gene in Indian isolates of Pasteurella multocida and expression of recombinant PlpE in vaccine strain of P. multocida serotype B: 2 (United States)

    Singh, Ajay Pratap; Singh, Satparkash; Gupta, Santosh Kumar; Singh, Vijendra Pal; Sharma, Bhaskar


    Outer membrane proteins of Pasteurella (P.) multocida have been known to be protective immunogens. Pasteurella lipoprotein E (PlpE) has been reported to be an important cross reactive outer membrane protein in P. multocida. The gene encoding the PlpE of P. multocida serotypes A: 3, B: 2 and D: 1 was amplified from the genomic DNA. The amplified products were cloned and the nucleotide sequence was determined. Sequence analysis of the recombinant clones revealed a single open reading frame of 1,011 bp, 1,008 bp and 1,017 bp encoding a protein with a calculated molecular mass of 37.829 kDa, 37.389 kDa and 37.965 kDa for serotypes A: 3, B: 2 and D: 1 respectively. The comparison of the plpE sequence in different capsular types revealed a high degree (>90%) of homology. Furthermore, the plpE gene of Haemorhhagic septicaemia causing serotype (B: 2) was expressed in E. coli and recombinant PlpE was strongly immunostained by antiserum against whole cell antigen, indicating that the protein is expressed in vivo. PMID:20706030

  19. The fluid control mechanism of bionic structural heterogeneous composite materials and its potential application in enhancing pump efficiency


    Limei Tian; Jin, E.; Ziyuan Li; Haoran Mei; Yinci Wang; Yangeng Shang


    Studies have shown that the structure of dolphin skin controls fluid media dynamically. Gaining inspiration from this phenomenon, a kind of bionic structural heterogeneous composite material was designed. The bionic structural heterogeneous composite material is composed of two materials: a rigid metal base layer with bionic structures and an elastic polymer surface layer with the corresponding mirror structures. The fluid control mechanism of the bionic structural heterogeneous composite mat...

  20. Contrast media osmolality and plasma volume changes. (United States)

    Hine, A L; Lui, D; Dawson, P


    A theoretical and experimental study of the plasma volume expansion consequent on the hyperosmolality of contrast media is presented. In the case of the ratio 1.5 media theory and experiment coincide closely but in the case of the ratio 3 media the observed changes exceed the predicted. It is proposed that this is due partly to the slower diffusion of the ratio 3 media out of the intravascular space and partly due to the fact that the osmotic load presented by these media is greater than would be expected from a study of their commercial solutions in which osmolality is reduced by molecular aggregation. The implications for the relative haemodynamic effects of different contrast media are discussed. The osmotic effects of contrast media also play a part in determining the image quality achievable in intravenous digital subtraction angiography (IV-DSA). It is predicted that ratio 3 contrast media will give better quality images in IV-DSA than ratio 1.5 media.

  1. Konservasi Media: Memori Kultural pada Media-Media Lama

    Directory of Open Access Journals (Sweden)

    Aloysius Ranggabumi Nuswantoro


    Full Text Available Abstract: Technology boosts the emergence of new communication tools and also creates the dichotomy of old media and new media. At first, it seems like there is nothing wrong with the dichotomy. However, in the context of communication value and meaning, there may be something missing when old media are being abandoned. Not merely the physical manifestation of old media, but rather the work it that contains useful information for the current generation. As a result, today’s people are now losing the root of their thoughts in the past. Thus, conservation is frankly needed to preserve the cultural memory in society Abstrak: Teknologi mendorong munculnya alat-alat komunikasi baru dan membuat dikotomi media lama dan media baru. Sekilas tidak ada yang salah dengan dikotomi tersebut dan konsekuensi yang menyertainya. Namun dalam konteks nilai dan makna komunikasi, ada sesuatu yang hilang ketika media lama ditinggalkan. Bukan semata-mata pada perwujudan fisik media lama, tetapi lebih kepada karya media lama yang memuat informasi berguna bagi generasi saat itu. Akibatnya orang zaman kini kehilangan jejak atau akar pikiran mereka di masa lalu. Maka konservasi media perlu dilakukan untuk mempertahankan memori kultural tersebut.

  2. Heterogeneity: multilingualism and democracy

    Directory of Open Access Journals (Sweden)

    Hans-Jürgen Krumm


    Full Text Available Linguistic diversity and multilingualism on the part of individuals are aprerequisite and a constitutive condition of enabling people to live togetherin a world of growing heterogeneity. Foreign language teaching plays animportant part in democratic education because it can be seen as a trainingin respecting otherness and developing an intercultural, non-ethnocentricperception and attitude. This is all the more important because of the neces-sity of integrating children from migrant families into school life.My article argues that language education policy has to take this per-spective into account, i.e., of establishing a planned diversification so thatpupils (and their parents will not feel satisfied with learning English only,but also become motivated to learn languages of their own neighbourhood,such as migrant and minority languages. However, in order to make use ofthe linguistic resources in the classroom, relating it to the democratic impetusof foreign language education, it is necessary to revise existing languagepolicies and to develop a multilingual perspective for all educational institutions.

  3. Theory of heterogeneous viscoelasticity (United States)

    Schirmacher, Walter; Ruocco, Giancarlo; Mazzone, Valerio


    We review a new theory of viscoelasticity of a glass-forming viscous liquid near and below the glass transition. In our model, we assume that each point in the material has a specific viscosity, which varies randomly in space according to a fluctuating activation free energy. We include a Maxwellian elastic term, and assume that the corresponding shear modulus fluctuates as well with the same distribution as that of the activation barriers. The model is solved in coherent potential approximation, for which a derivation is given. The theory predicts an Arrhenius-type temperature dependence of the viscosity in the vanishing frequency limit, independent of the distribution of the activation barriers. The theory implies that this activation energy is generally different from that of a diffusing particle with the same barrier height distribution. If the distribution of activation barriers is assumed to have the Gaussian form, the finite-frequency version of the theory describes well the typical low-temperature alpha relaxation peak of glasses. Beta relaxation can be included by adding another Gaussian with centre at much lower energies than that is responsible for the alpha relaxation. At high frequencies, our theory reduces to the description of an elastic medium with spatially fluctuating elastic moduli (heterogeneous elasticity theory), which explains the occurrence of the boson peak-related vibrational anomalies of glasses.

  4. Parsing Heterogeneous Striatal Activity

    Directory of Open Access Journals (Sweden)

    Kae Nakamura


    Full Text Available The striatum is an input channel of the basal ganglia and is well known to be involved in reward-based decision making and learning. At the macroscopic level, the striatum has been postulated to contain parallel functional modules, each of which includes neurons that perform similar computations to support selection of appropriate actions for different task contexts. At the single-neuron level, however, recent studies in monkeys and rodents have revealed heterogeneity in neuronal activity even within restricted modules of the striatum. Looking for generality in the complex striatal activity patterns, here we briefly survey several types of striatal activity, focusing on their usefulness for mediating behaviors. In particular, we focus on two types of behavioral tasks: reward-based tasks that use salient sensory cues and manipulate outcomes associated with the cues; and perceptual decision tasks that manipulate the quality of noisy sensory cues and associate all correct decisions with the same outcome. Guided by previous insights on the modular organization and general selection-related functions of the basal ganglia, we relate striatal activity patterns on these tasks to two types of computations: implementation of selection and evaluation. We suggest that a parsing with the selection/evaluation categories encourages a focus on the functional commonalities revealed by studies with different animal models and behavioral tasks, instead of a focus on aspects of striatal activity that may be specific to a particular task setting. We then highlight several questions in the selection-evaluation framework for future explorations.

  5. Les clusters moléculaires. Applications en catalyse homogène et hétérogène Molecular Clusters. Applications in Homogeneous and Heterogeneous Catalysis

    Directory of Open Access Journals (Sweden)

    Dorbon M.


    Full Text Available Le présent article ne prétend pas être une étude bibliographique complète. II ne s'agit que d'une synthèse dont le but est l'introduction à un secteur de la chimie encore jeune et surtout très vaste et plein d'avenir. Les clusters métalliques sont des composés constitués d'atomes métalliques liés entre eux et généralement entourés de ligands ; ils présentent à la fois certaines des caractéristiques des complexes uninucléaires d'une part et des métaux massiques d'autre part. D'un point de vue fondamental, la chimie des clusters représente un domaine encore neuf et particulièrement vaste. D'un point de vue pratique, leur principal intérêt réside dans le fait que bon nombre d'entre eux ont fait preuve de propriétés catalytiques remarquables tant en mode homogène qu'en mode hétérogène. Ils doivent être pris en considération par les industriels de la chimie car certains peuvent être impliqués dans des réactions aussi importantes que la synthèse de Fischer-Tropsch, l'hydrogénation des oléfines, la réaction de gaz à l'eau et la fixation biologique de l'azote atmosphérique. This article does not pretend to be an exhaustive bibliographic survey. It is merely a synthesis intended as an introduction to a sector of chemistry which is still young and especially is very vast and promising. Metal clusters are compounds made up of metal atours bonded together and generally surrounded by ligands. They have various characteristics of both mono-nuclear complexes and bulk metals. From a fundamental point of view, the chemistry of clusters is still a new and particularly vast field. From a practical point of view, the importance of clusters lies in the fact that a good number of them have shown proof of remarkable catalytic properties, both homogeneous and heterogeneous. They must henceforth be taken into consideration by chemical engineers because some of them may be involved in such important reactions as the Fischer

  6. Fiscal Consolidations and Heterogeneous Expectations

    NARCIS (Netherlands)

    Hommes, C.; Lustenhouwer, J.; Mavromatis, K.


    We analyze fiscal consolidations using a New Keynesian model where agents have heterogeneous expectations and are uncertain about the composition of consoidations. Heterogeneity in expectations may amplify expansions, stabilizing thus the debt-to-GDP ratio faster under tax based consolidations, in

  7. Query Expansion Using Heterogeneous Thesauri. (United States)

    Mandala, Rila; Tokunaga, Takenobu; Tanaka, Hozumi


    Proposes a method to improve the performance of information retrieval systems by expanding queries using heterogeneous thesauri. Experiments show that using heterogeneous thesauri with an appropriate weighting method results in better retrieval performance than using only one type of thesaurus. (Author/LRW)

  8. Dynamic heterogeneity in life histories. (United States)

    Tuljapurkar, Shripad; Steiner, Ulrich K; Orzack, Steven Hecht


    Longitudinal data on natural populations have been analysed using multistage models in which survival depends on reproductive stage, and individuals change stages according to a Markov chain. These models are special cases of stage-structured population models. We show that stage-structured models generate dynamic heterogeneity: life-history differences produced by stochastic stratum dynamics. We characterize dynamic heterogeneity in a range of species across taxa by properties of the Markov chain: the entropy, which describes the extent of heterogeneity, and the subdominant eigenvalue, which describes the persistence of reproductive success during the life of an individual. Trajectories of reproductive stage determine survivorship, and we analyse the variance in lifespan within and between trajectories of reproductive stage. We show how stage-structured models can be used to predict realized distributions of lifetime reproductive success. Dynamic heterogeneity contrasts with fixed heterogeneity: unobserved differences that generate variation between life histories. We show by an example that observed distributions of lifetime reproductive success are often consistent with the claim that little or no fixed heterogeneity influences this trait. We propose that dynamic heterogeneity provides a 'neutral' model for assessing the possible role of unobserved 'quality' differences between individuals. We discuss fitness for dynamic life histories, and the implications of dynamic heterogeneity for the evolution of life histories and senescence.

  9. Phenotype heterogeneity in cancer cell populations

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Luis [CNRS UMR 7598, LJLL, & INRIA MAMBA team, Sorbonne Universités, UPMC Univ Paris 06, Boîte courrier 187, 4 Pl. Jussieu, 75252 Paris cedex 05, France, (France); Chisholm, Rebecca [School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia, (Australia); Clairambault, Jean [INRIA MAMBA team & LJLL, UMR 7598, Sorbonne Universités, UPMC Univ Paris 06, Boîte courrier 187, 4 Pl. Jussieu, 75252 Paris cedex 05, France,, Corresponding author (France); Escargueil, Alexandre [INSERM “Cancer Biology and Therapeutics”, Sorbonne Universités, UPMC Univ Paris 06, UMR-S 938, CDR St Antoine, Hôpital St Antoine, 184 Fbg. St Antoine, 75571 Paris cedex 12, France, (France); Lorenzi, Tommaso [CMLA, ENS Cachan, 61, Av. du Président Wilson, 94230 Cachan cedex & INRIA MAMBA team, & LJLL, UMR 7598, UPMC Univ Paris 06, Boîte courrier 187, 4 Pl. Jussieu, 75252 Paris cedex 05, France, (France); Lorz, Alexander [Sorbonne Universités, UPMC Univ Paris 06, LJLL, UMR 7598 & INRIA Boîte courrier 187, 4 Pl. Jussieu, 75252 Paris cedex 05, France, (France); Trélat, Emmanuel [Institut Universitaire de France, Sorbonne Universités, UPMC Univ Paris 06, LJLL, UMR 7598, Boîte courrier 187, UPMC Univ Paris 06, 4 Pl. Jussieu, 75252 Paris cedex 05, France, (France)


    Phenotype heterogeneity in cancer cell populations, be it of genetic, epigenetic or stochastic origin, has been identified as a main source of resistance to drug treatments and a major source of therapeutic failures in cancers. The molecular mechanisms of drug resistance are partly understood at the single cell level (e.g., overexpression of ABC transporters or of detoxication enzymes), but poorly predictable in tumours, where they are hypothesised to rely on heterogeneity at the cell population scale, which is thus the right level to describe cancer growth and optimise its control by therapeutic strategies in the clinic. We review a few results from the biological literature on the subject, and from mathematical models that have been published to predict and control evolution towards drug resistance in cancer cell populations. We propose, based on the latter, optimisation strategies of combined treatments to limit emergence of drug resistance to cytotoxic drugs in cancer cell populations, in the monoclonal situation, which limited as it is still retains consistent features of cell population heterogeneity. The polyclonal situation, that may be understood as “bet hedging” of the tumour, thus protecting itself from different sources of drug insults, may lie beyond such strategies and will need further developments. In the monoclonal situation, we have designed an optimised therapeutic strategy relying on a scheduled combination of cytotoxic and cytostatic treatments that can be adapted to different situations of cancer treatments. Finally, we review arguments for biological theoretical frameworks proposed at different time and development scales, the so-called atavistic model (diachronic view relying on Darwinian genotype selection in the coursof billions of years) and the Waddington-like epigenetic landscape endowed with evolutionary quasi-potential (synchronic view relying on Lamarckian phenotype instruction of a given genome by reversible mechanisms), to

  10. Heterogeneous noise enhances spatial reciprocity

    CERN Document Server

    Yao, Y


    Recent research has identified the heterogeneity as crucial for the evolution of cooperation in spatial population. However, the influence of heterogeneous noise is still lack. Inspired by this interesting question, in this work, we try to incorporate heterogeneous noise into the evaluation of utility, where only a proportion of population possesses noise, whose range can also be tuned. We find that increasing heterogeneous noise monotonously promotes cooperation and even translates the full defection phase (of the homogeneous version) into the complete cooperation phase. Moreover, the promotion effect of this mechanism can be attributed to the leading role of cooperators who have the heterogeneous noise. These type of cooperators can attract more agents penetrating into the robust cooperator clusters, which is beyond the text of traditional spatial reciprocity. We hope that our work may shed light on the understanding of the cooperative behavior in the society.

  11. Field heterogeneity: some basic issues

    Energy Technology Data Exchange (ETDEWEB)

    Philip, J.R.


    Present-day soil-water physics enables useful quantitative predictions in the laboratory and in simple field situations. However, difficulties frequently arise for areas of appreciable size in the field. Two types of heterogeneity are distinguished: deterministic and stochastic. The first often demands an extension of established analyses and may involve important phenomena absent from the analogous homogeneous problem. Stochastic heterogeneity may involve many scales and is imperfectly known. The statistical properties may be stationary, but in more complicated cases, randomness may be embedded in (either known or unknown) systematic trends. Some aspects of unsaturated and generally unsteady flow in heterogeneous systems are reviewed: the mathematical nature of the flow equation; the concept of scale-heterogeneity; analytical and quasianalytical solutions. The enormity of the total problem of unsaturated unsteady flow in stochastic heterogeneous systems is illustrated through a dialectic of 8 successive stages of simplification. 37 references.


    Directory of Open Access Journals (Sweden)

    Anjar Sri Wahyuni


    Full Text Available Advances in technology in various fields, for example in communications and information technology at the moment, learning media has a central position in the learning process and not solely aids. The media is an integral part of the learning process. In this process, using instructional media associated with anything that can be done by the media. Instructional media used in learning activities can influence the learning efektitas. At first, learning media only serves as a tool for teachers. Two approaches / models of learning media in the electoral process, namely: selecting the model enclosed and open selection model. Closed election occurs when alternative media has been determined. Open selection model is the inverse of the secret ballot. We are still free to choose any type of media, according to our needs. Alternative media is still wide open. Choose open procedures more flexible in nature, because really we adjust to the needs and conditions.   Keywords :  Effectiveness, Media, Learning.

  13. Transcriptomic-anatomic analysis of the mouse habenula uncovers a high molecular heterogeneity among neurons in the lateral complex, while gene expression in the medial complex largely obeys subnuclear boundaries. (United States)

    Wagner, Franziska; French, Leon; Veh, Rüdiger W


    The mammalian habenula with its medial and lateral complexes has gained much interest in recent years, while knowledge on the detailed biological functions of these nuclei is still scarce. Novel strategies to differentiate and identify habenular cell types are required. Such attempts have largely failed, most likely due to the lack of appropriate molecular markers. One important tool to approach this dilemma is available in form of the Allen Brain Atlas (ABA), which provides detailed expression patterns of many genes in the mouse brain. In the present report, ABA tools in combination with visual inspection of ISH images were used to detect transcripts, which are strongly expressed in medial (MHb) and lateral (LHb) habenular complexes. Against our expectations, most transcripts were differentially distributed throughout the LHb, disregarding boundaries of subnuclear areas. Nine distinct distribution patterns were recognized. Yet, several transcripts could not be attributed to one of these, suggesting a high diversity of neuron types in the LHb. In the MHb, in contrast, many transcripts tended to obey subnuclear boundaries. The differential distribution of others like Adcyap1, Chrna3, or Trp53i11 suggests the presence of a novel subfield adjacent to the region of the MHbVm, which now is termed intermediate field of the ventral MHb. In addition, the localizations of Amigo2, Adcyap1, and a couple of other transcripts suggest a lateral extension of the MHb, which is here, termed HbX area. Apparently, this area is composed of intermingled MHb and LHb neurons and may allow functional interaction between the both habenular complexes.

  14. Fractional diffusion models of cardiac electrical propagation: role of structural heterogeneity in dispersion of repolarization. (United States)

    Bueno-Orovio, Alfonso; Kay, David; Grau, Vicente; Rodriguez, Blanca; Burrage, Kevin


    Impulse propagation in biological tissues is known to be modulated by structural heterogeneity. In cardiac muscle, improved understanding on how this heterogeneity influences electrical spread is key to advancing our interpretation of dispersion of repolarization. We propose fractional diffusion models as a novel mathematical description of structurally heterogeneous excitable media, as a means of representing the modulation of the total electric field by the secondary electrical sources associated with tissue inhomogeneities. Our results, analysed against in vivo human recordings and experimental data of different animal species, indicate that structural heterogeneity underlies relevant characteristics of cardiac electrical propagation at tissue level. These include conduction effects on action potential (AP) morphology, the shortening of AP duration along the activation pathway and the progressive modulation by premature beats of spatial patterns of dispersion of repolarization. The proposed approach may also have important implications in other research fields involving excitable complex media.

  15. Konservasi Media: Memori Kultural pada Media-Media Lama


    Aloysius Ranggabumi Nuswantoro


    Abstract: Technology boosts the emergence of new communication tools and also creates the dichotomy of old media and new media. At first, it seems like there is nothing wrong with the dichotomy. However, in the context of communication value and meaning, there may be something missing when old media are being abandoned. Not merely the physical manifestation of old media, but rather the work it that contains useful information for the current generation. As a result, today’s people are now l...

  16. Konservasi Media: Memori Kultural Pada Media-Media Lama


    Nuswantoro, Aloysius Ranggabumi


    : Technology boosts the emergence of new communication tools and also creates the dichotomy of old media and new media. At first, it seems like there is nothing wrong with the dichotomy. However, in the context of communication value and meaning, there may be something missing when old media are being abandoned. Not merely the physical manifestation of old media, but rather the work it that contains useful information for the current generation. As a result, today’s people are now losing th...

  17. Two-Level Domain Decomposition Methods for Highly Heterogeneous Darcy Equations. Connections with Multiscale Methods

    Directory of Open Access Journals (Sweden)

    Dolean Victorita


    Full Text Available Multiphase, compositional porous media flow models lead to the solution of highly heterogeneous systems of Partial Differential Equations (PDE. We focus on overlapping Schwarz type methods on parallel computers and on multiscale methods. We present a coarse space [Nataf F., Xiang H., Dolean V., Spillane N. (2011 SIAM J. Sci. Comput. 33, 4, 1623-1642] that is robust even when there are such heterogeneities. The two-level domain decomposition approach is compared to multiscale methods.

  18. Media Violence and Children. (United States)

    Groebel, Jo


    Presents the results of the UNESCO global study on media violence and children which was conducted between 1996 and 1997. Highlights include the role of the media, media heroes as role models, media violence and aggression, differences by gender, rural versus urban environments, the pervasiveness of television, and recommendations. (Author/LRW)

  19. Living within the Media (United States)

    Griffin, Erin


    In this article, the author shares how media affects her as a teenager. The author says that media has such a relationship with the world today, specifically with teenagers like her. Media gives off so much information that can be valid or invalid, positive or negative. The media can persuade anyone to do something or to think a certain way.…

  20. The Media Teacher's Handbook (United States)

    Scarratt, Elaine, Ed.; Davison, Jon, Ed.


    "The Media Teacher's Handbook" is an indispensible guide for all teachers, both specialist and non-specialist, delivering Media Studies and media education in secondary schools and colleges. It is the first text to draw together the three key elements of secondary sector teaching in relation to media study--the "theoretical",…

  1. Media Literacy Bibliography. (United States)

    Duncan, Barry


    Provides an up-to-date bibliography of resources available for teaching media literacy. Groups resources into the areas of media education methodology, mass media texts, general background, television, film, the news and medium of print, advertising, gender and the media, popular culture, popular music and rock video, periodicals, and…

  2. Molecular profiling of childhood cancer: Biomarkers and novel therapies

    Directory of Open Access Journals (Sweden)

    Federica Saletta


    General significance: The increasing recognition of the heterogeneity of molecular causes of cancer favors the continued development of molecularly targeted agents, and their transfer to pediatric and adolescent populations.

  3. Efektivitas Media Dalam Pembelajaran

    Directory of Open Access Journals (Sweden)

    Anjar Sri Wahyuni


    Full Text Available Advances in technology in various fields, for example in communications and information technology at the moment, learning media has a central position in the learning process and not solely aids. The media is an integral part of the learning process. In this process, using instructional media associated with anything that can be done by the media. Instructional media used in learning activities can influence the learning efektitas. At first, learning media only serves as a tool for teachers. Two approaches / models of learning media in the electoral process, namely: selecting the model enclosed and open selection model. Closed election occurs when alternative media has been determined. Open selection model is the inverse of the secret ballot. We are still free to choose any type of media, according to our needs. Alternative media is still wide open. Choose open procedures more flexible in nature, because really we adjust to the needs and conditions.

  4. Robust mechanobiological behavior emerges in heterogeneous myosin systems (United States)

    Egan, Paul F.; Moore, Jeffrey R.; Ehrlicher, Allen J.; Weitz, David A.; Schunn, Christian; Cagan, Jonathan; LeDuc, Philip


    Biological complexity presents challenges for understanding natural phenomenon and engineering new technologies, particularly in systems with molecular heterogeneity. Such complexity is present in myosin motor protein systems, and computational modeling is essential for determining how collective myosin interactions produce emergent system behavior. We develop a computational approach for altering myosin isoform parameters and their collective organization, and support predictions with in vitro experiments of motility assays with α-actinins as molecular force sensors. The computational approach models variations in single myosin molecular structure, system organization, and force stimuli to predict system behavior for filament velocity, energy consumption, and robustness. Robustness is the range of forces where a filament is expected to have continuous velocity and depends on used myosin system energy. Myosin systems are shown to have highly nonlinear behavior across force conditions that may be exploited at a systems level by combining slow and fast myosin isoforms heterogeneously. Results suggest some heterogeneous systems have lower energy use near stall conditions and greater energy consumption when unloaded, therefore promoting robustness. These heterogeneous system capabilities are unique in comparison with homogenous systems and potentially advantageous for high performance bionanotechnologies. Findings open doors at the intersections of mechanics and biology, particularly for understanding and treating myosin-related diseases and developing approaches for motor molecule-based technologies.

  5. Ethics of Media



    Events such as the phone-hacking scandal, Wikileaks and the Mohammed cartoons controversy have placed ethics of media at the centre of current debates. Media are not only centralised institutions, but also technologies and means through which we sustain relationships with each other. We live with and in media, and this book sketches and critiques the normative contours of our intensely mediated worlds. What are the 'ethics' of media? What forms would we expect them to take? Do digital media c...

  6. Social media influencer marketing


    Isosuo, Heli


    The marketing field is changing simultaneously with the digital world. Social media is getting more and more important to marketers, and there is a need to stand out in the social media noise. Social media influencer marketing could be a good alternative to other types of marketing. A need from the consignor and the interest of the author were the motivations for conducting the study. Sääskilahti Consulting has a social media influencer network Somevaikuttajat, which is offering social media ...

  7. Effect of heterogeneities on evaluating earthquake triggering of volcanic eruptions

    Directory of Open Access Journals (Sweden)

    J. Takekawa


    Full Text Available Recent researches have indicated coupling between volcanic eruptions and earthquakes. Some of them calculated static stress transfer in subsurface induced by the occurrences of earthquakes. Most of their analyses ignored the spatial heterogeneity in subsurface, or only took into account the rigidity layering in the crust. On the other hand, a smaller scale heterogeneity of around hundreds of meters has been suggested by geophysical investigations. It is difficult to reflect that kind of heterogeneity in analysis models because accurate distributions of fluctuation are not well understood in many cases. Thus, the effect of the ignorance of the smaller scale heterogeneity on evaluating the earthquake triggering of volcanic eruptions is also not well understood. In the present study, we investigate the influence of the assumption of homogeneity on evaluating earthquake triggering of volcanic eruptions using finite element simulations. The crust is treated as a stochastic media with different heterogeneous parameters (correlation length and magnitude of velocity perturbation in our simulations. We adopt exponential and von Karman functions as spatial auto-correlation functions (ACF. In all our simulation results, the ignorance of the smaller scale heterogeneity leads to underestimation of the failure pressure around a chamber wall, which relates to dyke initiation. The magnitude of the velocity perturbation has a larger effect on the tensile failure at the chamber wall than the difference of the ACF and the correlation length. The maximum effect on the failure pressure in all our simulations is about twice larger than that in the homogeneous case. This indicates that the estimation of the earthquake triggering due to static stress transfer should take account of the heterogeneity of around hundreds of meters.


    Carrel, A; Ebeling, A H


    The presence in a culture medium of heterogenic serum of various concentrations exerts a definite influence on the rate of multiplication of fibroblasts. Dog serum does not inhibit the growth of See PDF for Structure chicken fibroblasts markedly until its concentration reaches 15 per cent. Beyond this figure, each increase of the concentration brings about a rapid decrease in the rate of cell multiplication. When the concentration reaches from 30 to 45 per cent, no growth takes place. The inhibiting action of cat serum begins to manifest itself at a concentration of 25 per cent and prevents cell proliferation completely at a concentration of 55 and 60 per cent. The ratio, See PDF for Equation can be taken as expressing the action of the serum on fibroblast multiplication; that is, as the growth index of the serum. See PDF for Structure The inhibiting influence of heterogenic serum was found to vary in direct ratio to the age of the animal from which it was obtained. The rate of proliferation of chicken fibroblasts was studied comparatively in media containing varied concentrations of serum from young and old animals. For each concentration of serum, the rate of growth in the serum of the old animal was expressed in relation to the rate of growth in the serum of the young animal. When cat serum was used, the curve obtained in plotting this ratio in ordinates and the serum concentration in abscissae showed a rapid increase in the inhibiting action of the old serum as soon as the concentration reached 30 per cent. The same tests were repeated with the serum from young and old dogs. The general results were identical, although See PDF for Structure the quantitative inhibiting action of both sera was greater than that of cat serum. It may be concluded that under the conditions of the experiments: 1. Heterogenicsera inhibit and prevent the growth of chicken fibroblasts when their concentration is made to vary within certain limits. 2. A relation exists between the rate

  9. Impact of aquifer heterogeneity structure and local-scale dispersion on solute concentration uncertainty (United States)

    Srzic, Veljko; Cvetkovic, Vladimir; Andricevic, Roko; Gotovac, Hrvoje


    In this paper, we study the influence of high log-conductivity variance (σY2) and local-scale dispersion on the first two concentration moments as well as on higher-order moments, skewness, and kurtosis, in a 2-D heterogeneous aquifer. Three different heterogeneity structures are considered, defined with one and the same global isotropic Gaussian variogram. The three structures differ in terms of spatial connectivity patterns at extreme log-conductivity values. Our numerical approach to simulate contaminant transport through heterogeneous porous media is based on the Lagrangian framework with a reverse tracking formulation. Advection and local-scale dispersion are two competing and controlling mechanisms, with a relative ratio defined by the Peclet number (Pe); hydraulic log-conductivity variance σY2 in the simulations is assumed to be one or eight. The term local-scale dispersion is used as a combined effect of molecular diffusion and mechanical dispersion. Uncertainty of the concentration field is quantified by the second-order moment, or the coefficient of variation (CVC) as a function of the sampling position along a centerline, Peclet number, and σY2, as well as by higher-order moments, i.e., skewness and kurtosis. The parameter σY2 shows a strong influence on the concentration statistics, while the three different structures have a minor impact in the case of low heterogeneity. The results also indicate that for σY2=8, the influence of local-scale dispersion is significant after five integral scales (IY) from the source for the connected (CN) field, while in case of a disconnected field, the local-scale dispersion effect is observed after 20IY from the source. In the case of unit σY2, local-scale dispersion acts very slowly affecting concentration uncertainty at distances higher than 20IY from the source. Our inspection of Monte Carlo concentration skewness and kurtosis with the ones obtained from the Beta distribution show the discrepancies for high

  10. Assessment of Breast Cancer Risk Factors Reveals Subtype Heterogeneity. (United States)

    Holm, Johanna; Eriksson, Louise; Ploner, Alexander; Eriksson, Mikael; Rantalainen, Mattias; Li, Jingmei; Hall, Per; Czene, Kamila


    Subtype heterogeneity for breast cancer risk factors has been suspected, potentially reflecting etiologic differences and implicating risk prediction. However, reports are conflicting regarding the presence of heterogeneity for many exposures. To examine subtype heterogeneity across known breast cancer risk factors, we conducted a case-control analysis of 2,632 breast cancers and 15,945 controls in Sweden. Molecular subtype was predicted from pathology record-derived IHC markers by a classifier trained on PAM50 subtyping. Multinomial logistic regression estimated separate ORs for each subtype by the exposures parity, age at first birth, breastfeeding, menarche, hormone replacement therapy use, somatotype at age 18, benign breast disease, mammographic density, polygenic risk score, family history of breast cancer, and BRCA mutations. We found clear subtype heterogeneity for genetic factors and breastfeeding. Polygenic risk score was associated with all subtypes except for the basal-like (Pheterogeneity risk of basal-like subtype [OR 4.17; 95% confidence interval (CI) 1.89-9.21] compared with both nulliparity (reference) and breastfeeding. Breastfeeding was not associated with risk of HER2-overexpressing type, but protective for all other subtypes. The observed heterogeneity in risk of distinct breast cancer subtypes for germline variants supports heterogeneity in etiology and has implications for their use in risk prediction. The association between basal-like subtype and breastfeeding merits more research into potential causal mechanisms and confounders. Cancer Res; 77(13); 3708-17. ©2017 AACR. ©2017 American Association for Cancer Research.

  11. Regulatory Rewiring in a Cross Causes Extensive Genetic Heterogeneity. (United States)

    Matsui, Takeshi; Linder, Robert; Phan, Joann; Seidl, Fabian; Ehrenreich, Ian M


    Genetic heterogeneity occurs when individuals express similar phenotypes as a result of different underlying mechanisms. Although such heterogeneity is known to be a potential source of unexplained heritability in genetic mapping studies, its prevalence and molecular basis are not fully understood. Here we show that substantial genetic heterogeneity underlies a model phenotype--the ability to grow invasively--in a cross of two Saccharomyces cerevisiae strains. The heterogeneous basis of this trait across genotypes and environments makes it difficult to detect causal loci with standard genetic mapping techniques. However, using selective genotyping in the original cross, as well as in targeted backcrosses, we detected four loci that contribute to differences in the ability to grow invasively. Identification of causal genes at these loci suggests that they act by changing the underlying regulatory architecture of invasion. We verified this point by deleting many of the known transcriptional activators of invasion, as well as the gene encoding the cell surface protein Flo11 from five relevant segregants and showing that these individuals differ in the genes they require for invasion. Our work illustrates the extensive genetic heterogeneity that can underlie a trait and suggests that regulatory rewiring is a basic mechanism that gives rise to this heterogeneity. Copyright © 2015 by the Genetics Society of America.

  12. One microenvironment does not fit all: heterogeneity beyond cancer cells. (United States)

    Kim, Ik Sun; Zhang, Xiang H-F


    Human cancers exhibit formidable molecular heterogeneity, to a large extent accounting for the incomplete and transitory efficacy of current anti-cancer therapies. However, neoplastic cells alone do not manifest the disease, but conscript a battery of non-tumor cells to enable and sustain hallmark capabilities of cancer. Escaping immunosurveillance is one of such capabilities. Tumors evolve immunosuppressive microenvironment to subvert anti-tumor immunity. In this review, we will focus on tumor-associated myeloid cells, which constitute an essential part of the immune microenvironment and reciprocally interact with cancer cells to establish malignancy toward metastasis. The diversity and plasticity of these cells constitute another layer of heterogeneity, beyond the heterogeneity of cancer cells themselves. We envision that immune microenvironment co-evolves with the genetic heterogeneity of tumor. Addressing the question of how genetically distinct tumors shape and are shaped by unique immune microenvironment will provide an attractive rationale to develop novel immunotherapeutic modalities. Here, we discuss the complex nature of tumor microenvironment, with an emphasis on the cellular and functional heterogeneity among tumor-associated myeloid cells as well as immune environment heterogeneity in the context of a full spectrum of human breast cancers.

  13. Digital Humanities and networked digital media

    Directory of Open Access Journals (Sweden)

    Niels Ole Finnemann


    Full Text Available This article discusses digital humanities and the growing diversity of digital media, digital materials and digital methods. The first section describes the humanities computing tradition formed around the interpretation of computation as a rule-based process connected to a concept of digital materials centred on the digitisation of non-digital, finite works, corpora and oeuvres. The second section discusses “the big tent” of contemporary digital humanities. It is argued that there can be no unifying interpretation of digital humanities above the level of studying digital materials with the help of software-supported methods. This is so, in part, because of the complexity of the world and, in part, because digital media remain open to the projection of new epistemologies onto the functional architecture of these media. The third section discusses the heterogeneous character of digital materials and proposes that the study of digital materials should be established as a field in its own right.

  14. Digital Humanities and networked digital media

    Directory of Open Access Journals (Sweden)

    Niels Ole Finnemann


    Full Text Available This article discusses digital humanities and the growing diversity of digital media, digital materials and digital methods. The first section describes the humanities computing tradition formed around the interpretation of computation as a rule-based process connected to a concept of digital materials centred on the digitisation of non-digital, finite works, corpora and oeuvres. The second section discusses “the big tent” of contemporary digital humanities. It is argued that there can be no unifying interpretation of digital humanities above the level of studying digital materials with the help of software-supported methods. This is so, in part, because of the complexity of the world and, in part, because digital media remain open to the projection of new epistemologies onto the functional architecture of these media. The third section discusses the heterogeneous character of digital materials and proposes that the study of digital materials should be established as a field in its own right.

  15. Shock dynamics in layered periodic media

    KAUST Repository

    Ketcheson, David I.


    Solutions of constant-coeffcient nonlinear hyperbolic PDEs generically develop shocks, even if the initial data is smooth. Solutions of hyperbolic PDEs with variable coeffcients can behave very differently. We investigate formation and stability of shock waves in a one-dimensional periodic layered medium by a computational study of time-reversibility and entropy evolution. We find that periodic layered media tend to inhibit shock formation. For small initial conditions and large impedance variation, no shock formation is detected even after times much greater than the time of shock formation in a homogeneous medium. Furthermore, weak shocks are observed to be dynamically unstable in the sense that they do not lead to significant long-term entropy decay. We propose a characteristic condition for admissibility of shocks in heterogeneous media that generalizes the classical Lax entropy condition and accurately predicts the formation or absence of shocks in these media.

  16. Homogeneous, Heterogeneous, and Enzymatic Catalysis. (United States)

    Oyama, S. Ted; Somorjai, Gabor A.


    Discusses three areas of catalysis: homegeneous, heterogeneous, and enzymatic. Explains fundamentals and economic impact of catalysis. Lists and discusses common industrial catalysts. Provides a list of 107 references. (MVL)

  17. Formation of Rationally Heterogeneous Expectations

    NARCIS (Netherlands)

    Pfajfar, D.


    Abstract: This paper models expectation formation by taking into account that agents produce heterogeneous expectations due to model uncertainty, informational frictions and different capacities for processing information. We show that there are two general classes of steady states within this

  18. Electrocardiographic assessment of repolarization heterogeneity

    NARCIS (Netherlands)

    Hooft van Huysduynen, Bart


    Repolarization heterogeneity refers to differences in repolarization instants in the heart. Normally, repolarization in the human heart is a relatively smooth, continuous process, during which adjacent areas repolarize almost simultaneously. Several drugs or cardiac diseases may disturb the

  19. Optimizations in Heterogeneous Mobile Networks

    DEFF Research Database (Denmark)

    Popovska Avramova, Andrijana

    Heterogeneous Mobile Networks bring advantages over homogeneous deployments in achieving the demand for mobile network capacity and coverage not just outdoor rural and urban areas, but also to homes and enterprises where the large portion of the mobile traffic is generated. However......, the heterogeneity in the mobile networks bring many challenges that are discusses with this dissertation. More focus is placed on specific issues with indifferent areas of heterogeneity by proposing optimizations in order to overcome the considered problems.The heterogeneity of mobile networks, together...... with the densification of the base stations, bring into a very complex network management and operation control for the mobile operators. Furthermore, the need to provide always best connection and service with high quality demands for a joint overall network resource management. This thesis addresses this challenge...

  20. Genetic heterogeneity in familial hyperinsulinism. (United States)

    Nestorowicz, A; Glaser, B; Wilson, B A; Shyng, S L; Nichols, C G; Stanley, C A; Thornton, P S; Permutt, M A


    Familial hyperinsulinism (HI) is a disorder characterized by dysregulation of insulin secretion and profound hypoglycemia. Mutations in both the Kir6.2 and sulfonylurea receptor (SUR1) genes have been associated with the autosomal recessive form of this disorder. In this study, the spectrum and frequency of SUR1 mutations in HI and their significance to clinical manifestations of the disease were investigated by screening 45 HI probands of various ethnic origins for mutations in the SUR1 gene. Single-strand conformation polymorphism (SSCP) and nucleotide sequence analyses of genomic DNA revealed a total of 17 novel and three previously described mutations in SUR1 . The novel mutations comprised one nonsense and 10 missense mutations, two deletions, three mutations in consensus splice-site sequences and an in-frame insertion of six nucleotides. One mutation occurred in the first nucleotide binding domain (NBF-1) of the SUR1 molecule and another eight mutations were located in the second nucleotide binding domain (NBF-2), including two at highly conserved amino acid residues within the Walker A sequence motif. The majority of the remaining mutations was distributed throughout the three putative transmembrane domains of the SUR1 protein. With the exception of the 3993-9G-->A mutation, which was detected on 4.5% (4/88) disease chromosomes, allelic frequencies for the identified mutations varied between 1.1 and 2.3% for HI chromosomes, indicating that each mutation was rare within the patient cohort. The clinical manifestations of HI in those patients homozygous for mutations in the SUR1 gene are described. In contrast with the allelic homogeneity of HI previously described in Ashkenazi Jewish patients, these findings suggest that a large degree of allelic heterogeneity at the SUR1 locus exists in non-Ashkenazi HI patients. These data have important implications for genetic counseling and prenatal diagnosis of HI, and also provide a basis to further elucidate the